Merge pull request #25 from PonyLianna/development

Release 1.4.0

Author: PonyLianna

.github/workflows/python-package.yml

@@ -0,0 +1,50 @@
+# 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" ]
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-24.04
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [ "3.12", "3.13", "3.14" ]
+
+    steps:
+      - uses: actions/checkout@v6
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          version: latest
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
+      - name: Install dependencies
+        run: |
+          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
+
+      - 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))"

.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

.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

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):