diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml new file mode 100644 index 0000000..5206346 --- /dev/null +++ b/.github/workflows/python-publish.yml @@ -0,0 +1,84 @@ +# This workflow will upload a Python Package to PyPI when a release is created +# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries + +# This workflow uses actions that are not certified by GitHub. +# They are provided by a third-party and are governed by +# separate terms of service, privacy policy, and support +# documentation. + +name: Upload Python Package + +on: + release: + types: [published] + +permissions: + contents: read + +jobs: + release-build: + runs-on: ubuntu-24.04 + + steps: + - uses: actions/checkout@v6 + + - uses: actions/setup-python@v5 + with: + python-version: "3.x" + + - 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 --extras "rdkit gui" --no-interaction + + - name: Test with pytest (coverage) + run: | + poetry run pytest -q --cov=pythonQEPest --cov-report=term-missing --cov-fail-under=40 + + - name: Build release distributions + run: | + # NOTE: put your own distribution build steps here. + poetry build + + - name: Upload distributions + uses: actions/upload-artifact@v4 + with: + name: release-dists + path: dist/ + + pypi-publish: + runs-on: ubuntu-24.04 + needs: + - release-build + permissions: + # IMPORTANT: this permission is mandatory for trusted publishing + id-token: write + + # Dedicated environments with protections for publishing are strongly recommended. + # For more information, see: https://docs.github.com/en/actions/deployment/targeting-different-environments/using-environments-for-deployment#deployment-protection-rules + environment: + name: pypi + # OPTIONAL: uncomment and update to include your PyPI project URL in the deployment status: + # url: https://pypi.org/p/YOURPROJECT + # + # ALTERNATIVE: if your GitHub Release name is the PyPI project version string + # ALTERNATIVE: exactly, uncomment the following line instead: + # url: https://pypi.org/project/YOURPROJECT/${{ github.event.release.name }} + + steps: + - name: Retrieve release distributions + uses: actions/download-artifact@v4 + with: + name: release-dists + path: dist/ + + - name: Publish release distributions to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 + with: + packages-dir: dist/ diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..c5d888c --- /dev/null +++ b/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2026 PonyLianna + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/README.md b/README.md index 2e00635..3db697e 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ # pythonQEPest [![pythonQEPest](https://github.com/PonyLianna/pythonQEPest/actions/workflows/python-package.yml/badge.svg)](https://github.com/PonyLianna/pythonQEPest/actions/workflows/python-package.yml) +[![PyPI Version](https://img.shields.io/pypi/v/pythonQEPest)](https://pypi.org/project/pythonQEPest/) Python implementation of QEPest (Quantitative Estimation of Pesticide), a program for scoring molecules as herbicides (QEH), insecticides (QEI), and fungicides (QEF). diff --git a/poetry.lock b/poetry.lock index 17c8e08..b39f671 100644 --- a/poetry.lock +++ b/poetry.lock @@ -576,6 +576,18 @@ files = [ {file = "distlib-0.4.0.tar.gz", hash = "sha256:feec40075be03a04501a973d81f633735b4b69f98b05450592310c0f401a4e0d"}, ] +[[package]] +name = "docutils" +version = "0.22.4" +description = "Docutils -- Python Documentation Utilities" +optional = false +python-versions = ">=3.9" +groups = ["dev"] +files = [ + {file = "docutils-0.22.4-py3-none-any.whl", hash = "sha256:d0013f540772d1420576855455d050a2180186c91c15779301ac2ccb3eeb68de"}, + {file = "docutils-0.22.4.tar.gz", hash = "sha256:4db53b1fde9abecbb74d91230d32ab626d94f6badfc575d6db9194a49df29968"}, +] + [[package]] name = "dulwich" version = "1.1.0" @@ -739,6 +751,26 @@ http2 = ["h2 (>=3,<5)"] socks = ["socksio (==1.*)"] zstd = ["zstandard (>=0.18.0)"] +[[package]] +name = "id" +version = "1.6.1" +description = "A tool for generating OIDC identities" +optional = false +python-versions = ">=3.9" +groups = ["dev"] +files = [ + {file = "id-1.6.1-py3-none-any.whl", hash = "sha256:f5ec41ed2629a508f5d0988eda142e190c9c6da971100612c4de9ad9f9b237ca"}, + {file = "id-1.6.1.tar.gz", hash = "sha256:d0732d624fb46fd4e7bc4e5152f00214450953b9e772c182c1c22964def1a069"}, +] + +[package.dependencies] +urllib3 = ">=2,<3" + +[package.extras] +dev = ["build", "bump (>=1.3.2)", "id[lint,test]"] +lint = ["bandit", "interrogate", "mypy", "ruff (<0.14.15)"] +test = ["coverage[toml]", "pretend", "pytest", "pytest-cov"] + [[package]] name = "identify" version = "2.6.17" @@ -917,6 +949,42 @@ files = [ [package.dependencies] altgraph = ">=0.17" +[[package]] +name = "markdown-it-py" +version = "4.0.0" +description = "Python port of markdown-it. Markdown parsing, done right!" +optional = false +python-versions = ">=3.10" +groups = ["dev"] +files = [ + {file = "markdown_it_py-4.0.0-py3-none-any.whl", hash = "sha256:87327c59b172c5011896038353a81343b6754500a08cd7a4973bb48c6d578147"}, + {file = "markdown_it_py-4.0.0.tar.gz", hash = "sha256:cb0a2b4aa34f932c007117b194e945bd74e0ec24133ceb5bac59009cda1cb9f3"}, +] + +[package.dependencies] +mdurl = ">=0.1,<1.0" + +[package.extras] +benchmarking = ["psutil", "pytest", "pytest-benchmark"] +compare = ["commonmark (>=0.9,<1.0)", "markdown (>=3.4,<4.0)", "markdown-it-pyrs", "mistletoe (>=1.0,<2.0)", "mistune (>=3.0,<4.0)", "panflute (>=2.3,<3.0)"] +linkify = ["linkify-it-py (>=1,<3)"] +plugins = ["mdit-py-plugins (>=0.5.0)"] +profiling = ["gprof2dot"] +rtd = ["ipykernel", "jupyter_sphinx", "mdit-py-plugins (>=0.5.0)", "myst-parser", "pyyaml", "sphinx", "sphinx-book-theme (>=1.0,<2.0)", "sphinx-copybutton", "sphinx-design"] +testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions", "requests"] + +[[package]] +name = "mdurl" +version = "0.1.2" +description = "Markdown URL utilities" +optional = false +python-versions = ">=3.7" +groups = ["dev"] +files = [ + {file = "mdurl-0.1.2-py3-none-any.whl", hash = "sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8"}, + {file = "mdurl-0.1.2.tar.gz", hash = "sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba"}, +] + [[package]] name = "more-itertools" version = "10.8.0" @@ -1001,6 +1069,43 @@ files = [ {file = "msgpack-1.1.2.tar.gz", hash = "sha256:3b60763c1373dd60f398488069bcdc703cd08a711477b5d480eecc9f9626f47e"}, ] +[[package]] +name = "nh3" +version = "0.3.3" +description = "Python binding to Ammonia HTML sanitizer Rust crate" +optional = false +python-versions = ">=3.8" +groups = ["dev"] +files = [ + {file = "nh3-0.3.3-cp314-cp314t-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl", hash = 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[[package]] name = "nodeenv" version = "1.10.0" @@ -1957,6 +2062,26 @@ files = [ numpy = "*" Pillow = "*" +[[package]] +name = "readme-renderer" +version = "44.0" +description = "readme_renderer is a library for rendering readme descriptions for Warehouse" +optional = false +python-versions = ">=3.9" +groups = ["dev"] +files = [ + {file = "readme_renderer-44.0-py3-none-any.whl", hash = "sha256:2fbca89b81a08526aadf1357a8c2ae889ec05fb03f5da67f9769c9a592166151"}, + {file = "readme_renderer-44.0.tar.gz", hash = "sha256:8712034eabbfa6805cacf1402b4eeb2a73028f72d1166d6f5cb7f9c047c5d1e1"}, +] + +[package.dependencies] +docutils = ">=0.21.2" +nh3 = ">=0.2.14" +Pygments = ">=2.5.1" + +[package.extras] +md = ["cmarkgfm (>=0.8.0)"] + [[package]] name = "requests" version = "2.32.5" @@ -1994,6 +2119,40 @@ files = [ [package.dependencies] requests = ">=2.0.1,<3.0.0" +[[package]] +name = "rfc3986" +version = "2.0.0" +description = "Validating URI References per RFC 3986" +optional = false +python-versions = ">=3.7" +groups = ["dev"] +files = [ + {file = "rfc3986-2.0.0-py2.py3-none-any.whl", hash = "sha256:50b1502b60e289cb37883f3dfd34532b8873c7de9f49bb546641ce9cbd256ebd"}, + {file = "rfc3986-2.0.0.tar.gz", hash = "sha256:97aacf9dbd4bfd829baad6e6309fa6573aaf1be3f6fa735c8ab05e46cecb261c"}, +] + +[package.extras] +idna2008 = ["idna"] + +[[package]] +name = "rich" +version = "14.3.3" +description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal" +optional = false +python-versions = ">=3.8.0" +groups = ["dev"] +files = [ + {file = "rich-14.3.3-py3-none-any.whl", hash = "sha256:793431c1f8619afa7d3b52b2cdec859562b950ea0d4b6b505397612db8d5362d"}, + {file = "rich-14.3.3.tar.gz", hash = "sha256:b8daa0b9e4eef54dd8cf7c86c03713f53241884e814f4e2f5fb342fe520f639b"}, +] + +[package.dependencies] +markdown-it-py = ">=2.2.0" +pygments = ">=2.13.0,<3.0.0" + +[package.extras] +jupyter = ["ipywidgets (>=7.5.1,<9)"] + [[package]] name = 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["keyring (>=21.2.0)"] + [[package]] name = "typing-extensions" version = "4.15.0" @@ -2318,4 +2503,4 @@ rdkit = ["rdkit"] [metadata] lock-version = "2.1" python-versions = ">=3.12,<3.15" -content-hash = "f9b15c3b9031dbde28676ba432b90dd4ed02ce104ecdcccd0fa24adf51c56140" +content-hash = "efb02100e483c2c94b44302916d2976a562135b4e17ceac388e3e54e5452b4cf" diff --git a/pyproject.toml b/pyproject.toml index 5b9077e..8387ecd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "pythonQEPest" -version = "2.0.0a2" +version = "2.0.0a3" description = "Java QEPest but written in Python" readme = "README.md" requires-python = ">=3.12,<3.15" @@ -27,6 +27,7 @@ dev = [ "pyinstaller (>=6.18.0,<7.0.0)", "poethepoet[poetry_plugin] (>=0.39.0)", "pytest-cov (>=7.0.0,<8.0.0)", + "twine (>=6.2.0,<7.0.0)", ] [build-system] @@ -42,3 +43,4 @@ exclude = [".venv", ".git", "__pycache__", "build", "dist"] test = "pytest" build-simple = "pyinstaller --onefile pythonQEPest/main.py" build-gui = "pyinstaller --onefile --noconsole pythonQEPest/gui/gui.py" +publish-pypi = "twine upload --repository pythonQEPest dist/*"