From 4315f2f11d950d76fd952ca8b63cf4240c392bd4 Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Tue, 1 Jul 2025 11:53:29 +0200 Subject: [PATCH 1/9] Document (#1) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * :art: add flake8 and ruff line length default (to 90 characters) * :art: add formatting of jupyter notebooks per default * :memo: highlight that also a folder has to be renamed * :memo: document what extension are used for * :memo: document debian (ubuntu) package adding which might be needed * :art: use PyPI and GitHub integration instead of secret api token * 🙈 hide folders creating when locally building the documentation website * :memo: document desing choices and layout of Python package * :art: add copy button for code blocks per default * :art: small corrections after proof-reading * :art: make name generic and document it. Choose a Licence hint * :art: add design document to Sphinx documentation * :art: add some more common error checking - set line-length to black default of 88 characters * Apply suggestions from code review Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * :bug: correct python pkg configuration file * :bug: add missing changes for requirments.txt As noted by Angel using requirements.txt needed one additional change: - add dependencies to the dynamic field Add hint to section with dependencies * :memo: Add hint to GitHub Releases and Source distribution testing * :art: follow Pasquale's advices (.gitignore + unnecessary config) - add more to .gitignore and link template - remove line-length configuration as it is already on the default 88 of black formatter * :memo: add sebastians hints on other ressources * :art: add license key and remove from classifiers as suggested by Sebastian * :memo: docstring and src layout hints (noted by sebastian) * :bug: add missing key to pyproject.toml --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- .github/workflows/cicd.yml | 7 +- .gitignore | 27 ++ .readthedocs.yaml | 3 + LICENSE | 2 +- README.md | 17 +- developing.md | 561 +++++++++++++++++++++++++++++++++++++ docs/.gitignore | 3 + docs/conf.py | 21 +- docs/developing.md | 5 + docs/index.md | 1 + pyproject.toml | 26 +- setup.cfg | 0 12 files changed, 648 insertions(+), 25 deletions(-) create mode 100644 developing.md create mode 100644 docs/.gitignore create mode 100644 docs/developing.md create mode 100644 setup.cfg diff --git a/.github/workflows/cicd.yml b/.github/workflows/cicd.yml index f06e9ed..3d485ce 100644 --- a/.github/workflows/cicd.yml +++ b/.github/workflows/cicd.yml @@ -34,7 +34,7 @@ jobs: - name: Lint with ruff run: | # stop the build if there are Python syntax errors or undefined names - ruff check . + ruff check src test: name: Test runs-on: ubuntu-latest @@ -119,10 +119,9 @@ jobs: with: name: artifact path: ./dist - + # register PyPI integration: + # https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/ - uses: pypa/gh-action-pypi-publish@release/v1 with: # remove repository key to set the default to pypi (not test.pypi.org) repository-url: https://test.pypi.org/legacy/ - user: __token__ - password: ${{ secrets.PYPI_API_TOKEN }} diff --git a/.gitignore b/.gitignore index 84675af..1604d52 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,5 @@ +# find more examples here: +# https://github.com/github/gitignore/blob/main/Python.gitignore # Binaries (object files) produced by a compiler *.so *.o @@ -27,3 +29,28 @@ _templates # VSCode may create a config file with this name **.vscode + +# Ruff stuff: +.ruff_cache/ + +# Environments +.env +.envrc +.venv +env/ +venv/ + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py.cover +.hypothesis/ +.pytest_cache/ +cover/ diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 75f0fc0..29f28ee 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -14,6 +14,9 @@ build: # nodejs: "19" # rust: "1.64" # golang: "1.19" + # apt_packages: + # - some_package + # Build documentation in the "docs/" directory with Sphinx sphinx: diff --git a/LICENSE b/LICENSE index db82110..88a548a 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2023: Jakob Nybo Nissen. +Copyright (c) 2025: First Last. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the diff --git a/README.md b/README.md index 4e71da5..a248d35 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,8 @@ # Example Python package +All design principles are explained in the [developing.md](developing.md) file. +The Python package template was created by Jakob Nybo Nissen and Henry Webel. + ## How to use Can be used as GitHub template repository, @@ -8,10 +11,15 @@ see [GitHub documentation](https://docs.github.com/en/repositories/creating-and- You will need to find and replace occurences of - `python_package` -> `your_package_name` + - also the folder `src/python_package` - `RasmussenLab` -> `GitHub_user_name` (or `organization`) - with the name of your package and GitHub user name (or organization). +- look for `First Last` to see where to replace with your name +- choose a license, see [GitHub documentation](https://docs.github.com/en/repositories/creating-and-managing-repositories/licensing-a-repository) + and [Creative Commons](https://creativecommons.org/chooser/). + Replace [`LICENSE`](LICENSE) file with the license you choose. + ## Development environment Install package so that new code is picked up in a restared python interpreter: @@ -22,6 +30,8 @@ pip install -e ".[dev]" ## Basic usage +> works using this template + ```python from python_package import hello_world print (python_package.__version__) @@ -31,8 +41,9 @@ print(hello_world(4)) ## Readthedocs The documentation can be build using readthedocs automatically. See -[project on Readthedocs](https://readthedocs.org/projects/rasmussenlab-python-package/) for the project. A new project needs -to be registered. +[project on Readthedocs](https://readthedocs.org/projects/rasmussenlab-python-package/) +for the project based on this template. A new project needs +to [be registered on ReadTheDocs](https://docs.readthedocs.com/platform/stable/intro/add-project.html). - make sure to enable build from PRs in the settings (advanded settings) - checkout configuration file: [`.readthedocs.yaml`](.readthedocs.yaml) diff --git a/developing.md b/developing.md new file mode 100644 index 0000000..d5424c9 --- /dev/null +++ b/developing.md @@ -0,0 +1,561 @@ +# Design descriptions and details for the Python package template + +> Author: Henry Webel + +[packaging.python.org](https://packaging.python.org/en/latest/tutorials/packaging-projects/) +has an excellent tutorial on how to package a Python project. I read and used insights from +that website to help create the template which is available on GitHub at +[https://github.com/RasmussenLab/python_package](https://github.com/RasmussenLab/python_package) +and I want to give here an overview specifically to some details regarding this template. +Some are overlapping with the +[packaging.python.org](https://packaging.python.org/en/latest/tutorials/packaging-projects/) +tutorial, but as always we decided for a certain set of tools, conventions and complexity +which needs some explanation. + +Here a brief overview of external resources you can also look at: + +- [packaging.python.org](https://packaging.python.org/en/latest/tutorials/packaging-projects/) +- [setuptools documentation](https://setuptools.pypa.io/en/latest/userguide/index.html) +- [learn.scientific-python.org](https://learn.scientific-python.org/development/) +- [Py-Pkgs](https://py-pkgs.org/) + +## Project structure + +First an overview of the main folder structure. See line comments for details on what +is the purpose of each folder or file: + +```bash +python_package +├── docs # Documentation using Sphinx +├── src # the source code of the package +├── tests # pytest tests +├── LICENSE # License file specifying usage terms +├── MANIFEST.in # non-python files to include into the build package +├── pyproject.toml # python package metadata, dependencies and configurations (incl. build tools) +├── pytest.ini # pytest configuration +├── README.md # README which is rendered on GitHub (or other hosting services) +└── setup.cfg # old python configuration file, empty +└── setup.py # artefact for backward compatibility, do not change +``` + +## Core packaging files + +We will first look at [`pyproject.toml`](pyproject.toml) and its relation to the +[`src`](src) directory. The +[`pyproject.toml`](pyproject.toml) file is the main configuration file for the Python package +and is used to specify the package metadata, dependencies, build tools and configurations. +The [`src`](src) folder stores the actual source code of the package, where the package itself is +the subdirectories of the [`src`](src) directory. The (e.g. `src/python_package`). + +
+About setup.py and setup.cfg configuration files + +The [`setup.py`](setup.py) file is an artefact for backward compatibility and should not +be changed. Everything that used to be in [`setup.py`](setup.py) or +[`setup.cfg`](setup.cfg) is now largely in [`pyproject.toml`](pyproject.toml). +The notable exception would be the desired maximum line length in `setup.cfg` for +the tool [`flake8`](https://flake8.pycqa.org/), which does not yet supported +[`pyproject.toml`](pyproject.toml) configuration. As we use `ruff` as linter, +we left it empty, but in case you want to use `flake8`, you can add: + +```INI +; setup.cfg +[flake8] +exclude = docs +max-line-length = 88 +aggressive = 2 +``` + +
+ +### Changes required in `pyproject.toml` + +You have to change entries under the `[project]` section to match your project name, +description, author, license, etc. Make sure to pick a license that works for you, e.g. +using [choosealicense.com](https://choosealicense.com/). Also update the `LICENSE` file +accordingly. + +The `dependencies` key can +list the dependencies and is currently commented out. The dependencies could also be +specified in via a `requirements.txt`, if you already have such a file. + +```toml +# ref: https://setuptools.pypa.io/en/stable/userguide/pyproject_config.html +[project] +authors = [ + { name = "First Last", email = "first.last@gmail.com" }, +] +description = "A small example package" +name = "python_package" +# This means: Load the version from the package itself. +# See the section below: [tools.setuptools.dynamic] +dynamic = ["version", # version is loaded from the package +#"dependencies", # add if using requirements.txt +] +readme = "README.md" +requires-python = ">=3.9" +# These are keywords +classifiers = [ + "Programming Language :: Python :: 3", + "Operating System :: OS Independent", +] +license = "MIT" # https://choosealicense.com/ +# # add dependencies here: (use one of the two) +# dependencies = ["numpy", "pandas", "scipy", "matplotlib", "seaborn"] +# use requirements.txt instead of pyproject.toml for dependencies +# https://stackoverflow.com/a/73600610/9684872 +# [tool.setuptools.dynamic] +# dependencies = {file = ["requirements.txt"]} +``` + +The entry + +```toml +dynamic = ["version"] +``` + +means that the version is loaded dynamically using the extension +[setuptools_scm](https://setuptools-scm.readthedocs.io/) +we list under the `[build-system]` section in [`pyproject.toml`](pyproject.toml). +This is done to avoid having to manually update the version and integrate with automatic +versioning through releases on GitHub. It also +ensures that each commit has a unique version number, which is useful for attributing +errors to specific non-released versions. The dynamic version is picked up in the +`__version__` variable in the `__init__.py` file of the package, which is located in the +[`src/python_package`](src/python_package) directory. + +```toml +[build-system] +build-backend = "setuptools.build_meta" +requires = ["setuptools>=64", "setuptools_scm>=8"] + +[tool.setuptools_scm] +# https://setuptools-scm.readthedocs.io/ +# used to pick up the version from the git tags or the latest commit. +``` + +Please also update the project URL to your project: + +```toml +[project.urls] +"Bug Tracker" = "https://github.com/RasmussenLab/python_package/issues" +"Homepage" = "https://github.com/RasmussenLab/python_package" +``` + +## Source directory layout of the package + +The source code of the package is located in the `src` directory, to have a project +independent folder to look for the source code recognized by most tools you would need +to build a package +(read on [packagin namespace packages](https://packaging.python.org/en/latest/guides/packaging-namespace-packages/)). +It also allows to have multiple subpackages or modules +in the same project under the `python_package` package (see example +[here](https://setuptools.pypa.io/en/latest/userguide/package_discovery.html#src-layout)). + +```bash +├── src +│ └── python_package +│ ├── __init__.py # imported when the package is imported (import python_package) +│ └── mockup.py # a submodule of the package (import python_package.mockup) +``` + +So you will need to rename the `python_package` directory to your package name, +e.g. `my_package` and specify the package name in the [`pyproject.toml`](pyproject.toml) file +under the `[project]` section: + +```toml +name = "my_package" +``` + +Strictly speaking you can give different names in both places, but this will only confuse +potential users. Think of `scikit-learn` for an example of a package that uses a different +name in the [`pyproject.toml`](pyproject.toml) file and the source code directory name, +leading to the `sklearn` package name when imported. + +## Documentation + +The documentation is created using [Sphinx](https://www.sphinx-doc.org/en/master/), +which is common for Python documentation. It relies additionally on several extensions +enabling the use of `markdown` and `jupyter` notebooks. + +The documentation is located in the [`docs`](docs) directory. Sphinx is configured via +the [`conf.py`](docs/conf.py) file, where you can specify the extension you want: + +```python +# in docs/conf.py + +extensions = [ + "sphinx.ext.autodoc", # Core extension for generating documentation from docstrings + "sphinx.ext.autodoc.typehints", # Automatically document type hints in function signatures + "sphinx.ext.viewcode", # Include links to the source code in the documentation + "sphinx.ext.napoleon", # Support for Google and NumPy style docstrings + "sphinx.ext.intersphinx", # allows linking to other projects' documentation in API + "sphinx_new_tab_link", # each link opens in a new tab + "myst_nb", # Markdown and Jupyter Notebook support + "sphinx_copybutton", # add copy button to code blocks +] +``` + +These are added as dependencies through the +`pyproject.toml` file under the `[project.optional-dependencies]` section: + +```toml +[project.optional-dependencies] +# Optional dependencies to locally build the documentation, also used for +# readthedocs. +docs = [ + "sphinx", + "sphinx-book-theme", + "myst-nb", + "ipywidgets", + "sphinx-new-tab-link!=0.2.2", + "jupytext", +] +``` + +### Required changes in `conf.py` + +The required changes in [`conf.py`](docs/conf.py) are at the following places: + +```python +# in docs/conf.py + +project = "python_package" +copyright = "2025, First Last" +author = "First Last" +PACKAGE_VERSION = metadata.version("python_package") + +# ... + +# and again links to your project repository +html_theme_options = { + "github_url": "https://github.com/RasmussenLab/python_package", + "repository_url": "https://github.com/RasmussenLab/python_package", + # more... +} + +# ... + +# and one last line (the last below) +if os.environ.get("READTHEDOCS") == "True": + from pathlib import Path + + PROJECT_ROOT = Path(__file__).parent.parent + PACKAGE_ROOT = PROJECT_ROOT / "src" / "python_package" +``` + +The last block is for Read The Docs to be able to generate the API documentation of your +package on the fly. See the Read The Docs section below for more details. + +### Theme, autodoc and intersphinx + +We build the documentation based on the template +[sphinx_book_theme](https://sphinx-book-theme.readthedocs.io), which is set in the +[`conf.py`](docs/conf.py) file and parts of our docs requirements in +[`pyproject.toml`](pyproject.toml): + +```python +html_theme = "sphinx_book_theme" +``` + +> If you use a different theme, some of the settings in `conf.py` might not be applicable +> and need to be changed. Explore other themes here: +> [sphinx-themes.org](https://sphinx-themes.org/) + +The API of the Python package in the `src` directory is automatically included +in the documentation using the +[`autodoc` extension](https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html). +We use per default the `numpydoc` style for docstrings, see the format +[here](https://numpydoc.readthedocs.io/en/stable/format.html). +The API documentation can be augmented with highlights from other types from projects +using `intersphinx`: + +```python +# Intersphinx options +intersphinx_mapping = { + "python": ("https://docs.python.org/3", None), + # "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None), + # "scikit-learn": ("https://scikit-learn.org/stable/", None), + # "matplotlib": ("https://matplotlib.org/stable/", None), +} +``` + +Here we only add the core Python documentation, but you can add more projects +like `pandas`, `scikit-learn`, or `matplotlib` to the mapping. + +### Building the documentation locally (with integration tests) + +To build the documentation locally, you can follow the instructions in the +[`docs/README.md`](docs/README.md), which you should also update with your name changes. +In short, you can run the following commands in the [`docs`](docs ) directory: + +```bash +# in root of the project +pip install ".[docs]" +cd docs # change to docs directory +sphinx-apidoc --force --implicit-namespaces --module-first -o reference ../src/python_package +sphinx-build -n -W --keep-going -b html ./ ./_build/ +``` + +this will create a `reference` directory with the API documentation of the Python package +`python_package`, a `jupyter_execute` for the tutorial in [`docs/tutorial`](docs/tutorial) + and a `_build` directory with an HTML version of the documentation. You can open the +`_build/index.html` file in your browser to view the documentation built locally. + +The tutorial related configuration in `conf.py` is the following, specifying that +errors stop the build process ensuring that examples are tested: + +```python +# https://myst-nb.readthedocs.io/en/latest/computation/execute.html +nb_execution_mode = "auto" + +myst_enable_extensions = ["dollarmath", "amsmath"] + +# Plotly support through require javascript library +# https://myst-nb.readthedocs.io/en/latest/render/interactive.html#plotly +html_js_files = [ + "https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js" +] + +# https://myst-nb.readthedocs.io/en/latest/configuration.html +# Execution +nb_execution_raise_on_error = True +# Rendering +nb_merge_streams = True +``` + +The tutorials are meant as a sort of integration test, where you make sure that the core +functionality your project wants to support is working as expected. For easier github +diffs, we use [`jupytext`](https://jupytext.readthedocs.io), which allows to +have the tutorial in both a Jupyter Notebook format and a Python script format. +You have to keep the files in sync using: + +```bash +jupytext --sync docs/tutorial/*.ipynb +``` + +The [`docs/tutorial/.jupytext`](docs/tutorial/.jupytext) configuration sets the default +format to `py:percent` and automatically allows syncing of new notebooks. + +### Read The Docs + +To build the documentation on Read The Docs, you need to create a file called +[`.readthedocs.yaml`](.readthedocs.yaml), which is located in the root of the project and +specifies which dependencies are needed. The core is the following specifying where the +[`conf.py`](docs/conf.py) file is and from where to install the required dependencies: + +```yaml +# Build documentation in the "docs/" directory with Sphinx +sphinx: + configuration: docs/conf.py + +python: + install: + - method: pip + path: . + extra_requirements: + - docs +``` + +You will need to manually register your project repository on +[Read The Docs](https://readthedocs.org/) in order that it can build the documentation +by the service. I recommend to activate builds for Pull Requests, so that +the documentation is built for each PR and you can see if the documentation is gradually +breaking, i.e. your integration test using the notebooks in +[`docs/tutorial`](docs/tutorial) fail. See their documentation +[on adding a project](https://docs.readthedocs.com/platform/stable/intro/add-project.html) +for instructions. + +## Running tests + +The tests are located in the `tests` directory and can be run using `pytest`. +Pytest is specified as a dependency in the `pyproject.toml` file under the +`[project.optional-dependencies]` section along with the formatter `black` and the +linter `ruff`: + +```toml +[project.optional-dependencies] +# local development options +dev = ["black[jupyter]", "ruff", "pytest"] +``` + +Instead of running these tools manually, typing + +```bash +black . +ruff check . +pytest tests +``` + +read the next section to see how this is automated using `GitHub Actions`. + +## GitHub Actions + +We run these checks also on GitHub using GitHub Actions. The configuration +for the actions is located in the [`.github/workflows`](.github/workflows) directory +and is specified in the `cdci.yml` file. See the biosustain dsp tutorial on GitHub Actions +for more details (or any other resource you find): +[biosustain/dsp_actions_tutorial](https://github.com/biosustain/dsp_actions_tutorial) + +```yaml +# This workflow will install Python dependencies, run tests and lint with a single version of Python +# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python + +name: Python application + +on: + push: + pull_request: + branches: ["main"] + schedule: + - cron: "0 2 * * 3" + +permissions: + contents: read + +jobs: + format: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: psf/black@stable + lint: + name: Lint with ruff + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - uses: actions/setup-python@v5 + with: + python-version: "3.11" + - name: Install ruff + run: | + pip install ruff + - name: Lint with ruff + run: | + # stop the build if there are Python syntax errors or undefined names + ruff check . + test: + name: Test + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["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 }} + cache: "pip" # caching pip dependencies + cache-dependency-path: "**/pyproject.toml" + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install pytest + pip install -e . + - name: Run tests + run: python -m pytest tests +``` + +This workflow also allows to create `PyPI` releases automatically if you register your +project on `PyPI` (or `TestPyPI` for testing first) and create a GitHub release: + +```yaml + publish: + name: Publish package + if: startsWith(github.ref, 'refs/tags') + needs: + - format + - lint + - test + - build_source_dist + # - build_wheels + runs-on: ubuntu-latest + + steps: + - uses: actions/download-artifact@v4 + with: + name: artifact + path: ./dist + + - uses: pypa/gh-action-pypi-publish@release/v1 + with: + # remove repository key to set the default to pypi (not test.pypi.org) + repository-url: https://test.pypi.org/legacy/ +``` + +To setup the [`gh-action-pypi-publish`](https://github.com/pypa/gh-action-pypi-publish) +action, you need to register the repository +on [PyPI](https://pypi.org/) or [`TestPyPI`](https://test.pypi.org/), which allows PyPI +and GitHub to communicate securely. See the instructions on +[packaging.python.org](https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/). + +You then trigger new releases to PyPI by creating a new GitHub release, which will +automatically trigger the `publish` job in the workflow as it needs you to set a tag. +Have a look at [VueGen Releases]( https://github.com/Multiomics-Analytics-Group/vuegen/releases) +for an example. The release notes are automatically generated using the PR titles, +see GitHub's +[docs](https://docs.github.com/en/repositories/releasing-projects-on-github/automatically-generated-release-notes). + +
+Wheels and testing builds +The wheels are not built by default, but you can be necessary for packages which need +to be partly compiled, e.g. if you use `Cython`, `numpy` C extensions or Rust extensions. + +Also additionally you could use the artifact from the `build_source_dist` job +to test the build of the source distribution. This is useful to ensure that a package +with non-Python files (e.g. data files) is built correctly and that the package +can be installed correctly. You should probably best test this in as much isolation as +you can, e.g. by not pulling the repository using `actions/checkout@v4`. + +```yaml + test_sdist: + name: Install built source distribution + needs: build_source_dist + runs-on: ubuntu-latest + steps: + # - uses: actions/checkout@v4 + - uses: actions/download-artifact@v4 + with: + name: artifact + path: ./dist + - uses: actions/setup-python@v5 + with: + python-version: "3.11" + - name: Install built sdist + run: | + pip install ./dist/*.tar.gz + # ... some checks +``` +
+ + + +## Full project structure + +```bash +python_package +├── docs +│ ├── tutorial +│ │ ├── tutorial.ipynb # tutorial in Jupyter Notebook format +│ │ └── tutorial.py # tutorial in Python script format (created by jupytext) +│ ├── conf.py # configuration for Sphinx documentation +│ ├── index.md # defining the website structure +│ ├── Makefile # can be ignored +│ └── README.md # specifies how to build the documentation +├── src +│ └── python_package +│ ├── __init__.py # imported when the package is imported (import python_package) +│ └── mockup.py # a submodule of the package (import python_package.mockup) +├── tests +│ ├── __init__.py +│ └── test_mockup.py # files and test_function need to start with test_ to be recognized by pytest +├── LICENSE # License file specifying usage terms +├── MANIFEST.in # non-python files to include into the build package +├── pyproject.toml # python package metadata, dependencies and configurations (incl. build tools) +├── pytest.ini # pytest configuration +├── README.md # README which is rendered on GitHub (or other hosting services) +└── setup.cfg # old python configuration file, empty +└── setup.py # artefact for backward compatibility, do not change +``` diff --git a/docs/.gitignore b/docs/.gitignore new file mode 100644 index 0000000..14a2c18 --- /dev/null +++ b/docs/.gitignore @@ -0,0 +1,3 @@ +_build +reference +jupyter_execute diff --git a/docs/conf.py b/docs/conf.py index 12ccf81..4851ebe 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -16,8 +16,8 @@ # -- Project information ----------------------------------------------------- project = "python_package" -copyright = "2025, Jakob Nybo Nissen, Henry Webel" -author = "Jakob Nybo Nissen, Henry Webel" +copyright = "2025, First Last" +author = "First Last" PACKAGE_VERSION = metadata.version("python_package") version = PACKAGE_VERSION release = PACKAGE_VERSION @@ -29,13 +29,14 @@ # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ - "sphinx.ext.autodoc", - "sphinx.ext.autodoc.typehints", - "sphinx.ext.viewcode", - "sphinx.ext.napoleon", - "sphinx.ext.intersphinx", - "sphinx_new_tab_link", - "myst_nb", + "sphinx.ext.autodoc", # Core extension for generating documentation from docstrings + "sphinx.ext.autodoc.typehints", # Automatically document type hints in function signatures + "sphinx.ext.viewcode", # Include links to the source code in the documentation + "sphinx.ext.napoleon", # Support for Google and NumPy style docstrings + "sphinx.ext.intersphinx", # allows linking to other projects' documentation in API + "sphinx_new_tab_link", # each link opens in a new tab + "myst_nb", # Markdown and Jupyter Notebook support + "sphinx_copybutton", # add copy button to code blocks ] # https://myst-nb.readthedocs.io/en/latest/computation/execute.html @@ -43,7 +44,7 @@ myst_enable_extensions = ["dollarmath", "amsmath"] -# Plolty support through require javascript library +# Plotly support through require javascript library # https://myst-nb.readthedocs.io/en/latest/render/interactive.html#plotly html_js_files = [ "https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js" diff --git a/docs/developing.md b/docs/developing.md new file mode 100644 index 0000000..88bf941 --- /dev/null +++ b/docs/developing.md @@ -0,0 +1,5 @@ +```{include} ../developing.md +:start-line: 0 +:relative-docs: www.rasmussenlab.com/python_package/docs +:relative-images: +``` diff --git a/docs/index.md b/docs/index.md index 3d68bf7..e9c9db3 100644 --- a/docs/index.md +++ b/docs/index.md @@ -30,6 +30,7 @@ reference/python_package :hidden: true README +developing ``` ## Indices and tables diff --git a/pyproject.toml b/pyproject.toml index f0cf6dc..7a59c2e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,26 +1,28 @@ # ref: https://setuptools.pypa.io/en/stable/userguide/pyproject_config.html [project] authors = [ - { name = "Jakob Nybo Nissen", email = "jakobnybonissen@gmail.com" }, - { name = "Henry Webel", email = "henry.webel@sund.ku.dk" }, + { name = "First Last", email = "first.last@gmail.com" }, ] description = "A small example package" name = "python_package" # This means: Load the version from the package itself. # See the section below: [tools.setuptools.dynamic] -dynamic = ["version"] +dynamic = ["version", # version is loaded from the package +#"dependencies", # add if using requirements.txt +] readme = "README.md" -requires-python = ">=3.9" +requires-python = ">=3.9" # test all higher Python versions # These are keywords classifiers = [ "Programming Language :: Python :: 3", - "License :: OSI Approved :: MIT License", "Operating System :: OS Independent", ] +license = "MIT" # https://choosealicense.com/ # # add dependencies here: (use one of the two) # dependencies = ["numpy", "pandas", "scipy", "matplotlib", "seaborn"] # use requirements.txt instead of pyproject.toml for dependencies # https://stackoverflow.com/a/73600610/9684872 +# ! uncomment also dependencies in the dynamic section above # [tool.setuptools.dynamic] # dependencies = {file = ["requirements.txt"]} @@ -39,13 +41,23 @@ docs = [ "ipywidgets", "sphinx-new-tab-link!=0.2.2", "jupytext", + "sphinx-copybutton", ] # local development options -dev = ["black", "ruff", "pytest"] +dev = ["black[jupyter]", "ruff", "pytest"] # Configure the Ruff linter: Ignore error number 501 [tool.ruff] -lint.ignore = ["E501"] +# https://docs.astral.sh/ruff/rules/#flake8-bandit-s +# lint.ignore = ["E501"] # Ignore line length errors +# Allow lines to be as long as (default is 88 in black) + +[tool.ruff.lint] +# https://docs.astral.sh/ruff/tutorial/#rule-selection +# 1. Enable flake8-bugbear (`B`) rules +# 2. Enable pycodestyle (`E`) errors and (`W`) warnings +# 3. Pyflakes (`F`) errors +extend-select = ["E", "W", "F", "B"] [build-system] build-backend = "setuptools.build_meta" diff --git a/setup.cfg b/setup.cfg new file mode 100644 index 0000000..e69de29 From 6615d191d68c45914aafa2890eab9064abb951cf Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Mon, 14 Jul 2025 14:22:22 +0200 Subject: [PATCH 2/9] Update pyproject.toml (#4) * :art: format pyproject file * :bug: fix how line length errors can be ignored (deactivated per default) --- pyproject.toml | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 7a59c2e..8d614cd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,14 +1,13 @@ # ref: https://setuptools.pypa.io/en/stable/userguide/pyproject_config.html [project] -authors = [ - { name = "First Last", email = "first.last@gmail.com" }, -] +authors = [{ name = "First Last", email = "first.last@gmail.com" }] description = "A small example package" name = "python_package" # This means: Load the version from the package itself. # See the section below: [tools.setuptools.dynamic] -dynamic = ["version", # version is loaded from the package -#"dependencies", # add if using requirements.txt +dynamic = [ + "version", # version is loaded from the package + #"dependencies", # add if using requirements.txt ] readme = "README.md" requires-python = ">=3.9" # test all higher Python versions @@ -46,11 +45,8 @@ docs = [ # local development options dev = ["black[jupyter]", "ruff", "pytest"] -# Configure the Ruff linter: Ignore error number 501 [tool.ruff] # https://docs.astral.sh/ruff/rules/#flake8-bandit-s -# lint.ignore = ["E501"] # Ignore line length errors -# Allow lines to be as long as (default is 88 in black) [tool.ruff.lint] # https://docs.astral.sh/ruff/tutorial/#rule-selection @@ -58,6 +54,8 @@ dev = ["black[jupyter]", "ruff", "pytest"] # 2. Enable pycodestyle (`E`) errors and (`W`) warnings # 3. Pyflakes (`F`) errors extend-select = ["E", "W", "F", "B"] +# Ignore line length errors: +# ignore = ["E501"] [build-system] build-backend = "setuptools.build_meta" From 9d642ffbc13a5d3e51d871c6b1a8d525c60a8486 Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Wed, 13 Aug 2025 13:38:19 +0200 Subject: [PATCH 3/9] Contributing info (#6) * :memo::wrench: start adressing recommendations from Sebastian, see #5 * :art: add default citation --- CITATION.cff | 12 ++++++++++++ Contributing.md | 36 ++++++++++++++++++++++++++++++++++++ README.md | 7 ++++--- docs/tutorial/.jupytext | 6 +++++- pyproject.toml | 2 +- 5 files changed, 58 insertions(+), 5 deletions(-) create mode 100644 CITATION.cff create mode 100644 Contributing.md diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..b78dd26 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,12 @@ +# https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files +cff-version: 1.2.0 +message: "If you use this software, please cite it as below." +authors: +- family-names: "Last" + given-names: "First" + orcid: "https://orcid.org/0000-0000-0000-0000" +title: "Python Package Template repository" +version: 0.0.1 +doi: 10.5281/zenodo.1234 +date-released: 2025-07-23 +url: "https://github.com/biosustain/python_package" diff --git a/Contributing.md b/Contributing.md new file mode 100644 index 0000000..94d1032 --- /dev/null +++ b/Contributing.md @@ -0,0 +1,36 @@ +# Contributing code + +Install the code with development dependencies: + +```bash +pip install -e '.[dev]' +``` + +## Format code and sort imports + +```bash +black . +isort . +``` + +## lint code + +```bash +ruff check . +``` + +## Run tests + +```bash +pytest +``` + +## Sync notebooks with jupytext + +For easier diffs, you can use jupytext to sync notebooks in the `docs/tutorial` directory with the percent format. + +```bash +jupytext --sync docs/tutorial/*.ipynb +``` + +This is configured in the [`.jupytext`](docs/tutorial/.jupytext) file in that directory. diff --git a/README.md b/README.md index a248d35..0b2d238 100644 --- a/README.md +++ b/README.md @@ -11,14 +11,15 @@ see [GitHub documentation](https://docs.github.com/en/repositories/creating-and- You will need to find and replace occurences of - `python_package` -> `your_package_name` - - also the folder `src/python_package` + - also the folder `src/python_package` - `RasmussenLab` -> `GitHub_user_name` (or `organization`) -with the name of your package and GitHub user name (or organization). + with the name of your package and GitHub user name (or organization). - look for `First Last` to see where to replace with your name - choose a license, see [GitHub documentation](https://docs.github.com/en/repositories/creating-and-managing-repositories/licensing-a-repository) and [Creative Commons](https://creativecommons.org/chooser/). Replace [`LICENSE`](LICENSE) file with the license you choose. +- Update the `CITATION.cff` file with your information. ## Development environment @@ -41,7 +42,7 @@ print(hello_world(4)) ## Readthedocs The documentation can be build using readthedocs automatically. See -[project on Readthedocs](https://readthedocs.org/projects/rasmussenlab-python-package/) +[project on Readthedocs](https://readthedocs.org/projects/rasmussenlab-python-package/) for the project based on this template. A new project needs to [be registered on ReadTheDocs](https://docs.readthedocs.com/platform/stable/intro/add-project.html). diff --git a/docs/tutorial/.jupytext b/docs/tutorial/.jupytext index 46e9467..c213311 100644 --- a/docs/tutorial/.jupytext +++ b/docs/tutorial/.jupytext @@ -1,2 +1,6 @@ -# all notebooks in this directory are in the percent format +# all notebooks in this directory are synced percent format when typing +# (jupytext is a dev dependency) +# jupytext --sync *.ipynb +# or from root directory +# jupytext --sync docs/api_examples/*.ipynb formats = "ipynb,py:percent" diff --git a/pyproject.toml b/pyproject.toml index 8d614cd..1afdec2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -43,7 +43,7 @@ docs = [ "sphinx-copybutton", ] # local development options -dev = ["black[jupyter]", "ruff", "pytest"] +dev = ["black[jupyter]", "ruff", "pytest", "isort", "jupytext"] [tool.ruff] # https://docs.astral.sh/ruff/rules/#flake8-bandit-s From b64451032da7212d1995792ea35724e889efb22d Mon Sep 17 00:00:00 2001 From: "Angel L. P." <59593766+angelphanth@users.noreply.github.com> Date: Thu, 14 Aug 2025 14:27:45 +0200 Subject: [PATCH 4/9] :bug: add mandatory permissions for trusted publishing (#8) * :bug: add mandatory permissiones for trusted publishing * :art: move settings for rule to other settings for rule --------- Co-authored-by: Henry Webel --- .github/workflows/cicd.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/cicd.yml b/.github/workflows/cicd.yml index 3d485ce..315f0ee 100644 --- a/.github/workflows/cicd.yml +++ b/.github/workflows/cicd.yml @@ -106,6 +106,8 @@ jobs: publish: name: Publish package if: startsWith(github.ref, 'refs/tags') + permissions: + id-token: write needs: - format - lint @@ -125,3 +127,4 @@ jobs: with: # remove repository key to set the default to pypi (not test.pypi.org) repository-url: https://test.pypi.org/legacy/ + \ No newline at end of file From 5b0e65b347d607d8b44a4720be08efbaa5299316 Mon Sep 17 00:00:00 2001 From: "Angel L. P." <59593766+angelphanth@users.noreply.github.com> Date: Fri, 12 Sep 2025 15:09:15 +0200 Subject: [PATCH 5/9] init testing docs and added example tests (#9) * :memo: marp to create slides from readme * note pytest.ini for doctest * add function * add tests from demo * ruff lint and format * :art: format README.md * rm pres --------- Co-authored-by: Henry Webel --- src/python_package/__init__.py | 4 +- src/python_package/mockup.py | 28 +++++++++ tests/README.md | 112 +++++++++++++++++++++++++++++++++ tests/test_mockup.py | 26 +++++++- 4 files changed, 167 insertions(+), 3 deletions(-) create mode 100644 tests/README.md diff --git a/src/python_package/__init__.py b/src/python_package/__init__.py index 851aa6a..c0a0890 100644 --- a/src/python_package/__init__.py +++ b/src/python_package/__init__.py @@ -4,8 +4,8 @@ __version__ = metadata.version("python_package") -from .mockup import hello_world +from .mockup import hello_world, saved_world # The __all__ variable is a list of variables which are imported # when a user does "from example import *" -__all__ = ["hello_world"] +__all__ = ["hello_world", "saved_world"] diff --git a/src/python_package/mockup.py b/src/python_package/mockup.py index d8232c6..4b39c12 100644 --- a/src/python_package/mockup.py +++ b/src/python_package/mockup.py @@ -13,5 +13,33 @@ def hello_world(n: int) -> str: ------- str str of 'hello world' n-times + + Examples + -------- + >>> hello_world(3) + 'hello world hello world hello world' """ return " ".join(repeat("hello world", n)) + + +def saved_world(filename: str) -> int: + """ + Count how many times 'hello world' is in a file. + + Parameters + ---------- + filename : str + The file to read + + Returns + ------- + int + How many times 'hello world' is in the file + + Examples + -------- + >>> saved_world("not-real.txt") # doctest: +SKIP + """ + with open(filename, "r") as f: + content = f.read() + return content.count("hello world") diff --git a/tests/README.md b/tests/README.md new file mode 100644 index 0000000..3207159 --- /dev/null +++ b/tests/README.md @@ -0,0 +1,112 @@ +--- +marp: true +theme: uncover +paginate: true +backgroundColor: #fff +--- + +# **Getting started with pytesting** + +--- + +## Quick start + +### Installation + +Install pytest. e.g., from the "dev" dependencies + +```bash +pip install ".[dev]" +``` + +### How to use + +To execute the tests run e.g. + +```bash +pytest +``` + +--- + +## Test development tips + +--- + +### Folder and test naming + +1. The tests for functions in `.py` should go in `tests/test_.py` + + e.g., the tests for [python_package/mockup.py](../src/python_package/mockup.py) are in [tests/test_mockup.py](test_mockup.py) + +2. The test names should start with `def test_ ...` + + e.g., `def test_hello_world(): ...` + +--- + +### Some Pytest decorators + +1. To indicate that the test function is expected to fail you can prepend + + ```python + @pytest.mark.xfail(raises=TypeError) + def test_hello_world_str(): ... + ``` + +--- + +2. To setup and cleanup any resources for a test you can use [pytest fixtures with `yield`](https://dev.to/dawidbeno/understanding-yield-in-pytest-fixtures-4m38) + + ```python + @pytest.fixture + def temp_file(): + # set up + < code to create a file> + # return + yield + the_file + # clean up + < code to remove the file> + ``` + +--- + +### Doctests + +You can also include tests in your docstrings using `>>>` followed by the expected result e.g. + +```python +def hello_world(n): + """ + Prints 'hello world' n-times. + ... + + Examples + -------- + >>> hello_world(3) + 'hello world hello world hello world' + ... + """ +``` + +Needs `addopts = --doctest-modules` in `pytest.ini` in root of directory + +--- + +### Skipping in doctests + +If you know that the test cannot succeed but would like to include an example usage in the docstring still then you can add `# doctest: +SKIP` e.g. + +```python +def saved_world(filename): + """ + Count how many times 'hello world' is in a file. + ... + + Examples + -------- + >>> saved_world("not-real.txt") # doctest: +SKIP + ... + """ +``` diff --git a/tests/test_mockup.py b/tests/test_mockup.py index 80ebb89..9307ed3 100644 --- a/tests/test_mockup.py +++ b/tests/test_mockup.py @@ -1,7 +1,31 @@ -from python_package import hello_world +from python_package import hello_world, saved_world +import pytest def test_hello_world_3times(): expected = "hello world hello world hello world" result = hello_world(3) assert result == expected + + +@pytest.mark.xfail(raises=TypeError) +def test_hello_world_str(): + hello_world("3") + + +@pytest.fixture +def temp_file(): + # set up + filename = "temp_hellooo.txt" + with open(filename, "w") as f: + f.write("hello world hello world hello world") + yield filename + # clean up + import os + + os.remove(filename) + + +def test_saved_world_3times(temp_file): + result = saved_world(temp_file) + assert result == 3 From e16e715a36b29fea44548a757614976bede4dacc Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Thu, 18 Sep 2025 10:19:30 +0200 Subject: [PATCH 6/9] Plotly isort (#12) * :art: add sorting check of imports * :art: ensure plotly plots are rendered on readthedocs * :art: format conf.py * :art: apply isort --- .github/workflows/cicd.yml | 2 +- docs/conf.py | 1 + tests/test_mockup.py | 3 ++- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/cicd.yml b/.github/workflows/cicd.yml index 315f0ee..64abdbe 100644 --- a/.github/workflows/cicd.yml +++ b/.github/workflows/cicd.yml @@ -19,6 +19,7 @@ jobs: steps: - uses: actions/checkout@v4 - uses: psf/black@stable + - uses: isort/isort-action@v1 lint: name: Lint with ruff runs-on: ubuntu-latest @@ -127,4 +128,3 @@ jobs: with: # remove repository key to set the default to pypi (not test.pypi.org) repository-url: https://test.pypi.org/legacy/ - \ No newline at end of file diff --git a/docs/conf.py b/docs/conf.py index 4851ebe..fbaa22f 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -49,6 +49,7 @@ html_js_files = [ "https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js" ] +os.environ["PLOTLY_RENDERER"] = "notebook" # compatibility with plotly6 # https://myst-nb.readthedocs.io/en/latest/configuration.html # Execution diff --git a/tests/test_mockup.py b/tests/test_mockup.py index 9307ed3..295cb72 100644 --- a/tests/test_mockup.py +++ b/tests/test_mockup.py @@ -1,6 +1,7 @@ -from python_package import hello_world, saved_world import pytest +from python_package import hello_world, saved_world + def test_hello_world_3times(): expected = "hello world hello world hello world" From 17b8c67457de73783a8b023fc785565d505b7700 Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Thu, 18 Sep 2025 10:19:42 +0200 Subject: [PATCH 7/9] Contributing info (#10) * :memo::wrench: start adressing recommendations from Sebastian, see #5 * :art: add default citation From 5750798edd9e4cf7b9feca115ec7e13be3f49930 Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Thu, 18 Sep 2025 10:19:57 +0200 Subject: [PATCH 8/9] =?UTF-8?q?=F0=9F=94=A7=20set=20default=20license=20to?= =?UTF-8?q?=20GPL-3.0=20(#3)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - make sure code stays open source in other projects --- LICENSE | 696 +++++++++++++++++++++++++++++++++++++++++++++++-- pyproject.toml | 3 +- 2 files changed, 676 insertions(+), 23 deletions(-) diff --git a/LICENSE b/LICENSE index 88a548a..a5eae15 100644 --- a/LICENSE +++ b/LICENSE @@ -1,22 +1,674 @@ -MIT License - -Copyright (c) 2025: First Last. - -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. + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + +Copyright (C) 2007 Free Software Foundation, Inc. +Everyone is permitted to copy and distribute verbatim copies +of this license document, but changing it is not allowed. + + Preamble + +The GNU General Public License is a free, copyleft license for +software and other kinds of works. + +The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. We, the Free Software Foundation, use the +GNU General Public License for most of our software; it applies also to +any other work released this way by its authors. You can apply it to +your programs, too. + +When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +them if you wish), that you receive source code or can get it if you +want it, that you can change the software or use pieces of it in new +free programs, and that you know you can do these things. + +To protect your rights, we need to prevent others from denying you +these rights or asking you to surrender the rights. Therefore, you have +certain responsibilities if you distribute copies of the software, or if +you modify it: responsibilities to respect the freedom of others. + +For example, if you distribute copies of such a program, whether +gratis or for a fee, you must pass on to the recipients the same +freedoms that you received. You must make sure that they, too, receive +or can get the source code. And you must show them these terms so they +know their rights. + +Developers that use the GNU GPL protect your rights with two steps: +(1) assert copyright on the software, and (2) offer you this License +giving you legal permission to copy, distribute and/or modify it. + +For the developers' and authors' protection, the GPL clearly explains +that there is no warranty for this free software. For both users' and +authors' sake, the GPL requires that modified versions be marked as +changed, so that their problems will not be attributed erroneously to +authors of previous versions. + +Some devices are designed to deny users access to install or run +modified versions of the software inside them, although the manufacturer +can do so. This is fundamentally incompatible with the aim of +protecting users' freedom to change the software. The systematic +pattern of such abuse occurs in the area of products for individuals to +use, which is precisely where it is most unacceptable. Therefore, we +have designed this version of the GPL to prohibit the practice for those +products. If such problems arise substantially in other domains, we +stand ready to extend this provision to those domains in future versions +of the GPL, as needed to protect the freedom of users. + +Finally, every program is threatened constantly by software patents. +States should not allow patents to restrict development and use of +software on general-purpose computers, but in those that do, we wish to +avoid the special danger that patents applied to a free program could +make it effectively proprietary. To prevent this, the GPL assures that +patents cannot be used to render the program non-free. + +The precise terms and conditions for copying, distribution and +modification follow. + + TERMS AND CONDITIONS + +0. Definitions. + +"This License" refers to version 3 of the GNU General Public License. + +"Copyright" also means copyright-like laws that apply to other kinds of +works, such as semiconductor masks. + +"The Program" refers to any copyrightable work licensed under this +License. Each licensee is addressed as "you". "Licensees" and +"recipients" may be individuals or organizations. + +To "modify" a work means to copy from or adapt all or part of the work +in a fashion requiring copyright permission, other than the making of an +exact copy. The resulting work is called a "modified version" of the +earlier work or a work "based on" the earlier work. + +A "covered work" means either the unmodified Program or a work based +on the Program. + +To "propagate" a work means to do anything with it that, without +permission, would make you directly or secondarily liable for +infringement under applicable copyright law, except executing it on a +computer or modifying a private copy. Propagation includes copying, +distribution (with or without modification), making available to the +public, and in some countries other activities as well. + +To "convey" a work means any kind of propagation that enables other +parties to make or receive copies. Mere interaction with a user through +a computer network, with no transfer of a copy, is not conveying. + +An interactive user interface displays "Appropriate Legal Notices" +to the extent that it includes a convenient and prominently visible +feature that (1) displays an appropriate copyright notice, and (2) +tells the user that there is no warranty for the work (except to the +extent that warranties are provided), that licensees may convey the +work under this License, and how to view a copy of this License. If +the interface presents a list of user commands or options, such as a +menu, a prominent item in the list meets this criterion. + +1. Source Code. + +The "source code" for a work means the preferred form of the work +for making modifications to it. "Object code" means any non-source +form of a work. + +A "Standard Interface" means an interface that either is an official +standard defined by a recognized standards body, or, in the case of +interfaces specified for a particular programming language, one that +is widely used among developers working in that language. + +The "System Libraries" of an executable work include anything, other +than the work as a whole, that (a) is included in the normal form of +packaging a Major Component, but which is not part of that Major +Component, and (b) serves only to enable use of the work with that +Major Component, or to implement a Standard Interface for which an +implementation is available to the public in source code form. A +"Major Component", in this context, means a major essential component +(kernel, window system, and so on) of the specific operating system +(if any) on which the executable work runs, or a compiler used to +produce the work, or an object code interpreter used to run it. + +The "Corresponding Source" for a work in object code form means all +the source code needed to generate, install, and (for an executable +work) run the object code and to modify the work, including scripts to +control those activities. However, it does not include the work's +System Libraries, or general-purpose tools or generally available free +programs which are used unmodified in performing those activities but +which are not part of the work. For example, Corresponding Source +includes interface definition files associated with source files for +the work, and the source code for shared libraries and dynamically +linked subprograms that the work is specifically designed to require, +such as by intimate data communication or control flow between those +subprograms and other parts of the work. + +The Corresponding Source need not include anything that users +can regenerate automatically from other parts of the Corresponding +Source. + +The Corresponding Source for a work in source code form is that +same work. + +2. Basic Permissions. + +All rights granted under this License are granted for the term of +copyright on the Program, and are irrevocable provided the stated +conditions are met. This License explicitly affirms your unlimited +permission to run the unmodified Program. The output from running a +covered work is covered by this License only if the output, given its +content, constitutes a covered work. This License acknowledges your +rights of fair use or other equivalent, as provided by copyright law. + +You may make, run and propagate covered works that you do not +convey, without conditions so long as your license otherwise remains +in force. You may convey covered works to others for the sole purpose +of having them make modifications exclusively for you, or provide you +with facilities for running those works, provided that you comply with +the terms of this License in conveying all material for which you do +not control copyright. Those thus making or running the covered works +for you must do so exclusively on your behalf, under your direction +and control, on terms that prohibit them from making any copies of +your copyrighted material outside their relationship with you. + +Conveying under any other circumstances is permitted solely under +the conditions stated below. Sublicensing is not allowed; section 10 +makes it unnecessary. + +3. Protecting Users' Legal Rights From Anti-Circumvention Law. + +No covered work shall be deemed part of an effective technological +measure under any applicable law fulfilling obligations under article +11 of the WIPO copyright treaty adopted on 20 December 1996, or +similar laws prohibiting or restricting circumvention of such +measures. + +When you convey a covered work, you waive any legal power to forbid +circumvention of technological measures to the extent such circumvention +is effected by exercising rights under this License with respect to +the covered work, and you disclaim any intention to limit operation or +modification of the work as a means of enforcing, against the work's +users, your or third parties' legal rights to forbid circumvention of +technological measures. + +4. Conveying Verbatim Copies. + +You may convey verbatim copies of the Program's source code as you +receive it, in any medium, provided that you conspicuously and +appropriately publish on each copy an appropriate copyright notice; +keep intact all notices stating that this License and any +non-permissive terms added in accord with section 7 apply to the code; +keep intact all notices of the absence of any warranty; and give all +recipients a copy of this License along with the Program. + +You may charge any price or no price for each copy that you convey, +and you may offer support or warranty protection for a fee. + +5. Conveying Modified Source Versions. + +You may convey a work based on the Program, or the modifications to +produce it from the Program, in the form of source code under the +terms of section 4, provided that you also meet all of these conditions: + + a) The work must carry prominent notices stating that you modified + it, and giving a relevant date. + + b) The work must carry prominent notices stating that it is + released under this License and any conditions added under section + 7. This requirement modifies the requirement in section 4 to + "keep intact all notices". + + c) You must license the entire work, as a whole, under this + License to anyone who comes into possession of a copy. This + License will therefore apply, along with any applicable section 7 + additional terms, to the whole of the work, and all its parts, + regardless of how they are packaged. This License gives no + permission to license the work in any other way, but it does not + invalidate such permission if you have separately received it. + + d) If the work has interactive user interfaces, each must display + Appropriate Legal Notices; however, if the Program has interactive + interfaces that do not display Appropriate Legal Notices, your + work need not make them do so. + +A compilation of a covered work with other separate and independent +works, which are not by their nature extensions of the covered work, +and which are not combined with it such as to form a larger program, +in or on a volume of a storage or distribution medium, is called an +"aggregate" if the compilation and its resulting copyright are not +used to limit the access or legal rights of the compilation's users +beyond what the individual works permit. Inclusion of a covered work +in an aggregate does not cause this License to apply to the other +parts of the aggregate. + +6. Conveying Non-Source Forms. + +You may convey a covered work in object code form under the terms +of sections 4 and 5, provided that you also convey the +machine-readable Corresponding Source under the terms of this License, +in one of these ways: + + a) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by the + Corresponding Source fixed on a durable physical medium + customarily used for software interchange. + + b) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by a + written offer, valid for at least three years and valid for as + long as you offer spare parts or customer support for that product + model, to give anyone who possesses the object code either (1) a + copy of the Corresponding Source for all the software in the + product that is covered by this License, on a durable physical + medium customarily used for software interchange, for a price no + more than your reasonable cost of physically performing this + conveying of source, or (2) access to copy the + Corresponding Source from a network server at no charge. + + c) Convey individual copies of the object code with a copy of the + written offer to provide the Corresponding Source. This + alternative is allowed only occasionally and noncommercially, and + only if you received the object code with such an offer, in accord + with subsection 6b. + + d) Convey the object code by offering access from a designated + place (gratis or for a charge), and offer equivalent access to the + Corresponding Source in the same way through the same place at no + further charge. You need not require recipients to copy the + Corresponding Source along with the object code. If the place to + copy the object code is a network server, the Corresponding Source + may be on a different server (operated by you or a third party) + that supports equivalent copying facilities, provided you maintain + clear directions next to the object code saying where to find the + Corresponding Source. Regardless of what server hosts the + Corresponding Source, you remain obligated to ensure that it is + available for as long as needed to satisfy these requirements. + + e) Convey the object code using peer-to-peer transmission, provided + you inform other peers where the object code and Corresponding + Source of the work are being offered to the general public at no + charge under subsection 6d. + +A separable portion of the object code, whose source code is excluded +from the Corresponding Source as a System Library, need not be +included in conveying the object code work. + +A "User Product" is either (1) a "consumer product", which means any +tangible personal property which is normally used for personal, family, +or household purposes, or (2) anything designed or sold for incorporation +into a dwelling. In determining whether a product is a consumer product, +doubtful cases shall be resolved in favor of coverage. For a particular +product received by a particular user, "normally used" refers to a +typical or common use of that class of product, regardless of the status +of the particular user or of the way in which the particular user +actually uses, or expects or is expected to use, the product. A product +is a consumer product regardless of whether the product has substantial +commercial, industrial or non-consumer uses, unless such uses represent +the only significant mode of use of the product. + +"Installation Information" for a User Product means any methods, +procedures, authorization keys, or other information required to install +and execute modified versions of a covered work in that User Product from +a modified version of its Corresponding Source. The information must +suffice to ensure that the continued functioning of the modified object +code is in no case prevented or interfered with solely because +modification has been made. + +If you convey an object code work under this section in, or with, or +specifically for use in, a User Product, and the conveying occurs as +part of a transaction in which the right of possession and use of the +User Product is transferred to the recipient in perpetuity or for a +fixed term (regardless of how the transaction is characterized), the +Corresponding Source conveyed under this section must be accompanied +by the Installation Information. But this requirement does not apply +if neither you nor any third party retains the ability to install +modified object code on the User Product (for example, the work has +been installed in ROM). + +The requirement to provide Installation Information does not include a +requirement to continue to provide support service, warranty, or updates +for a work that has been modified or installed by the recipient, or for +the User Product in which it has been modified or installed. Access to a +network may be denied when the modification itself materially and +adversely affects the operation of the network or violates the rules and +protocols for communication across the network. + +Corresponding Source conveyed, and Installation Information provided, +in accord with this section must be in a format that is publicly +documented (and with an implementation available to the public in +source code form), and must require no special password or key for +unpacking, reading or copying. + +7. Additional Terms. + +"Additional permissions" are terms that supplement the terms of this +License by making exceptions from one or more of its conditions. +Additional permissions that are applicable to the entire Program shall +be treated as though they were included in this License, to the extent +that they are valid under applicable law. If additional permissions +apply only to part of the Program, that part may be used separately +under those permissions, but the entire Program remains governed by +this License without regard to the additional permissions. + +When you convey a copy of a covered work, you may at your option +remove any additional permissions from that copy, or from any part of +it. (Additional permissions may be written to require their own +removal in certain cases when you modify the work.) You may place +additional permissions on material, added by you to a covered work, +for which you have or can give appropriate copyright permission. + +Notwithstanding any other provision of this License, for material you +add to a covered work, you may (if authorized by the copyright holders of +that material) supplement the terms of this License with terms: + + a) Disclaiming warranty or limiting liability differently from the + terms of sections 15 and 16 of this License; or + + b) Requiring preservation of specified reasonable legal notices or + author attributions in that material or in the Appropriate Legal + Notices displayed by works containing it; or + + c) Prohibiting misrepresentation of the origin of that material, or + requiring that modified versions of such material be marked in + reasonable ways as different from the original version; or + + d) Limiting the use for publicity purposes of names of licensors or + authors of the material; or + + e) Declining to grant rights under trademark law for use of some + trade names, trademarks, or service marks; or + + f) Requiring indemnification of licensors and authors of that + material by anyone who conveys the material (or modified versions of + it) with contractual assumptions of liability to the recipient, for + any liability that these contractual assumptions directly impose on + those licensors and authors. + +All other non-permissive additional terms are considered "further +restrictions" within the meaning of section 10. If the Program as you +received it, or any part of it, contains a notice stating that it is +governed by this License along with a term that is a further +restriction, you may remove that term. If a license document contains +a further restriction but permits relicensing or conveying under this +License, you may add to a covered work material governed by the terms +of that license document, provided that the further restriction does +not survive such relicensing or conveying. + +If you add terms to a covered work in accord with this section, you +must place, in the relevant source files, a statement of the +additional terms that apply to those files, or a notice indicating +where to find the applicable terms. + +Additional terms, permissive or non-permissive, may be stated in the +form of a separately written license, or stated as exceptions; +the above requirements apply either way. + +8. Termination. + +You may not propagate or modify a covered work except as expressly +provided under this License. Any attempt otherwise to propagate or +modify it is void, and will automatically terminate your rights under +this License (including any patent licenses granted under the third +paragraph of section 11). + +However, if you cease all violation of this License, then your +license from a particular copyright holder is reinstated (a) +provisionally, unless and until the copyright holder explicitly and +finally terminates your license, and (b) permanently, if the copyright +holder fails to notify you of the violation by some reasonable means +prior to 60 days after the cessation. + +Moreover, your license from a particular copyright holder is +reinstated permanently if the copyright holder notifies you of the +violation by some reasonable means, this is the first time you have +received notice of violation of this License (for any work) from that +copyright holder, and you cure the violation prior to 30 days after +your receipt of the notice. + +Termination of your rights under this section does not terminate the +licenses of parties who have received copies or rights from you under +this License. If your rights have been terminated and not permanently +reinstated, you do not qualify to receive new licenses for the same +material under section 10. + +9. Acceptance Not Required for Having Copies. + +You are not required to accept this License in order to receive or +run a copy of the Program. Ancillary propagation of a covered work +occurring solely as a consequence of using peer-to-peer transmission +to receive a copy likewise does not require acceptance. However, +nothing other than this License grants you permission to propagate or +modify any covered work. These actions infringe copyright if you do +not accept this License. Therefore, by modifying or propagating a +covered work, you indicate your acceptance of this License to do so. + +10. Automatic Licensing of Downstream Recipients. + +Each time you convey a covered work, the recipient automatically +receives a license from the original licensors, to run, modify and +propagate that work, subject to this License. You are not responsible +for enforcing compliance by third parties with this License. + +An "entity transaction" is a transaction transferring control of an +organization, or substantially all assets of one, or subdividing an +organization, or merging organizations. If propagation of a covered +work results from an entity transaction, each party to that +transaction who receives a copy of the work also receives whatever +licenses to the work the party's predecessor in interest had or could +give under the previous paragraph, plus a right to possession of the +Corresponding Source of the work from the predecessor in interest, if +the predecessor has it or can get it with reasonable efforts. + +You may not impose any further restrictions on the exercise of the +rights granted or affirmed under this License. For example, you may +not impose a license fee, royalty, or other charge for exercise of +rights granted under this License, and you may not initiate litigation +(including a cross-claim or counterclaim in a lawsuit) alleging that +any patent claim is infringed by making, using, selling, offering for +sale, or importing the Program or any portion of it. + +11. Patents. + +A "contributor" is a copyright holder who authorizes use under this +License of the Program or a work on which the Program is based. The +work thus licensed is called the contributor's "contributor version". + +A contributor's "essential patent claims" are all patent claims +owned or controlled by the contributor, whether already acquired or +hereafter acquired, that would be infringed by some manner, permitted +by this License, of making, using, or selling its contributor version, +but do not include claims that would be infringed only as a +consequence of further modification of the contributor version. For +purposes of this definition, "control" includes the right to grant +patent sublicenses in a manner consistent with the requirements of +this License. + +Each contributor grants you a non-exclusive, worldwide, royalty-free +patent license under the contributor's essential patent claims, to +make, use, sell, offer for sale, import and otherwise run, modify and +propagate the contents of its contributor version. + +In the following three paragraphs, a "patent license" is any express +agreement or commitment, however denominated, not to enforce a patent +(such as an express permission to practice a patent or covenant not to +sue for patent infringement). To "grant" such a patent license to a +party means to make such an agreement or commitment not to enforce a +patent against the party. + +If you convey a covered work, knowingly relying on a patent license, +and the Corresponding Source of the work is not available for anyone +to copy, free of charge and under the terms of this License, through a +publicly available network server or other readily accessible means, +then you must either (1) cause the Corresponding Source to be so +available, or (2) arrange to deprive yourself of the benefit of the +patent license for this particular work, or (3) arrange, in a manner +consistent with the requirements of this License, to extend the patent +license to downstream recipients. "Knowingly relying" means you have +actual knowledge that, but for the patent license, your conveying the +covered work in a country, or your recipient's use of the covered work +in a country, would infringe one or more identifiable patents in that +country that you have reason to believe are valid. + +If, pursuant to or in connection with a single transaction or +arrangement, you convey, or propagate by procuring conveyance of, a +covered work, and grant a patent license to some of the parties +receiving the covered work authorizing them to use, propagate, modify +or convey a specific copy of the covered work, then the patent license +you grant is automatically extended to all recipients of the covered +work and works based on it. + +A patent license is "discriminatory" if it does not include within +the scope of its coverage, prohibits the exercise of, or is +conditioned on the non-exercise of one or more of the rights that are +specifically granted under this License. You may not convey a covered +work if you are a party to an arrangement with a third party that is +in the business of distributing software, under which you make payment +to the third party based on the extent of your activity of conveying +the work, and under which the third party grants, to any of the +parties who would receive the covered work from you, a discriminatory +patent license (a) in connection with copies of the covered work +conveyed by you (or copies made from those copies), or (b) primarily +for and in connection with specific products or compilations that +contain the covered work, unless you entered into that arrangement, +or that patent license was granted, prior to 28 March 2007. + +Nothing in this License shall be construed as excluding or limiting +any implied license or other defenses to infringement that may +otherwise be available to you under applicable patent law. + +12. No Surrender of Others' Freedom. + +If conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot convey a +covered work so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you may +not convey it at all. For example, if you agree to terms that obligate you +to collect a royalty for further conveying from those to whom you convey +the Program, the only way you could satisfy both those terms and this +License would be to refrain entirely from conveying the Program. + +13. Use with the GNU Affero General Public License. + +Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU Affero General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the special requirements of the GNU Affero General Public License, +section 13, concerning interaction through a network will apply to the +combination as such. + +14. Revised Versions of this License. + +The Free Software Foundation may publish revised and/or new versions of +the GNU General Public License from time to time. Such new versions will +be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + +Each version is given a distinguishing version number. If the +Program specifies that a certain numbered version of the GNU General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU General Public License, you may choose any version ever published +by the Free Software Foundation. + +If the Program specifies that a proxy can decide which future +versions of the GNU General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + +Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + +15. Disclaimer of Warranty. + +THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + +16. Limitation of Liability. + +IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + +17. Interpretation of Sections 15 and 16. + +If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + +If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + +To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + +If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + +You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + +The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/pyproject.toml b/pyproject.toml index 1afdec2..fc7ca38 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,7 +16,8 @@ classifiers = [ "Programming Language :: Python :: 3", "Operating System :: OS Independent", ] -license = "MIT" # https://choosealicense.com/ +# Also update LICENSE file if you pick another one +license = "GPL-3.0-or-later" # https://choosealicense.com/licenses/gpl-3.0/ # # add dependencies here: (use one of the two) # dependencies = ["numpy", "pandas", "scipy", "matplotlib", "seaborn"] # use requirements.txt instead of pyproject.toml for dependencies From b4e341295d4415d973f64423178d33883a42595b Mon Sep 17 00:00:00 2001 From: Henry Webel Date: Thu, 25 Sep 2025 13:00:28 +0200 Subject: [PATCH 9/9] create a minimal cli interface for template (#13) * :sparkles: create a minimal cli interface example * :memo: document command line entry point --- developing.md | 22 ++++++++++++++++++++++ pyproject.toml | 6 ++++++ src/python_package/cli.py | 17 +++++++++++++++++ 3 files changed, 45 insertions(+) create mode 100644 src/python_package/cli.py diff --git a/developing.md b/developing.md index d5424c9..4fce3ee 100644 --- a/developing.md +++ b/developing.md @@ -142,6 +142,28 @@ Please also update the project URL to your project: "Homepage" = "https://github.com/RasmussenLab/python_package" ``` +The template also sets a command line script entry point, which allows to run +the function `main` in the `mockup` module of the package as a command line script, +wrapping the `hello_world` function from the `mockup` module. +The template uses the standard library [argparse](https://docs.python.org/3/library/argparse.html) +module to parse parameters from the command line and creates a basic interface. + +```toml +# Script entry points, i.e. command line commands available after installing the package +# e.g. implemented using argparse +# Then you can type: `python-package-hello -h` in the terminal +[project.scripts] +python-package-hello = "python_package.cli:main" +``` + +You can therefore run the command line script using: + +```bash +python-package-hello -h +# print hello world 3 times +python-package-hello -n 3 +``` + ## Source directory layout of the package The source code of the package is located in the `src` directory, to have a project diff --git a/pyproject.toml b/pyproject.toml index fc7ca38..ec501b0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -68,3 +68,9 @@ requires = ["setuptools>=64", "setuptools_scm>=8"] [tool.isort] profile = "black" + +# Script entry points, i.e. command line commands available after installing the package +# e.g. implemented using argparse +# Then you can type: `python-package-hello -h` in the terminal +[project.scripts] +python-package-hello = "python_package.cli:main" diff --git a/src/python_package/cli.py b/src/python_package/cli.py new file mode 100644 index 0000000..dd1d220 --- /dev/null +++ b/src/python_package/cli.py @@ -0,0 +1,17 @@ +import argparse + +from .mockup import hello_world + + +def main(): + parser = argparse.ArgumentParser(description="Python Package CLI") + parser.add_argument( + "-n", + "--repeat", + type=int, + default=1, + help="Number of times to repeat the greeting hello world", + ) + args = parser.parse_args() + msg = hello_world(args.repeat) + print(msg)