diff --git a/.github/workflows/cicd.yml b/.github/workflows/cicd.yml index 3d485ce..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 @@ -106,6 +107,8 @@ jobs: publish: name: Publish package if: startsWith(github.ref, 'refs/tags') + permissions: + id-token: write needs: - format - lint 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/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. 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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/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/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/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/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 7a59c2e..ec501b0 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 @@ -17,7 +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 @@ -44,13 +44,10 @@ docs = [ "sphinx-copybutton", ] # local development options -dev = ["black[jupyter]", "ruff", "pytest"] +dev = ["black[jupyter]", "ruff", "pytest", "isort", "jupytext"] -# 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 +55,8 @@ 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" @@ -69,3 +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/__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/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) 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..295cb72 100644 --- a/tests/test_mockup.py +++ b/tests/test_mockup.py @@ -1,7 +1,32 @@ -from python_package import hello_world +import pytest + +from python_package import hello_world, saved_world 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