From a89218f723a5faea277e72d21dc27637676a2e8e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 11 Aug 2025 18:38:02 +0000 Subject: [PATCH 01/58] build(deps-dev): bump pre-commit from 4.2.0 to 4.3.0 Bumps [pre-commit](https://github.com/pre-commit/pre-commit) from 4.2.0 to 4.3.0. - [Release notes](https://github.com/pre-commit/pre-commit/releases) - [Changelog](https://github.com/pre-commit/pre-commit/blob/main/CHANGELOG.md) - [Commits](https://github.com/pre-commit/pre-commit/compare/v4.2.0...v4.3.0) --- updated-dependencies: - dependency-name: pre-commit dependency-version: 4.3.0 dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- poetry.lock | 77 +++++++++++++++++++++++++++++++++++++++----------- pyproject.toml | 2 +- 2 files changed, 61 insertions(+), 18 deletions(-) diff --git a/poetry.lock b/poetry.lock index c196542..88ffc23 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand. [[package]] name = "altgraph" @@ -6,6 +6,7 @@ version = "0.17.4" description = "Python graph (network) package" optional = false python-versions = "*" +groups = ["dev"] files = [ {file = "altgraph-0.17.4-py2.py3-none-any.whl", hash = "sha256:642743b4750de17e655e6711601b077bc6598dbfa3ba5fa2b2a35ce12b508dff"}, {file = "altgraph-0.17.4.tar.gz", hash = "sha256:1b5afbb98f6c4dcadb2e2ae6ab9fa994bbb8c1d75f4fa96d340f9437ae454406"}, @@ -17,6 +18,7 @@ version = "0.7.0" description = "Reusable constraint types to use with typing.Annotated" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, @@ -28,6 +30,7 @@ version = "3.4.0" description = "Validate configuration and produce human readable error messages." optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"}, {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"}, @@ -39,6 +42,8 @@ version = "0.4.6" description = "Cross-platform colored terminal text." optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" +groups = ["dev"] +markers = "sys_platform == \"win32\"" files = [ {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"}, {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"}, @@ -50,6 +55,7 @@ version = "0.4.0" description = "Distribution utilities" optional = false python-versions = "*" +groups = ["dev"] files = [ {file = "distlib-0.4.0-py2.py3-none-any.whl", hash = "sha256:9659f7d87e46584a30b5780e43ac7a2143098441670ff0a49d5f9034c54a6c16"}, {file = "distlib-0.4.0.tar.gz", hash = "sha256:feec40075be03a04501a973d81f633735b4b69f98b05450592310c0f401a4e0d"}, @@ -61,6 +67,8 @@ version = "1.3.0" description = "Backport of PEP 654 (exception groups)" optional = false python-versions = ">=3.7" +groups = ["dev"] +markers = "python_version < \"3.11\"" files = [ {file = "exceptiongroup-1.3.0-py3-none-any.whl", hash = "sha256:4d111e6e0c13d0644cad6ddaa7ed0261a0b36971f6d23e7ec9b4b9097da78a10"}, {file = "exceptiongroup-1.3.0.tar.gz", hash = "sha256:b241f5885f560bc56a59ee63ca4c6a8bfa46ae4ad651af316d4e81817bb9fd88"}, @@ -78,6 +86,7 @@ version = "3.18.0" description = "A platform independent file lock." optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "filelock-3.18.0-py3-none-any.whl", hash = "sha256:c401f4f8377c4464e6db25fff06205fd89bdd83b65eb0488ed1b160f780e21de"}, {file = "filelock-3.18.0.tar.gz", hash = "sha256:adbc88eabb99d2fec8c9c1b229b171f18afa655400173ddc653d5d01501fb9f2"}, @@ -86,7 +95,7 @@ files = [ [package.extras] docs = ["furo (>=2024.8.6)", "sphinx (>=8.1.3)", "sphinx-autodoc-typehints (>=3)"] testing = ["covdefaults (>=2.3)", "coverage (>=7.6.10)", "diff-cover (>=9.2.1)", "pytest (>=8.3.4)", "pytest-asyncio (>=0.25.2)", "pytest-cov (>=6)", "pytest-mock (>=3.14)", "pytest-timeout (>=2.3.1)", "virtualenv (>=20.28.1)"] -typing = ["typing-extensions (>=4.12.2)"] +typing = ["typing-extensions (>=4.12.2) ; python_version < \"3.11\""] [[package]] name = "identify" @@ -94,6 +103,7 @@ version = "2.6.12" description = "File identification library for Python" optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "identify-2.6.12-py2.py3-none-any.whl", hash = "sha256:ad9672d5a72e0d2ff7c5c8809b62dfa60458626352fb0eb7b55e69bdc45334a2"}, {file = "identify-2.6.12.tar.gz", hash = "sha256:d8de45749f1efb108badef65ee8386f0f7bb19a7f26185f74de6367bffbaf0e6"}, @@ -108,6 +118,8 @@ version = "8.7.0" description = "Read metadata from Python packages" optional = false python-versions = ">=3.9" +groups = ["dev"] +markers = "python_version < \"3.10\"" files = [ {file = "importlib_metadata-8.7.0-py3-none-any.whl", hash = "sha256:e5dd1551894c77868a30651cef00984d50e1002d06942a7101d34870c5f02afd"}, {file = "importlib_metadata-8.7.0.tar.gz", hash = "sha256:d13b81ad223b890aa16c5471f2ac3056cf76c5f10f82d6f9292f0b415f389000"}, @@ -117,12 +129,12 @@ files = [ zipp = ">=3.20" [package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] enabler = ["pytest-enabler (>=2.2)"] perf = ["ipython"] -test = ["flufl.flake8", "importlib_resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"] +test = ["flufl.flake8", "importlib_resources (>=1.3) ; python_version < \"3.9\"", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"] type = ["pytest-mypy"] [[package]] @@ -131,6 +143,7 @@ version = "2.1.0" description = "brain-dead simple config-ini parsing" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "iniconfig-2.1.0-py3-none-any.whl", hash = "sha256:9deba5723312380e77435581c6bf4935c94cbfab9b1ed33ef8d238ea168eb760"}, {file = "iniconfig-2.1.0.tar.gz", hash = "sha256:3abbd2e30b36733fee78f9c7f7308f2d0050e88f0087fd25c2645f63c773e1c7"}, @@ -142,6 +155,8 @@ version = "1.16.3" description = "Mach-O header analysis and editing" optional = false python-versions = "*" +groups = ["dev"] +markers = "sys_platform == \"darwin\"" files = [ {file = "macholib-1.16.3-py2.py3-none-any.whl", hash = "sha256:0e315d7583d38b8c77e815b1ecbdbf504a8258d8b3e17b61165c6feb60d18f2c"}, {file = "macholib-1.16.3.tar.gz", hash = "sha256:07ae9e15e8e4cd9a788013d81f5908b3609aa76f9b1421bae9c4d7606ec86a30"}, @@ -156,6 +171,7 @@ version = "1.9.1" description = "Node.js virtual environment builder" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" +groups = ["dev"] files = [ {file = "nodeenv-1.9.1-py2.py3-none-any.whl", hash = "sha256:ba11c9782d29c27c70ffbdda2d7415098754709be8a7056d79a737cd901155c9"}, {file = "nodeenv-1.9.1.tar.gz", hash = "sha256:6ec12890a2dab7946721edbfbcd91f3319c6ccc9aec47be7c7e6b7011ee6645f"}, @@ -167,6 +183,7 @@ version = "25.0" description = "Core utilities for Python packages" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "packaging-25.0-py3-none-any.whl", hash = "sha256:29572ef2b1f17581046b3a2227d5c611fb25ec70ca1ba8554b24b0e69331a484"}, {file = "packaging-25.0.tar.gz", hash = "sha256:d443872c98d677bf60f6a1f2f8c1cb748e8fe762d2bf9d3148b5599295b0fc4f"}, @@ -178,6 +195,7 @@ version = "0.2.1" description = "Bring colors to your terminal." optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +groups = ["dev"] files = [ {file = "pastel-0.2.1-py2.py3-none-any.whl", hash = "sha256:4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364"}, {file = "pastel-0.2.1.tar.gz", hash = "sha256:e6581ac04e973cac858828c6202c1e1e81fee1dc7de7683f3e1ffe0bfd8a573d"}, @@ -189,6 +207,8 @@ version = "2023.2.7" description = "Python PE parsing module" optional = false python-versions = ">=3.6.0" +groups = ["dev"] +markers = "sys_platform == \"win32\"" files = [ {file = "pefile-2023.2.7-py3-none-any.whl", hash = "sha256:da185cd2af68c08a6cd4481f7325ed600a88f6a813bad9dea07ab3ef73d8d8d6"}, {file = "pefile-2023.2.7.tar.gz", hash = "sha256:82e6114004b3d6911c77c3953e3838654b04511b8b66e8583db70c65998017dc"}, @@ -200,6 +220,7 @@ version = "4.3.8" description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`." optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "platformdirs-4.3.8-py3-none-any.whl", hash = "sha256:ff7059bb7eb1179e2685604f4aaf157cfd9535242bd23742eadc3c13542139b4"}, {file = "platformdirs-4.3.8.tar.gz", hash = "sha256:3d512d96e16bcb959a814c9f348431070822a6496326a4be0911c40b5a74c2bc"}, @@ -216,6 +237,7 @@ version = "1.6.0" description = "plugin and hook calling mechanisms for python" optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "pluggy-1.6.0-py3-none-any.whl", hash = "sha256:e920276dd6813095e9377c0bc5566d94c932c33b27a3e3945d8389c374dd4746"}, {file = "pluggy-1.6.0.tar.gz", hash = "sha256:7dcc130b76258d33b90f61b658791dede3486c3e6bfb003ee5c9bfb396dd22f3"}, @@ -231,6 +253,7 @@ version = "0.36.0" description = "A task runner that works well with poetry and uv." optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "poethepoet-0.36.0-py3-none-any.whl", hash = "sha256:693e3c1eae9f6731d3613c3c0c40f747d3c5c68a375beda42e590a63c5623308"}, {file = "poethepoet-0.36.0.tar.gz", hash = "sha256:2217b49cb4e4c64af0b42ff8c4814b17f02e107d38bc461542517348ede25663"}, @@ -242,17 +265,18 @@ pyyaml = ">=6.0.2,<7.0" tomli = {version = ">=1.2.2", markers = "python_version < \"3.11\""} [package.extras] -poetry-plugin = ["poetry (>=1.2.0,<3.0.0)"] +poetry-plugin = ["poetry (>=1.2.0,<3.0.0) ; python_version < \"4.0\""] [[package]] name = "pre-commit" -version = "4.2.0" +version = "4.3.0" description = "A framework for managing and maintaining multi-language pre-commit hooks." optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ - {file = "pre_commit-4.2.0-py2.py3-none-any.whl", hash = "sha256:a009ca7205f1eb497d10b845e52c838a98b6cdd2102a6c8e4540e94ee75c58bd"}, - {file = "pre_commit-4.2.0.tar.gz", hash = "sha256:601283b9757afd87d40c4c4a9b2b5de9637a8ea02eaff7adc2d0fb4e04841146"}, + {file = "pre_commit-4.3.0-py2.py3-none-any.whl", hash = "sha256:2b0747ad7e6e967169136edffee14c16e148a778a54e4f967921aa1ebf2308d8"}, + {file = "pre_commit-4.3.0.tar.gz", hash = "sha256:499fe450cc9d42e9d58e606262795ecb64dd05438943c62b66f6a8673da30b16"}, ] [package.dependencies] @@ -268,6 +292,7 @@ version = "2.11.7" description = "Data validation using Python type hints" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "pydantic-2.11.7-py3-none-any.whl", hash = "sha256:dde5df002701f6de26248661f6835bbe296a47bf73990135c7d07ce741b9623b"}, {file = "pydantic-2.11.7.tar.gz", hash = "sha256:d989c3c6cb79469287b1569f7447a17848c998458d49ebe294e975b9baf0f0db"}, @@ -281,7 +306,7 @@ typing-inspection = ">=0.4.0" [package.extras] email = ["email-validator (>=2.0.0)"] -timezone = ["tzdata"] +timezone = ["tzdata ; python_version >= \"3.9\" and platform_system == \"Windows\""] [[package]] name = "pydantic-core" @@ -289,6 +314,7 @@ version = "2.33.2" description = "Core functionality for Pydantic validation and serialization" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "pydantic_core-2.33.2-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:2b3d326aaef0c0399d9afffeb6367d5e26ddc24d351dbc9c636840ac355dc5d8"}, {file = "pydantic_core-2.33.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:0e5b2671f05ba48b94cb90ce55d8bdcaaedb8ba00cc5359f6810fc918713983d"}, @@ -400,6 +426,7 @@ version = "2.19.2" description = "Pygments is a syntax highlighting package written in Python." optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "pygments-2.19.2-py3-none-any.whl", hash = "sha256:86540386c03d588bb81d44bc3928634ff26449851e99741617ecb9037ee5ec0b"}, {file = "pygments-2.19.2.tar.gz", hash = "sha256:636cb2477cec7f8952536970bc533bc43743542f70392ae026374600add5b887"}, @@ -414,6 +441,7 @@ version = "6.15.0" description = "PyInstaller bundles a Python application and all its dependencies into a single package." optional = false python-versions = "<3.15,>=3.8" +groups = ["dev"] files = [ {file = "pyinstaller-6.15.0-py3-none-macosx_10_13_universal2.whl", hash = "sha256:9f00c71c40148cd1e61695b2c6f1e086693d3bcf9bfa22ab513aa4254c3b966f"}, {file = "pyinstaller-6.15.0-py3-none-manylinux2014_aarch64.whl", hash = "sha256:cbcc8eb77320c60722030ac875883b564e00768fe3ff1721c7ba3ad0e0a277e9"}, @@ -449,6 +477,7 @@ version = "2025.8" description = "Community maintained hooks for PyInstaller" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "pyinstaller_hooks_contrib-2025.8-py3-none-any.whl", hash = "sha256:8d0b8cfa0cb689a619294ae200497374234bd4e3994b3ace2a4442274c899064"}, {file = "pyinstaller_hooks_contrib-2025.8.tar.gz", hash = "sha256:3402ad41dfe9b5110af134422e37fc5d421ba342c6cb980bd67cb30b7415641c"}, @@ -465,6 +494,7 @@ version = "1.9.0" description = "A cross-platform clipboard module for Python. (Only handles plain text for now.)" optional = false python-versions = "*" +groups = ["ui"] files = [ {file = "pyperclip-1.9.0.tar.gz", hash = "sha256:b7de0142ddc81bfc5c7507eea19da920b92252b548b96186caf94a5e2527d310"}, ] @@ -475,6 +505,7 @@ version = "8.4.1" description = "pytest: simple powerful testing with Python" optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "pytest-8.4.1-py3-none-any.whl", hash = "sha256:539c70ba6fcead8e78eebbf1115e8b589e7565830d7d006a8723f19ac8a0afb7"}, {file = "pytest-8.4.1.tar.gz", hash = "sha256:7c67fd69174877359ed9371ec3af8a3d2b04741818c51e5e99cc1742251fa93c"}, @@ -498,6 +529,8 @@ version = "0.2.3" description = "A (partial) reimplementation of pywin32 using ctypes/cffi" optional = false python-versions = ">=3.6" +groups = ["dev"] +markers = "sys_platform == \"win32\"" files = [ {file = "pywin32-ctypes-0.2.3.tar.gz", hash = "sha256:d162dc04946d704503b2edc4d55f3dba5c1d539ead017afa00142c38b9885755"}, {file = "pywin32_ctypes-0.2.3-py3-none-any.whl", hash = "sha256:8a1513379d709975552d202d942d9837758905c8d01eb82b8bcc30918929e7b8"}, @@ -509,6 +542,7 @@ version = "6.0.2" description = "YAML parser and emitter for Python" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "PyYAML-6.0.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:0a9a2848a5b7feac301353437eb7d5957887edbf81d56e903999a75a3d743086"}, {file = "PyYAML-6.0.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:29717114e51c84ddfba879543fb232a6ed60086602313ca38cce623c1d62cfbf"}, @@ -571,19 +605,20 @@ version = "80.9.0" description = "Easily download, build, install, upgrade, and uninstall Python packages" optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "setuptools-80.9.0-py3-none-any.whl", hash = "sha256:062d34222ad13e0cc312a4c02d73f059e86a4acbfbdea8f8f76b28c99f306922"}, {file = "setuptools-80.9.0.tar.gz", hash = "sha256:f36b47402ecde768dbfafc46e8e4207b4360c654f1f3bb84475f0a28628fb19c"}, ] [package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)", "ruff (>=0.8.0)"] -core = ["importlib_metadata (>=6)", "jaraco.functools (>=4)", "jaraco.text (>=3.7)", "more_itertools", "more_itertools (>=8.8)", "packaging (>=24.2)", "platformdirs (>=4.2.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\"", "ruff (>=0.8.0) ; sys_platform != \"cygwin\""] +core = ["importlib_metadata (>=6) ; python_version < \"3.10\"", "jaraco.functools (>=4)", "jaraco.text (>=3.7)", "more_itertools", "more_itertools (>=8.8)", "packaging (>=24.2)", "platformdirs (>=4.2.2)", "tomli (>=2.0.1) ; python_version < \"3.11\"", "wheel (>=0.43.0)"] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier", "towncrier (<24.7)"] enabler = ["pytest-enabler (>=2.2)"] -test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.7.2)", "jaraco.test (>=5.5)", "packaging (>=24.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-home (>=0.5)", "pytest-perf", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"] -type = ["importlib_metadata (>=7.0.2)", "jaraco.develop (>=7.21)", "mypy (==1.14.*)", "pytest-mypy"] +test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21) ; python_version >= \"3.9\" and sys_platform != \"cygwin\"", "jaraco.envs (>=2.2)", "jaraco.path (>=3.7.2)", "jaraco.test (>=5.5)", "packaging (>=24.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-home (>=0.5)", "pytest-perf ; sys_platform != \"cygwin\"", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"] +type = ["importlib_metadata (>=7.0.2) ; python_version < \"3.10\"", "jaraco.develop (>=7.21) ; sys_platform != \"cygwin\"", "mypy (==1.14.*)", "pytest-mypy"] [[package]] name = "tomli" @@ -591,6 +626,8 @@ version = "2.2.1" description = "A lil' TOML parser" optional = false python-versions = ">=3.8" +groups = ["dev"] +markers = "python_version < \"3.11\"" files = [ {file = "tomli-2.2.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:678e4fa69e4575eb77d103de3df8a895e1591b48e740211bd1067378c69e8249"}, {file = "tomli-2.2.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:023aa114dd824ade0100497eb2318602af309e5a55595f76b626d6d9f3b7b0a6"}, @@ -632,10 +669,12 @@ version = "4.14.1" description = "Backported and Experimental Type Hints for Python 3.9+" optional = false python-versions = ">=3.9" +groups = ["main", "dev"] files = [ {file = "typing_extensions-4.14.1-py3-none-any.whl", hash = "sha256:d1e1e3b58374dc93031d6eda2420a48ea44a36c2b4766a4fdeb3710755731d76"}, {file = "typing_extensions-4.14.1.tar.gz", hash = "sha256:38b39f4aeeab64884ce9f74c94263ef78f3c22467c8724005483154c26648d36"}, ] +markers = {dev = "python_version < \"3.11\""} [[package]] name = "typing-inspection" @@ -643,6 +682,7 @@ version = "0.4.1" description = "Runtime typing introspection tools" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "typing_inspection-0.4.1-py3-none-any.whl", hash = "sha256:389055682238f53b04f7badcb49b989835495a96700ced5dab2d8feae4b26f51"}, {file = "typing_inspection-0.4.1.tar.gz", hash = "sha256:6ae134cc0203c33377d43188d4064e9b357dba58cff3185f22924610e70a9d28"}, @@ -657,6 +697,7 @@ version = "20.33.0" description = "Virtual Python Environment builder" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "virtualenv-20.33.0-py3-none-any.whl", hash = "sha256:106b6baa8ab1b526d5a9b71165c85c456fbd49b16976c88e2bc9352ee3bc5d3f"}, {file = "virtualenv-20.33.0.tar.gz", hash = "sha256:47e0c0d2ef1801fce721708ccdf2a28b9403fa2307c3268aebd03225976f61d2"}, @@ -669,7 +710,7 @@ platformdirs = ">=3.9.1,<5" [package.extras] docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] -test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"] +test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8) ; platform_python_implementation == \"PyPy\" or platform_python_implementation == \"GraalVM\" or platform_python_implementation == \"CPython\" and sys_platform == \"win32\" and python_version >= \"3.13\"", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10) ; platform_python_implementation == \"CPython\""] [[package]] name = "zipp" @@ -677,13 +718,15 @@ version = "3.23.0" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.9" +groups = ["dev"] +markers = "python_version < \"3.10\"" files = [ {file = "zipp-3.23.0-py3-none-any.whl", hash = "sha256:071652d6115ed432f5ce1d34c336c0adfd6a884660d1e9712a256d3d3bd4b14e"}, {file = "zipp-3.23.0.tar.gz", hash = "sha256:a07157588a12518c9d4034df3fbbee09c814741a33ff63c05fa29d26a2404166"}, ] [package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] enabler = ["pytest-enabler (>=2.2)"] @@ -691,6 +734,6 @@ test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more_it type = ["pytest-mypy"] [metadata] -lock-version = "2.0" +lock-version = "2.1" python-versions = ">=3.9,<3.13" -content-hash = "185677ed863787199abf62232ff60a1cbe30a06b054d5daf9adf690aee944002" +content-hash = "10e73b8ef8ce23a9129fafe16b30283f6edb17e5879e4133bdcd6be679330eb2" diff --git a/pyproject.toml b/pyproject.toml index 8a02438..5b15d5b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -13,7 +13,7 @@ pydantic = "2.11.7" [tool.poetry.group.dev.dependencies] pytest = "^8.4.1" -pre-commit = "^4.2.0" +pre-commit = "^4.3.0" pyinstaller = "^6.15.0" poethepoet = "^0.36.0" From 786eeacf741a3115d13cf8845c7ec0634ab879e9 Mon Sep 17 00:00:00 2001 From: Lina Date: Mon, 15 Sep 2025 15:48:50 +0200 Subject: [PATCH 02/58] update[pyproject]: pytest, pyinstaller, poethepoet, pydantic, chardet --- poetry.lock | 164 +++++++++++++++++++------------------------------ pyproject.toml | 9 +-- 2 files changed, 69 insertions(+), 104 deletions(-) diff --git a/poetry.lock b/poetry.lock index 88ffc23..8a8e5e0 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. [[package]] name = "altgraph" @@ -6,7 +6,6 @@ version = "0.17.4" description = "Python graph (network) package" optional = false python-versions = "*" -groups = ["dev"] files = [ {file = "altgraph-0.17.4-py2.py3-none-any.whl", hash = "sha256:642743b4750de17e655e6711601b077bc6598dbfa3ba5fa2b2a35ce12b508dff"}, {file = "altgraph-0.17.4.tar.gz", hash = "sha256:1b5afbb98f6c4dcadb2e2ae6ab9fa994bbb8c1d75f4fa96d340f9437ae454406"}, @@ -18,7 +17,6 @@ version = "0.7.0" description = "Reusable constraint types to use with typing.Annotated" optional = false python-versions = ">=3.8" -groups = ["main"] files = [ {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, @@ -30,20 +28,28 @@ version = "3.4.0" description = "Validate configuration and produce human readable error messages." optional = false python-versions = ">=3.8" -groups = ["dev"] files = [ {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"}, {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"}, ] +[[package]] +name = "chardet" +version = "5.2.0" +description = "Universal encoding detector for Python 3" +optional = false +python-versions = ">=3.7" +files = [ + {file = "chardet-5.2.0-py3-none-any.whl", hash = "sha256:e1cf59446890a00105fe7b7912492ea04b6e6f06d4b742b2c788469e34c82970"}, + {file = "chardet-5.2.0.tar.gz", hash = "sha256:1b3b6ff479a8c414bc3fa2c0852995695c4a026dcd6d0633b2dd092ca39c1cf7"}, +] + [[package]] name = "colorama" version = "0.4.6" description = "Cross-platform colored terminal text." optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" -groups = ["dev"] -markers = "sys_platform == \"win32\"" files = [ {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"}, {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"}, @@ -55,7 +61,6 @@ version = "0.4.0" description = "Distribution utilities" optional = false python-versions = "*" -groups = ["dev"] files = [ {file = "distlib-0.4.0-py2.py3-none-any.whl", hash = "sha256:9659f7d87e46584a30b5780e43ac7a2143098441670ff0a49d5f9034c54a6c16"}, {file = "distlib-0.4.0.tar.gz", hash = "sha256:feec40075be03a04501a973d81f633735b4b69f98b05450592310c0f401a4e0d"}, @@ -67,8 +72,6 @@ version = "1.3.0" description = "Backport of PEP 654 (exception groups)" optional = false python-versions = ">=3.7" -groups = ["dev"] -markers = "python_version < \"3.11\"" files = [ {file = "exceptiongroup-1.3.0-py3-none-any.whl", hash = "sha256:4d111e6e0c13d0644cad6ddaa7ed0261a0b36971f6d23e7ec9b4b9097da78a10"}, {file = "exceptiongroup-1.3.0.tar.gz", hash = "sha256:b241f5885f560bc56a59ee63ca4c6a8bfa46ae4ad651af316d4e81817bb9fd88"}, @@ -82,31 +85,24 @@ test = ["pytest (>=6)"] [[package]] name = "filelock" -version = "3.18.0" +version = "3.19.1" description = "A platform independent file lock." optional = false python-versions = ">=3.9" -groups = ["dev"] files = [ - {file = "filelock-3.18.0-py3-none-any.whl", hash = "sha256:c401f4f8377c4464e6db25fff06205fd89bdd83b65eb0488ed1b160f780e21de"}, - {file = "filelock-3.18.0.tar.gz", hash = "sha256:adbc88eabb99d2fec8c9c1b229b171f18afa655400173ddc653d5d01501fb9f2"}, + {file = "filelock-3.19.1-py3-none-any.whl", hash = "sha256:d38e30481def20772f5baf097c122c3babc4fcdb7e14e57049eb9d88c6dc017d"}, + {file = "filelock-3.19.1.tar.gz", hash = "sha256:66eda1888b0171c998b35be2bcc0f6d75c388a7ce20c3f3f37aa8e96c2dddf58"}, ] -[package.extras] -docs = ["furo (>=2024.8.6)", "sphinx (>=8.1.3)", "sphinx-autodoc-typehints (>=3)"] -testing = ["covdefaults (>=2.3)", "coverage (>=7.6.10)", "diff-cover (>=9.2.1)", "pytest (>=8.3.4)", "pytest-asyncio (>=0.25.2)", "pytest-cov (>=6)", "pytest-mock (>=3.14)", "pytest-timeout (>=2.3.1)", "virtualenv (>=20.28.1)"] -typing = ["typing-extensions (>=4.12.2) ; python_version < \"3.11\""] - [[package]] name = "identify" -version = "2.6.12" +version = "2.6.14" description = "File identification library for Python" optional = false python-versions = ">=3.9" -groups = ["dev"] files = [ - 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sys_platform != \"cygwin\""] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] enabler = ["pytest-enabler (>=2.2)"] @@ -734,6 +698,6 @@ test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more_it type = ["pytest-mypy"] [metadata] -lock-version = "2.1" +lock-version = "2.0" python-versions = ">=3.9,<3.13" -content-hash = "10e73b8ef8ce23a9129fafe16b30283f6edb17e5879e4133bdcd6be679330eb2" +content-hash = "090d0ec7c8c410647a0ab8b7b8eb1c9394ef5887e0f2c7cefd54828d879ac2da" diff --git a/pyproject.toml b/pyproject.toml index 5b15d5b..dd51b37 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,13 +9,14 @@ packages = [ ] [tool.poetry.dependencies] python = ">=3.9,<3.13" -pydantic = "2.11.7" +pydantic = "2.11.9" +chardet = "^5.2.0" [tool.poetry.group.dev.dependencies] -pytest = "^8.4.1" +pytest = "^8.4.2" pre-commit = "^4.3.0" -pyinstaller = "^6.15.0" -poethepoet = "^0.36.0" +pyinstaller = "^6.16.0" +poethepoet = "^0.37.0" [tool.poetry.group.ui.dependencies] pyperclip = "^1.9.0" From 1e5a130ecc5d46264062e6dbaa2674380b8c6af5 Mon Sep 17 00:00:00 2001 From: Lina Date: Mon, 15 Sep 2025 15:55:59 +0200 Subject: [PATCH 03/58] Create python-package.yml --- .github/workflows/python-package.yml | 40 ++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 .github/workflows/python-package.yml diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml new file mode 100644 index 0000000..2576ba8 --- /dev/null +++ b/.github/workflows/python-package.yml @@ -0,0 +1,40 @@ +# This workflow will install Python dependencies, run tests and lint with a variety of Python versions +# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python + +name: pythonQEPest + +on: + push: + branches: [ "development" ] + pull_request: + branches: [ "development" , "release" ] + +jobs: + build: + + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: ["3.9", "3.10", "3.11"] + + steps: + - uses: actions/checkout@v4 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v3 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + python -m pip install poetry + python -m poetry install + # - name: Lint with flake8 + # run: | + # # stop the build if there are Python syntax errors or undefined names + # flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + # # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide + # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + - name: Test with pytest + run: | + pytest From 5753c89a229310409c3c4e1032c5a48790d616cc Mon Sep 17 00:00:00 2001 From: Lina Date: Mon, 22 Sep 2025 22:09:45 +0200 Subject: [PATCH 04/58] update[pyproject]: poethepoet --- poetry.lock | 1214 +++++++++++++++++++++++++++++++++++++++++++++++- pyproject.toml | 5 +- 2 files changed, 1208 insertions(+), 11 deletions(-) diff --git a/poetry.lock b/poetry.lock index 8a8e5e0..ab84fe3 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. 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+1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand. [[package]] name = "altgraph" @@ -6,6 +6,7 @@ version = "0.17.4" description = "Python graph (network) package" optional = false python-versions = "*" +groups = ["dev"] files = [ {file = "altgraph-0.17.4-py2.py3-none-any.whl", hash = "sha256:642743b4750de17e655e6711601b077bc6598dbfa3ba5fa2b2a35ce12b508dff"}, {file = "altgraph-0.17.4.tar.gz", hash = "sha256:1b5afbb98f6c4dcadb2e2ae6ab9fa994bbb8c1d75f4fa96d340f9437ae454406"}, @@ -17,6 +18,7 @@ version = "0.7.0" description = "Reusable constraint types to use with typing.Annotated" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, @@ -28,6 +30,7 @@ version = "4.10.0" description = "High-level concurrency and networking framework on top of asyncio or Trio" optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "anyio-4.10.0-py3-none-any.whl", hash = "sha256:60e474ac86736bbfd6f210f7a61218939c318f43f9972497381f1c5e930ed3d1"}, {file = "anyio-4.10.0.tar.gz", hash = "sha256:3f3fae35c96039744587aa5b8371e7e8e603c0702999535961dd336026973ba6"}, @@ -48,6 +51,8 @@ version = "1.2.0" description = "Backport of CPython tarfile module" optional = false python-versions = ">=3.8" +groups = ["dev"] +markers = "python_version < \"3.12\"" files = [ {file = "backports.tarfile-1.2.0-py3-none-any.whl", hash = "sha256:77e284d754527b01fb1e6fa8a1afe577858ebe4e9dad8919e34c862cb399bc34"}, {file = "backports_tarfile-1.2.0.tar.gz", hash = "sha256:d75e02c268746e1b8144c278978b6e98e85de6ad16f8e4b0844a154557eca991"}, @@ -63,6 +68,7 @@ version = "1.3.0" description = "A simple, correct Python build frontend" optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "build-1.3.0-py3-none-any.whl", hash = "sha256:7145f0b5061ba90a1500d60bd1b13ca0a8a4cebdd0cc16ed8adf1c0e739f43b4"}, {file = "build-1.3.0.tar.gz", hash = "sha256:698edd0ea270bde950f53aed21f3a0135672206f3911e0176261a31e0e07b397"}, @@ -77,7 +83,7 @@ tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""} [package.extras] uv = ["uv (>=0.1.18)"] -virtualenv = ["virtualenv (>=20.11)", "virtualenv (>=20.17)", "virtualenv (>=20.31)"] +virtualenv = ["virtualenv (>=20.11) ; python_version < \"3.10\"", "virtualenv (>=20.17) ; python_version >= \"3.10\" and python_version < \"3.14\"", "virtualenv (>=20.31) ; python_version >= \"3.14\""] [[package]] name = "cachecontrol" @@ -85,6 +91,7 @@ version = "0.14.3" description = "httplib2 caching for requests" optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "cachecontrol-0.14.3-py3-none-any.whl", hash = "sha256:b35e44a3113f17d2a31c1e6b27b9de6d4405f84ae51baa8c1d3cc5b633010cae"}, {file = "cachecontrol-0.14.3.tar.gz", hash = "sha256:73e7efec4b06b20d9267b441c1f733664f989fb8688391b670ca812d70795d11"}, @@ -106,6 +113,7 @@ version = "2025.8.3" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.7" +groups = ["dev"] files = [ {file = "certifi-2025.8.3-py3-none-any.whl", hash = "sha256:f6c12493cfb1b06ba2ff328595af9350c65d6644968e5d3a2ffd78699af217a5"}, {file = "certifi-2025.8.3.tar.gz", hash = "sha256:e564105f78ded564e3ae7c923924435e1daa7463faeab5bb932bc53ffae63407"}, @@ -117,6 +125,8 @@ version = "2.0.0" description = "Foreign Function Interface for Python calling C code." optional = false python-versions = ">=3.9" +groups = ["dev"] +markers = "(sys_platform == \"linux\" or sys_platform == \"darwin\") and (platform_python_implementation != \"PyPy\" or sys_platform == \"darwin\")" files = [ {file = "cffi-2.0.0-cp310-cp310-macosx_10_13_x86_64.whl", hash = "sha256:0cf2d91ecc3fcc0625c2c530fe004f82c110405f101548512cce44322fa8ac44"}, {file = "cffi-2.0.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:f73b96c41e3b2adedc34a7356e64c8eb96e03a3782b535e043a986276ce12a49"}, @@ -213,6 +223,7 @@ version = "3.4.0" description = "Validate configuration and produce human readable error messages." optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"}, {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"}, @@ -224,6 +235,7 @@ version = "3.4.3" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." optional = false python-versions = ">=3.7" +groups = ["dev"] files = [ {file = "charset_normalizer-3.4.3-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:fb7f67a1bfa6e40b438170ebdc8158b78dc465a5a67b6dde178a46987b244a72"}, {file = "charset_normalizer-3.4.3-cp310-cp310-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:cc9370a2da1ac13f0153780040f465839e6cccb4a1e44810124b4e22483c93fe"}, @@ -312,6 +324,7 @@ version = "2.1.0" description = "Cleo allows you to create beautiful and testable command-line interfaces." optional = false python-versions = ">=3.7,<4.0" +groups = ["dev"] files = [ {file = "cleo-2.1.0-py3-none-any.whl", hash = "sha256:4a31bd4dd45695a64ee3c4758f583f134267c2bc518d8ae9a29cf237d009b07e"}, {file = "cleo-2.1.0.tar.gz", hash = "sha256:0b2c880b5d13660a7ea651001fb4acb527696c01f15c9ee650f377aa543fd523"}, @@ -327,6 +340,8 @@ version = "0.4.6" description = "Cross-platform colored terminal text." optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" +groups = ["dev"] +markers = "os_name == \"nt\" or sys_platform == \"win32\"" files = [ {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"}, {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"}, @@ -338,6 +353,7 @@ version = "0.4.1" description = "Manage Python errors with ease" optional = false python-versions = ">=3.7,<4.0" +groups = ["dev"] files = [ {file = "crashtest-0.4.1-py3-none-any.whl", hash = "sha256:8d23eac5fa660409f57472e3851dab7ac18aba459a8d19cbbba86d3d5aecd2a5"}, {file = "crashtest-0.4.1.tar.gz", hash = "sha256:80d7b1f316ebfbd429f648076d6275c877ba30ba48979de4191714a75266f0ce"}, @@ -349,6 +365,8 @@ version = "43.0.3" description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers." optional = false python-versions = ">=3.7" +groups = ["dev"] +markers = "sys_platform == \"linux\"" files = [ {file = "cryptography-43.0.3-cp37-abi3-macosx_10_9_universal2.whl", hash = "sha256:bf7a1932ac4176486eab36a19ed4c0492da5d97123f1406cf15e41b05e787d2e"}, {file = "cryptography-43.0.3-cp37-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:63efa177ff54aec6e1c0aefaa1a241232dcd37413835a9b674b6e3f0ae2bfd3e"}, @@ -398,6 +416,7 @@ version = "0.4.0" description = "Distribution utilities" optional = false python-versions = "*" +groups = ["dev"] files = [ {file = "distlib-0.4.0-py2.py3-none-any.whl", hash = "sha256:9659f7d87e46584a30b5780e43ac7a2143098441670ff0a49d5f9034c54a6c16"}, {file = "distlib-0.4.0.tar.gz", hash = "sha256:feec40075be03a04501a973d81f633735b4b69f98b05450592310c0f401a4e0d"}, @@ -409,6 +428,7 @@ version = "0.24.1" description = "Python Git Library" optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "dulwich-0.24.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:2169c36b7955b40e1ec9b0543301a3dd536718c3b7840959ca70e7ed17397c25"}, {file = "dulwich-0.24.1-cp310-cp310-manylinux_2_28_aarch64.whl", hash = "sha256:d16507ca6d6c2d29d7d942da4cc50fa589d58ab066030992dfa3932de6695062"}, @@ -459,6 +479,8 @@ version = "1.3.0" description = "Backport of PEP 654 (exception groups)" optional = false python-versions = ">=3.7" +groups = ["dev"] +markers = "python_version < \"3.11\"" files = [ {file = "exceptiongroup-1.3.0-py3-none-any.whl", hash = "sha256:4d111e6e0c13d0644cad6ddaa7ed0261a0b36971f6d23e7ec9b4b9097da78a10"}, {file = "exceptiongroup-1.3.0.tar.gz", hash = "sha256:b241f5885f560bc56a59ee63ca4c6a8bfa46ae4ad651af316d4e81817bb9fd88"}, @@ -476,6 +498,7 @@ version = "2.21.2" description = "Fastest Python implementation of JSON schema" optional = false python-versions = "*" +groups = ["dev"] files = [ {file = "fastjsonschema-2.21.2-py3-none-any.whl", hash = "sha256:1c797122d0a86c5cace2e54bf4e819c36223b552017172f32c5c024a6b77e463"}, {file = "fastjsonschema-2.21.2.tar.gz", hash = "sha256:b1eb43748041c880796cd077f1a07c3d94e93ae84bba5ed36800a33554ae05de"}, @@ -490,6 +513,7 @@ version = "3.19.1" description = "A platform independent file lock." optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "filelock-3.19.1-py3-none-any.whl", hash = "sha256:d38e30481def20772f5baf097c122c3babc4fcdb7e14e57049eb9d88c6dc017d"}, {file = "filelock-3.19.1.tar.gz", hash = "sha256:66eda1888b0171c998b35be2bcc0f6d75c388a7ce20c3f3f37aa8e96c2dddf58"}, @@ -501,6 +525,7 @@ version = "0.7.0" description = "A utility to find python versions on your system" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "findpython-0.7.0-py3-none-any.whl", hash = "sha256:f53cfcc29536f5b83c962cf922bba8ff6d6a3c2a05fda6a45aa58a47d005d8fc"}, {file = "findpython-0.7.0.tar.gz", hash = "sha256:8b31647c76352779a3c1a0806699b68e6a7bdc0b5c2ddd9af2a07a0d40c673dc"}, @@ -516,6 +541,7 @@ version = "0.16.0" description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "h11-0.16.0-py3-none-any.whl", hash = "sha256:63cf8bbe7522de3bf65932fda1d9c2772064ffb3dae62d55932da54b31cb6c86"}, {file = "h11-0.16.0.tar.gz", hash = "sha256:4e35b956cf45792e4caa5885e69fba00bdbc6ffafbfa020300e549b208ee5ff1"}, @@ -527,6 +553,7 @@ version = "1.0.9" description = "A minimal low-level HTTP client." optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "httpcore-1.0.9-py3-none-any.whl", hash = "sha256:2d400746a40668fc9dec9810239072b40b4484b640a8c38fd654a024c7a1bf55"}, {file = "httpcore-1.0.9.tar.gz", hash = "sha256:6e34463af53fd2ab5d807f399a9b45ea31c3dfa2276f15a2c3f00afff6e176e8"}, @@ -548,6 +575,7 @@ version = "0.28.1" description = "The next generation HTTP client." optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "httpx-0.28.1-py3-none-any.whl", hash = "sha256:d909fcccc110f8c7faf814ca82a9a4d816bc5a6dbfea25d6591d6985b8ba59ad"}, {file = "httpx-0.28.1.tar.gz", hash = "sha256:75e98c5f16b0f35b567856f597f06ff2270a374470a5c2392242528e3e3e42fc"}, @@ -560,7 +588,7 @@ httpcore = "==1.*" idna = "*" [package.extras] -brotli = ["brotli", "brotlicffi"] +brotli = ["brotli ; platform_python_implementation == \"CPython\"", "brotlicffi ; platform_python_implementation != \"CPython\""] cli = ["click (==8.*)", "pygments (==2.*)", "rich (>=10,<14)"] http2 = ["h2 (>=3,<5)"] socks = ["socksio (==1.*)"] @@ -572,6 +600,7 @@ version = "2.6.14" description = "File identification library for Python" optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "identify-2.6.14-py2.py3-none-any.whl", hash = "sha256:11a073da82212c6646b1f39bb20d4483bfb9543bd5566fec60053c4bb309bf2e"}, {file = "identify-2.6.14.tar.gz", hash = "sha256:663494103b4f717cb26921c52f8751363dc89db64364cd836a9bf1535f53cd6a"}, @@ -586,6 +615,7 @@ version = "3.10" description = "Internationalized Domain Names in Applications (IDNA)" optional = false python-versions = ">=3.6" +groups = ["dev"] files = [ {file = "idna-3.10-py3-none-any.whl", hash = "sha256:946d195a0d259cbba61165e88e65941f16e9b36ea6ddb97f00452bae8b1287d3"}, {file = "idna-3.10.tar.gz", hash = "sha256:12f65c9b470abda6dc35cf8e63cc574b1c52b11df2c86030af0ac09b01b13ea9"}, @@ -600,6 +630,8 @@ version = "8.7.0" description = "Read metadata from Python packages" optional = false python-versions = ">=3.9" +groups = ["dev"] +markers = "python_version < \"3.12\"" files = [ {file = "importlib_metadata-8.7.0-py3-none-any.whl", hash = "sha256:e5dd1551894c77868a30651cef00984d50e1002d06942a7101d34870c5f02afd"}, {file = "importlib_metadata-8.7.0.tar.gz", hash = "sha256:d13b81ad223b890aa16c5471f2ac3056cf76c5f10f82d6f9292f0b415f389000"}, @@ -609,12 +641,12 @@ files = [ zipp = ">=3.20" [package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] enabler = ["pytest-enabler (>=2.2)"] perf = ["ipython"] -test = ["flufl.flake8", "importlib_resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"] +test = ["flufl.flake8", "importlib_resources (>=1.3) ; python_version < \"3.9\"", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"] type = ["pytest-mypy"] [[package]] @@ -623,6 +655,7 @@ version = "2.1.0" description = "brain-dead simple config-ini parsing" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "iniconfig-2.1.0-py3-none-any.whl", hash = "sha256:9deba5723312380e77435581c6bf4935c94cbfab9b1ed33ef8d238ea168eb760"}, {file = "iniconfig-2.1.0.tar.gz", hash = "sha256:3abbd2e30b36733fee78f9c7f7308f2d0050e88f0087fd25c2645f63c773e1c7"}, @@ -634,6 +667,7 @@ version = "0.7.0" description = "A library for installing Python wheels." optional = false python-versions = ">=3.7" +groups = ["dev"] files = [ {file = "installer-0.7.0-py3-none-any.whl", hash = "sha256:05d1933f0a5ba7d8d6296bb6d5018e7c94fa473ceb10cf198a92ccea19c27b53"}, {file = "installer-0.7.0.tar.gz", hash = "sha256:a26d3e3116289bb08216e0d0f7d925fcef0b0194eedfa0c944bcaaa106c4b631"}, @@ -645,6 +679,7 @@ version = "3.4.0" description = "Utility functions for Python class constructs" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "jaraco.classes-3.4.0-py3-none-any.whl", hash = "sha256:f662826b6bed8cace05e7ff873ce0f9283b5c924470fe664fff1c2f00f581790"}, {file = "jaraco.classes-3.4.0.tar.gz", hash = "sha256:47a024b51d0239c0dd8c8540c6c7f484be3b8fcf0b2d85c13825780d3b3f3acd"}, @@ -663,6 +698,7 @@ version = "6.0.1" description = "Useful decorators and context managers" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "jaraco.context-6.0.1-py3-none-any.whl", hash = "sha256:f797fc481b490edb305122c9181830a3a5b76d84ef6d1aef2fb9b47ab956f9e4"}, {file = "jaraco_context-6.0.1.tar.gz", hash = "sha256:9bae4ea555cf0b14938dc0aee7c9f32ed303aa20a3b73e7dc80111628792d1b3"}, @@ -673,7 +709,7 @@ files = [ [package.extras] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -test = ["portend", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)"] +test = ["portend", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] [[package]] name = "jaraco-functools" @@ -681,6 +717,7 @@ version = "4.3.0" description = "Functools like those found in stdlib" optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "jaraco_functools-4.3.0-py3-none-any.whl", hash = "sha256:227ff8ed6f7b8f62c56deff101545fa7543cf2c8e7b82a7c2116e672f29c26e8"}, {file = "jaraco_functools-4.3.0.tar.gz", hash = "sha256:cfd13ad0dd2c47a3600b439ef72d8615d482cedcff1632930d6f28924d92f294"}, @@ -690,7 +727,7 @@ files = [ more_itertools = "*" [package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] enabler = ["pytest-enabler (>=2.2)"] @@ -703,13 +740,15 @@ version = "0.9.0" description = "Low-level, pure Python DBus protocol wrapper." optional = false python-versions = ">=3.7" +groups = ["dev"] +markers = "sys_platform == \"linux\"" files = [ {file = "jeepney-0.9.0-py3-none-any.whl", hash = "sha256:97e5714520c16fc0a45695e5365a2e11b81ea79bba796e26f9f1d178cb182683"}, {file = "jeepney-0.9.0.tar.gz", hash = "sha256:cf0e9e845622b81e4a28df94c40345400256ec608d0e55bb8a3feaa9163f5732"}, ] [package.extras] -test = ["async-timeout", "pytest", "pytest-asyncio (>=0.17)", "pytest-trio", "testpath", "trio"] +test = ["async-timeout ; python_version < \"3.11\"", "pytest", "pytest-asyncio (>=0.17)", "pytest-trio", "testpath", "trio"] trio = ["trio"] [[package]] @@ -718,6 +757,7 @@ version = "25.6.0" description = "Store and access your passwords safely." optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "keyring-25.6.0-py3-none-any.whl", hash = "sha256:552a3f7af126ece7ed5c89753650eec89c7eaae8617d0aa4d9ad2b75111266bd"}, {file = "keyring-25.6.0.tar.gz", hash = "sha256:0b39998aa941431eb3d9b0d4b2460bc773b9df6fed7621c2dfb291a7e0187a66"}, @@ -733,7 +773,7 @@ pywin32-ctypes = {version = ">=0.2.0", markers = "sys_platform == \"win32\""} SecretStorage = {version = ">=3.2", markers = "sys_platform == \"linux\""} [package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] completion = ["shtab (>=1.1.0)"] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] @@ -747,6 +787,8 @@ version = "1.16.3" description = "Mach-O header analysis and editing" optional = false python-versions = "*" +groups = ["dev"] +markers = "sys_platform == \"darwin\"" files = [ {file = "macholib-1.16.3-py2.py3-none-any.whl", hash = "sha256:0e315d7583d38b8c77e815b1ecbdbf504a8258d8b3e17b61165c6feb60d18f2c"}, {file = "macholib-1.16.3.tar.gz", hash = "sha256:07ae9e15e8e4cd9a788013d81f5908b3609aa76f9b1421bae9c4d7606ec86a30"}, @@ -761,6 +803,7 @@ version = "10.8.0" description = "More routines for operating on iterables, beyond itertools" optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "more_itertools-10.8.0-py3-none-any.whl", hash = "sha256:52d4362373dcf7c52546bc4af9a86ee7c4579df9a8dc268be0a2f949d376cc9b"}, {file = "more_itertools-10.8.0.tar.gz", hash = "sha256:f638ddf8a1a0d134181275fb5d58b086ead7c6a72429ad725c67503f13ba30bd"}, @@ -772,6 +815,7 @@ version = "1.1.1" description = "MessagePack serializer" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "msgpack-1.1.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:353b6fc0c36fde68b661a12949d7d49f8f51ff5fa019c1e47c87c4ff34b080ed"}, {file = "msgpack-1.1.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:79c408fcf76a958491b4e3b103d1c417044544b68e96d06432a189b43d1215c8"}, @@ -840,6 +884,7 @@ version = "1.9.1" description = "Node.js virtual environment builder" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" +groups = ["dev"] files = [ {file = "nodeenv-1.9.1-py2.py3-none-any.whl", hash = "sha256:ba11c9782d29c27c70ffbdda2d7415098754709be8a7056d79a737cd901155c9"}, {file = "nodeenv-1.9.1.tar.gz", hash = "sha256:6ec12890a2dab7946721edbfbcd91f3319c6ccc9aec47be7c7e6b7011ee6645f"}, @@ -851,6 +896,7 @@ version = "25.0" description = "Core utilities for Python packages" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "packaging-25.0-py3-none-any.whl", hash = "sha256:29572ef2b1f17581046b3a2227d5c611fb25ec70ca1ba8554b24b0e69331a484"}, {file = "packaging-25.0.tar.gz", hash = "sha256:d443872c98d677bf60f6a1f2f8c1cb748e8fe762d2bf9d3148b5599295b0fc4f"}, @@ -862,6 +908,7 @@ version = "0.2.1" description = "Bring colors to your terminal." optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +groups = ["dev"] files = [ {file = "pastel-0.2.1-py2.py3-none-any.whl", hash = "sha256:4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364"}, {file = "pastel-0.2.1.tar.gz", hash = "sha256:e6581ac04e973cac858828c6202c1e1e81fee1dc7de7683f3e1ffe0bfd8a573d"}, @@ -873,6 +920,7 @@ version = "2025.9.18" description = "Installer for Python Build Standalone" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "pbs_installer-2025.9.18-py3-none-any.whl", hash = "sha256:8ef55d7675698747505c237015d14c81759bd66a0d4c8b20cec9a2dc96e8434c"}, {file = "pbs_installer-2025.9.18.tar.gz", hash = "sha256:c0a51a7c1e015723bd8396f02e15b5876e439f74b0f45bbac436b189f903219f"}, @@ -893,6 +941,8 @@ version = "2023.2.7" description = "Python PE parsing module" optional = false python-versions = ">=3.6.0" +groups = ["dev"] +markers = "sys_platform == \"win32\"" files = [ {file = "pefile-2023.2.7-py3-none-any.whl", hash = "sha256:da185cd2af68c08a6cd4481f7325ed600a88f6a813bad9dea07ab3ef73d8d8d6"}, {file = "pefile-2023.2.7.tar.gz", hash = "sha256:82e6114004b3d6911c77c3953e3838654b04511b8b66e8583db70c65998017dc"}, @@ -904,6 +954,7 @@ version = "1.12.1.2" description = "Query metadata from sdists / bdists / installed packages." optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "pkginfo-1.12.1.2-py3-none-any.whl", hash = "sha256:c783ac885519cab2c34927ccfa6bf64b5a704d7c69afaea583dd9b7afe969343"}, {file = "pkginfo-1.12.1.2.tar.gz", hash = "sha256:5cd957824ac36f140260964eba3c6be6442a8359b8c48f4adf90210f33a04b7b"}, @@ -918,6 +969,7 @@ version = "4.4.0" description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`." optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "platformdirs-4.4.0-py3-none-any.whl", hash = "sha256:abd01743f24e5287cd7a5db3752faf1a2d65353f38ec26d98e25a6db65958c85"}, {file = "platformdirs-4.4.0.tar.gz", hash = "sha256:ca753cf4d81dc309bc67b0ea38fd15dc97bc30ce419a7f58d13eb3bf14c4febf"}, @@ -934,6 +986,7 @@ version = "1.6.0" description = "plugin and hook calling mechanisms for python" optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "pluggy-1.6.0-py3-none-any.whl", hash = "sha256:e920276dd6813095e9377c0bc5566d94c932c33b27a3e3945d8389c374dd4746"}, {file = "pluggy-1.6.0.tar.gz", hash = "sha256:7dcc130b76258d33b90f61b658791dede3486c3e6bfb003ee5c9bfb396dd22f3"}, @@ -949,6 +1002,7 @@ version = "0.37.0" description = "A task runner that works well with poetry and uv." optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "poethepoet-0.37.0-py3-none-any.whl", hash = "sha256:861790276315abcc8df1b4bd60e28c3d48a06db273edd3092f3c94e1a46e5e22"}, {file = "poethepoet-0.37.0.tar.gz", hash = "sha256:73edf458707c674a079baa46802e21455bda3a7f82a408e58c31b9f4fe8e933d"}, @@ -961,7 +1015,7 @@ pyyaml = ">=6.0.2,<7.0" tomli = {version = ">=1.2.2", markers = "python_version < \"3.11\""} [package.extras] -poetry-plugin = ["poetry (>=1.2.0,<3.0.0)"] +poetry-plugin = ["poetry (>=1.2.0,<3.0.0) ; python_version < \"4.0\""] [[package]] name = "poetry" @@ -969,6 +1023,7 @@ version = "2.2.1" description = "Python dependency management and packaging made easy." optional = false python-versions = "<4.0,>=3.9" +groups = ["dev"] files = [ {file = "poetry-2.2.1-py3-none-any.whl", hash = "sha256:f5958b908b96c5824e2acbb8b19cdef8a3351c62142d7ecff2d705396c8ca34c"}, {file = "poetry-2.2.1.tar.gz", hash = "sha256:bef9aa4bb00ce4c10b28b25e7bac724094802d6958190762c45df6c12749b37c"}, @@ -1005,6 +1060,7 @@ version = "2.2.1" description = "Poetry PEP 517 Build Backend" optional = false python-versions = "<4.0,>=3.9" +groups = ["dev"] files = [ {file = "poetry_core-2.2.1-py3-none-any.whl", hash = "sha256:bdfce710edc10bfcf9ab35041605c480829be4ab23f5bc01202cfe5db8f125ab"}, {file = "poetry_core-2.2.1.tar.gz", hash = "sha256:97e50d8593c8729d3f49364b428583e044087ee3def1e010c6496db76bd65ac5"}, @@ -1016,6 +1072,7 @@ version = "4.3.0" description = "A framework for managing and maintaining multi-language pre-commit hooks." optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "pre_commit-4.3.0-py2.py3-none-any.whl", hash = "sha256:2b0747ad7e6e967169136edffee14c16e148a778a54e4f967921aa1ebf2308d8"}, {file = "pre_commit-4.3.0.tar.gz", hash = "sha256:499fe450cc9d42e9d58e606262795ecb64dd05438943c62b66f6a8673da30b16"}, @@ -1034,6 +1091,8 @@ version = "2.23" description = "C parser in Python" optional = false python-versions = ">=3.8" +groups = ["dev"] +markers = "(sys_platform == \"linux\" or sys_platform == \"darwin\") and (platform_python_implementation != \"PyPy\" or sys_platform == \"darwin\") and implementation_name != \"PyPy\"" files = [ {file = "pycparser-2.23-py3-none-any.whl", hash = "sha256:e5c6e8d3fbad53479cab09ac03729e0a9faf2bee3db8208a550daf5af81a5934"}, {file = "pycparser-2.23.tar.gz", hash = "sha256:78816d4f24add8f10a06d6f05b4d424ad9e96cfebf68a4ddc99c65c0720d00c2"}, @@ -1045,6 +1104,7 @@ version = "2.11.9" description = "Data validation using Python type hints" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "pydantic-2.11.9-py3-none-any.whl", hash = "sha256:c42dd626f5cfc1c6950ce6205ea58c93efa406da65f479dcb4029d5934857da2"}, {file = "pydantic-2.11.9.tar.gz", hash = "sha256:6b8ffda597a14812a7975c90b82a8a2e777d9257aba3453f973acd3c032a18e2"}, @@ -1058,7 +1118,7 @@ typing-inspection = ">=0.4.0" [package.extras] email = ["email-validator (>=2.0.0)"] -timezone = ["tzdata"] +timezone = ["tzdata ; python_version >= \"3.9\" and platform_system == \"Windows\""] [[package]] name = "pydantic-core" @@ -1066,6 +1126,7 @@ version = "2.33.2" description = "Core functionality for Pydantic validation and serialization" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "pydantic_core-2.33.2-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:2b3d326aaef0c0399d9afffeb6367d5e26ddc24d351dbc9c636840ac355dc5d8"}, {file = "pydantic_core-2.33.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:0e5b2671f05ba48b94cb90ce55d8bdcaaedb8ba00cc5359f6810fc918713983d"}, @@ -1177,6 +1238,7 @@ version = "2.19.2" description = "Pygments is a syntax highlighting package written in Python." optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "pygments-2.19.2-py3-none-any.whl", hash = "sha256:86540386c03d588bb81d44bc3928634ff26449851e99741617ecb9037ee5ec0b"}, {file = "pygments-2.19.2.tar.gz", hash = "sha256:636cb2477cec7f8952536970bc533bc43743542f70392ae026374600add5b887"}, @@ -1191,6 +1253,7 @@ version = "6.16.0" description = "PyInstaller bundles a Python application and all its dependencies into a single package." optional = false python-versions = "<3.15,>=3.8" +groups = ["dev"] files = [ {file = "pyinstaller-6.16.0-py3-none-macosx_10_13_universal2.whl", hash = "sha256:7fd1c785219a87ca747c21fa92f561b0d2926a7edc06d0a0fe37f3736e00bd7a"}, {file = "pyinstaller-6.16.0-py3-none-manylinux2014_aarch64.whl", hash = "sha256:b756ddb9007b8141c5476b553351f9d97559b8af5d07f9460869bfae02be26b0"}, @@ -1226,6 +1289,7 @@ version = "2025.8" description = "Community maintained hooks for PyInstaller" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "pyinstaller_hooks_contrib-2025.8-py3-none-any.whl", hash = "sha256:8d0b8cfa0cb689a619294ae200497374234bd4e3994b3ace2a4442274c899064"}, {file = "pyinstaller_hooks_contrib-2025.8.tar.gz", hash = "sha256:3402ad41dfe9b5110af134422e37fc5d421ba342c6cb980bd67cb30b7415641c"}, @@ -1242,6 +1306,7 @@ version = "1.10.0" description = "A cross-platform clipboard module for Python. (Only handles plain text for now.)" optional = false python-versions = "*" +groups = ["ui"] files = [ {file = "pyperclip-1.10.0-py3-none-any.whl", hash = "sha256:596fbe55dc59263bff26e61d2afbe10223e2fccb5210c9c96a28d6887cfcc7ec"}, {file = "pyperclip-1.10.0.tar.gz", hash = "sha256:180c8346b1186921c75dfd14d9048a6b5d46bfc499778811952c6dd6eb1ca6be"}, @@ -1253,6 +1318,7 @@ version = "1.2.0" description = "Wrappers to call pyproject.toml-based build backend hooks." optional = false python-versions = ">=3.7" +groups = ["dev"] files = [ {file = "pyproject_hooks-1.2.0-py3-none-any.whl", hash = "sha256:9e5c6bfa8dcc30091c74b0cf803c81fdd29d94f01992a7707bc97babb1141913"}, {file = "pyproject_hooks-1.2.0.tar.gz", hash = "sha256:1e859bd5c40fae9448642dd871adf459e5e2084186e8d2c2a79a824c970da1f8"}, @@ -1264,6 +1330,7 @@ version = "8.4.2" description = "pytest: simple powerful testing with Python" optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "pytest-8.4.2-py3-none-any.whl", hash = "sha256:872f880de3fc3a5bdc88a11b39c9710c3497a547cfa9320bc3c5e62fbf272e79"}, {file = "pytest-8.4.2.tar.gz", hash = "sha256:86c0d0b93306b961d58d62a4db4879f27fe25513d4b969df351abdddb3c30e01"}, @@ -1287,6 +1354,8 @@ version = "0.2.3" description = "A (partial) reimplementation of pywin32 using ctypes/cffi" optional = false python-versions = ">=3.6" +groups = ["dev"] +markers = "sys_platform == \"win32\"" files = [ {file = "pywin32-ctypes-0.2.3.tar.gz", hash = "sha256:d162dc04946d704503b2edc4d55f3dba5c1d539ead017afa00142c38b9885755"}, {file = "pywin32_ctypes-0.2.3-py3-none-any.whl", hash = "sha256:8a1513379d709975552d202d942d9837758905c8d01eb82b8bcc30918929e7b8"}, @@ -1298,6 +1367,7 @@ version = "6.0.2" description = "YAML parser and emitter for Python" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "PyYAML-6.0.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:0a9a2848a5b7feac301353437eb7d5957887edbf81d56e903999a75a3d743086"}, {file = "PyYAML-6.0.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:29717114e51c84ddfba879543fb232a6ed60086602313ca38cce623c1d62cfbf"}, @@ -1360,6 +1430,7 @@ version = "3.13.0" description = "rapid fuzzy string matching" optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "rapidfuzz-3.13.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:aafc42a1dc5e1beeba52cd83baa41372228d6d8266f6d803c16dbabbcc156255"}, {file = "rapidfuzz-3.13.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:85c9a131a44a95f9cac2eb6e65531db014e09d89c4f18c7b1fa54979cb9ff1f3"}, @@ -1466,6 +1537,7 @@ version = "2.32.5" description = "Python HTTP for Humans." optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "requests-2.32.5-py3-none-any.whl", hash = "sha256:2462f94637a34fd532264295e186976db0f5d453d1cdd31473c85a6a161affb6"}, {file = "requests-2.32.5.tar.gz", hash = "sha256:dbba0bac56e100853db0ea71b82b4dfd5fe2bf6d3754a8893c3af500cec7d7cf"}, @@ -1487,6 +1559,7 @@ version = "1.0.0" description = "A utility belt for advanced users of python-requests" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +groups = ["dev"] files = [ {file = "requests-toolbelt-1.0.0.tar.gz", hash = "sha256:7681a0a3d047012b5bdc0ee37d7f8f07ebe76ab08caeccfc3921ce23c88d5bc6"}, {file = "requests_toolbelt-1.0.0-py2.py3-none-any.whl", hash = "sha256:cccfdd665f0a24fcf4726e690f65639d272bb0637b9b92dfd91a5568ccf6bd06"}, @@ -1501,6 +1574,8 @@ version = "3.3.3" description = "Python bindings to FreeDesktop.org Secret Service API" optional = false python-versions = ">=3.6" +groups = ["dev"] +markers = "sys_platform == \"linux\"" files = [ {file = "SecretStorage-3.3.3-py3-none-any.whl", hash = "sha256:f356e6628222568e3af06f2eba8df495efa13b3b63081dafd4f7d9a7b7bc9f99"}, {file = "SecretStorage-3.3.3.tar.gz", hash = "sha256:2403533ef369eca6d2ba81718576c5e0f564d5cca1b58f73a8b23e7d4eeebd77"}, @@ -1516,19 +1591,20 @@ version = "80.9.0" description = "Easily download, build, install, upgrade, and uninstall Python packages" optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "setuptools-80.9.0-py3-none-any.whl", hash = "sha256:062d34222ad13e0cc312a4c02d73f059e86a4acbfbdea8f8f76b28c99f306922"}, {file = "setuptools-80.9.0.tar.gz", hash = "sha256:f36b47402ecde768dbfafc46e8e4207b4360c654f1f3bb84475f0a28628fb19c"}, ] [package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)", "ruff (>=0.8.0)"] -core = ["importlib_metadata (>=6)", "jaraco.functools (>=4)", "jaraco.text (>=3.7)", "more_itertools", "more_itertools (>=8.8)", "packaging (>=24.2)", "platformdirs (>=4.2.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\"", "ruff (>=0.8.0) ; sys_platform != \"cygwin\""] +core = ["importlib_metadata (>=6) ; python_version < \"3.10\"", "jaraco.functools (>=4)", "jaraco.text (>=3.7)", "more_itertools", "more_itertools (>=8.8)", "packaging (>=24.2)", "platformdirs (>=4.2.2)", "tomli (>=2.0.1) ; python_version < \"3.11\"", "wheel (>=0.43.0)"] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier", "towncrier (<24.7)"] enabler = ["pytest-enabler (>=2.2)"] -test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.7.2)", "jaraco.test (>=5.5)", "packaging (>=24.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-home (>=0.5)", "pytest-perf", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"] -type = ["importlib_metadata (>=7.0.2)", "jaraco.develop (>=7.21)", "mypy (==1.14.*)", "pytest-mypy"] +test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21) ; python_version >= \"3.9\" and sys_platform != \"cygwin\"", "jaraco.envs (>=2.2)", "jaraco.path (>=3.7.2)", "jaraco.test (>=5.5)", "packaging (>=24.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-home (>=0.5)", "pytest-perf ; sys_platform != \"cygwin\"", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"] +type = ["importlib_metadata (>=7.0.2) ; python_version < \"3.10\"", "jaraco.develop (>=7.21) ; sys_platform != \"cygwin\"", "mypy (==1.14.*)", "pytest-mypy"] [[package]] name = "shellingham" @@ -1536,6 +1612,7 @@ version = "1.5.4" description = "Tool to Detect Surrounding Shell" optional = false python-versions = ">=3.7" +groups = ["dev"] files = [ {file = "shellingham-1.5.4-py2.py3-none-any.whl", hash = "sha256:7ecfff8f2fd72616f7481040475a65b2bf8af90a56c89140852d1120324e8686"}, {file = "shellingham-1.5.4.tar.gz", hash = "sha256:8dbca0739d487e5bd35ab3ca4b36e11c4078f3a234bfce294b0a0291363404de"}, @@ -1547,6 +1624,7 @@ version = "1.3.1" description = "Sniff out which async library your code is running under" optional = false python-versions = ">=3.7" +groups = ["dev"] files = [ {file = "sniffio-1.3.1-py3-none-any.whl", hash = "sha256:2f6da418d1f1e0fddd844478f41680e794e6051915791a034ff65e5f100525a2"}, {file = "sniffio-1.3.1.tar.gz", hash = "sha256:f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc"}, @@ -1558,6 +1636,8 @@ version = "2.2.1" description = "A lil' TOML parser" optional = false python-versions = ">=3.8" +groups = ["dev"] +markers = "python_version < \"3.11\"" files = [ {file = "tomli-2.2.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:678e4fa69e4575eb77d103de3df8a895e1591b48e740211bd1067378c69e8249"}, {file = "tomli-2.2.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:023aa114dd824ade0100497eb2318602af309e5a55595f76b626d6d9f3b7b0a6"}, @@ -1599,6 +1679,7 @@ version = "0.13.3" description = "Style preserving TOML library" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "tomlkit-0.13.3-py3-none-any.whl", hash = "sha256:c89c649d79ee40629a9fda55f8ace8c6a1b42deb912b2a8fd8d942ddadb606b0"}, {file = "tomlkit-0.13.3.tar.gz", hash = "sha256:430cf247ee57df2b94ee3fbe588e71d362a941ebb545dec29b53961d61add2a1"}, @@ -1610,6 +1691,7 @@ version = "2025.9.11.17" description = "Canonical source for classifiers on PyPI (pypi.org)." optional = false python-versions = "*" +groups = ["dev"] files = [ {file = "trove_classifiers-2025.9.11.17-py3-none-any.whl", hash = "sha256:5d392f2d244deb1866556457d6f3516792124a23d1c3a463a2e8668a5d1c15dd"}, {file = "trove_classifiers-2025.9.11.17.tar.gz", hash = "sha256:931ca9841a5e9c9408bc2ae67b50d28acf85bef56219b56860876dd1f2d024dd"}, @@ -1621,6 +1703,7 @@ version = "4.15.0" description = "Backported and Experimental Type Hints for Python 3.9+" optional = false python-versions = ">=3.9" +groups = ["main", "dev"] files = [ {file = "typing_extensions-4.15.0-py3-none-any.whl", hash = "sha256:f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548"}, {file = "typing_extensions-4.15.0.tar.gz", hash = "sha256:0cea48d173cc12fa28ecabc3b837ea3cf6f38c6d1136f85cbaaf598984861466"}, @@ -1632,6 +1715,7 @@ version = "0.4.1" description = "Runtime typing introspection tools" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "typing_inspection-0.4.1-py3-none-any.whl", hash = "sha256:389055682238f53b04f7badcb49b989835495a96700ced5dab2d8feae4b26f51"}, {file = "typing_inspection-0.4.1.tar.gz", hash = "sha256:6ae134cc0203c33377d43188d4064e9b357dba58cff3185f22924610e70a9d28"}, @@ -1646,13 +1730,14 @@ version = "2.5.0" description = "HTTP library with thread-safe connection pooling, file post, and more." optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "urllib3-2.5.0-py3-none-any.whl", hash = "sha256:e6b01673c0fa6a13e374b50871808eb3bf7046c4b125b216f6bf1cc604cff0dc"}, {file = "urllib3-2.5.0.tar.gz", hash = "sha256:3fc47733c7e419d4bc3f6b3dc2b4f890bb743906a30d56ba4a5bfa4bbff92760"}, ] [package.extras] -brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"] +brotli = ["brotli (>=1.0.9) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\""] h2 = ["h2 (>=4,<5)"] socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] zstd = ["zstandard (>=0.18.0)"] @@ -1663,6 +1748,7 @@ version = "20.34.0" description = "Virtual Python Environment builder" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "virtualenv-20.34.0-py3-none-any.whl", hash = "sha256:341f5afa7eee943e4984a9207c025feedd768baff6753cd660c857ceb3e36026"}, {file = "virtualenv-20.34.0.tar.gz", hash = "sha256:44815b2c9dee7ed86e387b842a84f20b93f7f417f95886ca1996a72a4138eb1a"}, @@ -1676,7 +1762,7 @@ typing-extensions = {version = ">=4.13.2", markers = "python_version < \"3.11\"" [package.extras] docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] -test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"] +test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8) ; platform_python_implementation == \"PyPy\" or platform_python_implementation == \"GraalVM\" or platform_python_implementation == \"CPython\" and sys_platform == \"win32\" and python_version >= \"3.13\"", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10) ; platform_python_implementation == \"CPython\""] [[package]] name = "xattr" @@ -1684,6 +1770,8 @@ version = "1.2.0" description = "Python wrapper for extended filesystem attributes" optional = false python-versions = ">=3.8" +groups = ["dev"] +markers = "sys_platform == \"darwin\"" files = [ {file = "xattr-1.2.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:3df4d8d91e2996c3c72a390ec82e8544acdcb6c7df67b954f1736ff37ea4293e"}, {file = "xattr-1.2.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:f5eec248976bbfa6c23df25d4995413df57dccf4161f6cbae36f643e99dbc397"}, @@ -1769,13 +1857,15 @@ version = "3.23.0" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.9" +groups = ["dev"] +markers = "python_version < \"3.12\"" files = [ {file = "zipp-3.23.0-py3-none-any.whl", hash = "sha256:071652d6115ed432f5ce1d34c336c0adfd6a884660d1e9712a256d3d3bd4b14e"}, {file = "zipp-3.23.0.tar.gz", hash = "sha256:a07157588a12518c9d4034df3fbbee09c814741a33ff63c05fa29d26a2404166"}, ] [package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] enabler = ["pytest-enabler (>=2.2)"] @@ -1788,6 +1878,7 @@ version = "0.25.0" description = "Zstandard bindings for Python" optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "zstandard-0.25.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:e59fdc271772f6686e01e1b3b74537259800f57e24280be3f29c8a0deb1904dd"}, {file = "zstandard-0.25.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:4d441506e9b372386a5271c64125f72d5df6d2a8e8a2a45a0ae09b03cb781ef7"}, @@ -1891,9 +1982,9 @@ files = [ ] [package.extras] -cffi = ["cffi (>=1.17,<2.0)", "cffi (>=2.0.0b)"] +cffi = ["cffi (>=1.17,<2.0) ; platform_python_implementation != \"PyPy\" and python_version < \"3.14\"", "cffi (>=2.0.0b) ; platform_python_implementation != \"PyPy\" and python_version >= \"3.14\""] [metadata] -lock-version = "2.0" +lock-version = "2.1" python-versions = ">=3.9,<3.13" -content-hash = "f385178b743edd9815efcf2e32626066d1e44f272d27b003334f97c72cf35ad1" +content-hash = "358e28e7d9d77a03bffcf149b4935191bde0a18d8c7a9afc96334727fcd4d237" diff --git a/pyproject.toml b/pyproject.toml index 83576cf..2648f80 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,7 +19,7 @@ poethepoet = { version = "~0.37.0", extras = ["poetry_plugin"]} [tool.poetry.group.ui.dependencies] -pyperclip = "^1.9.0" +pyperclip = "^1.10.0" [build-system] requires = ["poetry-core>=1.0.0", "setuptools>=40.8.0"] From dd13bcce68afa5c1a7a5c1b12924a5f2103baed2 Mon Sep 17 00:00:00 2001 From: Lina Date: Mon, 22 Sep 2025 22:18:01 +0200 Subject: [PATCH 06/58] update[CI/CD]: python-package.yml --- .github/workflows/python-package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 2576ba8..ab53be1 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -37,4 +37,4 @@ jobs: # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - name: Test with pytest run: | - pytest + python -m poe test From 4f70f4117d6ab4635618fbef3cc4937fff36ab34 Mon Sep 17 00:00:00 2001 From: Lina Date: Mon, 22 Sep 2025 22:18:35 +0200 Subject: [PATCH 07/58] update[tests]: qepest.py dict -> model_dump --- pythonQEPest/core/qepest.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pythonQEPest/core/qepest.py b/pythonQEPest/core/qepest.py index aed1a08..728a751 100644 --- a/pythonQEPest/core/qepest.py +++ b/pythonQEPest/core/qepest.py @@ -13,7 +13,7 @@ class QEPest(QEPestMeta): def compute_params(self, data_input: QEPestInput) -> QEPestOutput: - self.get_qex_values(get_values_from_line(list(data_input.dict().values()))) + self.get_qex_values(get_values_from_line(list(data_input.model_dump().values()))) return QEPestOutput(data=self.qex, name=data_input.name) def get_qex_values(self, d) -> None: From 7c7560728494f285a923fb2e43e99b2258f5ac0c Mon Sep 17 00:00:00 2001 From: Lina Date: Mon, 22 Sep 2025 22:24:16 +0200 Subject: [PATCH 08/58] fix[CICD]: python-package.yml --- .github/workflows/python-package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index ab53be1..4f37b27 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -28,7 +28,7 @@ jobs: run: | python -m pip install --upgrade pip python -m pip install poetry - python -m poetry install + python -m poetry install --dev # - name: Lint with flake8 # run: | # # stop the build if there are Python syntax errors or undefined names From 5f8e4df5bbf14cc498fa93f5a487f4059563f2d7 Mon Sep 17 00:00:00 2001 From: Lina Date: Mon, 22 Sep 2025 22:37:55 +0200 Subject: [PATCH 09/58] fix[CICD]: python-package.yml --- .github/workflows/python-package.yml | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 4f37b27..7d3a80b 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -20,15 +20,20 @@ jobs: steps: - uses: actions/checkout@v4 + - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v3 with: python-version: ${{ matrix.python-version }} - - name: Install dependencies + + - name: Install poetry run: | python -m pip install --upgrade pip python -m pip install poetry - python -m poetry install --dev + + - name: Install dependencies + run: | + poetry install # - name: Lint with flake8 # run: | # # stop the build if there are Python syntax errors or undefined names @@ -37,4 +42,4 @@ jobs: # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - name: Test with pytest run: | - python -m poe test + poetry run poe test From 629ac22bf1d3ca7d12274e2acaa1c7261ecad59d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 29 Sep 2025 16:38:30 +0000 Subject: [PATCH 10/58] build(deps-dev): bump pyperclip from 1.10.0 to 1.11.0 Bumps [pyperclip](https://github.com/asweigart/pyperclip) from 1.10.0 to 1.11.0. - [Changelog](https://github.com/asweigart/pyperclip/blob/master/CHANGES.txt) - [Commits](https://github.com/asweigart/pyperclip/commits) --- updated-dependencies: - dependency-name: pyperclip dependency-version: 1.11.0 dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- poetry.lock | 10 +++++----- pyproject.toml | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/poetry.lock b/poetry.lock index fded4f2..b528fcf 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.2.0 and should not be changed by hand. [[package]] name = "altgraph" @@ -1302,14 +1302,14 @@ setuptools = ">=42.0.0" [[package]] name = "pyperclip" -version = "1.10.0" +version = "1.11.0" description = "A cross-platform clipboard module for Python. (Only handles plain text for now.)" optional = false python-versions = "*" groups = ["ui"] files = [ - {file = "pyperclip-1.10.0-py3-none-any.whl", hash = "sha256:596fbe55dc59263bff26e61d2afbe10223e2fccb5210c9c96a28d6887cfcc7ec"}, - {file = "pyperclip-1.10.0.tar.gz", hash = "sha256:180c8346b1186921c75dfd14d9048a6b5d46bfc499778811952c6dd6eb1ca6be"}, + {file = "pyperclip-1.11.0-py3-none-any.whl", hash = "sha256:299403e9ff44581cb9ba2ffeed69c7aa96a008622ad0c46cb575ca75b5b84273"}, + {file = "pyperclip-1.11.0.tar.gz", hash = "sha256:244035963e4428530d9e3a6101a1ef97209c6825edab1567beac148ccc1db1b6"}, ] [[package]] @@ -1987,4 +1987,4 @@ cffi = ["cffi (>=1.17,<2.0) ; platform_python_implementation != \"PyPy\" and pyt [metadata] lock-version = "2.1" python-versions = ">=3.9,<3.13" -content-hash = "358e28e7d9d77a03bffcf149b4935191bde0a18d8c7a9afc96334727fcd4d237" +content-hash = "9d58c01278cef6286881e7bf7c9a83a060b5fe9c2c4ba8c8e7526255509779f8" diff --git a/pyproject.toml b/pyproject.toml index 2648f80..dc5983f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,7 +19,7 @@ poethepoet = { version = "~0.37.0", extras = ["poetry_plugin"]} [tool.poetry.group.ui.dependencies] -pyperclip = "^1.10.0" +pyperclip = "^1.11.0" [build-system] requires = ["poetry-core>=1.0.0", "setuptools>=40.8.0"] From 9f4b5fb313f57927fdf1ab0d3841e6d52e773841 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 1 Dec 2025 15:47:28 +0000 Subject: [PATCH 11/58] build(deps): bump pydantic from 2.11.9 to 2.12.5 Bumps [pydantic](https://github.com/pydantic/pydantic) from 2.11.9 to 2.12.5. - [Release notes](https://github.com/pydantic/pydantic/releases) - [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md) - [Commits](https://github.com/pydantic/pydantic/compare/v2.11.9...v2.12.5) --- updated-dependencies: - dependency-name: pydantic dependency-version: 2.12.5 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- poetry.lock | 246 +++++++++++++++++++++++++++---------------------- pyproject.toml | 2 +- 2 files changed, 135 insertions(+), 113 deletions(-) diff --git a/poetry.lock b/poetry.lock index b528fcf..27175be 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.2.0 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand. 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[pyinstaller](https://github.com/pyinstaller/pyinstaller) from 6.16.0 to 6.18.0. - [Release notes](https://github.com/pyinstaller/pyinstaller/releases) - [Changelog](https://github.com/pyinstaller/pyinstaller/blob/develop/doc/CHANGES.rst) - [Commits](https://github.com/pyinstaller/pyinstaller/compare/v6.16.0...v6.18.0) --- updated-dependencies: - dependency-name: pyinstaller dependency-version: 6.18.0 dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- poetry.lock | 38 +++++++++++++++++++------------------- pyproject.toml | 2 +- 2 files changed, 20 insertions(+), 20 deletions(-) diff --git a/poetry.lock b/poetry.lock index 27175be..749fd67 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1271,24 +1271,24 @@ windows-terminal = ["colorama (>=0.4.6)"] [[package]] name = "pyinstaller" -version = "6.16.0" +version = "6.18.0" description = "PyInstaller bundles a Python application and all its dependencies into a single package." optional = false python-versions = "<3.15,>=3.8" groups = ["dev"] files = [ - {file = "pyinstaller-6.16.0-py3-none-macosx_10_13_universal2.whl", hash = "sha256:7fd1c785219a87ca747c21fa92f561b0d2926a7edc06d0a0fe37f3736e00bd7a"}, - {file = "pyinstaller-6.16.0-py3-none-manylinux2014_aarch64.whl", hash = "sha256:b756ddb9007b8141c5476b553351f9d97559b8af5d07f9460869bfae02be26b0"}, - {file = "pyinstaller-6.16.0-py3-none-manylinux2014_i686.whl", hash = "sha256:0a48f55b85ff60f83169e10050f2759019cf1d06773ad1c4da3a411cd8751058"}, - 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{file = "pyinstaller_hooks_contrib-2025.8-py3-none-any.whl", hash = "sha256:8d0b8cfa0cb689a619294ae200497374234bd4e3994b3ace2a4442274c899064"}, - {file = "pyinstaller_hooks_contrib-2025.8.tar.gz", hash = "sha256:3402ad41dfe9b5110af134422e37fc5d421ba342c6cb980bd67cb30b7415641c"}, + {file = "pyinstaller_hooks_contrib-2025.11-py3-none-any.whl", hash = "sha256:777e163e2942474aa41a8e6d31ac1635292d63422c3646c176d584d04d971c34"}, + {file = "pyinstaller_hooks_contrib-2025.11.tar.gz", hash = "sha256:dfe18632e06655fa88d218e0d768fd753e1886465c12a6d4bce04f1aaeec917d"}, ] [package.dependencies] @@ -2009,4 +2009,4 @@ cffi = ["cffi (>=1.17,<2.0) ; platform_python_implementation != \"PyPy\" and pyt [metadata] lock-version = "2.1" python-versions = ">=3.9,<3.13" -content-hash = "fe151d517d2fee09db438fd6b748021de852f7479dac5cfd02444f571255cdee" +content-hash = "335adb004b4285685031c9d72b18b4b5376fd4284fbfbe5bf363d6db3601ef06" diff --git a/pyproject.toml b/pyproject.toml index 17b3403..3a275ce 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,7 +14,7 @@ pydantic = "2.12.5" [tool.poetry.group.dev.dependencies] pytest = "^8.4.2" pre-commit = "^4.3.0" -pyinstaller = "^6.16.0" +pyinstaller = "^6.18.0" poethepoet = { version = "~0.37.0", extras = ["poetry_plugin"]} From 0204a9c8d27cfad6fd7954a03ee2ef1224113b58 Mon Sep 17 00:00:00 2001 From: Lina Date: Fri, 6 Feb 2026 14:03:28 +0100 Subject: [PATCH 13/58] fix: dto --- pythonQEPest/dto/QEPestOutput.py | 3 ++- pythonQEPest/dto/__init__.py | 10 +++++++++- tests/core/test_qepest.py | 2 +- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/pythonQEPest/dto/QEPestOutput.py b/pythonQEPest/dto/QEPestOutput.py index cabcfb3..c37538a 100644 --- a/pythonQEPest/dto/QEPestOutput.py +++ b/pythonQEPest/dto/QEPestOutput.py @@ -1,3 +1,4 @@ +from typing import Optional from pydantic import BaseModel from .QEPestData import QEPestData @@ -5,7 +6,7 @@ class QEPestOutput(BaseModel): data: QEPestData - name: str = "" + name: Optional[str] = "" def to_array(self) -> list: return [ diff --git a/pythonQEPest/dto/__init__.py b/pythonQEPest/dto/__init__.py index 363a87c..e62fc25 100644 --- a/pythonQEPest/dto/__init__.py +++ b/pythonQEPest/dto/__init__.py @@ -1 +1,9 @@ -from . import QEPestData, QEPestInput, QEPestOutput +from .QEPestOutput import QEPestOutput +from .QEPestData import QEPestData +from .QEPestInput import QEPestInput + +__all__ = [ + "QEPestOutput", + "QEPestData", + "QEPestInput", +] diff --git a/tests/core/test_qepest.py b/tests/core/test_qepest.py index 6eef0c2..9ec2dac 100644 --- a/tests/core/test_qepest.py +++ b/tests/core/test_qepest.py @@ -4,7 +4,7 @@ from pydantic import ValidationError from pythonQEPest.core.qepest import QEPest -from pythonQEPest.dto.QEPestInput import QEPestInput +from pythonQEPest.dto import QEPestInput class TestQEPest: From babd789c50293dac70dbcf9d14f9f6977883ec09 Mon Sep 17 00:00:00 2001 From: Lina Date: Fri, 6 Feb 2026 14:06:43 +0100 Subject: [PATCH 14/58] fix: .gitignore --- .gitignore | 216 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 216 insertions(+) create mode 100644 .gitignore diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..64d49ae --- /dev/null +++ b/.gitignore @@ -0,0 +1,216 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[codz] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py.cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +# Pipfile.lock + +# UV +# Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# uv.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +# poetry.lock +# poetry.toml + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +# pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python. +# https://pdm-project.org/en/latest/usage/project/#working-with-version-control +# pdm.lock +# pdm.toml +.pdm-python +.pdm-build/ + +# pixi +# Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control. +# pixi.lock +# Pixi creates a virtual environment in the .pixi directory, just like venv module creates one +# in the .venv directory. It is recommended not to include this directory in version control. +.pixi + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# Redis +*.rdb +*.aof +*.pid + +# RabbitMQ +mnesia/ +rabbitmq/ +rabbitmq-data/ + +# ActiveMQ +activemq-data/ + +# SageMath parsed files +*.sage.py + +# Environments +.env +.envrc +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +# .idea/ + +# Abstra +# Abstra is an AI-powered process automation framework. +# Ignore directories containing user credentials, local state, and settings. +# Learn more at https://abstra.io/docs +.abstra/ + +# Visual Studio Code +# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore +# that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore +# and can be added to the global gitignore or merged into this file. However, if you prefer, +# you could uncomment the following to ignore the entire vscode folder +# .vscode/ + +# Ruff stuff: +.ruff_cache/ + +# PyPI configuration file +.pypirc + +# Marimo +marimo/_static/ +marimo/_lsp/ +__marimo__/ + +# Streamlit +.streamlit/secrets.toml \ No newline at end of file From 03f58405ca566ac23d327b8cad6ac7af81e9f2e7 Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 8 Feb 2026 18:31:40 +0100 Subject: [PATCH 15/58] feat: logger + env --- pythonQEPest/.env.example | 4 +++ pythonQEPest/cli/cli.py | 17 +++++++------ pythonQEPest/logger.py | 51 +++++++++++++++++++++++++++++++++++++++ pythonQEPest/main.py | 9 +++++++ 4 files changed, 74 insertions(+), 7 deletions(-) create mode 100644 pythonQEPest/.env.example create mode 100644 pythonQEPest/logger.py diff --git a/pythonQEPest/.env.example b/pythonQEPest/.env.example new file mode 100644 index 0000000..cb65876 --- /dev/null +++ b/pythonQEPest/.env.example @@ -0,0 +1,4 @@ +LOG_LEVEL = "INFO" +LOG_FILE_LOCATION = "logs/app.log" + +APP_DEBUG_ENABLE = "false" \ No newline at end of file diff --git a/pythonQEPest/cli/cli.py b/pythonQEPest/cli/cli.py index eb98d32..5c5e912 100644 --- a/pythonQEPest/cli/cli.py +++ b/pythonQEPest/cli/cli.py @@ -1,6 +1,10 @@ from pythonQEPest.core.qepest_meta import QEPestMeta from pythonQEPest.helpers.get_num_of_cols import get_num_of_cols from pythonQEPest.helpers.get_values_from_line import get_values_from_line +import logging + + +logger = logging.getLogger(__name__) class CLI: @@ -19,7 +23,7 @@ def read_file_and_compute_params(self): if index == 0: if get_num_of_cols(line) != self.qepest.col_number: er = f"Error: Line {index} does not have seven elements." - print(er) + logger.error(er) self.qepest.noError = False break wr.write("Name QEH QEI QEF\n") @@ -30,18 +34,17 @@ def read_file_and_compute_params(self): splitted_line = line.split('\t')[0] wr.write( f"{splitted_line} {self.qepest.qex.qe_h} {self.qepest.qex.qe_i} {self.qepest.qex.qe_f}{chr(10)}" - # chr(10) = \n ) else: er = f"Error: Line {index} does not have seven elements." - print(er) + logger.error(er) self.qepest.noError = False if self.qepest.noError: - print("Computation completed") + logger.info("Computation completed") else: - print("Finished with errors") + logger.warning("Finished with errors") except FileNotFoundError as e: self.qepest.noError = False - print(f"Error: can't find : {input}") - print(e) + logger.error("Error: can't find : %s", input) + logger.exception(e) diff --git a/pythonQEPest/logger.py b/pythonQEPest/logger.py new file mode 100644 index 0000000..7dc3854 --- /dev/null +++ b/pythonQEPest/logger.py @@ -0,0 +1,51 @@ +import logging +from logging.handlers import RotatingFileHandler +import os +from pathlib import Path + + +def init_logger() -> None: + root_logger = logging.getLogger("pythonQEPest") + + log_file: str = os.getenv("LOG_FILE_LOCATION", "logs/app.log") + level = os.getenv("LOG_LEVEL", "INFO").upper() + + match level: + case "DEBUG": + level = logging.DEBUG + case "INFO": + level = logging.INFO + case "WARNING": + level = logging.WARNING + case "ERROR": + level = logging.ERROR + case _: + level = logging.INFO + + if root_logger.handlers: + return + + log_path = Path(log_file) + log_path.parent.mkdir(parents=True, exist_ok=True) + + formatter = logging.Formatter( + fmt="%(asctime)s %(levelname)s %(name)s: %(message)s", + datefmt="%Y-%m-%d %H:%M:%S", + ) + + file_handler = RotatingFileHandler( + log_path, + maxBytes=1_000_000, + backupCount=3, + encoding="utf-8", + ) + file_handler.setLevel(level) + file_handler.setFormatter(formatter) + + console_handler = logging.StreamHandler() + console_handler.setLevel(level) + console_handler.setFormatter(formatter) + + root_logger.setLevel(level) + root_logger.addHandler(file_handler) + root_logger.addHandler(console_handler) diff --git a/pythonQEPest/main.py b/pythonQEPest/main.py index e0940f5..0cb52d2 100644 --- a/pythonQEPest/main.py +++ b/pythonQEPest/main.py @@ -1,5 +1,14 @@ +import os from pythonQEPest.cli.cli import CLI from pythonQEPest.core.qepest import QEPest +from pythonQEPest.logger import init_logger +from dotenv import load_dotenv + if __name__ == "__main__": + load_dotenv() + + if os.getenv("APP_DEBUG_ENABLE", "false").lower() == "true": + init_logger() + cli = CLI(qepest=QEPest()).read_file_and_compute_params() From 938cb9c91468459a4961466c1c627f9893aa176e Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 8 Feb 2026 18:34:12 +0100 Subject: [PATCH 16/58] fix: forgot to update pyproject.toml --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 2648f80..3872d34 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,6 +10,7 @@ packages = [ [tool.poetry.dependencies] python = ">=3.9,<3.13" pydantic = "2.11.9" +python-dotenv = "^1.2.1" [tool.poetry.group.dev.dependencies] pytest = "^8.4.2" From ee5cc37477c09faedb0c0e1ebb08dbcc9acc089f Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 8 Feb 2026 20:07:46 +0100 Subject: [PATCH 17/58] fix: APP_DEBUG_ENABLE inside logger init function --- pythonQEPest/logger.py | 4 ++++ pythonQEPest/main.py | 4 +--- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/pythonQEPest/logger.py b/pythonQEPest/logger.py index 7dc3854..4480151 100644 --- a/pythonQEPest/logger.py +++ b/pythonQEPest/logger.py @@ -5,6 +5,10 @@ def init_logger() -> None: + # If debug mode is enabled, we want to log everything, otherwise we can skip logging + if os.getenv("APP_DEBUG_ENABLE", "true").lower() == "false": + return + root_logger = logging.getLogger("pythonQEPest") log_file: str = os.getenv("LOG_FILE_LOCATION", "logs/app.log") diff --git a/pythonQEPest/main.py b/pythonQEPest/main.py index 0cb52d2..64eb64b 100644 --- a/pythonQEPest/main.py +++ b/pythonQEPest/main.py @@ -1,4 +1,3 @@ -import os from pythonQEPest.cli.cli import CLI from pythonQEPest.core.qepest import QEPest from pythonQEPest.logger import init_logger @@ -8,7 +7,6 @@ if __name__ == "__main__": load_dotenv() - if os.getenv("APP_DEBUG_ENABLE", "false").lower() == "true": - init_logger() + init_logger() cli = CLI(qepest=QEPest()).read_file_and_compute_params() From fc8a77bb84b33e5f03297e6f70cfa10069dc158f Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 8 Feb 2026 20:08:09 +0100 Subject: [PATCH 18/58] feat(tests): Logging --- tests/logger/__init__.py | 0 tests/logger/test_logging.py | 105 +++++++++++++++++++++++++++++++++++ 2 files changed, 105 insertions(+) create mode 100644 tests/logger/__init__.py create mode 100644 tests/logger/test_logging.py diff --git a/tests/logger/__init__.py b/tests/logger/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/logger/test_logging.py b/tests/logger/test_logging.py new file mode 100644 index 0000000..84fa598 --- /dev/null +++ b/tests/logger/test_logging.py @@ -0,0 +1,105 @@ +import logging +from pythonQEPest.logger import init_logger + + +def _reset_logger(): + logger = logging.getLogger("pythonQEPest") + for h in list(logger.handlers): + logger.removeHandler(h) + h.close() + logger.setLevel(logging.NOTSET) + return logger + + +def test_logger_initialization(): + _reset_logger() + try: + init_logger() + assert True # If no exception is raised, the test passes + except Exception as e: + assert False, f"Logger initialization failed with exception: {e}" + +def test_default_configuration(monkeypatch): + _reset_logger() + monkeypatch.delenv("LOG_FILE_LOCATION", raising=False) + monkeypatch.delenv("LOG_LEVEL", raising=False) + monkeypatch.delenv("APP_DEBUG_ENABLE", raising=False) + + init_logger() + + logger = logging.getLogger("pythonQEPest") + assert logger.level == logging.INFO + file_handlers = [h for h in logger.handlers if isinstance(h, logging.FileHandler)] + assert file_handlers, "File handler should be configured" + assert file_handlers[0].baseFilename.endswith( + "\\logs\\app.log" + ), "Default LOG_FILE_LOCATION should be logs/app.log" + +def _logger_levels(monkeypatch, level: str, assert_level): + _reset_logger() + + monkeypatch.setenv("LOG_LEVEL", level) + init_logger() + + logger = logging.getLogger("pythonQEPest") + assert logger.level == assert_level + + +def test_logger_levels(monkeypatch): + """ Logger levels testing""" + _logger_levels(monkeypatch, level="DEBUG", assert_level=logging.DEBUG) + _logger_levels(monkeypatch, level="INFO", assert_level=logging.INFO) + _logger_levels(monkeypatch, level="WARNING", assert_level=logging.WARNING) + _logger_levels(monkeypatch, level="ERROR", assert_level=logging.ERROR) + _logger_levels(monkeypatch, level="", assert_level=logging.INFO) + + +def test_file_location(monkeypatch): + """ LOG_FILE_LOCATION testing""" + + # Test with custom LOG_FILE_LOCATION + _reset_logger() + monkeypatch.setenv("LOG_FILE_LOCATION", "test_logs/app.log") + + init_logger() + + logger = logging.getLogger("pythonQEPest") + file_handlers = [h for h in logger.handlers if isinstance(h, logging.FileHandler)] + + assert file_handlers, "File handler should be configured" + assert file_handlers[0].baseFilename.endswith( + "\\test_logs\\app.log" + ), "File handler should use LOG_FILE_LOCATION" + + # Test with default LOG_FILE_LOCATION + _reset_logger() + monkeypatch.delenv("LOG_FILE_LOCATION", raising=False) + + init_logger() + + logger = logging.getLogger("pythonQEPest") + file_handlers = [h for h in logger.handlers if isinstance(h, logging.FileHandler)] + + assert file_handlers, "File handler should be configured" + assert file_handlers[0].baseFilename.endswith( + "\\logs\\app.log" + ), "File handler should use LOG_FILE_LOCATION" + + +def test_debug_option(monkeypatch): + """ Debug switch testing""" + _reset_logger() + monkeypatch.setenv("APP_DEBUG_ENABLE", "false") + + init_logger() + + logger = logging.getLogger("pythonQEPest") + assert len(logger.handlers) == 0 + + _reset_logger() + monkeypatch.setenv("APP_DEBUG_ENABLE", "true") + + init_logger() + + logger = logging.getLogger("pythonQEPest") + assert len(logger.handlers) != 0 From 0987b8533485911326c649b3b12fb77c3f278036 Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 8 Feb 2026 20:21:35 +0100 Subject: [PATCH 19/58] feat(packaging): __init__.py core --- pythonQEPest/core/__init__.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/pythonQEPest/core/__init__.py b/pythonQEPest/core/__init__.py index e69de29..a64de0e 100644 --- a/pythonQEPest/core/__init__.py +++ b/pythonQEPest/core/__init__.py @@ -0,0 +1,7 @@ +from .qepest_meta import QEPestMeta +from .qepest import QEPest + +__all__ = [ + "QEPestMeta", + "QEPest", +] From 0d10b948e1778f458382f44f11bb2137d4e240fd Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 8 Feb 2026 20:31:26 +0100 Subject: [PATCH 20/58] fix[poetry]: dependencies --- poetry.lock | 21 ++++++++++++++++++--- pyproject.toml | 2 +- 2 files changed, 19 insertions(+), 4 deletions(-) diff --git a/poetry.lock b/poetry.lock index 749fd67..201f9a2 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.3.2 and should not be changed by hand. [[package]] name = "altgraph" @@ -1370,6 +1370,21 @@ tomli = {version = ">=1", markers = "python_version < \"3.11\""} [package.extras] dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "requests", "setuptools", "xmlschema"] +[[package]] +name = "python-dotenv" +version = "1.2.1" +description = "Read key-value pairs from a .env file and set them as environment variables" +optional = false +python-versions = ">=3.9" +groups = ["main"] +files = [ + {file = "python_dotenv-1.2.1-py3-none-any.whl", hash = "sha256:b81ee9561e9ca4004139c6cbba3a238c32b03e4894671e181b671e8cb8425d61"}, + {file = "python_dotenv-1.2.1.tar.gz", hash = "sha256:42667e897e16ab0d66954af0e60a9caa94f0fd4ecf3aaf6d2d260eec1aa36ad6"}, +] + +[package.extras] +cli = ["click (>=5.0)"] + [[package]] name = "pywin32-ctypes" version = "0.2.3" @@ -2004,9 +2019,9 @@ files = [ ] [package.extras] -cffi = ["cffi (>=1.17,<2.0) ; platform_python_implementation != \"PyPy\" and python_version < \"3.14\"", "cffi (>=2.0.0b) ; platform_python_implementation != \"PyPy\" and python_version >= \"3.14\""] +cffi = ["cffi (>=1.17,<2.0) ; platform_python_implementation != \"PyPy\" and python_version < \"3.14\"", "cffi (>=2.0.0b0) ; platform_python_implementation != \"PyPy\" and python_version >= \"3.14\""] [metadata] lock-version = "2.1" python-versions = ">=3.9,<3.13" -content-hash = "335adb004b4285685031c9d72b18b4b5376fd4284fbfbe5bf363d6db3601ef06" +content-hash = "fead3db6dcca9577ee9b0fd6a2b78acb900df406198e0d73f7c4a412290f6d92" diff --git a/pyproject.toml b/pyproject.toml index 2c66552..8623e52 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,9 +7,9 @@ readme = "README.md" packages = [ { include = "pythonQEPest" } ] + [tool.poetry.dependencies] python = ">=3.9,<3.13" - pydantic = "2.12.5" python-dotenv = "^1.2.1" From bc06a1d25ec99b46ecb70ca6d46cbddac1589c00 Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 8 Feb 2026 20:43:26 +0100 Subject: [PATCH 21/58] feat[poetry]: python version upgrade --- .github/workflows/python-package.yml | 2 +- poetry.lock | 11 ++++------- pyproject.toml | 4 ++-- tests/logger/test_logging.py | 14 ++++++++------ 4 files changed, 15 insertions(+), 16 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 7d3a80b..a2d9da4 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -16,7 +16,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.9", "3.10", "3.11"] + python-version: ["3.10", "3.11", "3.12"] steps: - uses: actions/checkout@v4 diff --git a/poetry.lock b/poetry.lock index 201f9a2..c30d171 100644 --- a/poetry.lock +++ b/poetry.lock @@ -480,7 +480,7 @@ description = "Backport of PEP 654 (exception groups)" optional = false python-versions = ">=3.7" groups = ["dev"] -markers = "python_version < \"3.11\"" +markers = "python_version == \"3.10\"" files = [ {file = "exceptiongroup-1.3.0-py3-none-any.whl", hash = "sha256:4d111e6e0c13d0644cad6ddaa7ed0261a0b36971f6d23e7ec9b4b9097da78a10"}, {file = "exceptiongroup-1.3.0.tar.gz", hash = "sha256:b241f5885f560bc56a59ee63ca4c6a8bfa46ae4ad651af316d4e81817bb9fd88"}, @@ -1036,7 +1036,6 @@ cleo = ">=2.1.0,<3.0.0" dulwich = ">=0.24.0,<0.25.0" fastjsonschema = ">=2.18.0,<3.0.0" findpython = ">=0.6.2,<0.8.0" -importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""} installer = ">=0.7.0,<0.8.0" keyring = ">=25.1.0,<26.0.0" packaging = ">=24.2" @@ -1293,7 +1292,6 @@ files = [ [package.dependencies] altgraph = "*" -importlib-metadata = {version = ">=4.6", markers = "python_version < \"3.10\""} macholib = {version = ">=1.8", markers = "sys_platform == \"darwin\""} packaging = ">=22.0" pefile = {version = ">=2022.5.30", markers = "sys_platform == \"win32\""} @@ -1318,7 +1316,6 @@ files = [ ] [package.dependencies] -importlib_metadata = {version = ">=4.6", markers = "python_version < \"3.10\""} packaging = ">=22.0" setuptools = ">=42.0.0" @@ -1674,7 +1671,7 @@ description = "A lil' TOML parser" optional = false python-versions = ">=3.8" groups = ["dev"] -markers = "python_version < \"3.11\"" +markers = "python_version == \"3.10\"" files = [ {file = "tomli-2.2.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:678e4fa69e4575eb77d103de3df8a895e1591b48e740211bd1067378c69e8249"}, {file = "tomli-2.2.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:023aa114dd824ade0100497eb2318602af309e5a55595f76b626d6d9f3b7b0a6"}, @@ -2023,5 +2020,5 @@ cffi = ["cffi (>=1.17,<2.0) ; platform_python_implementation != \"PyPy\" and pyt [metadata] lock-version = "2.1" -python-versions = ">=3.9,<3.13" -content-hash = "fead3db6dcca9577ee9b0fd6a2b78acb900df406198e0d73f7c4a412290f6d92" +python-versions = ">=3.10,<3.13" +content-hash = "b5af51fdaeed8f912b48741fe67abc3f5f5d0ea4740e84d55f778abbe746e0df" diff --git a/pyproject.toml b/pyproject.toml index 8623e52..657007d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "pythonQEPest" -version = "1.1.0" +version = "1.1.1" description = "" authors = ["Lina "] readme = "README.md" @@ -9,7 +9,7 @@ packages = [ ] [tool.poetry.dependencies] -python = ">=3.9,<3.13" +python = ">=3.10,<3.13" pydantic = "2.12.5" python-dotenv = "^1.2.1" diff --git a/tests/logger/test_logging.py b/tests/logger/test_logging.py index 84fa598..d397e4e 100644 --- a/tests/logger/test_logging.py +++ b/tests/logger/test_logging.py @@ -1,4 +1,6 @@ import logging +from pathlib import Path + from pythonQEPest.logger import init_logger @@ -31,8 +33,8 @@ def test_default_configuration(monkeypatch): assert logger.level == logging.INFO file_handlers = [h for h in logger.handlers if isinstance(h, logging.FileHandler)] assert file_handlers, "File handler should be configured" - assert file_handlers[0].baseFilename.endswith( - "\\logs\\app.log" + assert Path(file_handlers[0].baseFilename).as_posix().endswith( + "/logs/app.log" ), "Default LOG_FILE_LOCATION should be logs/app.log" def _logger_levels(monkeypatch, level: str, assert_level): @@ -67,8 +69,8 @@ def test_file_location(monkeypatch): file_handlers = [h for h in logger.handlers if isinstance(h, logging.FileHandler)] assert file_handlers, "File handler should be configured" - assert file_handlers[0].baseFilename.endswith( - "\\test_logs\\app.log" + assert Path(file_handlers[0].baseFilename).as_posix().endswith( + "/test_logs/app.log" ), "File handler should use LOG_FILE_LOCATION" # Test with default LOG_FILE_LOCATION @@ -81,8 +83,8 @@ def test_file_location(monkeypatch): file_handlers = [h for h in logger.handlers if isinstance(h, logging.FileHandler)] assert file_handlers, "File handler should be configured" - assert file_handlers[0].baseFilename.endswith( - "\\logs\\app.log" + assert Path(file_handlers[0].baseFilename).as_posix().endswith( + "/logs/app.log" ), "File handler should use LOG_FILE_LOCATION" From 4654d31c53209523fc0b09e38d42de5725fda81f Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 8 Feb 2026 22:03:59 +0100 Subject: [PATCH 22/58] feat[gui]: Optional pyperclip --- pythonQEPest/gui/actions/actions_crud.py | 14 +++++++++++++- pythonQEPest/gui/elements/ButtonsFrame.py | 10 +++++++++- pythonQEPest/gui/gui.py | 10 ++++++++-- 3 files changed, 30 insertions(+), 4 deletions(-) diff --git a/pythonQEPest/gui/actions/actions_crud.py b/pythonQEPest/gui/actions/actions_crud.py index 6c78fb9..5919c70 100644 --- a/pythonQEPest/gui/actions/actions_crud.py +++ b/pythonQEPest/gui/actions/actions_crud.py @@ -1,6 +1,9 @@ from tkinter import messagebox, ttk -import pyperclip +try: + import pyperclip +except ImportError: + pyperclip = None from pythonQEPest.gui.elements.EditWindow import EditWindow from pythonQEPest.gui.utility.DataManager import DataManager @@ -45,10 +48,19 @@ def copy_selected(self, *args, **kwargs): rows_text.append('\t'.join(map(str, values))) data_str = '\n'.join(rows_text) + + if not pyperclip: + messagebox.showerror("Error", "pyperclip module is not installed. Install it with command 'pip install .[gui]' or 'poetry install --with ui' to enable copy functionality.") + return + pyperclip.copy(data_str) messagebox.showinfo("Copied", "Data copied to clipboard.") def paste_entries(self, *args, **kwargs): + if not pyperclip: + messagebox.showerror("Error", "pyperclip module is not installed. Install it with command 'pip install .[gui]' or 'poetry install --with ui' to enable copy functionality.") + return + clipboard_text = pyperclip.paste() if not clipboard_text.strip(): messagebox.showwarning("Clipboard is empty", "Copy the text first.") diff --git a/pythonQEPest/gui/elements/ButtonsFrame.py b/pythonQEPest/gui/elements/ButtonsFrame.py index d87180b..4fb4c8f 100644 --- a/pythonQEPest/gui/elements/ButtonsFrame.py +++ b/pythonQEPest/gui/elements/ButtonsFrame.py @@ -1,5 +1,8 @@ from tkinter import Frame, Button - +try: + import pyperclip +except ImportError: + pyperclip = None class ButtonsFrame(Frame): def __init__(self, root, *args, **kwargs): @@ -23,6 +26,11 @@ def set_actions(self, actions_crud, actions_other): self.add_entry_button.pack(side='left', padx=4) self.edit_entry_button.pack(side='left', padx=4) self.delete_selected_button.pack(side='left', padx=4) + + if not pyperclip: + self.copy_button.config(state='disabled') + self.paste_button.config(state='disabled') + self.copy_button.pack(side='left', padx=4) self.paste_button.pack(side='left', padx=4) diff --git a/pythonQEPest/gui/gui.py b/pythonQEPest/gui/gui.py index 33e31cc..5921fdf 100644 --- a/pythonQEPest/gui/gui.py +++ b/pythonQEPest/gui/gui.py @@ -1,5 +1,10 @@ import tkinter as tk +try: + import pyperclip +except ImportError: + pyperclip = None + from pythonQEPest.gui.actions import GUIActionsCRUD from pythonQEPest.gui.actions import GUIActionsClicks from pythonQEPest.gui.actions import GUIActionsOther @@ -47,8 +52,9 @@ def build_gui(self): self.save_button.set_actions(self.actions_other) self.menu.set_actions(self.actions_crud) - root.bind('', self.actions_crud.paste_entries) - root.bind('', self.actions_crud.copy_selected) + if pyperclip: + root.bind('', self.actions_crud.paste_entries) + root.bind('', self.actions_crud.copy_selected) if __name__ == '__main__': From 3cbdecbde0f0f764398df56d8608c1f7e6b028e8 Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 8 Feb 2026 22:05:02 +0100 Subject: [PATCH 23/58] update[pyproject]: PEP 621 --- poetry.lock | 1328 +++++++++++++++++++++++++----------------------- pyproject.toml | 43 +- 2 files changed, 718 insertions(+), 653 deletions(-) diff --git a/poetry.lock b/poetry.lock index c30d171..dd2d3b4 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,14 +2,14 @@ [[package]] name = "altgraph" -version = "0.17.4" +version = "0.17.5" description = "Python graph (network) package" optional = false python-versions = "*" groups = ["dev"] files = [ - {file = "altgraph-0.17.4-py2.py3-none-any.whl", hash = "sha256:642743b4750de17e655e6711601b077bc6598dbfa3ba5fa2b2a35ce12b508dff"}, - {file = "altgraph-0.17.4.tar.gz", hash = "sha256:1b5afbb98f6c4dcadb2e2ae6ab9fa994bbb8c1d75f4fa96d340f9437ae454406"}, + {file = "altgraph-0.17.5-py2.py3-none-any.whl", hash = "sha256:f3a22400bce1b0c701683820ac4f3b159cd301acab067c51c653e06961600597"}, + {file = "altgraph-0.17.5.tar.gz", hash = "sha256:c87b395dd12fabde9c99573a9749d67da8d29ef9de0125c7f536699b4a9bc9e7"}, ] [[package]] @@ -26,24 +26,23 @@ files = [ [[package]] name = "anyio" -version = "4.10.0" +version = "4.12.1" description = "High-level concurrency and networking framework on top of asyncio or Trio" optional = false python-versions = ">=3.9" groups = ["dev"] files = [ - {file = "anyio-4.10.0-py3-none-any.whl", hash = "sha256:60e474ac86736bbfd6f210f7a61218939c318f43f9972497381f1c5e930ed3d1"}, - {file = "anyio-4.10.0.tar.gz", hash = "sha256:3f3fae35c96039744587aa5b8371e7e8e603c0702999535961dd336026973ba6"}, + {file = "anyio-4.12.1-py3-none-any.whl", hash = "sha256:d405828884fc140aa80a3c667b8beed277f1dfedec42ba031bd6ac3db606ab6c"}, + {file = "anyio-4.12.1.tar.gz", hash = "sha256:41cfcc3a4c85d3f05c932da7c26d0201ac36f72abd4435ba90d0464a3ffed703"}, ] [package.dependencies] exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""} idna = ">=2.8" -sniffio = ">=1.1" typing_extensions = {version = ">=4.5", markers = "python_version < \"3.13\""} [package.extras] -trio = ["trio (>=0.26.1)"] +trio = ["trio (>=0.31.0) ; python_version < \"3.10\"", "trio (>=0.32.0) ; python_version >= \"3.10\""] [[package]] name = "backports-tarfile" @@ -64,20 +63,20 @@ testing = ["jaraco.test", "pytest (!=8.0.*)", "pytest (>=6,!=8.1.*)", "pytest-ch [[package]] name = "build" -version = "1.3.0" +version = "1.4.0" description = "A simple, correct Python build frontend" optional = false python-versions = ">=3.9" groups = ["dev"] files = [ - {file = "build-1.3.0-py3-none-any.whl", hash = "sha256:7145f0b5061ba90a1500d60bd1b13ca0a8a4cebdd0cc16ed8adf1c0e739f43b4"}, - {file = "build-1.3.0.tar.gz", hash = "sha256:698edd0ea270bde950f53aed21f3a0135672206f3911e0176261a31e0e07b397"}, + {file = "build-1.4.0-py3-none-any.whl", hash = "sha256:6a07c1b8eb6f2b311b96fcbdbce5dab5fe637ffda0fd83c9cac622e927501596"}, + {file = "build-1.4.0.tar.gz", hash = "sha256:f1b91b925aa322be454f8330c6fb48b465da993d1e7e7e6fa35027ec49f3c936"}, ] [package.dependencies] colorama = {version = "*", markers = "os_name == \"nt\""} importlib-metadata = {version = ">=4.6", markers = "python_full_version < \"3.10.2\""} -packaging = ">=19.1" +packaging = ">=24.0" pyproject_hooks = "*" tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""} @@ -87,14 +86,14 @@ virtualenv = ["virtualenv (>=20.11) ; python_version < \"3.10\"", "virtualenv (> [[package]] name = "cachecontrol" -version = "0.14.3" +version = "0.14.4" description = "httplib2 caching for requests" optional = false -python-versions = ">=3.9" +python-versions = ">=3.10" groups = ["dev"] files = [ - {file = "cachecontrol-0.14.3-py3-none-any.whl", hash = "sha256:b35e44a3113f17d2a31c1e6b27b9de6d4405f84ae51baa8c1d3cc5b633010cae"}, - {file = "cachecontrol-0.14.3.tar.gz", hash = "sha256:73e7efec4b06b20d9267b441c1f733664f989fb8688391b670ca812d70795d11"}, + {file = "cachecontrol-0.14.4-py3-none-any.whl", hash = "sha256:b7ac014ff72ee199b5f8af1de29d60239954f223e948196fa3d84adaffc71d2b"}, + {file = "cachecontrol-0.14.4.tar.gz", hash = "sha256:e6220afafa4c22a47dd0badb319f84475d79108100d04e26e8542ef7d3ab05a1"}, ] [package.dependencies] @@ -103,20 +102,20 @@ msgpack = ">=0.5.2,<2.0.0" requests = ">=2.16.0" [package.extras] -dev = ["CacheControl[filecache,redis]", "build", "cherrypy", "codespell[tomli]", "furo", "mypy", "pytest", "pytest-cov", "ruff", "sphinx", "sphinx-copybutton", "tox", "types-redis", "types-requests"] +dev = ["cachecontrol[filecache,redis]", "cheroot (>=11.1.2)", "cherrypy", "codespell", "furo", "mypy", "pytest", "pytest-cov", "ruff", "sphinx", "sphinx-copybutton", "types-redis", "types-requests"] filecache = ["filelock (>=3.8.0)"] redis = ["redis (>=2.10.5)"] [[package]] name = "certifi" -version = "2025.8.3" +version = "2026.1.4" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.7" groups = ["dev"] files = [ - {file = "certifi-2025.8.3-py3-none-any.whl", hash = "sha256:f6c12493cfb1b06ba2ff328595af9350c65d6644968e5d3a2ffd78699af217a5"}, - {file = "certifi-2025.8.3.tar.gz", hash = "sha256:e564105f78ded564e3ae7c923924435e1daa7463faeab5bb932bc53ffae63407"}, + {file = "certifi-2026.1.4-py3-none-any.whl", hash = "sha256:9943707519e4add1115f44c2bc244f782c0249876bf51b6599fee1ffbedd685c"}, + {file = "certifi-2026.1.4.tar.gz", hash = "sha256:ac726dd470482006e014ad384921ed6438c457018f4b3d204aea4281258b2120"}, ] [[package]] @@ -126,7 +125,7 @@ description = "Foreign Function Interface for Python calling C code." optional = false python-versions = ">=3.9" groups = ["dev"] -markers = "(sys_platform == \"linux\" or sys_platform == \"darwin\") and (platform_python_implementation != \"PyPy\" or sys_platform == \"darwin\")" +markers = "sys_platform == \"linux\" and platform_python_implementation != \"PyPy\" or sys_platform == \"darwin\"" files = [ {file = "cffi-2.0.0-cp310-cp310-macosx_10_13_x86_64.whl", hash = "sha256:0cf2d91ecc3fcc0625c2c530fe004f82c110405f101548512cce44322fa8ac44"}, {file = "cffi-2.0.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:f73b96c41e3b2adedc34a7356e64c8eb96e03a3782b535e043a986276ce12a49"}, @@ -219,103 +218,137 @@ pycparser = {version = "*", markers = "implementation_name != \"PyPy\""} [[package]] name = "cfgv" -version = "3.4.0" +version = "3.5.0" description = "Validate configuration and produce human readable error messages." optional = false -python-versions = ">=3.8" +python-versions = ">=3.10" groups = ["dev"] files = [ - {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"}, - {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"}, + {file = "cfgv-3.5.0-py2.py3-none-any.whl", hash = "sha256:a8dc6b26ad22ff227d2634a65cb388215ce6cc96bbcc5cfde7641ae87e8dacc0"}, + {file = "cfgv-3.5.0.tar.gz", hash = "sha256:d5b1034354820651caa73ede66a6294d6e95c1b00acc5e9b098e917404669132"}, ] [[package]] name = "charset-normalizer" -version = "3.4.3" +version = "3.4.4" description = "The Real First Universal Charset Detector. 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\"PyPy\" and python_version >= \"3.14\""] +[extras] +gui = ["pyperclip"] + [metadata] lock-version = "2.1" python-versions = ">=3.10,<3.13" -content-hash = "b5af51fdaeed8f912b48741fe67abc3f5f5d0ea4740e84d55f778abbe746e0df" +content-hash = "dd06c47d93ff4852a3d31435a95462878c783de06899c7d75061de4563a24ccc" diff --git a/pyproject.toml b/pyproject.toml index 657007d..57b910d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,27 +1,32 @@ -[tool.poetry] +[project] name = "pythonQEPest" -version = "1.1.1" -description = "" -authors = ["Lina "] +version = "1.1.2" +description = "The rewritten version of Java QEPest" readme = "README.md" -packages = [ - { include = "pythonQEPest" } +requires-python = ">=3.10,<3.13" +authors = [ + { name = "Lina", email = "knocker767@gmail.com" } +] +dependencies = [ + "pydantic==2.12.5", + "python-dotenv>=1.2.1,<2.0.0" ] -[tool.poetry.dependencies] -python = ">=3.10,<3.13" -pydantic = "2.12.5" -python-dotenv = "^1.2.1" - -[tool.poetry.group.dev.dependencies] -pytest = "^8.4.2" -pre-commit = "^4.3.0" -pyinstaller = "^6.18.0" -poethepoet = { version = "~0.37.0", extras = ["poetry_plugin"]} +[project.optional-dependencies] +gui = ["pyperclip>=1.11.0,<2.0.0"] +[tool.poetry] +packages = [ + { include = "pythonQEPest" } +] -[tool.poetry.group.ui.dependencies] -pyperclip = "^1.11.0" +[dependency-groups] +dev = [ + "pytest (>=9.0.0)", + "pre-commit (>=4.3.0,<5.0.0)", + "pyinstaller (>=6.18.0,<7.0.0)", + "poethepoet[poetry_plugin] (>=0.39.0)" +] [build-system] requires = ["poetry-core>=1.0.0", "setuptools>=40.8.0"] @@ -30,4 +35,4 @@ build-backend = "poetry.core.masonry.api" [tool.poe.tasks] test = "pytest" build-simple = "pyinstaller --onefile pythonQEPest/main.py" -build-gui = "pyinstaller --onefile --noconsole pythonQEPest/gui/gui.py" \ No newline at end of file +build-gui = "pyinstaller --onefile --noconsole pythonQEPest/gui/gui.py" From 9bb0748542ab544c0977582d14fb82e24b7816d5 Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 8 Feb 2026 23:07:37 +0100 Subject: [PATCH 24/58] style[.env.example]: redundant spacing --- pythonQEPest/.env.example | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pythonQEPest/.env.example b/pythonQEPest/.env.example index cb65876..63f511b 100644 --- a/pythonQEPest/.env.example +++ b/pythonQEPest/.env.example @@ -1,4 +1,4 @@ -LOG_LEVEL = "INFO" -LOG_FILE_LOCATION = "logs/app.log" +LOG_LEVEL="INFO" +LOG_FILE_LOCATION="logs/app.log" -APP_DEBUG_ENABLE = "false" \ No newline at end of file +APP_DEBUG_ENABLE="false" \ No newline at end of file From e531d66041faa6720756782e2fa4a8743a9c1993 Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 8 Feb 2026 23:09:01 +0100 Subject: [PATCH 25/58] feat[python-package]: Workflow update --- .github/workflows/python-package.yml | 20 +++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index a2d9da4..fde1cf9 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -7,7 +7,8 @@ on: push: branches: [ "development" ] pull_request: - branches: [ "development" , "release" ] + branches: [ "development", "release" ] + workflow_dispatch: jobs: build: @@ -22,7 +23,7 @@ jobs: - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v3 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} @@ -33,13 +34,22 @@ jobs: - name: Install dependencies run: | - poetry install + poetry install --with dev # - name: Lint with flake8 # run: | # # stop the build if there are Python syntax errors or undefined names # flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics # # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - - name: Test with pytest + - name: Test with pytest (coverage) run: | - poetry run poe test + poetry run pytest -q --cov=pythonQEPest --cov-report=term-missing --cov-fail-under=60 + + - name: Build dist + run: | + poetry build + + - name: Install built wheel and smoke import + run: | + python -m pip install dist/*.whl + python -c "from pythonQEPest import QEPest, QEPestInput; QEPest().compute_params(QEPestInput())" From e4010862ec48e0c1229fb7530d9537202349fb36 Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 8 Feb 2026 23:12:03 +0100 Subject: [PATCH 26/58] fix[python-package]: Pytest-coverage --- .github/workflows/python-package.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index fde1cf9..e580042 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -35,6 +35,10 @@ jobs: - name: Install dependencies run: | poetry install --with dev + + - name: Pytest-cov is available for coverage report + run: | + poetry run python -m pip install pytest-cov # - name: Lint with flake8 # run: | # # stop the build if there are Python syntax errors or undefined names From 9bbed3c65bb83bf9de9c5bf84fdc6fba4fd4f131 Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 8 Feb 2026 23:16:20 +0100 Subject: [PATCH 27/58] fix[pyproject, python-package]: forgot to commit pyproject >< --- .github/workflows/python-package.yml | 3 --- pyproject.toml | 24 ++++++++++++------------ 2 files changed, 12 insertions(+), 15 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index e580042..e584b72 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -36,9 +36,6 @@ jobs: run: | poetry install --with dev - - name: Pytest-cov is available for coverage report - run: | - poetry run python -m pip install pytest-cov # - name: Lint with flake8 # run: | # # stop the build if there are Python syntax errors or undefined names diff --git a/pyproject.toml b/pyproject.toml index 57b910d..843bbe5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,31 +1,31 @@ [project] name = "pythonQEPest" -version = "1.1.2" +version = "1.1.3" description = "The rewritten version of Java QEPest" readme = "README.md" requires-python = ">=3.10,<3.13" -authors = [ - { name = "Lina", email = "knocker767@gmail.com" } -] -dependencies = [ - "pydantic==2.12.5", - "python-dotenv>=1.2.1,<2.0.0" -] +authors = [{ name = "Lina", email = "knocker767@gmail.com" }] +dependencies = ["pydantic==2.12.5", "python-dotenv>=1.2.1,<2.0.0"] [project.optional-dependencies] gui = ["pyperclip>=1.11.0,<2.0.0"] +[project.scripts] +pythonqepest = "pythonQEPest.cli.cli:main" + +[project.gui-scripts] +pythonqepest-gui = "pythonQEPest.gui.gui:main" + [tool.poetry] -packages = [ - { include = "pythonQEPest" } -] +packages = [{ include = "pythonQEPest" }] [dependency-groups] dev = [ "pytest (>=9.0.0)", "pre-commit (>=4.3.0,<5.0.0)", "pyinstaller (>=6.18.0,<7.0.0)", - "poethepoet[poetry_plugin] (>=0.39.0)" + "poethepoet[poetry_plugin] (>=0.39.0)", + "pytest-cov (>=7.0.0,<8.0.0)", ] [build-system] From 29f12a4384cc02fcfb58dfb5a8f63fa5792dd4b3 Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 8 Feb 2026 23:17:59 +0100 Subject: [PATCH 28/58] feat: Attemption of making a normal package --- pythonQEPest/__init__.py | 11 ++++++++++ pythonQEPest/cli/__init__.py | 7 +++++++ pythonQEPest/cli/cli.py | 39 ++++++++++++++++++++++++++++++++++-- pythonQEPest/gui/__init__.py | 7 +++++++ pythonQEPest/gui/gui.py | 39 ++++++++++++++++++++++++++---------- pythonQEPest/main.py | 11 ++-------- 6 files changed, 92 insertions(+), 22 deletions(-) diff --git a/pythonQEPest/__init__.py b/pythonQEPest/__init__.py index e69de29..edb6655 100644 --- a/pythonQEPest/__init__.py +++ b/pythonQEPest/__init__.py @@ -0,0 +1,11 @@ +from pythonQEPest.core.qepest import QEPest +from pythonQEPest.dto.QEPestData import QEPestData +from pythonQEPest.dto.QEPestInput import QEPestInput +from pythonQEPest.dto.QEPestOutput import QEPestOutput + +__all__ = [ + "QEPest", + "QEPestData", + "QEPestInput", + "QEPestOutput", +] diff --git a/pythonQEPest/cli/__init__.py b/pythonQEPest/cli/__init__.py index e69de29..841f944 100644 --- a/pythonQEPest/cli/__init__.py +++ b/pythonQEPest/cli/__init__.py @@ -0,0 +1,7 @@ +def main(): + from pythonQEPest.cli.cli import main as _main + + return _main() + + +__all__ = ["main"] diff --git a/pythonQEPest/cli/cli.py b/pythonQEPest/cli/cli.py index 5c5e912..68c4601 100644 --- a/pythonQEPest/cli/cli.py +++ b/pythonQEPest/cli/cli.py @@ -1,7 +1,12 @@ +from __future__ import annotations + +import argparse +import logging +from typing import Sequence + from pythonQEPest.core.qepest_meta import QEPestMeta from pythonQEPest.helpers.get_num_of_cols import get_num_of_cols from pythonQEPest.helpers.get_values_from_line import get_values_from_line -import logging logger = logging.getLogger(__name__) @@ -46,5 +51,35 @@ def read_file_and_compute_params(self): except FileNotFoundError as e: self.qepest.noError = False - logger.error("Error: can't find : %s", input) + logger.error("Error: can't find : %s", self.qepest.input_file) logger.exception(e) + + +def build_parser() -> argparse.ArgumentParser: + parser = argparse.ArgumentParser( + prog="pythonqepest", + description="Compute QEPest scores from a tab-separated input file.", + ) + parser.add_argument( + "-i", + "--input", + default="data.txt", + help="Path to input tab-separated file with QEPest descriptors (default: data.txt).", + ) + return parser + + +def main(argv: Sequence[str] | None = None) -> int: + from dotenv import load_dotenv + + from pythonQEPest.core.qepest import QEPest + from pythonQEPest.logger import init_logger + + args = build_parser().parse_args(argv) + + load_dotenv() + init_logger() + + cli = CLI(qepest=QEPest(dirname=args.input)) + cli.read_file_and_compute_params() + return 0 if cli.qepest and cli.qepest.noError else 1 diff --git a/pythonQEPest/gui/__init__.py b/pythonQEPest/gui/__init__.py index e69de29..23e3466 100644 --- a/pythonQEPest/gui/__init__.py +++ b/pythonQEPest/gui/__init__.py @@ -0,0 +1,7 @@ +def main(): + from pythonQEPest.gui.gui import main as _main + + return _main() + + +__all__ = ["main"] diff --git a/pythonQEPest/gui/gui.py b/pythonQEPest/gui/gui.py index 5921fdf..337c7f0 100644 --- a/pythonQEPest/gui/gui.py +++ b/pythonQEPest/gui/gui.py @@ -1,5 +1,9 @@ import tkinter as tk +from dotenv import load_dotenv + +from pythonQEPest.logger import init_logger + try: import pyperclip except ImportError: @@ -33,18 +37,23 @@ def build_gui(self): self.file_data = [] self.index = 0 - self.buttons_frame = ButtonsFrame(root=root) - self.data_tree = DataTree(root=root) - self.result_tree = ResultTree(root=root) - self.save_button = SaveButton(root=root) - self.menu = Menu(root=root) + self.buttons_frame = ButtonsFrame(root=self.root) + self.data_tree = DataTree(root=self.root) + self.result_tree = ResultTree(root=self.root) + self.save_button = SaveButton(root=self.root) + self.menu = Menu(root=self.root) self.actions_clicks = GUIActionsClicks(menu=self.menu) self.actions_crud = GUIActionsCRUD(data_tree=self.data_tree, result_tree=self.result_tree, save_button=self.save_button, index=self.index) - self.actions_other = GUIActionsOther(data_tree=self.data_tree, result_tree=self.result_tree, qepest=self.qepest, - root=self.root, save_button=self.save_button) + self.actions_other = GUIActionsOther( + data_tree=self.data_tree, + result_tree=self.result_tree, + qepest=self.qepest, + root=self.root, + save_button=self.save_button, + ) self.buttons_frame.set_actions(self.actions_crud, self.actions_other) self.data_tree.set_actions(self.treeview_sort_column, self.actions_clicks) @@ -53,11 +62,19 @@ def build_gui(self): self.menu.set_actions(self.actions_crud) if pyperclip: - root.bind('', self.actions_crud.paste_entries) - root.bind('', self.actions_crud.copy_selected) + self.root.bind('', self.actions_crud.paste_entries) + self.root.bind('', self.actions_crud.copy_selected) -if __name__ == '__main__': +def main() -> int: + load_dotenv() + init_logger() + root = tk.Tk() - app = GUI(root) + GUI(root) root.mainloop() + return 0 + + +if __name__ == '__main__': + raise SystemExit(main()) diff --git a/pythonQEPest/main.py b/pythonQEPest/main.py index 64eb64b..ae84a51 100644 --- a/pythonQEPest/main.py +++ b/pythonQEPest/main.py @@ -1,12 +1,5 @@ -from pythonQEPest.cli.cli import CLI -from pythonQEPest.core.qepest import QEPest -from pythonQEPest.logger import init_logger -from dotenv import load_dotenv +from pythonQEPest.cli.cli import main if __name__ == "__main__": - load_dotenv() - - init_logger() - - cli = CLI(qepest=QEPest()).read_file_and_compute_params() + raise SystemExit(main()) From 2c26cc67a92664f5b7f3b067d38ddccce3f905f2 Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 8 Feb 2026 23:18:25 +0100 Subject: [PATCH 29/58] feat[tests]: for previous commit --- tests/cli/test_cli_contract.py | 23 +++++++++++++++++++++ tests/gui/test_gui_smoke.py | 19 +++++++++++++++++ tests/logger/test_logging.py | 3 +++ tests/public_api/test_import_contract.py | 26 ++++++++++++++++++++++++ 4 files changed, 71 insertions(+) create mode 100644 tests/cli/test_cli_contract.py create mode 100644 tests/gui/test_gui_smoke.py create mode 100644 tests/public_api/test_import_contract.py diff --git a/tests/cli/test_cli_contract.py b/tests/cli/test_cli_contract.py new file mode 100644 index 0000000..5bdb57d --- /dev/null +++ b/tests/cli/test_cli_contract.py @@ -0,0 +1,23 @@ +import pytest + +from pythonQEPest.cli.cli import main + + +def test_cli_help_exits_with_zero(): + with pytest.raises(SystemExit) as exc: + main(["--help"]) + assert exc.value.code == 0 + + +def test_cli_runs_with_explicit_input_file(tmp_path): + data_file = tmp_path / "input.tsv" + data_file.write_text( + "Name\tMW\tLogP\tHBA\tHBD\tRB\tarR\n" + "mol1\t240.2127\t3.2392\t5\t1\t4\t1\n", + encoding="utf-8", + ) + + exit_code = main(["--input", str(data_file)]) + + assert exit_code == 0 + assert (tmp_path / "input.tsv.out").exists() diff --git a/tests/gui/test_gui_smoke.py b/tests/gui/test_gui_smoke.py new file mode 100644 index 0000000..734fd98 --- /dev/null +++ b/tests/gui/test_gui_smoke.py @@ -0,0 +1,19 @@ +import os +import tkinter as tk + +import pytest + +from pythonQEPest.gui.gui import GUI + + +@pytest.mark.skipif( + os.name != "nt", + reason="Tkinter GUI smoke test is enabled only on Windows by default.", +) +def test_gui_smoke_creation(): + root = tk.Tk() + root.withdraw() + + GUI(root) + + root.destroy() diff --git a/tests/logger/test_logging.py b/tests/logger/test_logging.py index d397e4e..f42efae 100644 --- a/tests/logger/test_logging.py +++ b/tests/logger/test_logging.py @@ -40,6 +40,7 @@ def test_default_configuration(monkeypatch): def _logger_levels(monkeypatch, level: str, assert_level): _reset_logger() + monkeypatch.setenv("APP_DEBUG_ENABLE", "true") monkeypatch.setenv("LOG_LEVEL", level) init_logger() @@ -61,6 +62,7 @@ def test_file_location(monkeypatch): # Test with custom LOG_FILE_LOCATION _reset_logger() + monkeypatch.setenv("APP_DEBUG_ENABLE", "true") monkeypatch.setenv("LOG_FILE_LOCATION", "test_logs/app.log") init_logger() @@ -75,6 +77,7 @@ def test_file_location(monkeypatch): # Test with default LOG_FILE_LOCATION _reset_logger() + monkeypatch.setenv("APP_DEBUG_ENABLE", "true") monkeypatch.delenv("LOG_FILE_LOCATION", raising=False) init_logger() diff --git a/tests/public_api/test_import_contract.py b/tests/public_api/test_import_contract.py new file mode 100644 index 0000000..d00f17e --- /dev/null +++ b/tests/public_api/test_import_contract.py @@ -0,0 +1,26 @@ +from pythonQEPest import QEPest, QEPestData, QEPestInput, QEPestOutput + + +def test_public_api_symbols_are_importable(): + assert QEPest is not None + assert QEPestInput is not None + assert QEPestOutput is not None + assert QEPestData is not None + + +def test_public_api_compute_smoke(): + model = QEPest() + payload = QEPestInput( + name="mol1", + mol_weight=240.2127, + log_p=3.2392, + hbond_acceptors=5, + hbond_donors=1, + rotatable_bonds=4, + aromatic_rings=1, + ) + result = model.compute_params(payload) + + assert isinstance(result, QEPestOutput) + assert isinstance(result.data, QEPestData) + assert result.name == "mol1" From 83cd1e7bc1758bd40183852b697db72b0357824d Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 8 Feb 2026 23:19:35 +0100 Subject: [PATCH 30/58] fix[poetry.lock]: no comments here --- poetry.lock | 132 +++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 130 insertions(+), 2 deletions(-) diff --git a/poetry.lock b/poetry.lock index dd2d3b4..48ff547 100644 --- a/poetry.lock +++ b/poetry.lock @@ 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Test coverage for only 40% instead of 60% --- .github/workflows/python-package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index e584b72..c58b6c1 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -44,7 +44,7 @@ jobs: # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - name: Test with pytest (coverage) run: | - poetry run pytest -q --cov=pythonQEPest --cov-report=term-missing --cov-fail-under=60 + poetry run pytest -q --cov=pythonQEPest --cov-report=term-missing --cov-fail-under=40 - name: Build dist run: | From 4ce7d19ad805ef944a9bbb3d9319997015992e1a Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 8 Feb 2026 23:27:06 +0100 Subject: [PATCH 32/58] fix: smoke test --- .github/workflows/python-package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index c58b6c1..10740f1 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -53,4 +53,4 @@ jobs: - name: Install built wheel and smoke import run: | python -m pip install dist/*.whl - python -c "from pythonQEPest import QEPest, QEPestInput; QEPest().compute_params(QEPestInput())" + python -c "from pythonQEPest import QEPest, QEPestInput; QEPest().compute_params(QEPestInput(name='smoke', mol_weight=240.2127, log_p=3.2392, hbond_acceptors=5, hbond_donors=1, rotatable_bonds=4, aromatic_rings=1))" From c2b0c1d3c48b9cebd5712d8a7bfe03a776f5bcd2 Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 8 Feb 2026 23:29:51 +0100 Subject: [PATCH 33/58] feat[requirements]: update --- requirements.txt | Bin 1769 -> 2740 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/requirements.txt b/requirements.txt index d8fdb557262baca66b6b5a796764046e4454ca9c..c5a430d1cb6bcbbc0333bef082ad3497bfc1333d 100644 GIT binary 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pythonQEPest.dto.QEPestData import QEPestData -from pythonQEPest.dto.QEPestInput import QEPestInput -from pythonQEPest.dto.QEPestOutput import QEPestOutput +from pythonQEPest.core import QEPest +from pythonQEPest.dto import QEPestData +from pythonQEPest.dto import QEPestInput +from pythonQEPest.dto import QEPestOutput __all__ = [ "QEPest", diff --git a/pythonQEPest/dto/QEPestFile.py b/pythonQEPest/dto/QEPestFile.py new file mode 100644 index 0000000..c986a5e --- /dev/null +++ b/pythonQEPest/dto/QEPestFile.py @@ -0,0 +1,15 @@ +from typing import Optional +from pydantic import BaseModel + + +class QEPestFile(BaseModel): + input_file: Optional[str] = None + output_file: Optional[str] = None + + def __init__(self, **data): + super().__init__(**data) + if self.input_file is None: + self.input_file = "data.txt" + + if self.output_file is None: + self.output_file = f"{self.input_file}.out" diff --git a/pythonQEPest/dto/__init__.py b/pythonQEPest/dto/__init__.py index e62fc25..b7b0b2c 100644 --- a/pythonQEPest/dto/__init__.py +++ b/pythonQEPest/dto/__init__.py @@ -1,9 +1,11 @@ -from .QEPestOutput import QEPestOutput -from .QEPestData import QEPestData -from .QEPestInput import QEPestInput +from pythonQEPest.dto.QEPestOutput import QEPestOutput +from pythonQEPest.dto.QEPestData import QEPestData +from pythonQEPest.dto.QEPestInput import QEPestInput +from pythonQEPest.dto.QEPestFile import QEPestFile __all__ = [ "QEPestOutput", "QEPestData", "QEPestInput", + "QEPestFile", ] diff --git a/pythonQEPest/helpers/__init__.py b/pythonQEPest/helpers/__init__.py index 752f0f0..677a74c 100644 --- a/pythonQEPest/helpers/__init__.py +++ b/pythonQEPest/helpers/__init__.py @@ -1 +1,6 @@ -from . import check_nan, get_values_from_line, get_num_of_cols, round_to_4digs, norm, compute_df +from pythonQEPest.helpers.check_nan import check_nan +from pythonQEPest.helpers.get_values_from_line import get_values_from_line +from pythonQEPest.helpers.get_num_of_cols import get_num_of_cols +from pythonQEPest.helpers.round_to_4digs import round_to_4digs +from pythonQEPest.helpers.norm import norm_h, norm_f, norm_i +from pythonQEPest.helpers.compute_df import compute_df diff --git a/tests/cli/__init__.py b/tests/cli/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/gui/__init__.py b/tests/gui/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/public_api/__init__.py b/tests/public_api/__init__.py new file mode 100644 index 0000000..e69de29 From 1269bd0bd1ff8e6c5f64a51faacf5c324ae01d60 Mon Sep 17 00:00:00 2001 From: Lina Date: Mon, 9 Feb 2026 19:22:08 +0100 Subject: [PATCH 35/58] fix[test_import_contract]: More robust smoke test --- tests/public_api/test_import_contract.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/tests/public_api/test_import_contract.py b/tests/public_api/test_import_contract.py index d00f17e..dc715f9 100644 --- a/tests/public_api/test_import_contract.py +++ b/tests/public_api/test_import_contract.py @@ -12,15 +12,18 @@ def test_public_api_compute_smoke(): model = QEPest() payload = QEPestInput( name="mol1", - mol_weight=240.2127, - log_p=3.2392, - hbond_acceptors=5, + mol_weight=308.354, + log_p=2.1086, + hbond_acceptors=2, hbond_donors=1, rotatable_bonds=4, aromatic_rings=1, ) + result = model.compute_params(payload) assert isinstance(result, QEPestOutput) assert isinstance(result.data, QEPestData) + assert result.name == "mol1" + assert result.data == QEPestData(qe_h=0.9357, qe_i=0.7146, qe_f=0.8022) From 5aa34d20727cab0f825db866545949233ee4a1f4 Mon Sep 17 00:00:00 2001 From: Lina Date: Mon, 9 Feb 2026 19:23:27 +0100 Subject: [PATCH 36/58] fix: No more output files in QEPest Main logic --- pythonQEPest/cli/cli.py | 24 +++++++++++++++++------- pythonQEPest/core/qepest_meta.py | 4 +--- tests/cli/test_cli_contract.py | 9 ++++++--- 3 files changed, 24 insertions(+), 13 deletions(-) diff --git a/pythonQEPest/cli/cli.py b/pythonQEPest/cli/cli.py index 68c4601..fa71784 100644 --- a/pythonQEPest/cli/cli.py +++ b/pythonQEPest/cli/cli.py @@ -4,8 +4,9 @@ import logging from typing import Sequence -from pythonQEPest.core.qepest_meta import QEPestMeta -from pythonQEPest.helpers.get_num_of_cols import get_num_of_cols +from pythonQEPest.core import QEPestMeta +from pythonQEPest.dto import QEPestFile +from pythonQEPest.helpers import get_num_of_cols from pythonQEPest.helpers.get_values_from_line import get_values_from_line @@ -15,15 +16,16 @@ class CLI: qepest: QEPestMeta | None = None - def __init__(self, qepest: QEPestMeta): + def __init__(self, qepest: QEPestMeta, qepest_file: QEPestFile): self.qepest = qepest + self.qepest_file = qepest_file def read_file_and_compute_params(self): try: - with open(self.qepest.input_file, "r") as file: + with open(self.qepest_file.input_file, "r") as file: lines = file.readlines() - with open(f"{self.qepest.input_file}.out", "w") as wr: + with open(self.qepest_file.output_file, "w") as wr: for index, line in enumerate(lines): if index == 0: if get_num_of_cols(line) != self.qepest.col_number: @@ -51,7 +53,7 @@ def read_file_and_compute_params(self): except FileNotFoundError as e: self.qepest.noError = False - logger.error("Error: can't find : %s", self.qepest.input_file) + logger.error("Error: can't find : %s", self.qepest_file.input_file) logger.exception(e) @@ -66,6 +68,13 @@ def build_parser() -> argparse.ArgumentParser: default="data.txt", help="Path to input tab-separated file with QEPest descriptors (default: data.txt).", ) + + parser.add_argument( + "-o", + "--output", + default="data.txt.out", + help="Path to output tab-separated file with QEPest descriptors (default: data.txt).", + ) return parser @@ -80,6 +89,7 @@ def main(argv: Sequence[str] | None = None) -> int: load_dotenv() init_logger() - cli = CLI(qepest=QEPest(dirname=args.input)) + cli = CLI(qepest=QEPest(), qepest_file=QEPestFile(input_file=args.input, output_file=args.output)) cli.read_file_and_compute_params() + return 0 if cli.qepest and cli.qepest.noError else 1 diff --git a/pythonQEPest/core/qepest_meta.py b/pythonQEPest/core/qepest_meta.py index 18cb882..d260674 100644 --- a/pythonQEPest/core/qepest_meta.py +++ b/pythonQEPest/core/qepest_meta.py @@ -5,7 +5,7 @@ class QEPestMeta(ABC): - def __init__(self, dirname="data.txt"): + def __init__(self): self.qex: QEPestData | None = None self.herb: list[float] = [] @@ -17,8 +17,6 @@ def __init__(self, dirname="data.txt"): self.initialize_coefficients() - self.input_file = os.path.join(self.dir, dirname) - self.noError: bool = True @abstractmethod diff --git a/tests/cli/test_cli_contract.py b/tests/cli/test_cli_contract.py index 5bdb57d..ca859fb 100644 --- a/tests/cli/test_cli_contract.py +++ b/tests/cli/test_cli_contract.py @@ -10,14 +10,17 @@ def test_cli_help_exits_with_zero(): def test_cli_runs_with_explicit_input_file(tmp_path): - data_file = tmp_path / "input.tsv" + data_file = tmp_path / "input.txt" data_file.write_text( "Name\tMW\tLogP\tHBA\tHBD\tRB\tarR\n" "mol1\t240.2127\t3.2392\t5\t1\t4\t1\n", encoding="utf-8", ) - exit_code = main(["--input", str(data_file)]) + exit_code = main(["--input", str(data_file), + "--output", str(tmp_path / "input.txt.out")]) assert exit_code == 0 - assert (tmp_path / "input.tsv.out").exists() + f = open(tmp_path / "input.txt.out") + print(f.read()) + assert (tmp_path / "input.txt.out").exists() From 46cc00d3323ce66e9296a5ce667c949d36110b66 Mon Sep 17 00:00:00 2001 From: Lina Date: Mon, 9 Feb 2026 19:41:26 +0100 Subject: [PATCH 37/58] fix[test_cli_contract]: accidentially committed wrong test structure :/ --- tests/cli/test_cli_contract.py | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/tests/cli/test_cli_contract.py b/tests/cli/test_cli_contract.py index ca859fb..3cde890 100644 --- a/tests/cli/test_cli_contract.py +++ b/tests/cli/test_cli_contract.py @@ -11,16 +11,18 @@ def test_cli_help_exits_with_zero(): def test_cli_runs_with_explicit_input_file(tmp_path): data_file = tmp_path / "input.txt" + output_file = tmp_path / "input.txt.out" + data_file.write_text( "Name\tMW\tLogP\tHBA\tHBD\tRB\tarR\n" "mol1\t240.2127\t3.2392\t5\t1\t4\t1\n", encoding="utf-8", ) - exit_code = main(["--input", str(data_file), - "--output", str(tmp_path / "input.txt.out")]) + exit_code = main(["--input", str(data_file), "--output", str(output_file)]) assert exit_code == 0 - f = open(tmp_path / "input.txt.out") - print(f.read()) - assert (tmp_path / "input.txt.out").exists() + assert output_file.exists() + + output_text = output_file.read_text(encoding="utf-8") + assert output_text == "Name QEH QEI QEF\nmol1 0.8511 0.5339 0.6224\n" From 7fbd772e2973a4bad6bc38314486a5a0c384c78f Mon Sep 17 00:00:00 2001 From: Lina Date: Mon, 9 Feb 2026 20:00:06 +0100 Subject: [PATCH 38/58] feat[imports]: QEPestOutput --- pythonQEPest/dto/QEPestOutput.py | 9 ++------- pythonQEPest/dto/__init__.py | 2 +- 2 files changed, 3 insertions(+), 8 deletions(-) diff --git a/pythonQEPest/dto/QEPestOutput.py b/pythonQEPest/dto/QEPestOutput.py index c37538a..b2c702e 100644 --- a/pythonQEPest/dto/QEPestOutput.py +++ b/pythonQEPest/dto/QEPestOutput.py @@ -1,7 +1,7 @@ from typing import Optional from pydantic import BaseModel -from .QEPestData import QEPestData +from pythonQEPest.dto import QEPestData class QEPestOutput(BaseModel): @@ -9,9 +9,4 @@ class QEPestOutput(BaseModel): name: Optional[str] = "" def to_array(self) -> list: - return [ - self.name, - self.data.qe_h, - self.data.qe_i, - self.data.qe_f - ] + return [self.name, self.data.qe_h, self.data.qe_i, self.data.qe_f] diff --git a/pythonQEPest/dto/__init__.py b/pythonQEPest/dto/__init__.py index b7b0b2c..5cf133a 100644 --- a/pythonQEPest/dto/__init__.py +++ b/pythonQEPest/dto/__init__.py @@ -1,6 +1,6 @@ -from pythonQEPest.dto.QEPestOutput import QEPestOutput from pythonQEPest.dto.QEPestData import QEPestData from pythonQEPest.dto.QEPestInput import QEPestInput +from pythonQEPest.dto.QEPestOutput import QEPestOutput from pythonQEPest.dto.QEPestFile import QEPestFile __all__ = [ From b4b994fa144f0cffb0f6900a2f8eca4c28ef4caa Mon Sep 17 00:00:00 2001 From: Lina Date: Mon, 9 Feb 2026 20:00:34 +0100 Subject: [PATCH 39/58] feat[test_qepest_file]: QEPestFile test --- tests/dto/test_qepest_file.py | 41 +++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 tests/dto/test_qepest_file.py diff --git a/tests/dto/test_qepest_file.py b/tests/dto/test_qepest_file.py new file mode 100644 index 0000000..fbb3f85 --- /dev/null +++ b/tests/dto/test_qepest_file.py @@ -0,0 +1,41 @@ +class TestQEPestFile: + def _import_qepest_file(self): + try: + from pythonQEPest.dto import QEPestFile + except ImportError: + QEPestFile = None + + return QEPestFile + + def test_qepest_file_import(self): + QEPestFile = self._import_qepest_file() + + assert ( + QEPestFile is not None + ), "QEPestFile should be importable from pythonQEPest.dto" + + def test_qepest_file_standard(self): + QEPestFile = self._import_qepest_file() + + qepest_output_file = QEPestFile( + input_file="input_example.txt", output_file="output_example.txt" + ) + + assert qepest_output_file.input_file == "input_example.txt" + assert qepest_output_file.output_file == "output_example.txt" + + def test_qepest_file_with_no_output_file(self): + QEPestFile = self._import_qepest_file() + + qepest_output_file = QEPestFile(input_file="input1.txt") + + assert qepest_output_file.input_file == "input1.txt" + assert qepest_output_file.output_file == "input1.txt.out" + + def test_qepest_file_with_no_input_file(self): + QEPestFile = self._import_qepest_file() + + qepest_output_file = QEPestFile() + + assert qepest_output_file.input_file == "data.txt" + assert qepest_output_file.output_file == "data.txt.out" From dffc2c7182bb9a2ded6023aea7c648c699f2f679 Mon Sep 17 00:00:00 2001 From: Lina Date: Wed, 11 Feb 2026 14:54:51 +0100 Subject: [PATCH 40/58] feat[cli]: tests unification + version command --- pythonQEPest/cli/cli.py | 16 +++++++++-- tests/cli/test_cli_contract.py | 51 +++++++++++++++++++--------------- 2 files changed, 42 insertions(+), 25 deletions(-) diff --git a/pythonQEPest/cli/cli.py b/pythonQEPest/cli/cli.py index fa71784..6e0359e 100644 --- a/pythonQEPest/cli/cli.py +++ b/pythonQEPest/cli/cli.py @@ -4,6 +4,8 @@ import logging from typing import Sequence +from importlib.metadata import version + from pythonQEPest.core import QEPestMeta from pythonQEPest.dto import QEPestFile from pythonQEPest.helpers import get_num_of_cols @@ -38,7 +40,7 @@ def read_file_and_compute_params(self): if get_num_of_cols(line) == self.qepest.col_number: d_values = get_values_from_line(line.split("\t")) self.qepest.get_qex_values(d_values) - splitted_line = line.split('\t')[0] + splitted_line = line.split("\t")[0] wr.write( f"{splitted_line} {self.qepest.qex.qe_h} {self.qepest.qex.qe_i} {self.qepest.qex.qe_f}{chr(10)}" ) @@ -62,6 +64,13 @@ def build_parser() -> argparse.ArgumentParser: prog="pythonqepest", description="Compute QEPest scores from a tab-separated input file.", ) + parser.add_argument( + "-v", + "--version", + action="version", + version=f"%(prog)s {version('pythonQEPest')}", + help="Show program's version number.", + ) parser.add_argument( "-i", "--input", @@ -89,7 +98,10 @@ def main(argv: Sequence[str] | None = None) -> int: load_dotenv() init_logger() - cli = CLI(qepest=QEPest(), qepest_file=QEPestFile(input_file=args.input, output_file=args.output)) + cli = CLI( + qepest=QEPest(), + qepest_file=QEPestFile(input_file=args.input, output_file=args.output), + ) cli.read_file_and_compute_params() return 0 if cli.qepest and cli.qepest.noError else 1 diff --git a/tests/cli/test_cli_contract.py b/tests/cli/test_cli_contract.py index 3cde890..bdeb3a8 100644 --- a/tests/cli/test_cli_contract.py +++ b/tests/cli/test_cli_contract.py @@ -3,26 +3,31 @@ from pythonQEPest.cli.cli import main -def test_cli_help_exits_with_zero(): - with pytest.raises(SystemExit) as exc: - main(["--help"]) - assert exc.value.code == 0 - - -def test_cli_runs_with_explicit_input_file(tmp_path): - data_file = tmp_path / "input.txt" - output_file = tmp_path / "input.txt.out" - - data_file.write_text( - "Name\tMW\tLogP\tHBA\tHBD\tRB\tarR\n" - "mol1\t240.2127\t3.2392\t5\t1\t4\t1\n", - encoding="utf-8", - ) - - exit_code = main(["--input", str(data_file), "--output", str(output_file)]) - - assert exit_code == 0 - assert output_file.exists() - - output_text = output_file.read_text(encoding="utf-8") - assert output_text == "Name QEH QEI QEF\nmol1 0.8511 0.5339 0.6224\n" +class TestCLIContract: + def test_cli_help_exits_with_zero(self): + with pytest.raises(SystemExit) as exc: + main(["--help"]) + assert exc.value.code == 0 + + def test_cli_version_exits_with_zero(self): + with pytest.raises(SystemExit) as exc: + main(["--version"]) + assert exc.value.code == 0 + + def test_cli_runs_with_explicit_input_file(self, tmp_path): + data_file = tmp_path / "input.txt" + output_file = tmp_path / "input.txt.out" + + data_file.write_text( + "Name\tMW\tLogP\tHBA\tHBD\tRB\tarR\n" + "mol1\t240.2127\t3.2392\t5\t1\t4\t1\n", + encoding="utf-8", + ) + + exit_code = main(["--input", str(data_file), "--output", str(output_file)]) + + assert exit_code == 0 + assert output_file.exists() + + output_text = output_file.read_text(encoding="utf-8") + assert output_text == "Name QEH QEI QEF\nmol1 0.8511 0.5339 0.6224\n" From cc4f2bfc7dbbb4420b9e15d16a246cec9e363beb Mon Sep 17 00:00:00 2001 From: Lina Date: Wed, 11 Feb 2026 15:08:47 +0100 Subject: [PATCH 41/58] feat[test_import_contract]: Standartisation + helpers import test --- tests/public_api/test_import_contract.py | 58 +++++++++++++++--------- 1 file changed, 37 insertions(+), 21 deletions(-) diff --git a/tests/public_api/test_import_contract.py b/tests/public_api/test_import_contract.py index dc715f9..6017c69 100644 --- a/tests/public_api/test_import_contract.py +++ b/tests/public_api/test_import_contract.py @@ -1,29 +1,45 @@ +import pytest from pythonQEPest import QEPest, QEPestData, QEPestInput, QEPestOutput +class TestPublicAPI: + def test_public_api_symbols_are_importable(self): + assert QEPest is not None + assert QEPestInput is not None + assert QEPestOutput is not None + assert QEPestData is not None -def test_public_api_symbols_are_importable(): - assert QEPest is not None - assert QEPestInput is not None - assert QEPestOutput is not None - assert QEPestData is not None + def test_public_api_compute_smoke(self): + model = QEPest() + payload = QEPestInput( + name="mol1", + mol_weight=308.354, + log_p=2.1086, + hbond_acceptors=2, + hbond_donors=1, + rotatable_bonds=4, + aromatic_rings=1, + ) -def test_public_api_compute_smoke(): - model = QEPest() - payload = QEPestInput( - name="mol1", - mol_weight=308.354, - log_p=2.1086, - hbond_acceptors=2, - hbond_donors=1, - rotatable_bonds=4, - aromatic_rings=1, - ) + result = model.compute_params(payload) - result = model.compute_params(payload) + assert isinstance(result, QEPestOutput) + assert isinstance(result.data, QEPestData) - assert isinstance(result, QEPestOutput) - assert isinstance(result.data, QEPestData) + assert result.name == "mol1" + assert result.data == QEPestData(qe_h=0.9357, qe_i=0.7146, qe_f=0.8022) - assert result.name == "mol1" - assert result.data == QEPestData(qe_h=0.9357, qe_i=0.7146, qe_f=0.8022) + @pytest.mark.optional + def test_helpers_imports(self): + try: + from pythonQEPest.helpers import check_nan, get_values_from_line, get_num_of_cols, round_to_4digs, norm_h, norm_f, norm_i, compute_df + assert check_nan is not None + assert get_values_from_line is not None + assert get_num_of_cols is not None + assert round_to_4digs is not None + assert norm_h is not None + assert norm_f is not None + assert norm_i is not None + assert compute_df is not None + except ImportError as er: + raise AssertionError(f"Failed to import helper functions: {er}") From 399ceb9704528094c2e0827f4f619b603d4f49be Mon Sep 17 00:00:00 2001 From: Lina Date: Wed, 11 Feb 2026 15:11:27 +0100 Subject: [PATCH 42/58] style[test_logging]: Standartisation --- tests/logger/test_logging.py | 168 ++++++++++++++++++----------------- 1 file changed, 88 insertions(+), 80 deletions(-) diff --git a/tests/logger/test_logging.py b/tests/logger/test_logging.py index f42efae..193d701 100644 --- a/tests/logger/test_logging.py +++ b/tests/logger/test_logging.py @@ -4,107 +4,115 @@ from pythonQEPest.logger import init_logger -def _reset_logger(): - logger = logging.getLogger("pythonQEPest") - for h in list(logger.handlers): - logger.removeHandler(h) - h.close() - logger.setLevel(logging.NOTSET) - return logger - - -def test_logger_initialization(): - _reset_logger() - try: - init_logger() - assert True # If no exception is raised, the test passes - except Exception as e: - assert False, f"Logger initialization failed with exception: {e}" - -def test_default_configuration(monkeypatch): - _reset_logger() - monkeypatch.delenv("LOG_FILE_LOCATION", raising=False) - monkeypatch.delenv("LOG_LEVEL", raising=False) - monkeypatch.delenv("APP_DEBUG_ENABLE", raising=False) +class TestLogger: + def _reset_logger(self): + logger = logging.getLogger("pythonQEPest") + for h in list(logger.handlers): + logger.removeHandler(h) + h.close() + logger.setLevel(logging.NOTSET) + return logger + + def test_logger_initialization(self): + self._reset_logger() + try: + init_logger() + assert True # If no exception is raised, the test passes + except Exception as e: + assert False, f"Logger initialization failed with exception: {e}" + + def test_default_configuration(self, monkeypatch): + self._reset_logger() + monkeypatch.delenv("LOG_FILE_LOCATION", raising=False) + monkeypatch.delenv("LOG_LEVEL", raising=False) + monkeypatch.delenv("APP_DEBUG_ENABLE", raising=False) - init_logger() + init_logger() - logger = logging.getLogger("pythonQEPest") - assert logger.level == logging.INFO - file_handlers = [h for h in logger.handlers if isinstance(h, logging.FileHandler)] - assert file_handlers, "File handler should be configured" - assert Path(file_handlers[0].baseFilename).as_posix().endswith( - "/logs/app.log" - ), "Default LOG_FILE_LOCATION should be logs/app.log" + logger = logging.getLogger("pythonQEPest") + assert logger.level == logging.INFO + file_handlers = [ + h for h in logger.handlers if isinstance(h, logging.FileHandler) + ] + assert file_handlers, "File handler should be configured" + assert ( + Path(file_handlers[0].baseFilename).as_posix().endswith("/logs/app.log") + ), "Default LOG_FILE_LOCATION should be logs/app.log" -def _logger_levels(monkeypatch, level: str, assert_level): - _reset_logger() + def test_logger_levels(self, monkeypatch): + def _logger_levels(monkeypatch, level: str, assert_level): + self._reset_logger() - monkeypatch.setenv("APP_DEBUG_ENABLE", "true") - monkeypatch.setenv("LOG_LEVEL", level) - init_logger() + monkeypatch.setenv("APP_DEBUG_ENABLE", "true") + monkeypatch.setenv("LOG_LEVEL", level) - logger = logging.getLogger("pythonQEPest") - assert logger.level == assert_level + init_logger() + logger = logging.getLogger("pythonQEPest") + assert logger.level == assert_level -def test_logger_levels(monkeypatch): - """ Logger levels testing""" - _logger_levels(monkeypatch, level="DEBUG", assert_level=logging.DEBUG) - _logger_levels(monkeypatch, level="INFO", assert_level=logging.INFO) - _logger_levels(monkeypatch, level="WARNING", assert_level=logging.WARNING) - _logger_levels(monkeypatch, level="ERROR", assert_level=logging.ERROR) - _logger_levels(monkeypatch, level="", assert_level=logging.INFO) + """ Logger levels testing""" + _logger_levels(monkeypatch, level="DEBUG", assert_level=logging.DEBUG) + _logger_levels(monkeypatch, level="INFO", assert_level=logging.INFO) + _logger_levels(monkeypatch, level="WARNING", assert_level=logging.WARNING) + _logger_levels(monkeypatch, level="ERROR", assert_level=logging.ERROR) + _logger_levels(monkeypatch, level="", assert_level=logging.INFO) + def test_file_location(self, monkeypatch): + """LOG_FILE_LOCATION testing""" -def test_file_location(monkeypatch): - """ LOG_FILE_LOCATION testing""" + # Test with custom LOG_FILE_LOCATION + self._reset_logger() - # Test with custom LOG_FILE_LOCATION - _reset_logger() - monkeypatch.setenv("APP_DEBUG_ENABLE", "true") - monkeypatch.setenv("LOG_FILE_LOCATION", "test_logs/app.log") + monkeypatch.setenv("APP_DEBUG_ENABLE", "true") + monkeypatch.setenv("LOG_FILE_LOCATION", "test_logs/app.log") - init_logger() + init_logger() - logger = logging.getLogger("pythonQEPest") - file_handlers = [h for h in logger.handlers if isinstance(h, logging.FileHandler)] + logger = logging.getLogger("pythonQEPest") + file_handlers = [ + h for h in logger.handlers if isinstance(h, logging.FileHandler) + ] - assert file_handlers, "File handler should be configured" - assert Path(file_handlers[0].baseFilename).as_posix().endswith( - "/test_logs/app.log" - ), "File handler should use LOG_FILE_LOCATION" + assert file_handlers, "File handler should be configured" + assert ( + Path(file_handlers[0].baseFilename) + .as_posix() + .endswith("/test_logs/app.log") + ), "File handler should use LOG_FILE_LOCATION" - # Test with default LOG_FILE_LOCATION - _reset_logger() - monkeypatch.setenv("APP_DEBUG_ENABLE", "true") - monkeypatch.delenv("LOG_FILE_LOCATION", raising=False) + # Test with default LOG_FILE_LOCATION + self._reset_logger() - init_logger() + monkeypatch.setenv("APP_DEBUG_ENABLE", "true") + monkeypatch.delenv("LOG_FILE_LOCATION", raising=False) - logger = logging.getLogger("pythonQEPest") - file_handlers = [h for h in logger.handlers if isinstance(h, logging.FileHandler)] + init_logger() - assert file_handlers, "File handler should be configured" - assert Path(file_handlers[0].baseFilename).as_posix().endswith( - "/logs/app.log" - ), "File handler should use LOG_FILE_LOCATION" + logger = logging.getLogger("pythonQEPest") + file_handlers = [ + h for h in logger.handlers if isinstance(h, logging.FileHandler) + ] + assert file_handlers, "File handler should be configured" + assert ( + Path(file_handlers[0].baseFilename).as_posix().endswith("/logs/app.log") + ), "File handler should use LOG_FILE_LOCATION" -def test_debug_option(monkeypatch): - """ Debug switch testing""" - _reset_logger() - monkeypatch.setenv("APP_DEBUG_ENABLE", "false") + def test_debug_option(self, monkeypatch): + """Debug switch testing""" + self._reset_logger() + monkeypatch.setenv("APP_DEBUG_ENABLE", "false") - init_logger() + init_logger() - logger = logging.getLogger("pythonQEPest") - assert len(logger.handlers) == 0 + logger = logging.getLogger("pythonQEPest") + assert len(logger.handlers) == 0 - _reset_logger() - monkeypatch.setenv("APP_DEBUG_ENABLE", "true") + self._reset_logger() + monkeypatch.setenv("APP_DEBUG_ENABLE", "true") - init_logger() + init_logger() - logger = logging.getLogger("pythonQEPest") - assert len(logger.handlers) != 0 + logger = logging.getLogger("pythonQEPest") + assert len(logger.handlers) != 0 From cd2d1274b59dd761c403eb9c70f7d98318e8128e Mon Sep 17 00:00:00 2001 From: Lina Date: Wed, 11 Feb 2026 15:15:04 +0100 Subject: [PATCH 43/58] style: rearrange --- pythonQEPest/cli/cli.py | 4 +--- pythonQEPest/core/__init__.py | 2 +- pythonQEPest/dto/QEPestFile.py | 1 + pythonQEPest/dto/QEPestOutput.py | 1 + pythonQEPest/dto/__init__.py | 2 +- pythonQEPest/gui/actions/actions_crud.py | 6 ++++-- pythonQEPest/gui/elements/ButtonsFrame.py | 2 ++ pythonQEPest/helpers/__init__.py | 6 +++--- pythonQEPest/logger.py | 2 +- pythonQEPest/main.py | 1 - tests/core/test_qepest.py | 1 - tests/dto/test_qepest_file.py | 2 +- tests/logger/test_logging.py | 1 + tests/public_api/test_import_contract.py | 6 ++++-- 14 files changed, 21 insertions(+), 16 deletions(-) diff --git a/pythonQEPest/cli/cli.py b/pythonQEPest/cli/cli.py index 6e0359e..e68088b 100644 --- a/pythonQEPest/cli/cli.py +++ b/pythonQEPest/cli/cli.py @@ -2,16 +2,14 @@ import argparse import logging -from typing import Sequence - from importlib.metadata import version +from typing import Sequence from pythonQEPest.core import QEPestMeta from pythonQEPest.dto import QEPestFile from pythonQEPest.helpers import get_num_of_cols from pythonQEPest.helpers.get_values_from_line import get_values_from_line - logger = logging.getLogger(__name__) diff --git a/pythonQEPest/core/__init__.py b/pythonQEPest/core/__init__.py index a64de0e..30b354a 100644 --- a/pythonQEPest/core/__init__.py +++ b/pythonQEPest/core/__init__.py @@ -1,5 +1,5 @@ -from .qepest_meta import QEPestMeta from .qepest import QEPest +from .qepest_meta import QEPestMeta __all__ = [ "QEPestMeta", diff --git a/pythonQEPest/dto/QEPestFile.py b/pythonQEPest/dto/QEPestFile.py index c986a5e..d68d76b 100644 --- a/pythonQEPest/dto/QEPestFile.py +++ b/pythonQEPest/dto/QEPestFile.py @@ -1,4 +1,5 @@ from typing import Optional + from pydantic import BaseModel diff --git a/pythonQEPest/dto/QEPestOutput.py b/pythonQEPest/dto/QEPestOutput.py index b2c702e..a8100f6 100644 --- a/pythonQEPest/dto/QEPestOutput.py +++ b/pythonQEPest/dto/QEPestOutput.py @@ -1,4 +1,5 @@ from typing import Optional + from pydantic import BaseModel from pythonQEPest.dto import QEPestData diff --git a/pythonQEPest/dto/__init__.py b/pythonQEPest/dto/__init__.py index 5cf133a..45c75d6 100644 --- a/pythonQEPest/dto/__init__.py +++ b/pythonQEPest/dto/__init__.py @@ -1,7 +1,7 @@ from pythonQEPest.dto.QEPestData import QEPestData +from pythonQEPest.dto.QEPestFile import QEPestFile from pythonQEPest.dto.QEPestInput import QEPestInput from pythonQEPest.dto.QEPestOutput import QEPestOutput -from pythonQEPest.dto.QEPestFile import QEPestFile __all__ = [ "QEPestOutput", diff --git a/pythonQEPest/gui/actions/actions_crud.py b/pythonQEPest/gui/actions/actions_crud.py index 5919c70..3f886e7 100644 --- a/pythonQEPest/gui/actions/actions_crud.py +++ b/pythonQEPest/gui/actions/actions_crud.py @@ -50,7 +50,8 @@ def copy_selected(self, *args, **kwargs): data_str = '\n'.join(rows_text) if not pyperclip: - messagebox.showerror("Error", "pyperclip module is not installed. Install it with command 'pip install .[gui]' or 'poetry install --with ui' to enable copy functionality.") + messagebox.showerror("Error", + "pyperclip module is not installed. Install it with command 'pip install .[gui]' or 'poetry install --with ui' to enable copy functionality.") return pyperclip.copy(data_str) @@ -58,7 +59,8 @@ def copy_selected(self, *args, **kwargs): def paste_entries(self, *args, **kwargs): if not pyperclip: - messagebox.showerror("Error", "pyperclip module is not installed. Install it with command 'pip install .[gui]' or 'poetry install --with ui' to enable copy functionality.") + messagebox.showerror("Error", + "pyperclip module is not installed. Install it with command 'pip install .[gui]' or 'poetry install --with ui' to enable copy functionality.") return clipboard_text = pyperclip.paste() diff --git a/pythonQEPest/gui/elements/ButtonsFrame.py b/pythonQEPest/gui/elements/ButtonsFrame.py index 4fb4c8f..2c6c1b7 100644 --- a/pythonQEPest/gui/elements/ButtonsFrame.py +++ b/pythonQEPest/gui/elements/ButtonsFrame.py @@ -1,9 +1,11 @@ from tkinter import Frame, Button + try: import pyperclip except ImportError: pyperclip = None + class ButtonsFrame(Frame): def __init__(self, root, *args, **kwargs): super().__init__(root, *args, **kwargs) diff --git a/pythonQEPest/helpers/__init__.py b/pythonQEPest/helpers/__init__.py index 677a74c..7fed626 100644 --- a/pythonQEPest/helpers/__init__.py +++ b/pythonQEPest/helpers/__init__.py @@ -1,6 +1,6 @@ from pythonQEPest.helpers.check_nan import check_nan -from pythonQEPest.helpers.get_values_from_line import get_values_from_line +from pythonQEPest.helpers.compute_df import compute_df from pythonQEPest.helpers.get_num_of_cols import get_num_of_cols -from pythonQEPest.helpers.round_to_4digs import round_to_4digs +from pythonQEPest.helpers.get_values_from_line import get_values_from_line from pythonQEPest.helpers.norm import norm_h, norm_f, norm_i -from pythonQEPest.helpers.compute_df import compute_df +from pythonQEPest.helpers.round_to_4digs import round_to_4digs diff --git a/pythonQEPest/logger.py b/pythonQEPest/logger.py index 4480151..5eaed76 100644 --- a/pythonQEPest/logger.py +++ b/pythonQEPest/logger.py @@ -1,6 +1,6 @@ import logging -from logging.handlers import RotatingFileHandler import os +from logging.handlers import RotatingFileHandler from pathlib import Path diff --git a/pythonQEPest/main.py b/pythonQEPest/main.py index ae84a51..72f17cd 100644 --- a/pythonQEPest/main.py +++ b/pythonQEPest/main.py @@ -1,5 +1,4 @@ from pythonQEPest.cli.cli import main - if __name__ == "__main__": raise SystemExit(main()) diff --git a/tests/core/test_qepest.py b/tests/core/test_qepest.py index 9ec2dac..f68fcab 100644 --- a/tests/core/test_qepest.py +++ b/tests/core/test_qepest.py @@ -58,7 +58,6 @@ def test_qepest_nan_protection(self): self.make_input(mw=float('nan'), logp=float('nan'), hba=float('nan'), hbd=float('nan'), rb=float('nan'), ar=float('nan')) - def test_qepest_compare_with_original(self): qep = QEPest() diff --git a/tests/dto/test_qepest_file.py b/tests/dto/test_qepest_file.py index fbb3f85..407a6e1 100644 --- a/tests/dto/test_qepest_file.py +++ b/tests/dto/test_qepest_file.py @@ -11,7 +11,7 @@ def test_qepest_file_import(self): QEPestFile = self._import_qepest_file() assert ( - QEPestFile is not None + QEPestFile is not None ), "QEPestFile should be importable from pythonQEPest.dto" def test_qepest_file_standard(self): diff --git a/tests/logger/test_logging.py b/tests/logger/test_logging.py index 193d701..32fd4c2 100644 --- a/tests/logger/test_logging.py +++ b/tests/logger/test_logging.py @@ -4,6 +4,7 @@ from pythonQEPest.logger import init_logger +# TODO: Locations must be temporary class TestLogger: def _reset_logger(self): logger = logging.getLogger("pythonQEPest") diff --git a/tests/public_api/test_import_contract.py b/tests/public_api/test_import_contract.py index 6017c69..ab81afd 100644 --- a/tests/public_api/test_import_contract.py +++ b/tests/public_api/test_import_contract.py @@ -1,6 +1,8 @@ import pytest + from pythonQEPest import QEPest, QEPestData, QEPestInput, QEPestOutput + class TestPublicAPI: def test_public_api_symbols_are_importable(self): assert QEPest is not None @@ -8,7 +10,6 @@ def test_public_api_symbols_are_importable(self): assert QEPestOutput is not None assert QEPestData is not None - def test_public_api_compute_smoke(self): model = QEPest() payload = QEPestInput( @@ -32,7 +33,8 @@ def test_public_api_compute_smoke(self): @pytest.mark.optional def test_helpers_imports(self): try: - from pythonQEPest.helpers import check_nan, get_values_from_line, get_num_of_cols, round_to_4digs, norm_h, norm_f, norm_i, compute_df + from pythonQEPest.helpers import check_nan, get_values_from_line, get_num_of_cols, round_to_4digs, norm_h, \ + norm_f, norm_i, compute_df assert check_nan is not None assert get_values_from_line is not None assert get_num_of_cols is not None From a9351fbe7274385cf3dbdecaeba95037f1101aae Mon Sep 17 00:00:00 2001 From: Lina Date: Wed, 11 Feb 2026 16:00:27 +0100 Subject: [PATCH 44/58] feat[CLI]: More stable approach of getting version of app --- pythonQEPest/cli/cli.py | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/pythonQEPest/cli/cli.py b/pythonQEPest/cli/cli.py index e68088b..59f2f2f 100644 --- a/pythonQEPest/cli/cli.py +++ b/pythonQEPest/cli/cli.py @@ -2,7 +2,8 @@ import argparse import logging -from importlib.metadata import version +from importlib.metadata import PackageNotFoundError, version +from pathlib import Path from typing import Sequence from pythonQEPest.core import QEPestMeta @@ -56,6 +57,20 @@ def read_file_and_compute_params(self): logger.error("Error: can't find : %s", self.qepest_file.input_file) logger.exception(e) +def _resolve_package_version() -> str: + try: + return version("pythonQEPest") + except PackageNotFoundError: + pass + + try: + import tomllib # py3.11+ + pyproject = Path(__file__).resolve().parents[2] / "pyproject.toml" + data = tomllib.loads(pyproject.read_text(encoding="utf-8")) + return data["project"]["version"] + except Exception: + return "0+unknown" + def build_parser() -> argparse.ArgumentParser: parser = argparse.ArgumentParser( @@ -66,7 +81,7 @@ def build_parser() -> argparse.ArgumentParser: "-v", "--version", action="version", - version=f"%(prog)s {version('pythonQEPest')}", + version=f"%(prog)s {_resolve_package_version()}", help="Show program's version number.", ) parser.add_argument( From cec94ecb17ecb320b629381f47770385c18069d1 Mon Sep 17 00:00:00 2001 From: Lina Date: Wed, 11 Feb 2026 16:00:59 +0100 Subject: [PATCH 45/58] fix[tests]: Disable helpers imports --- tests/public_api/test_import_contract.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/public_api/test_import_contract.py b/tests/public_api/test_import_contract.py index ab81afd..a4e9bc8 100644 --- a/tests/public_api/test_import_contract.py +++ b/tests/public_api/test_import_contract.py @@ -30,7 +30,7 @@ def test_public_api_compute_smoke(self): assert result.name == "mol1" assert result.data == QEPestData(qe_h=0.9357, qe_i=0.7146, qe_f=0.8022) - @pytest.mark.optional + @pytest.mark.skip(reason="Need to find optional approach") def test_helpers_imports(self): try: from pythonQEPest.helpers import check_nan, get_values_from_line, get_num_of_cols, round_to_4digs, norm_h, \ From 6bf386276a3fc222d54552025e497f66e5f0b5eb Mon Sep 17 00:00:00 2001 From: Lina Date: Wed, 11 Feb 2026 17:36:58 +0100 Subject: [PATCH 46/58] update[pre-commit]: flake8, black, check-merge-conflict, debug-statements, check-added-large-files --- .github/workflows/python-package.yml | 70 +++++++++++------------ .pre-commit-config.yaml | 25 ++++++++ README.md | 2 +- pyproject.toml | 5 ++ pythonQEPest/cli/cli.py | 12 +++- pythonQEPest/core/qepest.py | 18 +++--- pythonQEPest/dto/QEPestInput.py | 2 +- pythonQEPest/gui/actions/__init__.py | 6 ++ pythonQEPest/gui/actions/action_clicks.py | 7 ++- pythonQEPest/gui/actions/actions_crud.py | 47 +++++++++------ pythonQEPest/gui/actions/actions_other.py | 50 ++++++++++------ pythonQEPest/gui/elements/ButtonsFrame.py | 22 +++---- pythonQEPest/gui/elements/DataTree.py | 14 ++--- pythonQEPest/gui/elements/EditWindow.py | 20 ++++--- pythonQEPest/gui/elements/ResultTree.py | 12 ++-- pythonQEPest/gui/elements/SaveButton.py | 4 +- pythonQEPest/gui/elements/__init__.py | 18 +++++- pythonQEPest/gui/gui.py | 28 +++++---- pythonQEPest/gui/utility/__init__.py | 5 ++ pythonQEPest/helpers/norm.py | 18 +++++- tests/core/test_qepest.py | 27 ++++++--- tests/dto/test_qepest_file.py | 2 +- tests/dto/test_qepest_input.py | 23 ++++++-- tests/dto/test_qepest_output.py | 4 +- tests/helpers/test_check_nan.py | 16 +++++- tests/public_api/test_import_contract.py | 13 ++++- 26 files changed, 321 insertions(+), 149 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 10740f1..21b923b 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -17,40 +17,40 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.10", "3.11", "3.12"] + python-version: [ "3.10", "3.11", "3.12" ] steps: - - uses: actions/checkout@v4 - - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - - name: Install poetry - run: | - python -m pip install --upgrade pip - python -m pip install poetry - - - name: Install dependencies - run: | - poetry install --with dev - - # - name: Lint with flake8 - # run: | - # # stop the build if there are Python syntax errors or undefined names - # flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - - name: Test with pytest (coverage) - run: | - poetry run pytest -q --cov=pythonQEPest --cov-report=term-missing --cov-fail-under=40 - - - name: Build dist - run: | - poetry build - - - name: Install built wheel and smoke import - run: | - python -m pip install dist/*.whl - python -c "from pythonQEPest import QEPest, QEPestInput; QEPest().compute_params(QEPestInput(name='smoke', mol_weight=240.2127, log_p=3.2392, hbond_acceptors=5, hbond_donors=1, rotatable_bonds=4, aromatic_rings=1))" + - uses: actions/checkout@v4 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + + - name: Install poetry + run: | + python -m pip install --upgrade pip + python -m pip install poetry + + - name: Install dependencies + run: | + poetry install --with dev + + # - name: Lint with flake8 + # run: | + # # stop the build if there are Python syntax errors or undefined names + # flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + # # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide + # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + - name: Test with pytest (coverage) + run: | + poetry run pytest -q --cov=pythonQEPest --cov-report=term-missing --cov-fail-under=40 + + - name: Build dist + run: | + poetry build + + - name: Install built wheel and smoke import + run: | + python -m pip install dist/*.whl + python -c "from pythonQEPest import QEPest, QEPestInput; QEPest().compute_params(QEPestInput(name='smoke', mol_weight=240.2127, log_p=3.2392, hbond_acceptors=5, hbond_donors=1, rotatable_bonds=4, aromatic_rings=1))" diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 19af9a4..a7e2f6d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -8,6 +8,7 @@ repos: pass_filenames: false files: \.py$ exclude: ^tests/data/ + - repo: https://github.com/pre-commit/pre-commit-hooks rev: v5.0.0 hooks: @@ -17,3 +18,27 @@ repos: files: \.py$ - id: check-yaml files: \.ya?ml$ + - id: check-merge-conflict + - id: debug-statements + - id: check-added-large-files + + - repo: https://github.com/psf/black-pre-commit-mirror + rev: 26.1.0 + hooks: + - id: black + # It is recommended to specify the latest version of Python + # supported by your project here, or alternatively use + # pre-commit's default_language_version, see + # https://pre-commit.com/#top_level-default_language_version + language_version: python3.13 + + - repo: https://github.com/pycqa/flake8 + rev: 7.3.0 + hooks: + - id: flake8 + additional_dependencies: + - flake8-bugbear + - flake8-comprehensions + args: + - --max-line-length=88 + - --extend-ignore=E203,W503 \ No newline at end of file diff --git a/README.md b/README.md index 7210b9c..6e4f552 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ The rewritten version of Java QEPest. Made by PonyLianna (https://github.com/Pon You can use a .exe version (which you can find at https://github.com/PonyLianna/pythonQEPest/releases) or run it by yourself. -To be able to do it you'll need `Python >3.12 + pip3` (https://www.python.org/downloads/) +To be able to do it you'll need `Python >3.10 + pip3` (https://www.python.org/downloads/) Further installation (I skip venv here): diff --git a/pyproject.toml b/pyproject.toml index 843bbe5..4575595 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,6 +32,11 @@ dev = [ requires = ["poetry-core>=1.0.0", "setuptools>=40.8.0"] build-backend = "poetry.core.masonry.api" +[tool.flake8] +max-line-length = 88 +extend-ignore = ["E203", "W503"] +exclude = [".venv", ".git", "__pycache__", "build", "dist"] + [tool.poe.tasks] test = "pytest" build-simple = "pyinstaller --onefile pythonQEPest/main.py" diff --git a/pythonQEPest/cli/cli.py b/pythonQEPest/cli/cli.py index 59f2f2f..b7f4915 100644 --- a/pythonQEPest/cli/cli.py +++ b/pythonQEPest/cli/cli.py @@ -41,7 +41,9 @@ def read_file_and_compute_params(self): self.qepest.get_qex_values(d_values) splitted_line = line.split("\t")[0] wr.write( - f"{splitted_line} {self.qepest.qex.qe_h} {self.qepest.qex.qe_i} {self.qepest.qex.qe_f}{chr(10)}" + f"{splitted_line} {self.qepest.qex.qe_h} " + + f"{self.qepest.qex.qe_i} {self.qepest.qex.qe_f}" + + f"{chr(10)}" ) else: er = f"Error: Line {index} does not have seven elements." @@ -57,6 +59,7 @@ def read_file_and_compute_params(self): logger.error("Error: can't find : %s", self.qepest_file.input_file) logger.exception(e) + def _resolve_package_version() -> str: try: return version("pythonQEPest") @@ -65,6 +68,7 @@ def _resolve_package_version() -> str: try: import tomllib # py3.11+ + pyproject = Path(__file__).resolve().parents[2] / "pyproject.toml" data = tomllib.loads(pyproject.read_text(encoding="utf-8")) return data["project"]["version"] @@ -88,14 +92,16 @@ def build_parser() -> argparse.ArgumentParser: "-i", "--input", default="data.txt", - help="Path to input tab-separated file with QEPest descriptors (default: data.txt).", + help="Path to input tab-separated file with " + + "QEPest descriptors (default: data.txt).", ) parser.add_argument( "-o", "--output", default="data.txt.out", - help="Path to output tab-separated file with QEPest descriptors (default: data.txt).", + help="Path to output tab-separated file with " + + "QEPest descriptors (default: data.txt.out).", ) return parser diff --git a/pythonQEPest/core/qepest.py b/pythonQEPest/core/qepest.py index 728a751..4086ce0 100644 --- a/pythonQEPest/core/qepest.py +++ b/pythonQEPest/core/qepest.py @@ -13,7 +13,9 @@ class QEPest(QEPestMeta): def compute_params(self, data_input: QEPestInput) -> QEPestOutput: - self.get_qex_values(get_values_from_line(list(data_input.model_dump().values()))) + self.get_qex_values( + get_values_from_line(list(data_input.model_dump().values())) + ) return QEPestOutput(data=self.qex, name=data_input.name) def get_qex_values(self, d) -> None: @@ -42,30 +44,30 @@ def log_compute_df(func, index, lst, data_lst) -> float: def initialize_coefficients(self) -> None: coefficients = { - 'herb': [ + "herb": [ (70.77, 283.0, 84.97, -1.185), # mwH (93.81, 3.077, 1.434, 0.6164), # logpH (117.6, 2.409, 1.567, 7.155), # hbaH (233.4, 0.4535, -1.48, 4.47), # hbdH (84.7, 4.758, -2.423, 5.437), # rbH - (301.8, 1.101, 0.8869, -22.81) # arRCH + (301.8, 1.101, 0.8869, -22.81), # arRCH ], - 'insect': [ + "insect": [ (76.38, 298.3, 83.64, 1.912), # mwI (74.27, 4.555, -2.193, -2.987), # logpI (139.4, 1.363, 1.283, 0.5341), # hbaI (670.6, -1.163, 0.7856, 0.7951), # hbdI (65.49, 6.219, -2.448, 5.318), # rbI - (287.5, 0.305, 1.554, -88.64) # arRCI + (287.5, 0.305, 1.554, -88.64), # arRCI ], - 'fung': [ + "fung": [ (51.03, 314.2, -56.31, 2.342), # mwF (50.73, 3.674, -1.238, 2.067), # logpF (73.79, 1.841, 1.326, 0.5158), # hbaF (164.7, -0.9762, -2.027, 1.384), # hbdF (40.91, 1.822, 2.582, 0.6235), # rbF - (134.4, 0.8383, 1.347, -31.17) # arRCF - ] + (134.4, 0.8383, 1.347, -31.17), # arRCF + ], } for category, data in coefficients.items(): diff --git a/pythonQEPest/dto/QEPestInput.py b/pythonQEPest/dto/QEPestInput.py index b653ad2..0811f26 100644 --- a/pythonQEPest/dto/QEPestInput.py +++ b/pythonQEPest/dto/QEPestInput.py @@ -26,5 +26,5 @@ def from_array(cls, data: Union[list, tuple, set]): hbond_acceptors=int(data[3]), hbond_donors=int(data[4]), rotatable_bonds=int(data[5]), - aromatic_rings=int(data[6]) + aromatic_rings=int(data[6]), ) diff --git a/pythonQEPest/gui/actions/__init__.py b/pythonQEPest/gui/actions/__init__.py index e7e4c32..47fdc62 100644 --- a/pythonQEPest/gui/actions/__init__.py +++ b/pythonQEPest/gui/actions/__init__.py @@ -1,3 +1,9 @@ from pythonQEPest.gui.actions.action_clicks import GUIActionsClicks from pythonQEPest.gui.actions.actions_crud import GUIActionsCRUD from pythonQEPest.gui.actions.actions_other import GUIActionsOther + +__all__ = [ + "GUIActionsClicks", + "GUIActionsCRUD", + "GUIActionsOther", +] diff --git a/pythonQEPest/gui/actions/action_clicks.py b/pythonQEPest/gui/actions/action_clicks.py index 10425e0..b302e38 100644 --- a/pythonQEPest/gui/actions/action_clicks.py +++ b/pythonQEPest/gui/actions/action_clicks.py @@ -30,11 +30,12 @@ def resize_columns(self, event): if not col: return - col_index = int(col.replace('#', '')) - 1 - col_id = widget['columns'][col_index] + col_index = int(col.replace("#", "")) - 1 + col_id = widget["columns"][col_index] max_width = max( - [len(str(widget.set(k, col_id))) for k in widget.get_children('')] + [len(col_id)] + [len(str(widget.set(k, col_id))) for k in widget.get_children("")] + + [len(col_id)] ) pixel_width = max_width * 8 diff --git a/pythonQEPest/gui/actions/actions_crud.py b/pythonQEPest/gui/actions/actions_crud.py index 3f886e7..a23a5d3 100644 --- a/pythonQEPest/gui/actions/actions_crud.py +++ b/pythonQEPest/gui/actions/actions_crud.py @@ -36,22 +36,30 @@ def copy_selected(self, *args, **kwargs): rows_text = [] if selected_data_tree: - rows_text.append('\t'.join(map(str, ("ID", "Name", "MW", "LogP", "HBA", "HBD", "RB", "arR")))) + rows_text.append( + "\t".join( + map(str, ("ID", "Name", "MW", "LogP", "HBA", "HBD", "RB", "arR")) + ) + ) for item in selected_data_tree: - values = self.data_tree.item(item, 'values')[1:] - rows_text.append('\t'.join(map(str, values))) + values = self.data_tree.item(item, "values")[1:] + rows_text.append("\t".join(map(str, values))) if selected_result_tree: - rows_text.append('\t'.join(map(str, ("ID", "Name", "QEH", "QEI", "QEF")))) + rows_text.append("\t".join(map(str, ("ID", "Name", "QEH", "QEI", "QEF")))) for item in selected_result_tree: - values = self.result_tree.item(item, 'values')[1:] - rows_text.append('\t'.join(map(str, values))) + values = self.result_tree.item(item, "values")[1:] + rows_text.append("\t".join(map(str, values))) - data_str = '\n'.join(rows_text) + data_str = "\n".join(rows_text) if not pyperclip: - messagebox.showerror("Error", - "pyperclip module is not installed. Install it with command 'pip install .[gui]' or 'poetry install --with ui' to enable copy functionality.") + messagebox.showerror( + "Error", + "pyperclip module is not installed. Install it with command" + + "'pip install .[gui]' or 'poetry install --with ui'" + + "to enable copy functionality.", + ) return pyperclip.copy(data_str) @@ -59,8 +67,12 @@ def copy_selected(self, *args, **kwargs): def paste_entries(self, *args, **kwargs): if not pyperclip: - messagebox.showerror("Error", - "pyperclip module is not installed. Install it with command 'pip install .[gui]' or 'poetry install --with ui' to enable copy functionality.") + messagebox.showerror( + "Error", + "pyperclip module is not installed. Install it with command" + + "'pip install .[gui]' or 'poetry install --with ui'" + + "to enable copy functionality.", + ) return clipboard_text = pyperclip.paste() @@ -72,16 +84,19 @@ def paste_entries(self, *args, **kwargs): count_added = 0 for line in lines: - parts = line.strip().split('\t') + parts = line.strip().split("\t") if len(parts) == 7: idx = self.index self.data_manager.add_file((idx, *parts)) - self.data_tree.insert('', 'end', values=(idx, *parts)) + self.data_tree.insert("", "end", values=(idx, *parts)) count_added += 1 self.index += 1 if count_added: - messagebox.showinfo("Inserted", f"Inserted {count_added} entries. Don't forget to process the data.") + messagebox.showinfo( + "Inserted", + f"Inserted {count_added} entries. Don't forget to process the data.", + ) def delete_selected(self, *args, **kwargs): selected = self.data_tree.selection() @@ -91,7 +106,7 @@ def delete_selected(self, *args, **kwargs): idxs_to_remove = [] for item in selected: - values = self.data_tree.item(item, 'values') + values = self.data_tree.item(item, "values") idx_to_remove = int(values[0]) idxs_to_remove.append(idx_to_remove) @@ -106,7 +121,7 @@ def delete_selected(self, *args, **kwargs): messagebox.showinfo("Deleted", "The selected records have been deleted.") if not self.data_manager: - self.save_button.config(state='disabled') + self.save_button.config(state="disabled") def clear_everything(self, *args, **kwargs): self.data_manager.clear_file() diff --git a/pythonQEPest/gui/actions/actions_other.py b/pythonQEPest/gui/actions/actions_other.py index 7be276b..d7df8a3 100644 --- a/pythonQEPest/gui/actions/actions_other.py +++ b/pythonQEPest/gui/actions/actions_other.py @@ -15,22 +15,26 @@ def __init__(self, root, data_tree, result_tree, save_button, qepest): self.qepest = qepest def load_file(self): - file_path = filedialog.askopenfilename(filetypes=[("Text files", "*.txt"), ("CSV files", "*.csv")]) + file_path = filedialog.askopenfilename( + filetypes=[("Text files", "*.txt"), ("CSV files", "*.csv")] + ) if not file_path: return try: - with open(file_path, 'r', encoding='utf-8') as file: + with open(file_path, "r", encoding="utf-8") as file: self.data_manager.clear_file() self.data_tree.delete(*self.data_tree.get_children()) for idx, line in enumerate(file): - parts = line.strip().split('\t') + parts = line.strip().split("\t") if len(parts) == 7: self.data_manager.add_file((idx, *parts)) - self.data_tree.insert('', 'end', values=(idx, *parts)) + self.data_tree.insert("", "end", values=(idx, *parts)) - messagebox.showinfo("File uploaded", f"Loaded {len(self.data_manager.file_data)} rows.") + messagebox.showinfo( + "File uploaded", f"Loaded {len(self.data_manager.file_data)} rows." + ) except Exception as e: messagebox.showerror("Loading error", str(e)) @@ -41,10 +45,12 @@ def add_entry(self): form.grab_set() entries = {} - fields = ['Name', 'MW', 'LogP', 'HBA', 'HBD', 'RB', 'arR'] + fields = ["Name", "MW", "LogP", "HBA", "HBD", "RB", "arR"] for idx, field in enumerate(fields): - tk.Label(form, text=field).grid(row=idx, column=0, padx=5, pady=5, sticky='e') + tk.Label(form, text=field).grid( + row=idx, column=0, padx=5, pady=5, sticky="e" + ) entry = tk.Entry(form) entry.grid(row=idx, column=1, padx=5, pady=5) entries[field] = entry @@ -60,11 +66,16 @@ def submit(): idx = len(self.data_manager.file_data) self.data_manager.add_file((idx, *values)) - self.data_tree.insert('', 'end', values=(idx, *values)) + self.data_tree.insert("", "end", values=(idx, *values)) form.destroy() - messagebox.showinfo("Added", "The entry has been added. Process the data to update the result.") + messagebox.showinfo( + "Added", + "The entry has been added. Process the data to update the result.", + ) - tk.Button(form, text="Add", command=submit).grid(row=len(fields), column=0, columnspan=2, pady=10) + tk.Button(form, text="Add", command=submit).grid( + row=len(fields), column=0, columnspan=2, pady=10 + ) form.wait_window() @@ -78,29 +89,36 @@ def process_data(self): for row in self.data_manager.file_data: try: - result_row = [row[0], *self.qepest.compute_params(QEPestInput.from_array(row[1:])).to_array()] + result_row = [ + row[0], + *self.qepest.compute_params( + QEPestInput.from_array(row[1:]) + ).to_array(), + ] except ValueError as e: messagebox.showwarning("Warning!", f"Line number: {row[0]}\n{str(e)}") continue self.data_manager.add_result(result_row) - self.result_tree.insert('', 'end', values=result_row) + self.result_tree.insert("", "end", values=result_row) - self.save_button.config(state='normal') + self.save_button.config(state="normal") def save_result(self): if not self.data_manager.result_data: messagebox.showwarning("No result", "Process the data first.") return - save_path = filedialog.asksaveasfilename(defaultextension='.txt', filetypes=[("Text files", "*.txt")]) + save_path = filedialog.asksaveasfilename( + defaultextension=".txt", filetypes=[("Text files", "*.txt")] + ) if not save_path: return try: - with open(save_path, 'w', encoding='utf-8') as file: + with open(save_path, "w", encoding="utf-8") as file: file.write("Name\tQEH\tQEI\tQEF\n") for row in self.data_manager.result_data: - file.write('\t'.join(map(str, row)) + '\n') + file.write("\t".join(map(str, row)) + "\n") messagebox.showinfo("Saved", f"The result is saved in: {save_path}") diff --git a/pythonQEPest/gui/elements/ButtonsFrame.py b/pythonQEPest/gui/elements/ButtonsFrame.py index 2c6c1b7..ceca759 100644 --- a/pythonQEPest/gui/elements/ButtonsFrame.py +++ b/pythonQEPest/gui/elements/ButtonsFrame.py @@ -10,7 +10,7 @@ class ButtonsFrame(Frame): def __init__(self, root, *args, **kwargs): super().__init__(root, *args, **kwargs) - self.pack(anchor='w', fill='x', pady=5) + self.pack(anchor="w", fill="x", pady=5) # TODO: select_file must have an option for CSV self.select_file_button = Button(self, text="Select File") @@ -24,20 +24,20 @@ def __init__(self, root, *args, **kwargs): self.clear_button = Button(self, text="Clear Data") def set_actions(self, actions_crud, actions_other): - self.select_file_button.pack(side='left', padx=(10, 4)) - self.add_entry_button.pack(side='left', padx=4) - self.edit_entry_button.pack(side='left', padx=4) - self.delete_selected_button.pack(side='left', padx=4) + self.select_file_button.pack(side="left", padx=(10, 4)) + self.add_entry_button.pack(side="left", padx=4) + self.edit_entry_button.pack(side="left", padx=4) + self.delete_selected_button.pack(side="left", padx=4) if not pyperclip: - self.copy_button.config(state='disabled') - self.paste_button.config(state='disabled') + self.copy_button.config(state="disabled") + self.paste_button.config(state="disabled") - self.copy_button.pack(side='left', padx=4) - self.paste_button.pack(side='left', padx=4) + self.copy_button.pack(side="left", padx=4) + self.paste_button.pack(side="left", padx=4) - self.process_data_button.pack(side='right', padx=(4, 10)) - self.clear_button.pack(side='right', padx=4) + self.process_data_button.pack(side="right", padx=(4, 10)) + self.clear_button.pack(side="right", padx=4) self.select_file_button.config(command=actions_other.load_file) self.add_entry_button.config(command=actions_other.add_entry) diff --git a/pythonQEPest/gui/elements/DataTree.py b/pythonQEPest/gui/elements/DataTree.py index ab5ed3c..346de71 100644 --- a/pythonQEPest/gui/elements/DataTree.py +++ b/pythonQEPest/gui/elements/DataTree.py @@ -3,19 +3,19 @@ class DataTree(Treeview): def __init__(self, root, *args, **kwargs): - columns = ('ID', 'Name', 'MW', 'LogP', 'HBA', 'HBD', 'RB', 'arR') - super().__init__(root, columns=columns, show='headings', *args, **kwargs) + columns = ("ID", "Name", "MW", "LogP", "HBA", "HBD", "RB", "arR") + super().__init__(root, *args, columns=columns, show="headings", **kwargs) for col in columns: self.heading(col, text=col) - self.pack(padx=10, pady=10, fill='both', expand=True) + self.pack(padx=10, pady=10, fill="both", expand=True) def set_actions(self, sort_column, actions_clicks): - for col in self['columns']: - self.heading(col, - text=col, - command=lambda _col=col: sort_column(self, _col, False)) + for col in self["columns"]: + self.heading( + col, text=col, command=lambda _col=col: sort_column(self, _col, False) + ) self.bind("", actions_clicks.on_treeview_click_left) self.bind("", actions_clicks.on_treeview_click_right) diff --git a/pythonQEPest/gui/elements/EditWindow.py b/pythonQEPest/gui/elements/EditWindow.py index d671e7f..36a8a94 100644 --- a/pythonQEPest/gui/elements/EditWindow.py +++ b/pythonQEPest/gui/elements/EditWindow.py @@ -6,25 +6,27 @@ class EditWindow(tk.Toplevel): def __init__(self, tree: Treeview, child_tree: Treeview, item_id, *args, **kwargs): - super().__init__(master=tree, *args, **kwargs) + super().__init__(*args, master=tree, **kwargs) self.title("Edit Entry") # self.geometry("200x300") self.data_manager = DataManager() - values = tree.item(item_id, 'values') + values = tree.item(item_id, "values") old_id = values[0] entries = [] - columns = tree['columns'] + columns = tree["columns"] self.grid_columnconfigure(0, weight=0) self.grid_columnconfigure(1, weight=3) self.resizable(True, False) for idx, col in enumerate(columns): - tk.Label(self, text=col).grid(row=idx, column=0, padx=5, pady=5, sticky='ew') + tk.Label(self, text=col).grid( + row=idx, column=0, padx=5, pady=5, sticky="ew" + ) entry = tk.Entry(self) entry.insert(0, values[idx]) entry.grid(row=idx, column=1, padx=(5, 5), pady=5, sticky="ew") @@ -34,7 +36,7 @@ def save_changes() -> None: new_values = [entry.get() for entry in entries] if child_tree.exists(item_id): - new_child_values = list(child_tree.item(item_id, 'values')) + new_child_values = list(child_tree.item(item_id, "values")) if new_child_values[0] != new_values[0]: new_child_values[0] = new_values[0] child_tree.item(item_id, values=new_child_values) @@ -46,12 +48,16 @@ def save_changes() -> None: update_file_data(new_values) def update_file_data(values: list) -> None: - element = list(filter(lambda x: str(x[0]) == str(old_id), self.data_manager.file_data))[0] + element = list( + filter(lambda x: str(x[0]) == str(old_id), self.data_manager.file_data) + )[0] if element: self.data_manager.update_file(index=element[0], new_entry=values) self.destroy() - tk.Button(self, text="Save", command=save_changes).grid(row=len(columns), column=0, columnspan=2, pady=10) + tk.Button(self, text="Save", command=save_changes).grid( + row=len(columns), column=0, columnspan=2, pady=10 + ) self.grab_set() self.wait_window() diff --git a/pythonQEPest/gui/elements/ResultTree.py b/pythonQEPest/gui/elements/ResultTree.py index d9b940e..843911f 100644 --- a/pythonQEPest/gui/elements/ResultTree.py +++ b/pythonQEPest/gui/elements/ResultTree.py @@ -3,16 +3,18 @@ class ResultTree(Treeview): def __init__(self, root, *args, **kwargs): - columns = ('ID', 'Name', 'QEH', 'QEI', 'QEF') - super().__init__(root, columns=columns, show='headings', *args, **kwargs) + columns = ("ID", "Name", "QEH", "QEI", "QEF") + super().__init__(root, *args, columns=columns, show="headings", **kwargs) for col in columns: self.heading(col, text=col) - self.pack(padx=10, pady=10, fill='both', expand=True) + self.pack(padx=10, pady=10, fill="both", expand=True) def set_actions(self, sort_column, actions_clicks): - for col in self['columns']: - self.heading(col, text=col, command=lambda _col=col: sort_column(self, _col, False)) + for col in self["columns"]: + self.heading( + col, text=col, command=lambda _col=col: sort_column(self, _col, False) + ) self.bind("", actions_clicks.on_treeview_click_left) self.bind("", actions_clicks.on_treeview_click_right) diff --git a/pythonQEPest/gui/elements/SaveButton.py b/pythonQEPest/gui/elements/SaveButton.py index 35c42f3..ec30efd 100644 --- a/pythonQEPest/gui/elements/SaveButton.py +++ b/pythonQEPest/gui/elements/SaveButton.py @@ -3,8 +3,8 @@ class SaveButton(Button): def __init__(self, root, *args, **kwargs): - super().__init__(root, text="Save Results", state='disabled', *args, **kwargs) - self.pack(padx=10, pady=10, side='right') + super().__init__(root, *args, text="Save Results", state="disabled", **kwargs) + self.pack(padx=10, pady=10, side="right") def set_actions(self, actions_other): self.config(command=actions_other.save_result) diff --git a/pythonQEPest/gui/elements/__init__.py b/pythonQEPest/gui/elements/__init__.py index bdd240f..67e44da 100644 --- a/pythonQEPest/gui/elements/__init__.py +++ b/pythonQEPest/gui/elements/__init__.py @@ -1 +1,17 @@ -from pythonQEPest.gui.elements import ResultTree, DataTree, ButtonsFrame, Menu, SaveButton, EditWindow +from pythonQEPest.gui.elements import ( + ResultTree, + DataTree, + ButtonsFrame, + Menu, + SaveButton, + EditWindow, +) + +__all__ = [ + "ResultTree", + "DataTree", + "ButtonsFrame", + "Menu", + "SaveButton", + "EditWindow", +] diff --git a/pythonQEPest/gui/gui.py b/pythonQEPest/gui/gui.py index 337c7f0..9996522 100644 --- a/pythonQEPest/gui/gui.py +++ b/pythonQEPest/gui/gui.py @@ -22,16 +22,18 @@ class GUI(QEPestMeta): def treeview_sort_column(self, treeview, col, reverse): - l = [(treeview.set(k, col), k) for k in treeview.get_children('')] + treeview_lst = [(treeview.set(k, col), k) for k in treeview.get_children("")] try: - l.sort(key=lambda t: float(t[0]), reverse=reverse) + treeview_lst.sort(key=lambda t: float(t[0]), reverse=reverse) except ValueError: - l.sort(key=lambda t: t[0], reverse=reverse) + treeview_lst.sort(key=lambda t: t[0], reverse=reverse) - for index, (val, k) in enumerate(l): - treeview.move(k, '', index) + for index, (_, k) in enumerate(treeview_lst): + treeview.move(k, "", index) - treeview.heading(col, command=lambda: self.treeview_sort_column(treeview, col, not reverse)) + treeview.heading( + col, command=lambda: self.treeview_sort_column(treeview, col, not reverse) + ) def build_gui(self): self.file_data = [] @@ -44,8 +46,12 @@ def build_gui(self): self.menu = Menu(root=self.root) self.actions_clicks = GUIActionsClicks(menu=self.menu) - self.actions_crud = GUIActionsCRUD(data_tree=self.data_tree, result_tree=self.result_tree, - save_button=self.save_button, index=self.index) + self.actions_crud = GUIActionsCRUD( + data_tree=self.data_tree, + result_tree=self.result_tree, + save_button=self.save_button, + index=self.index, + ) self.actions_other = GUIActionsOther( data_tree=self.data_tree, @@ -62,8 +68,8 @@ def build_gui(self): self.menu.set_actions(self.actions_crud) if pyperclip: - self.root.bind('', self.actions_crud.paste_entries) - self.root.bind('', self.actions_crud.copy_selected) + self.root.bind("", self.actions_crud.paste_entries) + self.root.bind("", self.actions_crud.copy_selected) def main() -> int: @@ -76,5 +82,5 @@ def main() -> int: return 0 -if __name__ == '__main__': +if __name__ == "__main__": raise SystemExit(main()) diff --git a/pythonQEPest/gui/utility/__init__.py b/pythonQEPest/gui/utility/__init__.py index bf52550..48dc389 100644 --- a/pythonQEPest/gui/utility/__init__.py +++ b/pythonQEPest/gui/utility/__init__.py @@ -1 +1,6 @@ from pythonQEPest.gui.utility import DataManager, DataManagerMeta + +__all__ = [ + "DataManager", + "DataManagerMeta", +] diff --git a/pythonQEPest/helpers/norm.py b/pythonQEPest/helpers/norm.py index 4786b1d..74dd865 100644 --- a/pythonQEPest/helpers/norm.py +++ b/pythonQEPest/helpers/norm.py @@ -10,12 +10,24 @@ def norm(arr: Union[list, tuple], d: Union[int, float], descr: int) -> float: def norm_h(d: Union[int, float], descr: int) -> float: - return norm((69.5849922, 94.4228257, 120.4572352, 228.1589796, 89.7012502, 276.9634213), d, descr) + return norm( + (69.5849922, 94.4228257, 120.4572352, 228.1589796, 89.7012502, 276.9634213), + d, + descr, + ) def norm_i(d: Union[int, float], descr: int) -> float: - return norm((78.2919965, 71.2829691, 133.9224801, 331.170104, 70.5540709, 193.0023343), d, descr) + return norm( + (78.2919965, 71.2829691, 133.9224801, 331.170104, 70.5540709, 193.0023343), + d, + descr, + ) def norm_f(d: Union[int, float], descr: int) -> float: - return norm((53.3719946, 52.773116, 73.7976536, 144.9887053, 41.4385926, 102.3024319), d, descr) + return norm( + (53.3719946, 52.773116, 73.7976536, 144.9887053, 41.4385926, 102.3024319), + d, + descr, + ) diff --git a/tests/core/test_qepest.py b/tests/core/test_qepest.py index f68fcab..6549d40 100644 --- a/tests/core/test_qepest.py +++ b/tests/core/test_qepest.py @@ -17,7 +17,7 @@ def make_input(self, name="test", mw=120.5, logp=3.1, hba=2, hbd=1, rb=4, ar=1): hbond_acceptors=hba, hbond_donors=hbd, rotatable_bonds=rb, - aromatic_rings=ar + aromatic_rings=ar, ) def test_qepest_compute_params_basic(self): @@ -55,14 +55,21 @@ def test_qepest_nan_protection(self): qep = QEPest() qep.initialize_coefficients() with pytest.raises(ValidationError): - self.make_input(mw=float('nan'), logp=float('nan'), hba=float('nan'), - hbd=float('nan'), rb=float('nan'), ar=float('nan')) + self.make_input( + mw=float("nan"), + logp=float("nan"), + hba=float("nan"), + hbd=float("nan"), + rb=float("nan"), + ar=float("nan"), + ) def test_qepest_compare_with_original(self): qep = QEPest() result = qep.compute_params( - self.make_input("mol1", 240.2127, 3.2392, 5, 1, 4, 1)) + self.make_input("mol1", 240.2127, 3.2392, 5, 1, 4, 1) + ) assert result.name == "mol1" assert result.data.qe_h == 0.8511 @@ -71,7 +78,8 @@ def test_qepest_compare_with_original(self): assert result.to_array() == ["mol1", 0.8511, 0.5339, 0.6224] result = qep.compute_params( - self.make_input("mol2", 249.091, 3.0273, 3, 1, 5, 1)) + self.make_input("mol2", 249.091, 3.0273, 3, 1, 5, 1) + ) assert result.name == "mol2" assert result.data.qe_h == 0.975 assert result.data.qe_i == 0.6913 @@ -79,7 +87,8 @@ def test_qepest_compare_with_original(self): assert result.to_array() == ["mol2", 0.975, 0.6913, 0.731] result = qep.compute_params( - self.make_input("mol3", 308.354, 2.1086, 1, 0, 7, 1)) + self.make_input("mol3", 308.354, 2.1086, 1, 0, 7, 1) + ) assert result.name == "mol3" assert result.data.qe_h == 0.798 assert result.data.qe_i == 0.9018 @@ -87,7 +96,8 @@ def test_qepest_compare_with_original(self): assert result.to_array() == ["mol3", 0.798, 0.9018, 0.732] result = qep.compute_params( - self.make_input("mol4", 360.444, 4.0137, 3, 0, 8, 0)) + self.make_input("mol4", 360.444, 4.0137, 3, 0, 8, 0) + ) assert result.name == "mol4" assert result.data.qe_h == 0.5839 assert result.data.qe_i == 0.8382 @@ -95,7 +105,8 @@ def test_qepest_compare_with_original(self): assert result.to_array() == ["mol4", 0.5839, 0.8382, 0.6594] result = qep.compute_params( - self.make_input("mol5", 295.335, 4.9335, 2, 0, 1, 1)) + self.make_input("mol5", 295.335, 4.9335, 2, 0, 1, 1) + ) assert result.name == "mol5" assert result.data.qe_h == 0.8099 assert result.data.qe_i == 0.8118 diff --git a/tests/dto/test_qepest_file.py b/tests/dto/test_qepest_file.py index 407a6e1..fbb3f85 100644 --- a/tests/dto/test_qepest_file.py +++ b/tests/dto/test_qepest_file.py @@ -11,7 +11,7 @@ def test_qepest_file_import(self): QEPestFile = self._import_qepest_file() assert ( - QEPestFile is not None + QEPestFile is not None ), "QEPestFile should be importable from pythonQEPest.dto" def test_qepest_file_standard(self): diff --git a/tests/dto/test_qepest_input.py b/tests/dto/test_qepest_input.py index 937406c..f2ca35b 100644 --- a/tests/dto/test_qepest_input.py +++ b/tests/dto/test_qepest_input.py @@ -26,9 +26,15 @@ def test_qepest_input(self): assert qepest_input.aromatic_rings == 0 def test_qepest_input_with_changing(self): - qepest_input = QEPestInput(name=self.name, mol_weight=self.mol_weight, log_p=self.log_p, - hbond_acceptors=self.hbond_acceptors, hbond_donors=self.hbond_donors, - rotatable_bonds=self.rotatable_bonds, aromatic_rings=self.aromatic_rings) + qepest_input = QEPestInput( + name=self.name, + mol_weight=self.mol_weight, + log_p=self.log_p, + hbond_acceptors=self.hbond_acceptors, + hbond_donors=self.hbond_donors, + rotatable_bonds=self.rotatable_bonds, + aromatic_rings=self.aromatic_rings, + ) assert qepest_input.name == self.name @@ -42,8 +48,15 @@ def test_qepest_input_with_changing(self): assert qepest_input.aromatic_rings == self.aromatic_rings def test_qepest_output_functions(self): - arr = (self.name, self.mol_weight, self.log_p, self.hbond_acceptors, - self.hbond_donors, self.rotatable_bonds, self.aromatic_rings) + arr = ( + self.name, + self.mol_weight, + self.log_p, + self.hbond_acceptors, + self.hbond_donors, + self.rotatable_bonds, + self.aromatic_rings, + ) qepest_input = QEPestInput.from_array(arr) diff --git a/tests/dto/test_qepest_output.py b/tests/dto/test_qepest_output.py index 72b0b0e..c34c955 100644 --- a/tests/dto/test_qepest_output.py +++ b/tests/dto/test_qepest_output.py @@ -21,7 +21,9 @@ def test_qepest_output_with_changing(self): qepest_data = QEPestData(qe_h=self.qe_h, qe_i=self.qe_i, qe_f=self.qe_f) qepest_output = QEPestOutput(name=self.name, data=qepest_data) - new_qepest_data = QEPestData(qe_h=self.new_qe_h, qe_i=self.new_qe_i, qe_f=self.new_qe_f) + new_qepest_data = QEPestData( + qe_h=self.new_qe_h, qe_i=self.new_qe_i, qe_f=self.new_qe_f + ) qepest_output.name = self.new_name qepest_output.data = new_qepest_data diff --git a/tests/helpers/test_check_nan.py b/tests/helpers/test_check_nan.py index 189dba1..fc6e4f3 100644 --- a/tests/helpers/test_check_nan.py +++ b/tests/helpers/test_check_nan.py @@ -5,10 +5,22 @@ class TestCheckNAN: lst_good = [0.0, 0.1, 0.2] - lst_bad = [math.nan, float('nan'), 0.0] + lst_bad = [math.nan, float("nan"), 0.0] lst_bad_result = [0.0, 0.0, 0.0] lst_strange = [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 1, -45.43, math.nan, float("inf")] - lst_strange_result = [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 1, -45.43, 0.0, float("inf")] + lst_strange_result = [ + 0.0, + 0.1, + 0.2, + 0.3, + 0.4, + 0.5, + 0.6, + 1, + -45.43, + 0.0, + float("inf"), + ] def test_check_nan(self): result = check_nan(self.lst_good) diff --git a/tests/public_api/test_import_contract.py b/tests/public_api/test_import_contract.py index a4e9bc8..1a53560 100644 --- a/tests/public_api/test_import_contract.py +++ b/tests/public_api/test_import_contract.py @@ -33,8 +33,17 @@ def test_public_api_compute_smoke(self): @pytest.mark.skip(reason="Need to find optional approach") def test_helpers_imports(self): try: - from pythonQEPest.helpers import check_nan, get_values_from_line, get_num_of_cols, round_to_4digs, norm_h, \ - norm_f, norm_i, compute_df + from pythonQEPest.helpers import ( + check_nan, + get_values_from_line, + get_num_of_cols, + round_to_4digs, + norm_h, + norm_f, + norm_i, + compute_df, + ) + assert check_nan is not None assert get_values_from_line is not None assert get_num_of_cols is not None From 81d96fc73160bd61740b92d5e0a235af9346840f Mon Sep 17 00:00:00 2001 From: Lina Date: Wed, 11 Feb 2026 17:57:38 +0100 Subject: [PATCH 47/58] fix[version]: 1.1.4 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 4575595..b7a03cd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "pythonQEPest" -version = "1.1.3" +version = "1.1.4" description = "The rewritten version of Java QEPest" readme = "README.md" requires-python = ">=3.10,<3.13" From 7257830b0e9a106535b0f4865e0be7852fb200f3 Mon Sep 17 00:00:00 2001 From: Lina Date: Wed, 11 Feb 2026 18:09:34 +0100 Subject: [PATCH 48/58] fix[helpers]: Forgot to add __all__ --- pythonQEPest/helpers/__init__.py | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/pythonQEPest/helpers/__init__.py b/pythonQEPest/helpers/__init__.py index 7fed626..ae7b2f4 100644 --- a/pythonQEPest/helpers/__init__.py +++ b/pythonQEPest/helpers/__init__.py @@ -4,3 +4,14 @@ from pythonQEPest.helpers.get_values_from_line import get_values_from_line from pythonQEPest.helpers.norm import norm_h, norm_f, norm_i from pythonQEPest.helpers.round_to_4digs import round_to_4digs + +__all__ = [ + "check_nan", + "compute_df", + "get_num_of_cols", + "get_values_from_line", + "norm_h", + "norm_f", + "norm_i", + "round_to_4digs", +] From 7ddaaf78028c37b6bed1aa126ddb9c919f1dc5bc Mon Sep 17 00:00:00 2001 From: Lina Date: Wed, 11 Feb 2026 18:11:21 +0100 Subject: [PATCH 49/58] fix[test_logging]: B011 --- tests/logger/test_logging.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/logger/test_logging.py b/tests/logger/test_logging.py index 32fd4c2..2685094 100644 --- a/tests/logger/test_logging.py +++ b/tests/logger/test_logging.py @@ -20,7 +20,7 @@ def test_logger_initialization(self): init_logger() assert True # If no exception is raised, the test passes except Exception as e: - assert False, f"Logger initialization failed with exception: {e}" + raise AssertionError(f"Logger initialization failed with exception: {e}") def test_default_configuration(self, monkeypatch): self._reset_logger() From 898c6e7493a241688d3dc89d5dcafeb1fbd0e7e3 Mon Sep 17 00:00:00 2001 From: Lina Date: Wed, 11 Feb 2026 18:13:35 +0100 Subject: [PATCH 50/58] fix[version]: 1.1.5 Minor fix flake8 errors --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index b7a03cd..4a9f523 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "pythonQEPest" -version = "1.1.4" +version = "1.1.5" description = "The rewritten version of Java QEPest" readme = "README.md" requires-python = ">=3.10,<3.13" From c8d50d3349397cb7b44e67d3575b60a1a36a59b7 Mon Sep 17 00:00:00 2001 From: Lina Date: Thu, 12 Feb 2026 17:26:01 +0100 Subject: [PATCH 51/58] fix[qepest]: self.noError is a mistake --- pythonQEPest/cli/cli.py | 16 +++++++++++----- pythonQEPest/core/qepest_meta.py | 3 --- 2 files changed, 11 insertions(+), 8 deletions(-) diff --git a/pythonQEPest/cli/cli.py b/pythonQEPest/cli/cli.py index b7f4915..493c013 100644 --- a/pythonQEPest/cli/cli.py +++ b/pythonQEPest/cli/cli.py @@ -21,6 +21,8 @@ def __init__(self, qepest: QEPestMeta, qepest_file: QEPestFile): self.qepest = qepest self.qepest_file = qepest_file + self.error: bool = False + def read_file_and_compute_params(self): try: with open(self.qepest_file.input_file, "r") as file: @@ -32,8 +34,10 @@ def read_file_and_compute_params(self): if get_num_of_cols(line) != self.qepest.col_number: er = f"Error: Line {index} does not have seven elements." logger.error(er) - self.qepest.noError = False + + self.error = True break + wr.write("Name QEH QEI QEF\n") else: if get_num_of_cols(line) == self.qepest.col_number: @@ -48,14 +52,16 @@ def read_file_and_compute_params(self): else: er = f"Error: Line {index} does not have seven elements." logger.error(er) - self.qepest.noError = False - if self.qepest.noError: + + self.error = True + if not self.error: logger.info("Computation completed") else: logger.warning("Finished with errors") except FileNotFoundError as e: - self.qepest.noError = False + self.error = True + logger.error("Error: can't find : %s", self.qepest_file.input_file) logger.exception(e) @@ -123,4 +129,4 @@ def main(argv: Sequence[str] | None = None) -> int: ) cli.read_file_and_compute_params() - return 0 if cli.qepest and cli.qepest.noError else 1 + return 0 if not cli.error else 1 diff --git a/pythonQEPest/core/qepest_meta.py b/pythonQEPest/core/qepest_meta.py index d260674..f7f9d8b 100644 --- a/pythonQEPest/core/qepest_meta.py +++ b/pythonQEPest/core/qepest_meta.py @@ -1,6 +1,5 @@ import os from abc import abstractmethod, ABC - from pythonQEPest.dto import QEPestInput, QEPestOutput, QEPestData @@ -17,8 +16,6 @@ def __init__(self): self.initialize_coefficients() - self.noError: bool = True - @abstractmethod def compute_params(self, data_input: QEPestInput) -> QEPestOutput: pass From b1c47cc0a9a0b2ad493c770c7ed46162f744c193 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 16 Feb 2026 13:39:49 +0000 Subject: [PATCH 52/58] build(deps-dev): bump pyinstaller from 6.18.0 to 6.19.0 Bumps [pyinstaller](https://github.com/pyinstaller/pyinstaller) from 6.18.0 to 6.19.0. - [Release notes](https://github.com/pyinstaller/pyinstaller/releases) - [Changelog](https://github.com/pyinstaller/pyinstaller/blob/develop/doc/CHANGES.rst) - [Commits](https://github.com/pyinstaller/pyinstaller/compare/v6.18.0...v6.19.0) --- updated-dependencies: - dependency-name: pyinstaller dependency-version: 6.19.0 dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- poetry.lock | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/poetry.lock b/poetry.lock index 48ff547..20db0cc 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.3.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand. 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platform_python_implementation != \"PyPy\" and python_version < \"3.14\"", "cffi (>=2.0.0b0) ; platform_python_implementation != \"PyPy\" and python_version >= \"3.14\""] +cffi = ["cffi (>=1.17,<2.0) ; platform_python_implementation != \"PyPy\" and python_version < \"3.14\"", "cffi (>=2.0.0b) ; platform_python_implementation != \"PyPy\" and python_version >= \"3.14\""] [extras] gui = ["pyperclip"] @@ -2209,4 +2209,4 @@ gui = ["pyperclip"] [metadata] lock-version = "2.1" python-versions = ">=3.10,<3.13" -content-hash = "c02d0b3e7c9c86fe2934c2ae7158a7365a749831a445ad2f7793c47d383023ec" +content-hash = "8ba93ad768359952eb49357899071f484c212fc3b6d29cd85926a49c5b1b6400" From d8c833b10dcd9e16f3eb29f40f90ee148310ef62 Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 1 Mar 2026 01:18:19 +0100 Subject: [PATCH 53/58] refactor[QEPest]: Management initialisation Refactor QEPestMeta and related classes for improved coefficient handling and normalization - Updated QEPestMeta to accept coefficients and normalizers as optional parameters during initialization. - Introduced QEPestCoefficient, QEPestCoefficientNumerics, and QEPestCoefficientList for structured coefficient management. - Added Normaliser class for normalization functionality. - Modified QEPestOutput to use BaseModel for data representation. - Enhanced tests for coefficients and normalization to ensure robustness. - Removed deprecated normalization helper functions and consolidated tests. --- .github/workflows/python-package.yml | 26 +- pyproject.toml | 6 +- pythonQEPest/cli/cli.py | 7 +- pythonQEPest/config/__init__.py | 7 + pythonQEPest/config/normalise.py | 12 + pythonQEPest/config/qepest.py | 26 ++ pythonQEPest/core/qepest.py | 114 +++--- pythonQEPest/core/qepest_meta.py | 20 +- pythonQEPest/dto/QEPestOutput.py | 6 +- pythonQEPest/dto/__init__.py | 2 +- .../dto/coefficients/QEPestCoefficient.py | 57 +++ .../dto/coefficients/QEPestCoefficientList.py | 29 ++ .../coefficients/QEPestCoefficientNumerics.py | 44 +++ pythonQEPest/dto/coefficients/__init__.py | 7 + pythonQEPest/dto/normalisation/Normaliser.py | 16 + pythonQEPest/dto/normalisation/__init__.py | 3 + tests/config/__init__.py | 0 tests/config/test_coefficients.py | 369 ++++++++++++++++++ tests/config/test_normalisation.py | 36 ++ tests/core/test_qepest.py | 101 ++--- tests/dto/test_norm.py | 74 ++++ tests/helpers/test_norm.py | 47 --- tests/public_api/test_import_contract.py | 9 +- 23 files changed, 852 insertions(+), 166 deletions(-) create mode 100644 pythonQEPest/config/__init__.py create mode 100644 pythonQEPest/config/normalise.py create mode 100644 pythonQEPest/config/qepest.py create mode 100644 pythonQEPest/dto/coefficients/QEPestCoefficient.py create mode 100644 pythonQEPest/dto/coefficients/QEPestCoefficientList.py create mode 100644 pythonQEPest/dto/coefficients/QEPestCoefficientNumerics.py create mode 100644 pythonQEPest/dto/coefficients/__init__.py create mode 100644 pythonQEPest/dto/normalisation/Normaliser.py create mode 100644 pythonQEPest/dto/normalisation/__init__.py create mode 100644 tests/config/__init__.py create mode 100644 tests/config/test_coefficients.py create mode 100644 tests/config/test_normalisation.py create mode 100644 tests/dto/test_norm.py delete mode 100644 tests/helpers/test_norm.py diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 21b923b..b8eb251 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -12,36 +12,32 @@ on: jobs: build: - - runs-on: ubuntu-latest + runs-on: ubuntu-24.04 strategy: fail-fast: false matrix: - python-version: [ "3.10", "3.11", "3.12" ] + python-version: [ "3.12", "3.13", "3.14" ] steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 + uses: actions/setup-python@v6 with: python-version: ${{ matrix.python-version }} + cache: poetry + cache-dependency-path: poetry.lock - - name: Install poetry + - name: Install Poetry (pipx) run: | python -m pip install --upgrade pip - python -m pip install poetry + python -m pip install pipx + pipx install poetry - name: Install dependencies run: | - poetry install --with dev - - # - name: Lint with flake8 - # run: | - # # stop the build if there are Python syntax errors or undefined names - # flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + poetry install --with dev --no-interaction + - name: Test with pytest (coverage) run: | poetry run pytest -q --cov=pythonQEPest --cov-report=term-missing --cov-fail-under=40 diff --git a/pyproject.toml b/pyproject.toml index 4a9f523..9d0b121 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,9 +1,9 @@ [project] name = "pythonQEPest" -version = "1.1.5" -description = "The rewritten version of Java QEPest" +version = "1.3.0" +description = "Java QEPest in Python" readme = "README.md" -requires-python = ">=3.10,<3.13" +requires-python = ">=3.12,<3.15" authors = [{ name = "Lina", email = "knocker767@gmail.com" }] dependencies = ["pydantic==2.12.5", "python-dotenv>=1.2.1,<2.0.0"] diff --git a/pythonQEPest/cli/cli.py b/pythonQEPest/cli/cli.py index 493c013..86eca20 100644 --- a/pythonQEPest/cli/cli.py +++ b/pythonQEPest/cli/cli.py @@ -44,9 +44,12 @@ def read_file_and_compute_params(self): d_values = get_values_from_line(line.split("\t")) self.qepest.get_qex_values(d_values) splitted_line = line.split("\t")[0] + + # TODO: BUG, AFTER REWORK NEEDS TO BE FIXED !!!!!!!!!!! wr.write( - f"{splitted_line} {self.qepest.qex.qe_h} " - + f"{self.qepest.qex.qe_i} {self.qepest.qex.qe_f}" + f"{splitted_line} {self.qepest.qex.qe_herb} " + + f"{self.qepest.qex.qe_insect} " + + f"{self.qepest.qex.qe_fung}" + f"{chr(10)}" ) else: diff --git a/pythonQEPest/config/__init__.py b/pythonQEPest/config/__init__.py new file mode 100644 index 0000000..0d59601 --- /dev/null +++ b/pythonQEPest/config/__init__.py @@ -0,0 +1,7 @@ +from .qepest import qepest_default +from .normalise import normalise_default + +__all__ = [ + "normalise_default", + "qepest_default", +] diff --git a/pythonQEPest/config/normalise.py b/pythonQEPest/config/normalise.py new file mode 100644 index 0000000..666d681 --- /dev/null +++ b/pythonQEPest/config/normalise.py @@ -0,0 +1,12 @@ +normalise_default = { + "herb": (69.5849922, 94.4228257, 120.4572352, 228.1589796, 89.7012502, 276.9634213), + "insect": ( + 78.2919965, + 71.2829691, + 133.9224801, + 331.170104, + 70.5540709, + 193.0023343, + ), + "fung": (53.3719946, 52.773116, 73.7976536, 144.9887053, 41.4385926, 102.3024319), +} diff --git a/pythonQEPest/config/qepest.py b/pythonQEPest/config/qepest.py new file mode 100644 index 0000000..93293c7 --- /dev/null +++ b/pythonQEPest/config/qepest.py @@ -0,0 +1,26 @@ +qepest_default = { + "herb": [ + (70.77, 283.0, 84.97, -1.185), # mwH + (93.81, 3.077, 1.434, 0.6164), # logpH + (117.6, 2.409, 1.567, 7.155), # hbaH + (233.4, 0.4535, -1.48, 4.47), # hbdH + (84.7, 4.758, -2.423, 5.437), # rbH + (301.8, 1.101, 0.8869, -22.81), # arRCH + ], + "insect": [ + (76.38, 298.3, 83.64, 1.912), # mwI + (74.27, 4.555, -2.193, -2.987), # logpI + (139.4, 1.363, 1.283, 0.5341), # hbaI + (670.6, -1.163, 0.7856, 0.7951), # hbdI + (65.49, 6.219, -2.448, 5.318), # rbI + (287.5, 0.305, 1.554, -88.64), # arRCI + ], + "fung": [ + (51.03, 314.2, -56.31, 2.342), # mwF + (50.73, 3.674, -1.238, 2.067), # logpF + (73.79, 1.841, 1.326, 0.5158), # hbaF + (164.7, -0.9762, -2.027, 1.384), # hbdF + (40.91, 1.822, 2.582, 0.6235), # rbF + (134.4, 0.8383, 1.347, -31.17), # arRCF + ], +} diff --git a/pythonQEPest/core/qepest.py b/pythonQEPest/core/qepest.py index 4086ce0..09fa569 100644 --- a/pythonQEPest/core/qepest.py +++ b/pythonQEPest/core/qepest.py @@ -1,74 +1,98 @@ +import logging import math +from typing import Optional + +from pydantic import create_model, BaseModel from pythonQEPest.core.qepest_meta import QEPestMeta -from pythonQEPest.dto.QEPestData import QEPestData from pythonQEPest.dto.QEPestInput import QEPestInput from pythonQEPest.dto.QEPestOutput import QEPestOutput +from pythonQEPest.dto.normalisation.Normaliser import Normaliser from pythonQEPest.helpers.check_nan import check_nan from pythonQEPest.helpers.compute_df import compute_df from pythonQEPest.helpers.get_values_from_line import get_values_from_line -from pythonQEPest.helpers.norm import norm_h, norm_f, norm_i from pythonQEPest.helpers.round_to_4digs import round_to_4digs +logger = logging.getLogger(__name__) + class QEPest(QEPestMeta): + + def __init__(self, *args, **kwargs): + super().__init__(*args, **kwargs) + + def _log_compute_df(self, func, index, lst, data_lst) -> float: + df_result = compute_df(lst[index], *data_lst[index]) + return math.log(func(df_result, index)) + def compute_params(self, data_input: QEPestInput) -> QEPestOutput: self.get_qex_values( get_values_from_line(list(data_input.model_dump().values())) ) return QEPestOutput(data=self.qex, name=data_input.name) - def get_qex_values(self, d) -> None: - def log_compute_df(func, index, lst, data_lst) -> float: - df_result = compute_df(lst[index], *data_lst[index]) - return math.log(func(df_result, index)) + def get_qex_values(self, d) -> BaseModel: + names = [n.split("_")[1] for n in dir(self) if n.startswith("coefficient_")] + + # Coefficients names = ("coefficients_fung, coefficient_herb...) + coefficients_names = [n for n in dir(self) if n.startswith("coefficient_")] + if len(coefficients_names) == 0: + raise ValueError( + "No coefficient_ keys, needs to call " + + "initialize_coefficient and workable config to work" + ) - qe_h = 0.0 - qe_i = 0.0 - qe_f = 0.0 + # coefficients = [{i: getattr(self, i)} for i in coefficients_names] + + # Splitting by _ to get (fung, herb, etc...) to form qe_fung, qe_herb... + # qe_lst = [] + for z in names: + name = f"qe_{z}" + setattr(self, name, 0.0) d_num = len(d) for i in range(d_num): - qe_h += log_compute_df(func=norm_h, index=i, lst=d, data_lst=self.herb) - qe_i += log_compute_df(func=norm_i, index=i, lst=d, data_lst=self.insect) - qe_f += log_compute_df(func=norm_f, index=i, lst=d, data_lst=self.fung) + for name in names: + self.__dict__[f"qe_{name}"] += self._log_compute_df( + func=self.__dict__[f"normaliser_{name}"].norm, + index=i, + lst=d, + data_lst=self.__dict__[f"coefficient_{name}"], + ) q = [ - round_to_4digs(math.exp(qe_h / d_num)), - round_to_4digs(math.exp(qe_i / d_num)), - round_to_4digs(math.exp(qe_f / d_num)), + round_to_4digs(math.exp(self.__dict__[f"qe_{name}"] / d_num)) + for name in names ] result = check_nan(q) - self.qex = QEPestData(qe_h=result[0], qe_i=result[1], qe_f=result[2]) - - def initialize_coefficients(self) -> None: - coefficients = { - "herb": [ - (70.77, 283.0, 84.97, -1.185), # mwH - (93.81, 3.077, 1.434, 0.6164), # logpH - (117.6, 2.409, 1.567, 7.155), # hbaH - (233.4, 0.4535, -1.48, 4.47), # hbdH - (84.7, 4.758, -2.423, 5.437), # rbH - (301.8, 1.101, 0.8869, -22.81), # arRCH - ], - "insect": [ - (76.38, 298.3, 83.64, 1.912), # mwI - (74.27, 4.555, -2.193, -2.987), # logpI - (139.4, 1.363, 1.283, 0.5341), # hbaI - (670.6, -1.163, 0.7856, 0.7951), # hbdI - (65.49, 6.219, -2.448, 5.318), # rbI - (287.5, 0.305, 1.554, -88.64), # arRCI - ], - "fung": [ - (51.03, 314.2, -56.31, 2.342), # mwF - (50.73, 3.674, -1.238, 2.067), # logpF - (73.79, 1.841, 1.326, 0.5158), # hbaF - (164.7, -0.9762, -2.027, 1.384), # hbdF - (40.91, 1.822, 2.582, 0.6235), # rbF - (134.4, 0.8383, 1.347, -31.17), # arRCF - ], - } + + fields = {f"qe_{name}": (float, 0.0) for name in names} + dynamic_model = create_model("QEPestData", **fields) + self.qex = dynamic_model( + **{f"qe_{names[idx]}": name for idx, name in enumerate(result)} + ) + + return self.qex + + # TODO: Coefficients must be in other class + def initialize_coefficients(self, coefficients: Optional = None) -> None: + coefficients = super().initialize_coefficients() for category, data in coefficients.items(): - getattr(self, category).extend(data) + setattr(self, f"coefficient_{category}", data) + + # TODO: Same with Normalisers + def initialize_normalisers(self, normalisers: Optional = None) -> None: + normalisers = super().initialize_normalisers() + + for category, data in normalisers.items(): + setattr(self, f"normaliser_{category}", Normaliser(data)) + + +if __name__ == "__main__": + qepest = QEPest() + qepest.initialize_coefficients() + qepest.initialize_normalisers() + qepest.get_qex_values(1) + print(1) diff --git a/pythonQEPest/core/qepest_meta.py b/pythonQEPest/core/qepest_meta.py index f7f9d8b..0151790 100644 --- a/pythonQEPest/core/qepest_meta.py +++ b/pythonQEPest/core/qepest_meta.py @@ -1,10 +1,11 @@ import os from abc import abstractmethod, ABC + from pythonQEPest.dto import QEPestInput, QEPestOutput, QEPestData class QEPestMeta(ABC): - def __init__(self): + def __init__(self, *args, **kwargs): self.qex: QEPestData | None = None self.herb: list[float] = [] @@ -15,6 +16,7 @@ def __init__(self): self.dir: str = os.getcwd() self.initialize_coefficients() + self.initialize_normalisers() @abstractmethod def compute_params(self, data_input: QEPestInput) -> QEPestOutput: @@ -25,5 +27,17 @@ def get_qex_values(self, d) -> None: pass @abstractmethod - def initialize_coefficients(self) -> None: - pass + def initialize_coefficients(self, coefficients=None) -> None: + if coefficients is None: + from pythonQEPest.config.qepest import qepest_default + + coefficients = qepest_default + return coefficients + + @abstractmethod + def initialize_normalisers(self, normalisers=None) -> None: + if normalisers is None: + from pythonQEPest.config.normalise import normalise_default + + normalisers = normalise_default + return normalisers diff --git a/pythonQEPest/dto/QEPestOutput.py b/pythonQEPest/dto/QEPestOutput.py index a8100f6..d5415b2 100644 --- a/pythonQEPest/dto/QEPestOutput.py +++ b/pythonQEPest/dto/QEPestOutput.py @@ -2,12 +2,10 @@ from pydantic import BaseModel -from pythonQEPest.dto import QEPestData - class QEPestOutput(BaseModel): - data: QEPestData + data: BaseModel name: Optional[str] = "" def to_array(self) -> list: - return [self.name, self.data.qe_h, self.data.qe_i, self.data.qe_f] + return [self.name] + list(self.data.model_dump().values()) diff --git a/pythonQEPest/dto/__init__.py b/pythonQEPest/dto/__init__.py index 45c75d6..aa218a7 100644 --- a/pythonQEPest/dto/__init__.py +++ b/pythonQEPest/dto/__init__.py @@ -1,6 +1,6 @@ from pythonQEPest.dto.QEPestData import QEPestData -from pythonQEPest.dto.QEPestFile import QEPestFile from pythonQEPest.dto.QEPestInput import QEPestInput +from pythonQEPest.dto.QEPestFile import QEPestFile from pythonQEPest.dto.QEPestOutput import QEPestOutput __all__ = [ diff --git a/pythonQEPest/dto/coefficients/QEPestCoefficient.py b/pythonQEPest/dto/coefficients/QEPestCoefficient.py new file mode 100644 index 0000000..27c450f --- /dev/null +++ b/pythonQEPest/dto/coefficients/QEPestCoefficient.py @@ -0,0 +1,57 @@ +from pydantic import BaseModel + +from pythonQEPest.dto.coefficients import QEPestCoefficientNumerics + + +class QEPestCoefficient(BaseModel): + name: str + coefficients: QEPestCoefficientNumerics + + def __init__(self, *args, **kwargs): + if args: + if len(args) != 1: + raise ValueError(f"Expected len(args) == 1, got {len(args)}") + + # In case of {"test": [[1,2,3,4],[1,2,3,4],[1,2,3,4]} + if len(args[0]) == 1: + must_be_dict = args[0] + if isinstance(must_be_dict, dict): + key = list(must_be_dict.keys())[0] + coefficients = QEPestCoefficientNumerics(must_be_dict[key]) + super().__init__(name=key, coefficients=coefficients) + + # In case of ["test", [[1,2,3,4],[1,2,3,4],[1,2,3,4]] + elif len(args[0]) == 2: + arr = args[0] + if ( + isinstance(arr, tuple) + or isinstance(arr, set) + or isinstance(arr, list) + ): + name = arr[0] + coefficients = QEPestCoefficientNumerics(arr[1]) + super().__init__(name=name, coefficients=coefficients) + + elif kwargs: + super().__init__(**kwargs) + else: + raise ValueError( + "No name and coefficients provided. Please provide either a " + + "name and coefficients tuple or keyword arguments." + ) + + +if __name__ == "__main__": + # Example usage + coefficients = QEPestCoefficient( + mw=[0.1, 0.2, 0.3, 0.4], + logp=[0.1, 0.2, 0.3, 0.4], + hba=[0.1, 0.2, 0.3, 0.4], + hbd=[0.1, 0.2, 0.3, 0.4], + rb=[0.1, 0.2, 0.3, 0.4], + ar=[0.1, 0.2, 0.3, 0.4], + ) + print(coefficients) + + coefficients_alternative = QEPestCoefficient([[0.1, 0.2, 0.3, 0.4] * 6]) + print(coefficients_alternative) diff --git a/pythonQEPest/dto/coefficients/QEPestCoefficientList.py b/pythonQEPest/dto/coefficients/QEPestCoefficientList.py new file mode 100644 index 0000000..4975a5d --- /dev/null +++ b/pythonQEPest/dto/coefficients/QEPestCoefficientList.py @@ -0,0 +1,29 @@ +from typing import Optional, List + +from pydantic import BaseModel + +from pythonQEPest.dto.coefficients import QEPestCoefficient + + +class QEPestCoefficientList(BaseModel): + name: Optional[str] + named_coefficients: List[QEPestCoefficient] + + # TODO: Done all the cases and make some sort of docs here, pls + def __init__(self, *args, **kwargs): + if args: + named_coeff = args[0] + if len(named_coeff) == 1: + pass + elif len(named_coeff) > 1: + if isinstance(named_coeff, dict): + lst = [QEPestCoefficient({i: z}) for i, z in named_coeff.items()] + super().__init__(name="generic", named_coefficients=lst) + + elif kwargs: + super().__init__(**kwargs) + else: + raise ValueError( + "No name and coefficients provided. Please provide either a " + + "name and coefficients tuple or keyword arguments." + ) diff --git a/pythonQEPest/dto/coefficients/QEPestCoefficientNumerics.py b/pythonQEPest/dto/coefficients/QEPestCoefficientNumerics.py new file mode 100644 index 0000000..8c51224 --- /dev/null +++ b/pythonQEPest/dto/coefficients/QEPestCoefficientNumerics.py @@ -0,0 +1,44 @@ +from pydantic import BaseModel + +CoefficientTuple = tuple[float, float, float, float] + + +class QEPestCoefficientNumerics(BaseModel): + mw: CoefficientTuple + logp: CoefficientTuple + hba: CoefficientTuple + hbd: CoefficientTuple + rb: CoefficientTuple + ar: CoefficientTuple + + def __init__(self, *args, **kwargs): + if args: + # In case of [[1,2,3,4],[1,2,3,4],[1,2,3,4]] + # I don't want it to be a pain to init D: + if len(args) != 1: + raise ValueError( + f"Expected a single list of coefficients, got {len(args)}" + ) + + coefficients = args[0] + if len(coefficients) != 6: + raise ValueError( + "Expected list with structure [[1,2,3,4,5,6], ", + "[1,2,3,4,5,6], [1,...] ...] got ", + f"{len(coefficients)} and {coefficients}", + ) + + coefficients_mapped = { + field: coefficients[i] + for i, field in enumerate(["mw", "logp", "hba", "hbd", "rb", "ar"]) + } + super().__init__(**coefficients_mapped) + + elif kwargs: + super().__init__(**kwargs) + + else: + raise ValueError( + "No coefficients provided. Please provide either a ", + "list of coefficient tuples or keyword arguments.", + ) diff --git a/pythonQEPest/dto/coefficients/__init__.py b/pythonQEPest/dto/coefficients/__init__.py new file mode 100644 index 0000000..94e829f --- /dev/null +++ b/pythonQEPest/dto/coefficients/__init__.py @@ -0,0 +1,7 @@ +from pythonQEPest.dto.coefficients.QEPestCoefficientNumerics import ( + QEPestCoefficientNumerics, +) +from pythonQEPest.dto.coefficients.QEPestCoefficient import QEPestCoefficient +from pythonQEPest.dto.coefficients.QEPestCoefficientList import QEPestCoefficientList + +__all__ = ["QEPestCoefficientNumerics", "QEPestCoefficient", "QEPestCoefficientList"] diff --git a/pythonQEPest/dto/normalisation/Normaliser.py b/pythonQEPest/dto/normalisation/Normaliser.py new file mode 100644 index 0000000..ace3606 --- /dev/null +++ b/pythonQEPest/dto/normalisation/Normaliser.py @@ -0,0 +1,16 @@ +from typing import Union + + +class Normaliser: + def __init__(self, arr: Union[tuple, list]): + # if len(arr) != 6: + # raise ValueError(f"Array must be exact length of 6. Given: {len(arr)}") + + self.arr = arr + + def norm(self, d: Union[int, float], descr: int) -> float: + if descr > len(self.arr): + raise KeyError(f"Out of array. {descr} > {len(self.arr)}") + + max_val = self.arr[int(descr)] + return d / max_val if max_val != 0 else 0.0 diff --git a/pythonQEPest/dto/normalisation/__init__.py b/pythonQEPest/dto/normalisation/__init__.py new file mode 100644 index 0000000..3c2db34 --- /dev/null +++ b/pythonQEPest/dto/normalisation/__init__.py @@ -0,0 +1,3 @@ +from pythonQEPest.dto.normalisation.Normaliser import Normaliser + +__all__ = ["Normaliser"] diff --git a/tests/config/__init__.py b/tests/config/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/config/test_coefficients.py b/tests/config/test_coefficients.py new file mode 100644 index 0000000..8816b23 --- /dev/null +++ b/tests/config/test_coefficients.py @@ -0,0 +1,369 @@ +from pythonQEPest.dto.coefficients import ( + QEPestCoefficient, + QEPestCoefficientNumerics, + QEPestCoefficientList, +) + + +class TestQEPestCoefficients: + def test_qepest_coefficient_numerics_strict(self): + qep_coeff_num = QEPestCoefficientNumerics( + mw=(0.1, 0.2, 0.3, 0.4), + logp=(0.1, 0.2, 0.3, 0.4), + hba=(0.1, 0.2, 0.3, 0.4), + hbd=(0.1, 0.2, 0.3, 0.4), + rb=(0.1, 0.2, 0.3, 0.4), + ar=(0.1, 0.2, 0.3, 0.4), + ) + + assert qep_coeff_num.mw == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff_num.logp == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff_num.hba == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff_num.hbd == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff_num.rb == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff_num.ar == (0.1, 0.2, 0.3, 0.4) + + def test_qepest_coefficient_numerics_unstrict(self): + qep_coeff_num = QEPestCoefficientNumerics([[0.1, 0.2, 0.3, 0.4]] * 6) + + assert qep_coeff_num.mw == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff_num.logp == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff_num.hba == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff_num.hbd == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff_num.rb == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff_num.ar == (0.1, 0.2, 0.3, 0.4) + + def test_qepest_coefficients_strict(self): + coefficients_name = "herb" + coefficients_dict = [ + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + ] + qep_coeff = QEPestCoefficient( + name=coefficients_name, + coefficients=QEPestCoefficientNumerics(coefficients_dict), + ) + + assert qep_coeff.name == "herb" + assert qep_coeff.coefficients.mw == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.logp == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.hba == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.hbd == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.rb == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.ar == (0.1, 0.2, 0.3, 0.4) + + def test_qepest_coefficients_unstrict(self): + coefficients_dict = { + "herb": [ + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + ] + } + qep_coeff = QEPestCoefficient(coefficients_dict) + + assert qep_coeff.name == "herb" + assert qep_coeff.coefficients.mw == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.logp == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.hba == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.hbd == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.rb == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.ar == (0.1, 0.2, 0.3, 0.4) + + def test_qepest_coefficients_unstrict_chaos(self): + coefficients_dict = [ + "herb", + [ + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + [0.1, 0.2, 0.3, 0.4], + ], + ] + + qep_coeff = QEPestCoefficient(coefficients_dict) + + assert qep_coeff.name == "herb" + assert qep_coeff.coefficients.mw == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.logp == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.hba == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.hbd == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.rb == (0.1, 0.2, 0.3, 0.4) + assert qep_coeff.coefficients.ar == (0.1, 0.2, 0.3, 0.4) + + def test_qepest_coefficients_lst_basic(self): + coefficients_dict = { + "test1": [ + (0.1, 0.2, 0.3, 0.4), # mwI + (0.1, 0.2, 0.3, 0.4), # logpI + (0.1, 0.2, 0.3, 0.4), # hbaI + (0.1, 0.2, 0.3, 0.4), # hbdI + (0.1, 0.2, 0.3, 0.4), # rbI + (0.1, 0.2, 0.3, 0.4), # arRCI + ], + "test2": [ + (0.1, 0.2, 0.3, 0.4), # mwF + (0.1, 0.2, 0.3, 0.4), # logpF + (0.1, 0.2, 0.3, 0.4), # hbaF + (0.1, 0.2, 0.3, 0.4), # hbdF + (0.1, 0.2, 0.3, 0.4), # rbF + (0.1, 0.2, 0.3, 0.4), # arRCF + ], + } + + qep_coeff_lst = QEPestCoefficientList(coefficients_dict) + + assert qep_coeff_lst.name == "generic" + assert qep_coeff_lst.named_coefficients is not None + + assert len(qep_coeff_lst.named_coefficients) == 2 + + assert qep_coeff_lst.named_coefficients[0].name == "test1" + + assert qep_coeff_lst.named_coefficients[0].coefficients.mw == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + assert qep_coeff_lst.named_coefficients[0].coefficients.logp == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + assert qep_coeff_lst.named_coefficients[0].coefficients.hba == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + assert qep_coeff_lst.named_coefficients[0].coefficients.hbd == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + assert qep_coeff_lst.named_coefficients[0].coefficients.rb == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + assert qep_coeff_lst.named_coefficients[0].coefficients.ar == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + + assert qep_coeff_lst.named_coefficients[1].name == "test2" + + assert qep_coeff_lst.named_coefficients[1].coefficients.mw == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + assert qep_coeff_lst.named_coefficients[1].coefficients.logp == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + assert qep_coeff_lst.named_coefficients[1].coefficients.hba == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + assert qep_coeff_lst.named_coefficients[1].coefficients.hbd == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + assert qep_coeff_lst.named_coefficients[1].coefficients.rb == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + assert qep_coeff_lst.named_coefficients[1].coefficients.ar == ( + 0.1, + 0.2, + 0.3, + 0.4, + ) + + def test_qepest_coefficients_lst_w_import(self): + from pythonQEPest.config.qepest import qepest_default + + qep_coeff_lst = QEPestCoefficientList(qepest_default) + + assert qep_coeff_lst.name == "generic" + assert qep_coeff_lst.named_coefficients is not None + + assert len(qep_coeff_lst.named_coefficients) == 3 + + assert qep_coeff_lst.named_coefficients[0].name == "herb" + + assert qep_coeff_lst.named_coefficients[0].coefficients.mw == ( + 70.77, + 283.0, + 84.97, + -1.185, + ) + assert qep_coeff_lst.named_coefficients[0].coefficients.logp == ( + 93.81, + 3.077, + 1.434, + 0.6164, + ) + assert qep_coeff_lst.named_coefficients[0].coefficients.hba == ( + 117.6, + 2.409, + 1.567, + 7.155, + ) + assert qep_coeff_lst.named_coefficients[0].coefficients.hbd == ( + 233.4, + 0.4535, + -1.48, + 4.47, + ) + assert qep_coeff_lst.named_coefficients[0].coefficients.rb == ( + 84.7, + 4.758, + -2.423, + 5.437, + ) + assert qep_coeff_lst.named_coefficients[0].coefficients.ar == ( + 301.8, + 1.101, + 0.8869, + -22.81, + ) + + assert qep_coeff_lst.named_coefficients[1].name == "insect" + + assert qep_coeff_lst.named_coefficients[1].coefficients.mw == ( + 76.38, + 298.3, + 83.64, + 1.912, + ) + assert qep_coeff_lst.named_coefficients[1].coefficients.logp == ( + 74.27, + 4.555, + -2.193, + -2.987, + ) + assert qep_coeff_lst.named_coefficients[1].coefficients.hba == ( + 139.4, + 1.363, + 1.283, + 0.5341, + ) + assert qep_coeff_lst.named_coefficients[1].coefficients.hbd == ( + 670.6, + -1.163, + 0.7856, + 0.7951, + ) + assert qep_coeff_lst.named_coefficients[1].coefficients.rb == ( + 65.49, + 6.219, + -2.448, + 5.318, + ) + assert qep_coeff_lst.named_coefficients[1].coefficients.ar == ( + 287.5, + 0.305, + 1.554, + -88.64, + ) + + assert qep_coeff_lst.named_coefficients[2].name == "fung" + + assert qep_coeff_lst.named_coefficients[2].coefficients.mw == ( + 51.03, + 314.2, + -56.31, + 2.342, + ) + assert qep_coeff_lst.named_coefficients[2].coefficients.logp == ( + 50.73, + 3.674, + -1.238, + 2.067, + ) + assert qep_coeff_lst.named_coefficients[2].coefficients.hba == ( + 73.79, + 1.841, + 1.326, + 0.5158, + ) + assert qep_coeff_lst.named_coefficients[2].coefficients.hbd == ( + 164.7, + -0.9762, + -2.027, + 1.384, + ) + assert qep_coeff_lst.named_coefficients[2].coefficients.rb == ( + 40.91, + 1.822, + 2.582, + 0.6235, + ) + assert qep_coeff_lst.named_coefficients[2].coefficients.ar == ( + 134.4, + 0.8383, + 1.347, + -31.17, + ) + + def test_qepest_default_coefficients(self): + from pythonQEPest.config.qepest import qepest_default + + assert "fung" in qepest_default + assert "herb" in qepest_default + assert "insect" in qepest_default + + coefficients = { + "herb": [ + (70.77, 283.0, 84.97, -1.185), # mwH + (93.81, 3.077, 1.434, 0.6164), # logpH + (117.6, 2.409, 1.567, 7.155), # hbaH + (233.4, 0.4535, -1.48, 4.47), # hbdH + (84.7, 4.758, -2.423, 5.437), # rbH + (301.8, 1.101, 0.8869, -22.81), # arRCH + ], + "insect": [ + (76.38, 298.3, 83.64, 1.912), # mwI + (74.27, 4.555, -2.193, -2.987), # logpI + (139.4, 1.363, 1.283, 0.5341), # hbaI + (670.6, -1.163, 0.7856, 0.7951), # hbdI + (65.49, 6.219, -2.448, 5.318), # rbI + (287.5, 0.305, 1.554, -88.64), # arRCI + ], + "fung": [ + (51.03, 314.2, -56.31, 2.342), # mwF + (50.73, 3.674, -1.238, 2.067), # logpF + (73.79, 1.841, 1.326, 0.5158), # hbaF + (164.7, -0.9762, -2.027, 1.384), # hbdF + (40.91, 1.822, 2.582, 0.6235), # rbF + (134.4, 0.8383, 1.347, -31.17), # arRCF + ], + } + + assert qepest_default == coefficients diff --git a/tests/config/test_normalisation.py b/tests/config/test_normalisation.py new file mode 100644 index 0000000..88350bd --- /dev/null +++ b/tests/config/test_normalisation.py @@ -0,0 +1,36 @@ +class TestQEPestNormalisation: + def test_qepest_default_coefficients(self): + from pythonQEPest.config.normalise import normalise_default + + assert "fung" in normalise_default + assert "herb" in normalise_default + assert "insect" in normalise_default + + normalise = { + "herb": ( + 69.5849922, + 94.4228257, + 120.4572352, + 228.1589796, + 89.7012502, + 276.9634213, + ), + "insect": ( + 78.2919965, + 71.2829691, + 133.9224801, + 331.170104, + 70.5540709, + 193.0023343, + ), + "fung": ( + 53.3719946, + 52.773116, + 73.7976536, + 144.9887053, + 41.4385926, + 102.3024319, + ), + } + + assert normalise_default == normalise diff --git a/tests/core/test_qepest.py b/tests/core/test_qepest.py index 6549d40..eb7fc46 100644 --- a/tests/core/test_qepest.py +++ b/tests/core/test_qepest.py @@ -2,7 +2,6 @@ import pytest from pydantic import ValidationError - from pythonQEPest.core.qepest import QEPest from pythonQEPest.dto import QEPestInput @@ -21,39 +20,46 @@ def make_input(self, name="test", mw=120.5, logp=3.1, hba=2, hbd=1, rb=4, ar=1): ) def test_qepest_compute_params_basic(self): - qep = QEPest() - qep.initialize_coefficients() + qepest = QEPest() + + qepest.initialize_coefficients() + qepest.initialize_normalisers() + inp = self.make_input() - result = qep.compute_params(inp) + result = qepest.compute_params(inp) + assert hasattr(result, "data") - assert hasattr(result.data, "qe_f") - assert hasattr(result.data, "qe_h") - assert hasattr(result.data, "qe_i") - assert math.isfinite(result.data.qe_h) - assert math.isfinite(result.data.qe_i) - assert math.isfinite(result.data.qe_f) + assert hasattr(result.data, "qe_fung") + assert hasattr(result.data, "qe_herb") + assert hasattr(result.data, "qe_insect") + + assert math.isfinite(result.data.qe_herb) + assert math.isfinite(result.data.qe_insect) + assert math.isfinite(result.data.qe_fung) + assert hasattr(result, "name") assert result.name == inp.name def test_qepest_zero_input(self): - qep = QEPest() - qep.initialize_coefficients() + qepest = QEPest() + inp = self.make_input(mw=0, logp=0, hba=0, hbd=0, rb=0, ar=0) + with pytest.raises(ValueError): - qep.compute_params(inp) + qepest.compute_params(inp) def test_qepest_multiple_names(self): - qep = QEPest() - qep.initialize_coefficients() + qepest = QEPest() + for i in range(3): name = f"test_{i}" inp = self.make_input(name=name) - result = qep.compute_params(inp) + result = qepest.compute_params(inp) assert result.name == name def test_qepest_nan_protection(self): - qep = QEPest() - qep.initialize_coefficients() + # qepest = QEPest() + with pytest.raises(ValidationError): self.make_input( mw=float("nan"), @@ -65,50 +71,57 @@ def test_qepest_nan_protection(self): ) def test_qepest_compare_with_original(self): - qep = QEPest() + qepest = QEPest() - result = qep.compute_params( + result = qepest.compute_params( self.make_input("mol1", 240.2127, 3.2392, 5, 1, 4, 1) ) assert result.name == "mol1" - assert result.data.qe_h == 0.8511 - assert result.data.qe_i == 0.5339 - assert result.data.qe_f == 0.6224 - assert result.to_array() == ["mol1", 0.8511, 0.5339, 0.6224] + assert result.data.qe_herb == 0.8511 + assert result.data.qe_insect == 0.5339 + assert result.data.qe_fung == 0.6224 + + assert result.to_array() == ["mol1", 0.6224, 0.8511, 0.5339] - result = qep.compute_params( + result = qepest.compute_params( self.make_input("mol2", 249.091, 3.0273, 3, 1, 5, 1) ) assert result.name == "mol2" - assert result.data.qe_h == 0.975 - assert result.data.qe_i == 0.6913 - assert result.data.qe_f == 0.731 - assert result.to_array() == ["mol2", 0.975, 0.6913, 0.731] - result = qep.compute_params( + assert result.data.qe_herb == 0.975 + assert result.data.qe_insect == 0.6913 + assert result.data.qe_fung == 0.731 + + assert result.to_array() == ["mol2", 0.731, 0.975, 0.6913] + + result = qepest.compute_params( self.make_input("mol3", 308.354, 2.1086, 1, 0, 7, 1) ) assert result.name == "mol3" - assert result.data.qe_h == 0.798 - assert result.data.qe_i == 0.9018 - assert result.data.qe_f == 0.732 - assert result.to_array() == ["mol3", 0.798, 0.9018, 0.732] - result = qep.compute_params( + assert result.data.qe_herb == 0.798 + assert result.data.qe_insect == 0.9018 + assert result.data.qe_fung == 0.732 + + assert result.to_array() == ["mol3", 0.732, 0.798, 0.9018] + + result = qepest.compute_params( self.make_input("mol4", 360.444, 4.0137, 3, 0, 8, 0) ) assert result.name == "mol4" - assert result.data.qe_h == 0.5839 - assert result.data.qe_i == 0.8382 - assert result.data.qe_f == 0.6594 - assert result.to_array() == ["mol4", 0.5839, 0.8382, 0.6594] + assert result.data.qe_herb == 0.5839 + assert result.data.qe_insect == 0.8382 + assert result.data.qe_fung == 0.6594 - result = qep.compute_params( + assert result.to_array() == ["mol4", 0.6594, 0.5839, 0.8382] + + result = qepest.compute_params( self.make_input("mol5", 295.335, 4.9335, 2, 0, 1, 1) ) assert result.name == "mol5" - assert result.data.qe_h == 0.8099 - assert result.data.qe_i == 0.8118 - assert result.data.qe_f == 0.8742 - assert result.to_array() == ["mol5", 0.8099, 0.8118, 0.8742] + assert result.data.qe_herb == 0.8099 + assert result.data.qe_insect == 0.8118 + assert result.data.qe_fung == 0.8742 + + assert result.to_array() == ["mol5", 0.8742, 0.8099, 0.8118] diff --git a/tests/dto/test_norm.py b/tests/dto/test_norm.py new file mode 100644 index 0000000..2125c1a --- /dev/null +++ b/tests/dto/test_norm.py @@ -0,0 +1,74 @@ +import pytest + +from pythonQEPest.dto.normalisation.Normaliser import Normaliser + +# from pythonQEPest.helpers.norm import norm_i, norm_h, norm, norm_f + + +class TestNorm: + def test_norm_basic(self): + arr = [10, 20, 30] + d = 20 + + normaliser = Normaliser(arr) + + assert normaliser.norm(d, 1) == 1.0 + assert normaliser.norm(d, 2) == 20 / 30 + assert normaliser.norm(d, 0) == 2.0 + + def test_norm_zero_div(self): + arr = [10, 0, 30] + d = 5 + + normaliser = Normaliser(arr) + + assert normaliser.norm(d, 1) == 0.0 + + def test_norm_out_of_range(self): + arr = [1, 2, 3] + + normaliser = Normaliser(arr) + with pytest.raises(KeyError): + normaliser.norm(2, 5) + + def test_norm_negative_descr(self): + arr = [1, 2, 3] + + normaliser = Normaliser(arr) + + assert normaliser.norm(2, -1) == 2 / 3 + + def test_norm_h(self): + from pythonQEPest.config import normalise_default + + normaliser = Normaliser(normalise_default["herb"]) + + assert normaliser.norm(69.5849922, 0) == 1.0 + assert normaliser.norm(0, 2) == 0.0 + assert pytest.approx(normaliser.norm(60, 1), rel=1e-6) == 60 / 94.4228257 + + def test_norm_i(self): + from pythonQEPest.config import normalise_default + + normaliser = Normaliser(normalise_default["insect"]) + + assert normaliser.norm(78.2919965, 0) == 1.0 + assert normaliser.norm(0, 3) == 0.0 + assert pytest.approx(normaliser.norm(66, 1), rel=1e-6) == 66 / 71.2829691 + + def test_norm_f(self): + from pythonQEPest.config import normalise_default + + normaliser = Normaliser(normalise_default["fung"]) + + assert normaliser.norm(53.3719946, 0) == 1.0 + assert normaliser.norm(0, 5) == 0.0 + assert pytest.approx(normaliser.norm(70, 2), rel=1e-6) == 70 / 73.7976536 + + def test_norm_invalid_descr_type(self): + arr = [1, 2, 3] + + normaliser = Normaliser(arr) + + with pytest.raises(TypeError): + normaliser.norm(1, "not_an_int") diff --git a/tests/helpers/test_norm.py b/tests/helpers/test_norm.py deleted file mode 100644 index 6e1ebd3..0000000 --- a/tests/helpers/test_norm.py +++ /dev/null @@ -1,47 +0,0 @@ -import pytest - -from pythonQEPest.helpers.norm import norm_i, norm_h, norm, norm_f - - -class TestNorm: - def test_norm_basic(self): - arr = [10, 20, 30] - d = 20 - - assert norm(arr, d, 1) == 1.0 - assert norm(arr, d, 2) == 20 / 30 - assert norm(arr, d, 0) == 2.0 - - def test_norm_zero_div(self): - arr = [10, 0, 30] - d = 5 - assert norm(arr, d, 1) == 0.0 - - def test_norm_out_of_range(self): - arr = [1, 2, 3] - with pytest.raises(KeyError): - norm(arr, 2, 5) - - def test_norm_negative_descr(self): - arr = [1, 2, 3] - assert norm(arr, 2, -1) == 2 / 3 - - def test_norm_h(self): - assert norm_h(69.5849922, 0) == 1.0 - assert norm_h(0, 2) == 0.0 - assert pytest.approx(norm_h(60, 1), rel=1e-6) == 60 / 94.4228257 - - def test_norm_i(self): - assert norm_i(78.2919965, 0) == 1.0 - assert norm_i(0, 3) == 0.0 - assert pytest.approx(norm_i(66, 1), rel=1e-6) == 66 / 71.2829691 - - def test_norm_f(self): - assert norm_f(53.3719946, 0) == 1.0 - assert norm_f(0, 5) == 0.0 - assert pytest.approx(norm_f(70, 2), rel=1e-6) == 70 / 73.7976536 - - def test_norm_invalid_descr_type(self): - arr = [1, 2, 3] - with pytest.raises(TypeError): - norm(arr, 1, "not_an_int") diff --git a/tests/public_api/test_import_contract.py b/tests/public_api/test_import_contract.py index 1a53560..9880604 100644 --- a/tests/public_api/test_import_contract.py +++ b/tests/public_api/test_import_contract.py @@ -1,4 +1,5 @@ import pytest +from pydantic import BaseModel from pythonQEPest import QEPest, QEPestData, QEPestInput, QEPestOutput @@ -25,10 +26,14 @@ def test_public_api_compute_smoke(self): result = model.compute_params(payload) assert isinstance(result, QEPestOutput) - assert isinstance(result.data, QEPestData) + assert isinstance(result.data, BaseModel) assert result.name == "mol1" - assert result.data == QEPestData(qe_h=0.9357, qe_i=0.7146, qe_f=0.8022) + assert result.data.model_dump() == { + "qe_herb": 0.9357, + "qe_insect": 0.7146, + "qe_fung": 0.8022, + } @pytest.mark.skip(reason="Need to find optional approach") def test_helpers_imports(self): From 2bf62b91a1b952c698dbaa998587dd80f63d91e2 Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 1 Mar 2026 01:25:36 +0100 Subject: [PATCH 54/58] fix[python-package]: poetry --- .github/workflows/python-package.yml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index b8eb251..3453804 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -28,11 +28,12 @@ jobs: cache: poetry cache-dependency-path: poetry.lock - - name: Install Poetry (pipx) - run: | - python -m pip install --upgrade pip - python -m pip install pipx - pipx install poetry + - name: Install Poetry + uses: snok/install-poetry@v1 + with: + version: latest + virtualenvs-create: true + virtualenvs-in-project: true - name: Install dependencies run: | From 725f77af3e71421e6146a20f159d204249077fea Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 1 Mar 2026 01:29:31 +0100 Subject: [PATCH 55/58] fix[workflow]: Again? --- .github/workflows/python-package.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 3453804..57b2ddc 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -20,13 +20,10 @@ jobs: steps: - uses: actions/checkout@v6 - - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v6 with: python-version: ${{ matrix.python-version }} - cache: poetry - cache-dependency-path: poetry.lock - name: Install Poetry uses: snok/install-poetry@v1 From 35ea8e468a9f1565ee484562898f3b3fd978edab Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 1 Mar 2026 01:30:53 +0100 Subject: [PATCH 56/58] fix[poetry]: lock ;/ --- poetry.lock | 166 ++-------------------------------------------------- 1 file changed, 5 insertions(+), 161 deletions(-) diff --git a/poetry.lock b/poetry.lock index 20db0cc..5910abe 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.3.1 and should not be changed by hand. [[package]] name = "altgraph" @@ -37,30 +37,12 @@ files = [ ] [package.dependencies] -exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""} idna = ">=2.8" typing_extensions = {version = ">=4.5", markers = "python_version < \"3.13\""} [package.extras] trio = ["trio (>=0.31.0) ; python_version < \"3.10\"", "trio (>=0.32.0) ; python_version >= \"3.10\""] -[[package]] -name = "backports-tarfile" -version = "1.2.0" -description = "Backport of CPython tarfile module" -optional = false -python-versions = ">=3.8" -groups = ["dev"] -markers = "python_version < \"3.12\"" -files = [ - {file = "backports.tarfile-1.2.0-py3-none-any.whl", hash = "sha256:77e284d754527b01fb1e6fa8a1afe577858ebe4e9dad8919e34c862cb399bc34"}, - {file = "backports_tarfile-1.2.0.tar.gz", hash = "sha256:d75e02c268746e1b8144c278978b6e98e85de6ad16f8e4b0844a154557eca991"}, -] - -[package.extras] -docs = ["furo", "jaraco.packaging (>=9.3)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["jaraco.test", "pytest (!=8.0.*)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)"] - [[package]] name = "build" version = "1.4.0" @@ -75,10 +57,8 @@ files = [ [package.dependencies] colorama = {version = "*", markers = "os_name == \"nt\""} -importlib-metadata = {version = ">=4.6", markers = "python_full_version < \"3.10.2\""} packaging = ">=24.0" pyproject_hooks = "*" -tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""} [package.extras] uv = ["uv (>=0.1.18)"] @@ -482,9 +462,6 @@ files = [ {file = "coverage-7.13.3.tar.gz", hash = "sha256:f7f6182d3dfb8802c1747eacbfe611b669455b69b7c037484bb1efbbb56711ac"}, ] -[package.dependencies] -tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""} - [package.extras] toml = ["tomli ; python_full_version <= \"3.11.0a6\""] @@ -562,7 +539,6 @@ files = [ [package.dependencies] cffi = {version = ">=2.0.0", markers = "python_full_version >= \"3.9.0\" and platform_python_implementation != \"PyPy\""} -typing-extensions = {version = ">=4.13.2", markers = "python_full_version < \"3.11.0\""} [package.extras] docs = ["sphinx (>=5.3.0)", "sphinx-inline-tabs", "sphinx-rtd-theme (>=3.0.0)"] @@ -623,7 +599,6 @@ files = [ ] [package.dependencies] -typing_extensions = {version = ">=4.6.0", markers = "python_version < \"3.12\""} urllib3 = ">=2.2.2" [package.extras] @@ -638,25 +613,6 @@ paramiko = ["paramiko"] patiencediff = ["patiencediff"] pgp = ["gpg"] -[[package]] -name = "exceptiongroup" -version = "1.3.1" -description = "Backport of PEP 654 (exception groups)" -optional = false -python-versions = ">=3.7" -groups = ["dev"] -markers = "python_version == \"3.10\"" -files = [ - 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{file = "zipp-3.23.0-py3-none-any.whl", hash = "sha256:071652d6115ed432f5ce1d34c336c0adfd6a884660d1e9712a256d3d3bd4b14e"}, - {file = "zipp-3.23.0.tar.gz", hash = "sha256:a07157588a12518c9d4034df3fbbee09c814741a33ff63c05fa29d26a2404166"}, -] - -[package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] -cover = ["pytest-cov"] -doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -enabler = ["pytest-enabler (>=2.2)"] -test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more_itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] -type = ["pytest-mypy"] - [[package]] name = "zstandard" version = "0.25.0" @@ -2201,12 +2045,12 @@ files = [ ] [package.extras] -cffi = ["cffi (>=1.17,<2.0) ; platform_python_implementation != \"PyPy\" and python_version < \"3.14\"", "cffi (>=2.0.0b) ; platform_python_implementation != \"PyPy\" and python_version >= \"3.14\""] +cffi = ["cffi (>=1.17,<2.0) ; platform_python_implementation != \"PyPy\" and python_version < \"3.14\"", "cffi (>=2.0.0b0) ; platform_python_implementation != \"PyPy\" and python_version >= \"3.14\""] [extras] gui = ["pyperclip"] [metadata] lock-version = "2.1" -python-versions = ">=3.10,<3.13" -content-hash = "8ba93ad768359952eb49357899071f484c212fc3b6d29cd85926a49c5b1b6400" +python-versions = ">=3.12,<3.15" +content-hash = "29c0863bfefcb10cd0abfe597cd27281c5e3149ffbbe502e0fed03241e73826c" From 17f21a88b915ebe10ca8e981674066e9d4d8d6b5 Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 1 Mar 2026 16:11:47 +0100 Subject: [PATCH 57/58] feat[cli]: update version to 1.4.0 and refactor CLI and file handling --- pyproject.toml | 2 +- pythonQEPest/cli/cli.py | 82 +++++-------------- pythonQEPest/config/__init__.py | 2 +- .../config/{qepest.py => qepest_default.py} | 0 pythonQEPest/core/qepest.py | 42 ++++++++-- pythonQEPest/core/qepest_meta.py | 12 ++- pythonQEPest/dto/QEPestFile.py | 27 ++++-- pythonQEPest/dto/__init__.py | 9 +- pythonQEPest/gui/gui.py | 1 + pythonQEPest/logger.py | 3 + pythonQEPest/services/QEPestFileService.py | 66 +++++++++++++++ pythonQEPest/services/__init__.py | 3 + tests/cli/test_cli_contract.py | 78 ++++++++++++++++-- tests/config/test_coefficients.py | 4 +- tests/dto/test_qepest_file.py | 6 +- 15 files changed, 236 insertions(+), 101 deletions(-) rename pythonQEPest/config/{qepest.py => qepest_default.py} (100%) create mode 100644 pythonQEPest/services/QEPestFileService.py create mode 100644 pythonQEPest/services/__init__.py diff --git a/pyproject.toml b/pyproject.toml index 9d0b121..5f25736 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "pythonQEPest" -version = "1.3.0" +version = "1.4.0" description = "Java QEPest in Python" readme = "README.md" requires-python = ">=3.12,<3.15" diff --git a/pythonQEPest/cli/cli.py b/pythonQEPest/cli/cli.py index 86eca20..80a01ca 100644 --- a/pythonQEPest/cli/cli.py +++ b/pythonQEPest/cli/cli.py @@ -6,69 +6,12 @@ from pathlib import Path from typing import Sequence -from pythonQEPest.core import QEPestMeta from pythonQEPest.dto import QEPestFile -from pythonQEPest.helpers import get_num_of_cols -from pythonQEPest.helpers.get_values_from_line import get_values_from_line +from pythonQEPest.services.QEPestFileService import QEPestFileService logger = logging.getLogger(__name__) -class CLI: - qepest: QEPestMeta | None = None - - def __init__(self, qepest: QEPestMeta, qepest_file: QEPestFile): - self.qepest = qepest - self.qepest_file = qepest_file - - self.error: bool = False - - def read_file_and_compute_params(self): - try: - with open(self.qepest_file.input_file, "r") as file: - lines = file.readlines() - - with open(self.qepest_file.output_file, "w") as wr: - for index, line in enumerate(lines): - if index == 0: - if get_num_of_cols(line) != self.qepest.col_number: - er = f"Error: Line {index} does not have seven elements." - logger.error(er) - - self.error = True - break - - wr.write("Name QEH QEI QEF\n") - else: - if get_num_of_cols(line) == self.qepest.col_number: - d_values = get_values_from_line(line.split("\t")) - self.qepest.get_qex_values(d_values) - splitted_line = line.split("\t")[0] - - # TODO: BUG, AFTER REWORK NEEDS TO BE FIXED !!!!!!!!!!! - wr.write( - f"{splitted_line} {self.qepest.qex.qe_herb} " - + f"{self.qepest.qex.qe_insect} " - + f"{self.qepest.qex.qe_fung}" - + f"{chr(10)}" - ) - else: - er = f"Error: Line {index} does not have seven elements." - logger.error(er) - - self.error = True - if not self.error: - logger.info("Computation completed") - else: - logger.warning("Finished with errors") - - except FileNotFoundError as e: - self.error = True - - logger.error("Error: can't find : %s", self.qepest_file.input_file) - logger.exception(e) - - def _resolve_package_version() -> str: try: return version("pythonQEPest") @@ -108,10 +51,17 @@ def build_parser() -> argparse.ArgumentParser: parser.add_argument( "-o", "--output", - default="data.txt.out", + default="data.out.txt", help="Path to output tab-separated file with " + "QEPest descriptors (default: data.txt.out).", ) + + parser.add_argument( + "-f", + "--format", + default="txt", + help="Format to output file with " + "QEPest (json, txt).", + ) return parser @@ -126,10 +76,16 @@ def main(argv: Sequence[str] | None = None) -> int: load_dotenv() init_logger() - cli = CLI( + logger.debug("CLI initiated") + logger.info(f"CLI args: {argv}") + + service = QEPestFileService( qepest=QEPest(), - qepest_file=QEPestFile(input_file=args.input, output_file=args.output), + qepest_file=QEPestFile( + input_file=args.input, output_file=args.output, format=args.format + ), ) - cli.read_file_and_compute_params() - return 0 if not cli.error else 1 + service.read_file_and_compute_params() + + return 0 if not service.error else 1 diff --git a/pythonQEPest/config/__init__.py b/pythonQEPest/config/__init__.py index 0d59601..1f050c1 100644 --- a/pythonQEPest/config/__init__.py +++ b/pythonQEPest/config/__init__.py @@ -1,4 +1,4 @@ -from .qepest import qepest_default +from .qepest_default import qepest_default from .normalise import normalise_default __all__ = [ diff --git a/pythonQEPest/config/qepest.py b/pythonQEPest/config/qepest_default.py similarity index 100% rename from pythonQEPest/config/qepest.py rename to pythonQEPest/config/qepest_default.py diff --git a/pythonQEPest/core/qepest.py b/pythonQEPest/core/qepest.py index 09fa569..f0716ef 100644 --- a/pythonQEPest/core/qepest.py +++ b/pythonQEPest/core/qepest.py @@ -1,6 +1,6 @@ import logging import math -from typing import Optional +from typing import Optional, List from pydantic import create_model, BaseModel @@ -19,12 +19,32 @@ class QEPest(QEPestMeta): def __init__(self, *args, **kwargs): + self.coefficients_names = None + self.names = None + + logger.debug("QEPest initialisation") + + logger.info(f"QEPest args: {args}") + logger.info(f"QEPest kwargs: {kwargs}") + super().__init__(*args, **kwargs) + logger.debug("QEPest initialisation successful") + def _log_compute_df(self, func, index, lst, data_lst) -> float: df_result = compute_df(lst[index], *data_lst[index]) return math.log(func(df_result, index)) + def get_names(self) -> List[str]: + self.names = [ + n.split("_")[1] for n in dir(self) if n.startswith("coefficient_") + ] + return self.names + + def get_coefficients_names(self) -> List[str]: + self.coefficients_names = [f"coefficient_{name}" for name in self.names] + return self.coefficients_names + def compute_params(self, data_input: QEPestInput) -> QEPestOutput: self.get_qex_values( get_values_from_line(list(data_input.model_dump().values())) @@ -32,10 +52,11 @@ def compute_params(self, data_input: QEPestInput) -> QEPestOutput: return QEPestOutput(data=self.qex, name=data_input.name) def get_qex_values(self, d) -> BaseModel: - names = [n.split("_")[1] for n in dir(self) if n.startswith("coefficient_")] + names = self.get_names() # Coefficients names = ("coefficients_fung, coefficient_herb...) - coefficients_names = [n for n in dir(self) if n.startswith("coefficient_")] + coefficients_names = self.get_coefficients_names() + if len(coefficients_names) == 0: raise ValueError( "No coefficient_ keys, needs to call " @@ -75,24 +96,31 @@ def get_qex_values(self, d) -> BaseModel: return self.qex - # TODO: Coefficients must be in other class + # TODO: Coefficients must be in other class. + # TODO: Ability to provide whatever we want is a good thingy def initialize_coefficients(self, coefficients: Optional = None) -> None: + logger.debug("QEPest coefficients initialisation") coefficients = super().initialize_coefficients() + logger.debug("QEPest coefficients initialisation successful") for category, data in coefficients.items(): setattr(self, f"coefficient_{category}", data) + logger.info(f"QEPest coefficients initialisation with {coefficients.items()}") + # TODO: Same with Normalisers def initialize_normalisers(self, normalisers: Optional = None) -> None: + logger.debug("QEPest normalisers initialisation") normalisers = super().initialize_normalisers() + logger.debug("QEPest normalisers initialisation successful") + for category, data in normalisers.items(): setattr(self, f"normaliser_{category}", Normaliser(data)) + logger.info(f"QEPest normalisers initialisation with {normalisers.items()}") + if __name__ == "__main__": qepest = QEPest() - qepest.initialize_coefficients() - qepest.initialize_normalisers() qepest.get_qex_values(1) - print(1) diff --git a/pythonQEPest/core/qepest_meta.py b/pythonQEPest/core/qepest_meta.py index 0151790..a808daf 100644 --- a/pythonQEPest/core/qepest_meta.py +++ b/pythonQEPest/core/qepest_meta.py @@ -1,16 +1,14 @@ import os from abc import abstractmethod, ABC -from pythonQEPest.dto import QEPestInput, QEPestOutput, QEPestData +from pydantic import BaseModel + +from pythonQEPest.dto import QEPestInput, QEPestOutput class QEPestMeta(ABC): def __init__(self, *args, **kwargs): - self.qex: QEPestData | None = None - - self.herb: list[float] = [] - self.insect: list[float] = [] - self.fung: list[float] = [] + self.qex: BaseModel | None = None self.col_number: int = 7 self.dir: str = os.getcwd() @@ -29,7 +27,7 @@ def get_qex_values(self, d) -> None: @abstractmethod def initialize_coefficients(self, coefficients=None) -> None: if coefficients is None: - from pythonQEPest.config.qepest import qepest_default + from pythonQEPest.config.qepest_default import qepest_default coefficients = qepest_default return coefficients diff --git a/pythonQEPest/dto/QEPestFile.py b/pythonQEPest/dto/QEPestFile.py index d68d76b..5ccf5c7 100644 --- a/pythonQEPest/dto/QEPestFile.py +++ b/pythonQEPest/dto/QEPestFile.py @@ -1,16 +1,33 @@ +from enum import Enum from typing import Optional -from pydantic import BaseModel +from pydantic import BaseModel, model_validator + + +class QEPestFormat(Enum): + TXT = "txt" + JSON = "json" class QEPestFile(BaseModel): input_file: Optional[str] = None output_file: Optional[str] = None + format: Optional[QEPestFormat] = QEPestFormat.TXT + + model_config = {"arbitrary_types_allowed": True} - def __init__(self, **data): - super().__init__(**data) + @model_validator(mode="after") + def set_defaults(self): if self.input_file is None: self.input_file = "data.txt" - if self.output_file is None: - self.output_file = f"{self.input_file}.out" + if self.format is None: + self.format = QEPestFormat.TXT + + formatted_output = self.input_file.replace(".txt", "").replace(".json", "") + if self.format == QEPestFormat.JSON: + self.output_file = f"{formatted_output}.out.json" + else: + self.output_file = f"{formatted_output}.out.txt" + + return self diff --git a/pythonQEPest/dto/__init__.py b/pythonQEPest/dto/__init__.py index aa218a7..3db3c11 100644 --- a/pythonQEPest/dto/__init__.py +++ b/pythonQEPest/dto/__init__.py @@ -1,11 +1,6 @@ from pythonQEPest.dto.QEPestData import QEPestData from pythonQEPest.dto.QEPestInput import QEPestInput -from pythonQEPest.dto.QEPestFile import QEPestFile +from pythonQEPest.dto.QEPestFile import QEPestFile, QEPestFormat from pythonQEPest.dto.QEPestOutput import QEPestOutput -__all__ = [ - "QEPestOutput", - "QEPestData", - "QEPestInput", - "QEPestFile", -] +__all__ = ["QEPestOutput", "QEPestData", "QEPestInput", "QEPestFile", "QEPestFormat"] diff --git a/pythonQEPest/gui/gui.py b/pythonQEPest/gui/gui.py index 9996522..d172cfb 100644 --- a/pythonQEPest/gui/gui.py +++ b/pythonQEPest/gui/gui.py @@ -20,6 +20,7 @@ from pythonQEPest.gui.gui_meta import QEPestMeta +# TODO: Outdated. Must be dynamic class GUI(QEPestMeta): def treeview_sort_column(self, treeview, col, reverse): treeview_lst = [(treeview.set(k, col), k) for k in treeview.get_children("")] diff --git a/pythonQEPest/logger.py b/pythonQEPest/logger.py index 5eaed76..575b247 100644 --- a/pythonQEPest/logger.py +++ b/pythonQEPest/logger.py @@ -53,3 +53,6 @@ def init_logger() -> None: root_logger.setLevel(level) root_logger.addHandler(file_handler) root_logger.addHandler(console_handler) + + root_logger.info("Logger started Successfully") + root_logger.info(f"Level: {level}") diff --git a/pythonQEPest/services/QEPestFileService.py b/pythonQEPest/services/QEPestFileService.py new file mode 100644 index 0000000..2796b2e --- /dev/null +++ b/pythonQEPest/services/QEPestFileService.py @@ -0,0 +1,66 @@ +import logging +import json + +from pythonQEPest.core import QEPestMeta +from pythonQEPest.dto import QEPestFile +from pythonQEPest.dto.QEPestFile import QEPestFormat +from pythonQEPest.helpers.get_values_from_line import get_values_from_line +from pythonQEPest.helpers.get_num_of_cols import get_num_of_cols + +logger = logging.getLogger(__name__) + + +class QEPestFileService: + + def __init__(self, qepest: QEPestMeta, qepest_file: QEPestFile): + self.qepest = qepest + self.qepest_file = qepest_file + self.error = False + + def _write_txt_line(self, line: str, file) -> None: + splitted_line = line.split("\t")[0] + qex_headers = " ".join(self.qepest.qex.model_dump().keys()) + qex_values = " ".join(str(x) for x in self.qepest.qex.model_dump().values()) + + file.write(f"Name {qex_headers.upper()}\n") + file.write(f"{splitted_line} {qex_values}\n") + + def _write_json_line(self, line: str, file) -> None: + splitted_line = line.split("\t")[0] + data = {"name": splitted_line, **self.qepest.qex.model_dump()} + file.write(json.dumps(data) + "\n") + + def read_file_and_compute_params(self) -> None: + try: + with open(self.qepest_file.input_file, "r") as f: + lines = f.readlines() + + with open(self.qepest_file.output_file, "w") as wr: + for index, line in enumerate(lines): + if get_num_of_cols(line) != self.qepest.col_number: + logger.error( + f"Error: Line {index} does not have the " + "expected number of columns." + ) + self.error = True + break + + if index == 0: + continue + + d_values = get_values_from_line(line.split("\t")) + self.qepest.get_qex_values(d_values) + + if self.qepest_file.format == QEPestFormat.TXT: + self._write_txt_line(line, wr) + else: + self._write_json_line(line, wr) + + if not self.error: + logger.info("Computation completed") + else: + logger.warning("Finished with errors") + + except FileNotFoundError: + self.error = True + logger.error(f"Error: can't find: {self.qepest_file.input_file}") diff --git a/pythonQEPest/services/__init__.py b/pythonQEPest/services/__init__.py new file mode 100644 index 0000000..7df49da --- /dev/null +++ b/pythonQEPest/services/__init__.py @@ -0,0 +1,3 @@ +from pythonQEPest.services.QEPestFileService import QEPestFileService + +__all__ = ["QEPestFileService"] diff --git a/tests/cli/test_cli_contract.py b/tests/cli/test_cli_contract.py index bdeb3a8..da70cc9 100644 --- a/tests/cli/test_cli_contract.py +++ b/tests/cli/test_cli_contract.py @@ -4,19 +4,25 @@ class TestCLIContract: - def test_cli_help_exits_with_zero(self): + def test_cli_help_exits_with_zero(self, monkeypatch): + monkeypatch.setenv("APP_DEBUG_ENABLE", "false") + with pytest.raises(SystemExit) as exc: main(["--help"]) assert exc.value.code == 0 - def test_cli_version_exits_with_zero(self): + def test_cli_version_exits_with_zero(self, monkeypatch): + monkeypatch.setenv("APP_DEBUG_ENABLE", "false") + with pytest.raises(SystemExit) as exc: main(["--version"]) assert exc.value.code == 0 - def test_cli_runs_with_explicit_input_file(self, tmp_path): + def test_cli_runs_with_explicit_input_file(self, monkeypatch, tmp_path): + monkeypatch.setenv("APP_DEBUG_ENABLE", "false") + data_file = tmp_path / "input.txt" - output_file = tmp_path / "input.txt.out" + output_file = tmp_path / "input.out.txt" data_file.write_text( "Name\tMW\tLogP\tHBA\tHBD\tRB\tarR\n" @@ -30,4 +36,66 @@ def test_cli_runs_with_explicit_input_file(self, tmp_path): assert output_file.exists() output_text = output_file.read_text(encoding="utf-8") - assert output_text == "Name QEH QEI QEF\nmol1 0.8511 0.5339 0.6224\n" + assert output_file.name == "input.out.txt" + assert ( + output_text == "Name QE_FUNG QE_HERB QE_INSECT\nmol1 0.6224 0.8511 0.5339\n" + ) + + def test_cli_runs_with_explicit_input_file_format(self, monkeypatch, tmp_path): + monkeypatch.setenv("APP_DEBUG_ENABLE", "false") + + data_file = tmp_path / "input.txt" + output_file = tmp_path / "input.out.txt" + + data_file.write_text( + "Name\tMW\tLogP\tHBA\tHBD\tRB\tarR\n" + "mol1\t240.2127\t3.2392\t5\t1\t4\t1\n", + encoding="utf-8", + ) + + exit_code = main( + ["--input", str(data_file), "--output", str(output_file), "--format=txt"] + ) + + assert exit_code == 0 + assert output_file.exists() + + output_text = output_file.read_text(encoding="utf-8") + + assert output_file.name == "input.out.txt" + assert isinstance(output_text, str) + + assert ( + output_text == "Name QE_FUNG QE_HERB QE_INSECT\nmol1 0.6224 0.8511 0.5339\n" + ) + + def test_cli_runs_with_input_file_format(self, monkeypatch, tmp_path): + monkeypatch.setenv("APP_DEBUG_ENABLE", "false") + + data_file = tmp_path / "input.txt" + output_file = tmp_path / "input.out.json" + + data_file.write_text( + "Name\tMW\tLogP\tHBA\tHBD\tRB\tarR\n" + "mol1\t240.2127\t3.2392\t5\t1\t4\t1\n", + encoding="utf-8", + ) + + exit_code = main(["--input", str(data_file), "--format=json"]) + + assert exit_code == 0 + assert output_file.exists() + + output_text = output_file.read_text(encoding="utf-8") + + assert output_file.name == "input.out.json" + assert isinstance(output_text, str) + + import json + + assert json.loads(output_text) == { + "name": "mol1", + "qe_fung": 0.6224, + "qe_herb": 0.8511, + "qe_insect": 0.5339, + } diff --git a/tests/config/test_coefficients.py b/tests/config/test_coefficients.py index 8816b23..7f564a3 100644 --- a/tests/config/test_coefficients.py +++ b/tests/config/test_coefficients.py @@ -206,7 +206,7 @@ def test_qepest_coefficients_lst_basic(self): ) def test_qepest_coefficients_lst_w_import(self): - from pythonQEPest.config.qepest import qepest_default + from pythonQEPest.config.qepest_default import qepest_default qep_coeff_lst = QEPestCoefficientList(qepest_default) @@ -333,7 +333,7 @@ def test_qepest_coefficients_lst_w_import(self): ) def test_qepest_default_coefficients(self): - from pythonQEPest.config.qepest import qepest_default + from pythonQEPest.config.qepest_default import qepest_default assert "fung" in qepest_default assert "herb" in qepest_default diff --git a/tests/dto/test_qepest_file.py b/tests/dto/test_qepest_file.py index fbb3f85..67a4bc6 100644 --- a/tests/dto/test_qepest_file.py +++ b/tests/dto/test_qepest_file.py @@ -22,7 +22,7 @@ def test_qepest_file_standard(self): ) assert qepest_output_file.input_file == "input_example.txt" - assert qepest_output_file.output_file == "output_example.txt" + assert qepest_output_file.output_file == "input_example.out.txt" def test_qepest_file_with_no_output_file(self): QEPestFile = self._import_qepest_file() @@ -30,7 +30,7 @@ def test_qepest_file_with_no_output_file(self): qepest_output_file = QEPestFile(input_file="input1.txt") assert qepest_output_file.input_file == "input1.txt" - assert qepest_output_file.output_file == "input1.txt.out" + assert qepest_output_file.output_file == "input1.out.txt" def test_qepest_file_with_no_input_file(self): QEPestFile = self._import_qepest_file() @@ -38,4 +38,4 @@ def test_qepest_file_with_no_input_file(self): qepest_output_file = QEPestFile() assert qepest_output_file.input_file == "data.txt" - assert qepest_output_file.output_file == "data.txt.out" + assert qepest_output_file.output_file == "data.out.txt" From 0d901b89be9f23fcb5a6634ad3812e749feca339 Mon Sep 17 00:00:00 2001 From: Lina Date: Sun, 1 Mar 2026 16:18:29 +0100 Subject: [PATCH 58/58] update[poetry.lock]: new versions --- poetry.lock | 444 +++++++++++++++++++++++++---------------------- requirements.txt | Bin 2740 -> 2658 bytes 2 files changed, 240 insertions(+), 204 deletions(-) diff --git a/poetry.lock b/poetry.lock index 5910abe..90ab610 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.3.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.3.2 and should not be changed by hand. [[package]] name = "altgraph" @@ -88,14 +88,14 @@ redis = ["redis (>=2.10.5)"] [[package]] name = "certifi" -version = "2026.1.4" +version = "2026.2.25" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.7" groups = ["dev"] files = [ - {file = "certifi-2026.1.4-py3-none-any.whl", hash = "sha256:9943707519e4add1115f44c2bc244f782c0249876bf51b6599fee1ffbedd685c"}, - {file = "certifi-2026.1.4.tar.gz", hash = "sha256:ac726dd470482006e014ad384921ed6438c457018f4b3d204aea4281258b2120"}, + {file = "certifi-2026.2.25-py3-none-any.whl", hash = "sha256:027692e4402ad994f1c42e52a4997a9763c646b73e4096e4d5d6db8af1d6f0fa"}, + {file = "certifi-2026.2.25.tar.gz", hash = "sha256:e887ab5cee78ea814d3472169153c2d12cd43b14bd03329a39a9c6e2e80bfba7"}, ] [[package]] @@ -362,104 +362,118 @@ files = [ [[package]] name = "coverage" -version = "7.13.3" +version = "7.13.4" description = "Code coverage measurement for Python" optional = false python-versions = 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[[package]] name = "python-dotenv" version = "1.2.1" @@ -1849,24 +1888,21 @@ zstd = ["backports-zstd (>=1.0.0) ; python_version < \"3.14\""] [[package]] name = "virtualenv" -version = "20.36.1" +version = "21.1.0" description = "Virtual Python Environment builder" optional = false python-versions = ">=3.8" groups = ["dev"] files = [ - {file = "virtualenv-20.36.1-py3-none-any.whl", hash = "sha256:575a8d6b124ef88f6f51d56d656132389f961062a9177016a50e4f507bbcc19f"}, - {file = "virtualenv-20.36.1.tar.gz", hash = "sha256:8befb5c81842c641f8ee658481e42641c68b5eab3521d8e092d18320902466ba"}, + {file = "virtualenv-21.1.0-py3-none-any.whl", hash = "sha256:164f5e14c5587d170cf98e60378eb91ea35bf037be313811905d3a24ea33cc07"}, + {file = "virtualenv-21.1.0.tar.gz", hash = "sha256:1990a0188c8f16b6b9cf65c9183049007375b26aad415514d377ccacf1e4fb44"}, ] [package.dependencies] distlib = ">=0.3.7,<1" -filelock = {version = ">=3.20.1,<4", markers = "python_version >= \"3.10\""} +filelock = {version = ">=3.24.2,<4", markers = "python_version >= \"3.10\""} platformdirs = ">=3.9.1,<5" - -[package.extras] -docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] -test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8) ; platform_python_implementation == \"PyPy\" or platform_python_implementation == \"GraalVM\" or platform_python_implementation == \"CPython\" and sys_platform == \"win32\" and python_version >= \"3.13\"", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10) ; platform_python_implementation == \"CPython\""] +python-discovery = ">=1" [[package]] name = "xattr" diff --git a/requirements.txt b/requirements.txt index 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