diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 0000000..71d8479 --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,29 @@ +// For format details, see https://aka.ms/devcontainer.json. For config options, see the +// README at: https://github.com/devcontainers/templates/tree/main/src/python +{ + "name": "python-package", + // Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile + "image": "mcr.microsoft.com/devcontainers/python:1-3.11-bullseye", + "runArgs": [ + // avoid UID/GID remapping under rootless Podman + "--userns=keep-id" + ], + "features": {}, + + // Use 'postCreateCommand' to run commands after the container is created. + "postCreateCommand": "./.devcontainer/postCreateCommand.sh", + + // Configure tool-specific properties. + "customizations": { + "vscode": { + "extensions": ["ms-python.python", "editorconfig.editorconfig"], + "settings": { + "python.testing.pytestArgs": ["tests"], + "python.testing.unittestEnabled": false, + "python.testing.pytestEnabled": true, + "python.defaultInterpreterPath": "/workspaces/python-package/.venv/bin/python", + "python.testing.pytestPath": "/workspaces/python-package/.venv/bin/pytest" + } + } + } +} diff --git a/.devcontainer/postCreateCommand.sh b/.devcontainer/postCreateCommand.sh new file mode 100755 index 0000000..0f40854 --- /dev/null +++ b/.devcontainer/postCreateCommand.sh @@ -0,0 +1,10 @@ +#! /usr/bin/env bash + +# Install uv +curl -LsSf https://astral.sh/uv/install.sh | sh + +# Install Dependencies +uv sync + +# Install pre-commit hooks +uv run pre-commit install --install-hooks diff --git a/.github/actions/setup-python-env/action.yml b/.github/actions/setup-python-env/action.yml new file mode 100644 index 0000000..7e8f6b3 --- /dev/null +++ b/.github/actions/setup-python-env/action.yml @@ -0,0 +1,30 @@ +name: "Setup Python Environment" +description: "Set up Python environment for the given Python version" + +inputs: + python-version: + description: "Python version to use" + required: true + default: "3.12" + uv-version: + description: "uv version to use" + required: true + default: "0.6.14" + +runs: + using: "composite" + steps: + - uses: actions/setup-python@v5 + with: + python-version: ${{ inputs.python-version }} + + - name: Install uv + uses: astral-sh/setup-uv@v6 + with: + version: ${{ inputs.uv-version }} + enable-cache: 'true' + cache-suffix: ${{ matrix.python-version }} + + - name: Install Python dependencies + run: uv sync --frozen + shell: bash diff --git a/.github/workflows/labels.yml b/.github/workflows/labels.yml index 52c578c..188466c 100644 --- a/.github/workflows/labels.yml +++ b/.github/workflows/labels.yml @@ -26,4 +26,4 @@ jobs: https://raw.githubusercontent.com/biocommons/.github/main/etc/labels.yml .github/labels.yml - delete-other-labels: false \ No newline at end of file + delete-other-labels: false diff --git a/.github/workflows/python-ci-cd.yml b/.github/workflows/python-ci-cd.yml new file mode 100644 index 0000000..e46e311 --- /dev/null +++ b/.github/workflows/python-ci-cd.yml @@ -0,0 +1,22 @@ +name: Python CI/CD +permissions: + contents: write + id-token: write + +on: + pull_request: + branches: [ "main" ] + push: + tags: + - "[0-9]+.[0-9]+.[0-9]+" + +jobs: + python-ci-cd: + name: python-ci-cd + permissions: + contents: write + id-token: write + uses: biocommons/.github/.github/workflows/python-ci-cd.yml@main + with: + run-deploy: ${{ github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v') }} + secrets: inherit diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml deleted file mode 100644 index e511102..0000000 --- a/.github/workflows/python-package.yml +++ /dev/null @@ -1,139 +0,0 @@ -# https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/ -name: Python package - -on: - push: - tags: - - '[0-9]+.[0-9]+.[0-9]+' # release - - '[0-9]+.[0-9]+.[0-9]+a[0-9]+' # alpha - - '[0-9]+.[0-9]+.[0-9]+b[0-9]+' # beta - - '[0-9]+.[0-9]+.[0-9]+rc[0-9]+' # release candidate - - '[0-9]+.[0-9]+.[0-9]+.dev[0-9]+' # dev (not semver compliant) - - '[0-9]+.[0-9]+.[0-9]+.post[0-9]+' # post (not semver compliant) - pull_request: - -jobs: - cqa: - runs-on: ubuntu-latest - - steps: - - uses: actions/checkout@v4 - - - uses: awalsh128/cache-apt-pkgs-action@latest - with: - packages: zsh - version: 1.0 - - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: "3.12" - cache: pip - cache-dependency-path: '**/pyproject.yaml' - - - name: Install dev dependencies - run: | - python -m pip install --upgrade pip - pip install --use-deprecated=legacy-resolver '.[dev]' - - - name: Lint with Ruff - run: | - ruff check . - - - name: Format check with Ruff - run: | - ruff format --check . - - test: - runs-on: ubuntu-latest - - strategy: - fail-fast: false - matrix: - python-version: ["3.10", "3.11", "3.12"] - - steps: - - uses: actions/checkout@v4 - - - uses: awalsh128/cache-apt-pkgs-action@latest - with: - packages: zsh - version: 1.0 - - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - cache: pip - cache-dependency-path: '**/setup.cfg' - - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install --use-deprecated=legacy-resolver '.[tests]' - - - name: Test with pytest - run: | - make test - - - name: Upload coverage data to Codecov - run: | - # Verify integrity of codecov download - curl https://uploader.codecov.io/verification.gpg | gpg --no-default-keyring --keyring trustedkeys.gpg --import - curl -Os https://uploader.codecov.io/latest/linux/codecov - curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM - curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM.sig - gpgv codecov.SHA256SUM.sig codecov.SHA256SUM - shasum -a 256 -c codecov.SHA256SUM - # Upload coverage report - chmod +x codecov - ./codecov - - build: - name: Build distribution - if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') - runs-on: ubuntu-latest - needs: - - cqa - - test - steps: - - uses: actions/checkout@v4 - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: "3.12" - cache: pip - cache-dependency-path: '**/setup.cfg' - - name: Install pypa/build - run: >- - python3 -m - pip install - build - --user - - name: Build a binary wheel and a source tarball - run: python3 -m build - - name: Store the distribution packages - uses: actions/upload-artifact@v4 - with: - name: python-package-distributions - path: dist/ - - publish-to-pypi: - name: >- - Publish Python distribution to PyPI - needs: - - build - runs-on: ubuntu-latest - environment: - name: pypi - url: https://pypi.org/p/biocommons.example - permissions: - id-token: write # IMPORTANT: mandatory for trusted publishing - steps: - - name: Download all the dists - uses: actions/download-artifact@v4 - with: - name: python-package-distributions - path: dist/ - - name: Publish distribution to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/.github/workflows/stale.yml b/.github/workflows/stale.yml index d7a6cd4..db9f8bc 100644 --- a/.github/workflows/stale.yml +++ b/.github/workflows/stale.yml @@ -1,5 +1,3 @@ -# https://github.com/actions/stale - name: 'Close stale issues and PRs' on: workflow_dispatch: diff --git a/.github/workflows/validate-codecov-config.yml b/.github/workflows/validate-codecov-config.yml new file mode 100644 index 0000000..1e653f5 --- /dev/null +++ b/.github/workflows/validate-codecov-config.yml @@ -0,0 +1,17 @@ +name: validate-codecov-config + +on: + pull_request: + paths: [codecov.yaml] + push: + branches: [main] + +jobs: + validate-codecov-config: + runs-on: ubuntu-latest + permissions: + contents: read + steps: + - uses: actions/checkout@v4 + - name: Validate codecov configuration + run: curl -sSL --fail-with-body --data-binary @codecov.yaml https://codecov.io/validate diff --git a/.gitignore b/.gitignore index f26bdb1..2604f7b 100644 --- a/.gitignore +++ b/.gitignore @@ -1,143 +1,92 @@ -# Byte-compiled / optimized / DLL files +__marimo__/ __pycache__/ -*.py[cod] -*$py.class - -# C extensions -*.so - -# Distribution / packaging +__pypackages__/ +.abstra/ +.cache +.coverage +.coverage.* +.cursorignore +.cursorindexingignore +.dmypy.json +.DS_Store +.eggs/ +.env +.envrc +.hypothesis/ +.installed.cfg +.ipynb_checkpoints +.mypy_cache/ +.nox/ +.pdm-build/ +.pdm-python +.pixi +.pybuilder/ +.pypirc +.pyre/ +.pytest_cache/ .Python +.pytype/ +.ropeproject +.ruff_cache/ +.scrapy +.spyderproject +.spyproject +.tox/ +.venv +.vscode +.webassets-cache +*.cover +*.egg +*.egg-info/ +*.log +*.manifest +*.mo +*.pot +*.py.cover +*.py[codz] +*.sage.py +*.so +*.spec +*.sqlite3 +*.sqlite3-journal +*~ +*$py.class +/site +archive build/ +celerybeat-schedule +celerybeat.pid +cover/ +coverage.xml +cython_debug/ develop-eggs/ dist/ +dmypy.json +docs/_build/ +docs/source downloads/ eggs/ -.eggs/ +env.bak/ +env/ +ENV/ +htmlcov/ +instance/ +ipython_config.py lib/ lib64/ +local_settings.py +MANIFEST +marimo/_lsp/ +marimo/_static/ +nosetests.xml parts/ +pip-delete-this-directory.txt +pip-log.txt +profile_default/ sdist/ -var/ -wheels/ share/python-wheels/ -*.egg-info/ -.installed.cfg -*.egg -MANIFEST - -# PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. -*.manifest -*.spec - -# Installer logs -pip-log.txt -pip-delete-this-directory.txt - -# Unit test / coverage reports -htmlcov/ -.tox/ -.nox/ -.coverage -.coverage.* -.cache -nosetests.xml -coverage.xml -*.cover -*.py,cover -.hypothesis/ -.pytest_cache/ -cover/ - -# Translations -*.mo -*.pot - -# Django stuff: -*.log -local_settings.py -*.sqlite3 -db.sqlite3-journal - -# Flask stuff: -instance/ -.webassets-cache - -# Scrapy stuff: -.scrapy - -# Sphinx documentation -docs/_build/ - -# PyBuilder -.pybuilder/ target/ - -# Jupyter Notebook -.ipynb_checkpoints - -# IPython -profile_default/ -ipython_config.py - -# package/env management -.python-version -.env -.venv -env/ +var/ +venv.bak/ venv/ -ENV/ -*.bak -Pipfile.lock -poetry.lock -pdm.lock -.pdm.toml -.pdm-python -.pdm-build/ -uv.lock - -# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm -__pypackages__/ - -# Celery stuff -celerybeat-schedule -celerybeat.pid - -# SageMath parsed files -*.sage.py - -# Spyder project settings -.spyderproject -.spyproject - -# Rope project settings -.ropeproject - -# mkdocs documentation -/site - -# mypy -.mypy_cache/ -.dmypy.json -dmypy.json - -# Pyre type checker -.pyre/ - -# pytype static type analyzer -.pytype/ - -# Cython debug symbols -cython_debug/ - -# IDEs -.idea/ -.vscode - -# misc -*.orig -archive -*~ -**/.DS_Store +wheels/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f60689b..e42ff48 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,7 +1,22 @@ repos: -- repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.4.4 - hooks: - - id: ruff - - id: ruff-format - args: [ --check ] + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: "v5.0.0" + hooks: + - id: check-case-conflict + - id: check-merge-conflict + - id: check-toml + - id: check-yaml + - id: check-json + exclude: ^.devcontainer/devcontainer.json + - id: pretty-format-json + exclude: ^.devcontainer/devcontainer.json + args: [--autofix, --no-sort-keys] + - id: end-of-file-fixer + - id: trailing-whitespace + + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: "v0.12.7" + hooks: + - id: ruff-check + args: [ --exit-non-zero-on-fix ] + - id: ruff-format diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..de9287f --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,6 @@ +Thank you for your interest in contributing to the biocommons community! +Contributions are welcome and greatly appreciated. There are many types of +contributions and you don't need to be a developer! + +To get started, see https://biocommons.org/contributing/. We look forward to +hearing from you! diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..5bbe636 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,21 @@ +# Install uv +FROM python:3.12-slim +COPY --from=ghcr.io/astral-sh/uv:latest /uv /bin/uv + +# Change the working directory to the `app` directory +WORKDIR /app + +# Copy the lockfile and `pyproject.toml` into the image +COPY uv.lock /app/uv.lock +COPY pyproject.toml /app/pyproject.toml + +# Install dependencies +RUN uv sync --frozen --no-install-project + +# Copy the project into the image +COPY . /app + +# Sync the project +RUN uv sync --frozen + +CMD [ "python", "python_package/foo.py" ] diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..d645695 --- /dev/null +++ b/LICENSE @@ -0,0 +1,202 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/Makefile b/Makefile index bbcce4d..90f6fa2 100644 --- a/Makefile +++ b/Makefile @@ -1,154 +1,54 @@ -# Makefile for Python project - -.DELETE_ON_ERROR: -.PHONY: FORCE -.PRECIOUS: -.SUFFIXES: - -ifeq ("","$(shell command -v zsh)") -$(error "zsh not found; you must install zsh first") -endif - -SHELL:=zsh -eu -o pipefail -o null_glob -SELF:=$(firstword $(MAKEFILE_LIST)) - -VE_DIR=venv - -TEST_DIRS:=tests -DOC_TESTS:=src ./README.md - - -############################################################################ -#= BASIC USAGE -default: help - -#=> help -- display this help message -help: - @sbin/makefile-extract-documentation "${SELF}" - - -############################################################################ -#= SETUP, INSTALLATION, PACKAGING - -#=> devready: create venv, install prerequisites, install pkg in develop mode -.PHONY: devready -devready: - make ${VE_DIR} && source ${VE_DIR}/bin/activate && make develop - @echo '#################################################################################' - @echo '### Do not forget to `source ${VE_DIR}/bin/activate` to use this environment ###' - @echo '#################################################################################' - -#=> venv: make a Python 3 virtual environment -${VE_DIR}: - python3 --version - python3 -mvenv $@; \ - source $@/bin/activate; \ - python3 -m ensurepip --upgrade; \ - pip install --upgrade pip setuptools wheel - -#=> develop: install package in develop mode -.PHONY: develop -develop: - pip install -e ".[dev,tests]" - pre-commit install - -#=> install: install package .PHONY: install -install: - pip install "." +install: ## Install the virtual environment and install the pre-commit hooks + @echo "🚀 Creating virtual environment using uv" + @uv sync + @uv run pre-commit install + +.PHONY: check +check: ## Run code quality tools. + @echo "🚀 Checking lock file consistency with 'pyproject.toml'" + @uv lock --locked + @echo "🚀 Linting code: Running pre-commit" + @uv run pre-commit run -a + #@echo "🚀 Static type checking: Running ty" + #@uv run ty check + @echo "🚀 Checking for obsolete dependencies: Running deptry" + @uv run deptry src + +.PHONY: test +test: ## Test the code with pytest + @echo "🚀 Testing code: Running pytest" + @uv run python -m pytest # --cov --cov-config=pyproject.toml --cov-report=xml -#=> build: make sdist and wheel .PHONY: build -build: %: - python -m build - - -############################################################################ -#= TESTING -# see test configuration in setup.cfg - -#=> test: execute tests -#=> test-code: test code (including embedded doctests) -#=> test-docs: test example code in docs -.PHONY: test test-code test-docs -test: - pytest --cov src -test-docs: - pytest docs -test-code: - pytest src -test-%: - pytest -m '$*' src +build: clean-build ## Build wheel file + @echo "🚀 Creating wheel file" + @uvx --from build pyproject-build --installer uv -#=> tox -- run all tox tests -tox: - tox +.PHONY: clean-build +clean-build: ## Clean build artifacts + @echo "🚀 Removing build artifacts" + @uv run python -c "import shutil; import os; shutil.rmtree('dist') if os.path.exists('dist') else None" -#=> cqa: execute code quality tests -cqa: - ruff format --check - ruff check +.PHONY: publish +publish: ## Publish a release to PyPI. + @echo "🚀 Publishing." + @uvx twine upload --repository-url https://upload.pypi.org/legacy/ dist/* -#=> reformat: reformat code -.PHONY: reformat -reformat: - ruff check --fix - ruff format +.PHONY: build-and-publish +build-and-publish: build publish ## Build and publish. -############################################################################ -#= UTILITY TARGETS +.PHONY: docs-test +docs-test: ## Test if documentation can be built without warnings or errors + @uv run mkdocs build -s -#=> rename: rename files and substitute content for new repo name -.PHONY: rename -rename: - ./sbin/rename-package - -#=> docs -- make sphinx docs .PHONY: docs -docs: develop - # RTD makes json. Build here to ensure that it works. - make -C doc html json - -############################################################################ -#= CLEANUP - -#=> clean: remove temporary and backup files -.PHONY: clean -clean: - rm -frv **/*~ **/*.bak +docs: ## Build and serve the documentation + @uv run mkdocs serve -#=> cleaner: remove files and directories that are easily rebuilt -.PHONY: cleaner -cleaner: clean - rm -frv .cache build dist docs/_build - rm -frv **/__pycache__ - rm -frv **/*.egg-info - rm -frv **/*.pyc - rm -frv **/*.orig - rm -frv **/*.rej - -#=> cleanest: remove files and directories that require more time/network fetches to rebuild -.PHONY: cleanest -cleanest: cleaner - rm -frv .eggs .tox venv - -#=> distclean: remove untracked files and other detritus -.PHONY: distclean -distclean: cleanest - git clean -df +.PHONY: help +help: + @uv run python -c "import re; \ + [[print(f'\033[36m{m[0]:<20}\033[0m {m[1]}') for m in re.findall(r'^([a-zA-Z_-]+):.*?## (.*)$$', open(makefile).read(), re.M)] for makefile in ('$(MAKEFILE_LIST)').strip().split()]" -## -## Copyright 2023 Source Code Committers -## -## Licensed under the Apache License, Version 2.0 (the "License"); -## you may not use this file except in compliance with the License. -## You may obtain a copy of the License at -## -## http://www.apache.org/licenses/LICENSE-2.0 -## -## Unless required by applicable law or agreed to in writing, software -## distributed under the License is distributed on an "AS IS" BASIS, -## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -## See the License for the specific language governing permissions and -## limitations under the License. -## +.DEFAULT_GOAL := help diff --git a/README.md b/README.md index 212e681..fa7ffa4 100644 --- a/README.md +++ b/README.md @@ -1,83 +1,74 @@ -# biocommons.example Test Package +# python-package -[![codecov](https://codecov.io/gh/biocommons/biocommons.example/graph/badge.svg?token=CCUMQQV5R6)](https://codecov.io/gh/biocommons/biocommons.example) +[![Release](https://img.shields.io/github/v/release/biocommons/python-package)](https://img.shields.io/github/v/release/biocommons/python-package) +[![Build status](https://img.shields.io/github/actions/workflow/status/biocommons/python-package/main.yml?branch=main)](https://github.com/biocommons/python-package/actions/workflows/main.yml?query=branch%3Amain) +[![codecov](https://codecov.io/gh/biocommons/python-package/branch/main/graph/badge.svg)](https://codecov.io/gh/biocommons/python-package) +[![Commit activity](https://img.shields.io/github/commit-activity/m/biocommons/python-package)](https://img.shields.io/github/commit-activity/m/biocommons/python-package) +[![License](https://img.shields.io/github/license/biocommons/python-package)](https://img.shields.io/github/license/biocommons/python-package) -This repo provides a template for biocommons Python packages. Here's how to use it: +Package Description -1. Click the [Use this template](https://github.com/biocommons/example/generate) - button. Name the new repo like "biocommons.something". -1. Clone your repo locally. -1. In the repo, type `make rename`. The new name will be chosen based on the repo name. -1. Remove this header. -1. Commit and push. +- **Github repository**: +- **Documentation** -## Installation +## Getting started with your project -To install from pypi: ```pip install biocommons.example``` +### 1. Create a New Repository -## Developer Setup +First, create a repository on GitHub with the same name as this project, and then run the following commands: -Developers must install zsh, which is required by the Makefile. zsh is included by default in MacOS, and is readily available on all modern Linux distributions. +```bash +git init -b main +git add . +git commit -m "init commit" +git remote add origin git@github.com:biocommons/python-package.git +git push -u origin main +``` -Setup like this: +### 2. Set Up Your Development Environment - make devready - source venv/bin/activate +Then, install the environment and the pre-commit hooks with -Code reformatting: +```bash +make install +``` - make reformat +This will also generate your `uv.lock` file -Install pre-commit hook: +### 3. Run the pre-commit hooks - # included in `make devready`, not necessary for new installations - pre-commit install +Initially, the CI/CD pipeline might be failing due to formatting issues. To resolve those run: -Test: +```bash +uv run pre-commit run -a +``` - make test # for current environment - make tox # for all supported versions +### 4. Commit the changes -Build: +Lastly, commit the changes made by the two steps above to your repository. - git tag 0.0.0 - make build +```bash +git add . +git commit -m 'Fix formatting issues' +git push origin main +``` -Try it: +You are now ready to start development on your project! +The CI/CD pipeline will be triggered when you open a pull request, merge to main, or when you create a new release. - $ python3 -m biocommons.example - Marvin says: - There's only one life-form as intelligent as me within thirty parsecs... +To finalize the set-up for publishing to PyPI, see [here](https://fpgmaas.github.io/cookiecutter-uv/features/publishing/#set-up-for-pypi). +For activating the automatic documentation with MkDocs, see [here](https://fpgmaas.github.io/cookiecutter-uv/features/mkdocs/#enabling-the-documentation-on-github). +To enable the code coverage reports, see [here](https://fpgmaas.github.io/cookiecutter-uv/features/codecov/). - $ marvin-quote - Marvin says: - You think you've got problems? What are you supposed to do if you... +## Releasing a new version - $ ipython - >>> from biocommons.example import __version__, get_quote_from_marvin - >>> __version__ - '0.1.dev8+gd5519a8.d20211123' - >>> get_quote() - "The first ten million years were the worst, ... +- Create an API Token on [PyPI](https://pypi.org/). +- Add the API Token to your projects secrets with the name `PYPI_TOKEN` by visiting [this page](https://github.com/biocommons/python-package/settings/secrets/actions/new). +- Create a [new release](https://github.com/biocommons/python-package/releases/new) on Github. +- Create a new tag in the form `*.*.*`. +For more details, see [here](https://fpgmaas.github.io/cookiecutter-uv/features/cicd/#how-to-trigger-a-release). -# Features +--- -## Code structure and features - -* Modern pyproject.toml with setuptools -* Versioning based on git tag (only) -* Easy development setup -* Support for namespaces -* Testing with coverage using pytest; tests may be in `tests/`, embedded in the package, and in doc strings -* Examples for logging and package data -* Command-line with argument parsing with argparse - -## DevOps - -* Quality tools: Code linting and reformatting with Ruff -* GitHub Actions for testing and packaging - -## ToDo - -* Add devcontainer support +Repository initiated with [fpgmaas/cookiecutter-uv](https://github.com/fpgmaas/cookiecutter-uv). diff --git a/TODO b/TODO new file mode 100644 index 0000000..85869d3 --- /dev/null +++ b/TODO @@ -0,0 +1,9 @@ +- [x] use toml-sort to keep pyproject.toml in a canonical order + +- [ ] merge old and new makefiles + +- [ ] make github actions/workflows use makefile targets + +- [x] mv python ci/cd to biocommons/.github + +- [ ] release github actions / update branch spec in .github/workflows diff --git a/codecov.yaml b/codecov.yaml new file mode 100644 index 0000000..058cfb7 --- /dev/null +++ b/codecov.yaml @@ -0,0 +1,9 @@ +coverage: + range: 70..100 + round: down + precision: 1 + status: + project: + default: + target: 90% + threshold: 0.5% diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..51671c3 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,8 @@ +# python-package + +[![Release](https://img.shields.io/github/v/release/biocommons/python-package)](https://img.shields.io/github/v/release/biocommons/python-package) +[![Build status](https://img.shields.io/github/actions/workflow/status/biocommons/python-package/main.yml?branch=main)](https://github.com/biocommons/python-package/actions/workflows/main.yml?query=branch%3Amain) +[![Commit activity](https://img.shields.io/github/commit-activity/m/biocommons/python-package)](https://img.shields.io/github/commit-activity/m/biocommons/python-package) +[![License](https://img.shields.io/github/license/biocommons/python-package)](https://img.shields.io/github/license/biocommons/python-package) + +Package Description diff --git a/docs/modules.md b/docs/modules.md new file mode 100644 index 0000000..918cdf4 --- /dev/null +++ b/docs/modules.md @@ -0,0 +1 @@ +::: biocommons.example.marvin diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000..975a025 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,52 @@ +site_name: python-package +repo_url: https://github.com/biocommons/python-package +site_url: https://biocommons.github.io/python-package +site_description: Package Description +site_author: Biocommons Contributors +edit_uri: edit/main/docs/ +repo_name: biocommons/python-package +copyright: Maintained by biocommons. + +nav: + - Home: index.md + - Modules: modules.md +plugins: + - search + - mkdocstrings: + handlers: + python: + paths: ["src/biocommons/example"] +theme: + name: material + feature: + tabs: true + palette: + - media: "(prefers-color-scheme: light)" + scheme: default + primary: white + accent: deep orange + toggle: + icon: material/brightness-7 + name: Switch to dark mode + - media: "(prefers-color-scheme: dark)" + scheme: slate + primary: black + accent: deep orange + toggle: + icon: material/brightness-4 + name: Switch to light mode + icon: + repo: fontawesome/brands/github + +extra: + social: + - icon: fontawesome/brands/github + link: https://github.com/biocommons/python-package + - icon: fontawesome/brands/python + link: https://pypi.org/project/python-package + +markdown_extensions: + - toc: + permalink: true + - pymdownx.arithmatex: + generic: true diff --git a/orig/Makefile b/orig/Makefile new file mode 100644 index 0000000..bbcce4d --- /dev/null +++ b/orig/Makefile @@ -0,0 +1,154 @@ +# Makefile for Python project + +.DELETE_ON_ERROR: +.PHONY: FORCE +.PRECIOUS: +.SUFFIXES: + +ifeq ("","$(shell command -v zsh)") +$(error "zsh not found; you must install zsh first") +endif + +SHELL:=zsh -eu -o pipefail -o null_glob +SELF:=$(firstword $(MAKEFILE_LIST)) + +VE_DIR=venv + +TEST_DIRS:=tests +DOC_TESTS:=src ./README.md + + +############################################################################ +#= BASIC USAGE +default: help + +#=> help -- display this help message +help: + @sbin/makefile-extract-documentation "${SELF}" + + +############################################################################ +#= SETUP, INSTALLATION, PACKAGING + +#=> devready: create venv, install prerequisites, install pkg in develop mode +.PHONY: devready +devready: + make ${VE_DIR} && source ${VE_DIR}/bin/activate && make develop + @echo '#################################################################################' + @echo '### Do not forget to `source ${VE_DIR}/bin/activate` to use this environment ###' + @echo '#################################################################################' + +#=> venv: make a Python 3 virtual environment +${VE_DIR}: + python3 --version + python3 -mvenv $@; \ + source $@/bin/activate; \ + python3 -m ensurepip --upgrade; \ + pip install --upgrade pip setuptools wheel + +#=> develop: install package in develop mode +.PHONY: develop +develop: + pip install -e ".[dev,tests]" + pre-commit install + +#=> install: install package +.PHONY: install +install: + pip install "." + +#=> build: make sdist and wheel +.PHONY: build +build: %: + python -m build + + +############################################################################ +#= TESTING +# see test configuration in setup.cfg + +#=> test: execute tests +#=> test-code: test code (including embedded doctests) +#=> test-docs: test example code in docs +.PHONY: test test-code test-docs +test: + pytest --cov src +test-docs: + pytest docs +test-code: + pytest src +test-%: + pytest -m '$*' src + +#=> tox -- run all tox tests +tox: + tox + +#=> cqa: execute code quality tests +cqa: + ruff format --check + ruff check + +#=> reformat: reformat code +.PHONY: reformat +reformat: + ruff check --fix + ruff format + +############################################################################ +#= UTILITY TARGETS + +#=> rename: rename files and substitute content for new repo name +.PHONY: rename +rename: + ./sbin/rename-package + +#=> docs -- make sphinx docs +.PHONY: docs +docs: develop + # RTD makes json. Build here to ensure that it works. + make -C doc html json + +############################################################################ +#= CLEANUP + +#=> clean: remove temporary and backup files +.PHONY: clean +clean: + rm -frv **/*~ **/*.bak + +#=> cleaner: remove files and directories that are easily rebuilt +.PHONY: cleaner +cleaner: clean + rm -frv .cache build dist docs/_build + rm -frv **/__pycache__ + rm -frv **/*.egg-info + rm -frv **/*.pyc + rm -frv **/*.orig + rm -frv **/*.rej + +#=> cleanest: remove files and directories that require more time/network fetches to rebuild +.PHONY: cleanest +cleanest: cleaner + rm -frv .eggs .tox venv + +#=> distclean: remove untracked files and other detritus +.PHONY: distclean +distclean: cleanest + git clean -df + +## +## Copyright 2023 Source Code Committers +## +## Licensed under the Apache License, Version 2.0 (the "License"); +## you may not use this file except in compliance with the License. +## You may obtain a copy of the License at +## +## http://www.apache.org/licenses/LICENSE-2.0 +## +## Unless required by applicable law or agreed to in writing, software +## distributed under the License is distributed on an "AS IS" BASIS, +## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +## See the License for the specific language governing permissions and +## limitations under the License. +## diff --git a/orig/README.md b/orig/README.md new file mode 100644 index 0000000..212e681 --- /dev/null +++ b/orig/README.md @@ -0,0 +1,83 @@ +# biocommons.example Test Package + +[![codecov](https://codecov.io/gh/biocommons/biocommons.example/graph/badge.svg?token=CCUMQQV5R6)](https://codecov.io/gh/biocommons/biocommons.example) + +This repo provides a template for biocommons Python packages. Here's how to use it: + +1. Click the [Use this template](https://github.com/biocommons/example/generate) + button. Name the new repo like "biocommons.something". +1. Clone your repo locally. +1. In the repo, type `make rename`. The new name will be chosen based on the repo name. +1. Remove this header. +1. Commit and push. + +## Installation + +To install from pypi: ```pip install biocommons.example``` + +## Developer Setup + +Developers must install zsh, which is required by the Makefile. zsh is included by default in MacOS, and is readily available on all modern Linux distributions. + +Setup like this: + + make devready + source venv/bin/activate + +Code reformatting: + + make reformat + +Install pre-commit hook: + + # included in `make devready`, not necessary for new installations + pre-commit install + +Test: + + make test # for current environment + make tox # for all supported versions + +Build: + + git tag 0.0.0 + make build + +Try it: + + $ python3 -m biocommons.example + Marvin says: + There's only one life-form as intelligent as me within thirty parsecs... + + $ marvin-quote + Marvin says: + You think you've got problems? What are you supposed to do if you... + + $ ipython + >>> from biocommons.example import __version__, get_quote_from_marvin + >>> __version__ + '0.1.dev8+gd5519a8.d20211123' + >>> get_quote() + "The first ten million years were the worst, ... + + +# Features + +## Code structure and features + +* Modern pyproject.toml with setuptools +* Versioning based on git tag (only) +* Easy development setup +* Support for namespaces +* Testing with coverage using pytest; tests may be in `tests/`, embedded in the package, and in doc strings +* Examples for logging and package data +* Command-line with argument parsing with argparse + +## DevOps + +* Quality tools: Code linting and reformatting with Ruff +* GitHub Actions for testing and packaging + +## ToDo + +* Add devcontainer support diff --git a/orig/pyproject.toml b/orig/pyproject.toml new file mode 100644 index 0000000..9e0da19 --- /dev/null +++ b/orig/pyproject.toml @@ -0,0 +1,166 @@ +[project] +name = "biocommons.example" +authors = [ + { name = "biocommons contributors", email = "biocommons-dev@googlegroups.com" }, +] +description = "Example Package" +readme = "README.md" +license = { file = "LICENSE.txt" } +requires-python = ">=3.10" +classifiers = [ + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", +] +dynamic = ["version"] +dependencies = ["coloredlogs ~= 15.0", "pyyaml ~= 6.0"] + +[project.optional-dependencies] +dev = [ + "build ~= 0.8", + "ipython ~= 8.4", + "pre-commit ~= 3.4", + "ruff == 0.4.4", +] +tests = [ + "pytest-cov ~= 4.1", + "pytest ~= 7.1", + "vcrpy", + "tox ~= 4.15", +] +docs = ["mkdocs"] + +[project.scripts] +marvin-quote = "biocommons.example.__main__:main" + +[project.urls] +"Homepage" = "https://github.com/biocommons/biocommons.example" +"Bug Tracker" = "https://github.com/biocommons/biocommons.example/issues" + + +[build-system] +requires = ["setuptools >= 70.1", "setuptools_scm[toml] ~= 8.1"] +build-backend = "setuptools.build_meta" + + +[tool.setuptools] +include-package-data = true + +[tool.setuptools.packages.find] +where = ["src"] +exclude = ["__pycache__", "*.pyc"] +namespaces = true + +[tool.setuptools.package-data] +"*" = ["*.gz", "*.json", "*.yaml"] + + +[tool.setuptools_scm] + + +# https://docs.pytest.org/en/6.2.x/customize.html#pyproject-toml +[tool.pytest.ini_options] +addopts = "-s -v -x --strict-markers -m 'not extra' --doctest-modules --cov=src" +doctest_optionflags = [ + "ALLOW_BYTES", + "ALLOW_UNICODE", + "ELLIPSIS", + "IGNORE_EXCEPTION_DETAIL", + "NORMALIZE_WHITESPACE", +] +markers = [ + "network: tests that require network connectivity", + "slow: slow tests that should be run infrequently", +] + + +[tool.coverage.run] +branch = true +source = ["biocommons.example"] +omit = ["*_test.py", "*/test/*", "*/tests/*"] + + +[tool.coverage.report] +show_missing = true +exclude_lines = [ + # Have to re-enable the standard pragma + "pragma: no cover", + + # Don't complain about missing debug-only code: + "def __repr__", + "if self.debug", + + # Don't complain if tests don't hit defensive assertion code: + "raise AssertionError", + "raise NotImplementedError", + + # Don't complain if non-runnable code isn't run: + "if __name__ == .__main__.:", +] + +[tool.ruff] +src = ["src", "tests"] +line-length = 100 + +[tool.ruff.lint] +select = [ + "F", # https://docs.astral.sh/ruff/rules/#pyflakes-f + "E", + "W", # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w + "I", # https://docs.astral.sh/ruff/rules/#isort-i + "N", # https://docs.astral.sh/ruff/rules/#pep8-naming-n + "UP", # https://docs.astral.sh/ruff/rules/#pyupgrade-up + "YTT", # https://docs.astral.sh/ruff/rules/#flake8-2020-ytt + "S", # https://docs.astral.sh/ruff/rules/#flake8-bandit-s + "B", # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b + "A", # https://docs.astral.sh/ruff/rules/#flake8-builtins-a + "C4", # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4 + "DTZ", # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz + "EM", # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em + "LOG", # https://docs.astral.sh/ruff/rules/#flake8-logging-log + "G", # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g + "PIE", # https://docs.astral.sh/ruff/rules/#flake8-pie-pie + "PT", # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt + "RSE", # https://docs.astral.sh/ruff/rules/#flake8-raise-rse + "RET", # https://docs.astral.sh/ruff/rules/#flake8-return-ret + "SIM", # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim + "ARG", # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg + "PTH", # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth + "PL", # https://docs.astral.sh/ruff/rules/#pylint-pl + "TRY", # https://docs.astral.sh/ruff/rules/#tryceratops-try + "PERF", # https://docs.astral.sh/ruff/rules/#perflint-perf + "RUF", # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf +] +fixable = [ + "F401", + "F541", + "I", + "D", + "UP", + "B", + "C4", + "EM", + "PIE", + "PT", + "RSE", + "RET", + "SIM", + "PERF", + "RUF", +] +ignore = [ + # ignore for compatibility with formatter + "W191", + "E111", + "E114", + "E117", + "S321", + # other + "PLR0913", +] + +[tool.ruff.lint.per-file-ignores] +"tests/*" = ["S101"] diff --git a/orig2/Makefile b/orig2/Makefile new file mode 100644 index 0000000..41d2a74 --- /dev/null +++ b/orig2/Makefile @@ -0,0 +1,165 @@ +# Makefile for Python project + +.DELETE_ON_ERROR: +.PHONY: FORCE +.PRECIOUS: +.SUFFIXES: + +ifeq ("","$(shell command -v zsh)") +$(error "zsh not found; you must install zsh first") +endif + +SHELL:=zsh -eu -o pipefail -o null_glob +SELF:=$(firstword $(MAKEFILE_LIST)) + +VE_DIR:=.venv +PY_VERSION:=3.13 + +SRC_DIRS:=src +TEST_DIRS:=tests +DOC_TESTS:=${SRC_DIRS} # ./README.md + + +############################################################################ +#= BASIC USAGE +default: help + +#=> help -- display this help message +help: + @sbin/makefile-extract-documentation "${SELF}" + + +############################################################################ +#= SETUP, INSTALLATION, PACKAGING + +#=> devready: create venv, install prerequisites, install pkg in develop mode +.PHONY: devready +devready: + make ${VE_DIR} && source ${VE_DIR}/bin/activate && make develop + @echo '#################################################################################' + @echo '### Do not forget to `source ${VE_DIR}/bin/activate` to use this environment ###' + @echo '#################################################################################' + +#=> venv: make a Python 3 virtual environment +${VE_DIR}: + uv venv --python ${PY_VERSION} $@ + +#=> develop: install package in develop mode +.PHONY: develop +develop: + uv sync --extra dev --extra tests + pre-commit install + +#=> install: install package +.PHONY: install +install: + uv sync + +#=> build: make sdist and wheel +.PHONY: build +build: %: + python -m build + + +############################################################################ +#= TESTING +# see test configuration in setup.cfg + +#=> test: execute tests +#=> test-code: test code (including embedded doctests) +#=> test-docs: test example code in docs +.PHONY: test test-code test-docs +test: + pytest --cov ${SRC_DIRS} +test-code: + pytest ${TEST_DIRS} +test-docs: + pytest ${DOC_TESTS} +stest: + pytest -vvv -s -k ${t} +test-%: + pytest -m '$*' ${TEST_DIRS} + +#=> tox -- run all tox tests +tox: + uvx tox + +#=> cqa: execute code quality tests +cqa: + uvx ruff format --check + uvx ruff check + +############################################################################ +#= UTILITY TARGETS + +#=> reformat: reformat code +.PHONY: reformat +reformat: + uvx ruff check --fix + uvx ruff format + +#=> docs -- make sphinx docs +.PHONY: docs +docs: develop + # RTD makes json. Build here to ensure that it works. + make -C docs html json + +############################################################################ +#= CLEANUP + +#=> clean: remove temporary and backup files +.PHONY: clean +clean: + rm -frv **/*~ **/*.bak + -make -C docs $@ + -make -C examples $@ + +#=> cleaner: remove files and directories that are easily rebuilt +.PHONY: cleaner +cleaner: clean + rm -frv .cache build dist docs/_build + rm -frv **/__pycache__ + rm -frv **/*.egg-info + rm -frv **/*.pyc + rm -frv **/*.orig + rm -frv **/*.rej + -make -C docs $@ + -make -C examples $@ + +#=> cleanest: remove files and directories that are more expensive to rebuild +.PHONY: cleanest +cleanest: cleaner + rm -frv .eggs .tox venv + -make -C docs $@ + -make -C examples $@ + +#=> distclean: remove untracked files and other detritus +.PHONY: distclean +distclean: cleanest + git clean -df + + +############################################################################ +#= Repo renamer + +#=> rename: rename files and substitute content for new repo name +.PHONY: rename +rename: + ./sbin/rename-package + + +## +## Copyright 2023 Source Code Committers +## +## Licensed under the Apache License, Version 2.0 (the "License"); +## you may not use this file except in compliance with the License. +## You may obtain a copy of the License at +## +## http://www.apache.org/licenses/LICENSE-2.0 +## +## Unless required by applicable law or agreed to in writing, software +## distributed under the License is distributed on an "AS IS" BASIS, +## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +## See the License for the specific language governing permissions and +## limitations under the License. +## diff --git a/orig2/README.md b/orig2/README.md new file mode 100644 index 0000000..87525ea --- /dev/null +++ b/orig2/README.md @@ -0,0 +1,96 @@ +# biocommons.example Test Package + +[![codecov](https://codecov.io/gh/biocommons/biocommons.example/graph/badge.svg?token=CCUMQQV5R6)](https://codecov.io/gh/biocommons/biocommons.example) + +--- + +This repo provides a template for biocommons Python packages. Here's how to use it: + +1. Click the [Use this template](https://github.com/biocommons/example/generate) + button. Name the new repo like "biocommons.something". +1. Clone your repo locally. +1. In the repo, type `make rename`. The new name will be chosen based on the repo name. +1. Remove this header. +1. Commit and push. + +Delete this section in your generated template. + +--- + +## Installation + +To install from pypi: ```pip install biocommons.example``` + +## Developer Setup + +### Prerequisites + +- [GNU make](https://www.gnu.org/software/make/): Current mechanism for consistent invocation of developer tools. + - Mac: [Install brew](https://brew.sh/), then [install make](https://formulae.brew.sh/formula/make) + - Ubuntu: `sudo apt install make` +- [uv](https://docs.astral.sh/uv/): An extremely fast Python package and project manager, written in Rust. + - All platforms: See the [uv installation instructions](https://docs.astral.sh/uv/getting-started/installation/). +- [zsh](https://www.zsh.org/): Shell used by the Makefile + - Mac: included by default + - Ubuntu: `sudo apt install zsh` + +### One-time developer setup + +Create a Python virtual environment and install dependencies: + + make devready + +### Development + +Activate your environment: + + source venv/bin/activate + +Code reformatting: + + make reformat + +Test: + + make test # for current environment + make tox # for all supported versions + +Build: + + git tag 0.0.0 + make build + +Try it: + + $ python3 -m biocommons.example + Marvin says: + There's only one life-form as intelligent as me within thirty parsecs... + + $ marvin-quote + Marvin says: + You think you've got problems? What are you supposed to do if you... + + $ ipython + >>> from biocommons.example import __version__, get_quote_from_marvin + >>> __version__ + '0.1.dev8+gd5519a8.d20211123' + >>> get_quote() + "The first ten million years were the worst, ... + + +# Features + +## Code structure and features + +* Modern pyproject.toml with setuptools +* Versioning based on git tag (only) +* Easy development setup +* Support for namespaces +* Testing with coverage using pytest; tests may be in `tests/`, embedded in the package, and in doc strings +* Examples for logging and package data +* Command-line with argument parsing with argparse + +## DevOps + +* Quality tools: Code linting and reformatting with Ruff +* GitHub Actions for testing and packaging diff --git a/orig2/pyproject.toml b/orig2/pyproject.toml new file mode 100644 index 0000000..c3a12dc --- /dev/null +++ b/orig2/pyproject.toml @@ -0,0 +1,177 @@ +[project] +name = "biocommons.example" +authors = [ + { name = "biocommons contributors", email = "biocommons-dev@googlegroups.com" }, +] +description = "Example Package" +readme = "README.md" +license = { file = "LICENSE.txt" } +requires-python = ">=3.10" +classifiers = [ + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", +] +dynamic = ["version"] +dependencies = [ + "coloredlogs ~= 15.0", + "pyyaml ~= 6.0", +] + +[project.optional-dependencies] +dev = [ + "deptry>=0.23.0", + "ipython ~= 8.4", + "mkdocs-material>=8.5.10", + "mkdocs>=1.4.2", + "mkdocstrings[python]>=0.26.1", + "pre-commit>=3.8.0", + "pytest-cov>=4.0.0", + "pytest>=7.2.0", + "ruff>=0.11.5", + "tox-uv>=1.11.3", + "ty>=0.0.1a16", + +] +tests = [ + "pytest-cov ~= 4.1", + "pytest ~= 7.1", + "vcrpy", + "tox ~= 4.15", +] +docs = ["mkdocs"] + +[project.scripts] +marvin-quote = "biocommons.example.__main__:main" + +[project.urls] +"Homepage" = "https://github.com/biocommons/biocommons.example" +"Bug Tracker" = "https://github.com/biocommons/biocommons.example/issues" + + +[build-system] +requires = ["setuptools >= 70.1", "setuptools_scm[toml] ~= 8.1"] +build-backend = "setuptools.build_meta" + + +[tool.setuptools] +include-package-data = true + +[tool.setuptools.packages.find] +where = ["src"] +exclude = ["__pycache__", "*.pyc"] +namespaces = true + +[tool.setuptools.package-data] +"*" = ["*.gz", "*.json", "*.yaml"] + + +[tool.setuptools_scm] + + +# https://docs.pytest.org/en/6.2.x/customize.html#pyproject-toml +[tool.pytest.ini_options] +addopts = "-s -v -x --strict-markers -m 'not extra' --doctest-modules --cov=src" +doctest_optionflags = [ + "ALLOW_BYTES", + "ALLOW_UNICODE", + "ELLIPSIS", + "IGNORE_EXCEPTION_DETAIL", + "NORMALIZE_WHITESPACE", +] +markers = [ + "network: tests that require network connectivity", + "slow: slow tests that should be run infrequently", +] + + +[tool.coverage.run] +branch = true +source = ["biocommons.example"] +omit = ["*_test.py", "*/test/*", "*/tests/*"] + + +[tool.coverage.report] +show_missing = true +exclude_lines = [ + # Have to re-enable the standard pragma + "pragma: no cover", + + # Don't complain about missing debug-only code: + "def __repr__", + "if self.debug", + + # Don't complain if tests don't hit defensive assertion code: + "raise AssertionError", + "raise NotImplementedError", + + # Don't complain if non-runnable code isn't run: + "if __name__ == .__main__.:", +] + +[tool.ruff] +src = ["src", "tests"] +line-length = 100 + +[tool.ruff.lint] +select = [ + "F", # https://docs.astral.sh/ruff/rules/#pyflakes-f + "E", + "W", # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w + "I", # https://docs.astral.sh/ruff/rules/#isort-i + "N", # https://docs.astral.sh/ruff/rules/#pep8-naming-n + "UP", # https://docs.astral.sh/ruff/rules/#pyupgrade-up + "YTT", # https://docs.astral.sh/ruff/rules/#flake8-2020-ytt + "S", # https://docs.astral.sh/ruff/rules/#flake8-bandit-s + "B", # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b + "A", # https://docs.astral.sh/ruff/rules/#flake8-builtins-a + "C4", # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4 + "DTZ", # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz + "EM", # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em + "LOG", # https://docs.astral.sh/ruff/rules/#flake8-logging-log + "G", # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g + "PIE", # https://docs.astral.sh/ruff/rules/#flake8-pie-pie + "PT", # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt + "RSE", # https://docs.astral.sh/ruff/rules/#flake8-raise-rse + "RET", # https://docs.astral.sh/ruff/rules/#flake8-return-ret + "SIM", # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim + "ARG", # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg + "PTH", # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth + "PL", # https://docs.astral.sh/ruff/rules/#pylint-pl + "TRY", # https://docs.astral.sh/ruff/rules/#tryceratops-try + "PERF", # https://docs.astral.sh/ruff/rules/#perflint-perf + "RUF", # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf +] +fixable = [ + "F401", + "F541", + "I", + "D", + "UP", + "B", + "C4", + "EM", + "PIE", + "PT", + "RSE", + "RET", + "SIM", + "PERF", + "RUF", +] +ignore = [ + # ignore for compatibility with formatter + "W191", + "E111", + "E114", + "E117", + "S321", + # other + "PLR0913", +] + +[tool.ruff.lint.per-file-ignores] +"tests/*" = ["S101"] diff --git a/pyproject.toml b/pyproject.toml index 9e0da19..5e2198e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,104 +1,86 @@ +[build-system] +requires = ["setuptools >= 70.1", "setuptools_scm[toml] ~= 8.1"] +build-backend = "setuptools.build_meta" + +[dependency-groups] +dev = [ + "deptry>=0.23.0", + "mkdocs-material>=8.5.10", + "mkdocs>=1.4.2", + "mkdocstrings[python]>=0.26.1", + "mypy>=0.991", + "pre-commit>=2.20.0", + "pytest-cov>=4.0.0", + "pytest>=7.2.0", + "ruff>=0.11.5", + "tox-uv>=1.11.3", + "ty>=0.0.1a16" +] + [project] -name = "biocommons.example" +name = "biocommons-example" authors = [ - { name = "biocommons contributors", email = "biocommons-dev@googlegroups.com" }, + {name = "biocommons contributors", email = "biocommons-dev@googlegroups.com"} ] -description = "Example Package" +description = "biocommons.example package (namespaced)" readme = "README.md" -license = { file = "LICENSE.txt" } +license = "Apache-2.0" requires-python = ">=3.10" classifiers = [ - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", - "Programming Language :: Python :: 3.12", - "License :: OSI Approved :: MIT License", - "Operating System :: OS Independent", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Operating System :: OS Independent" ] -dynamic = ["version"] dependencies = ["coloredlogs ~= 15.0", "pyyaml ~= 6.0"] - -[project.optional-dependencies] -dev = [ - "build ~= 0.8", - "ipython ~= 8.4", - "pre-commit ~= 3.4", - "ruff == 0.4.4", -] -tests = [ - "pytest-cov ~= 4.1", - "pytest ~= 7.1", - "vcrpy", - "tox ~= 4.15", -] -docs = ["mkdocs"] +dynamic = ["version"] [project.scripts] marvin-quote = "biocommons.example.__main__:main" [project.urls] -"Homepage" = "https://github.com/biocommons/biocommons.example" -"Bug Tracker" = "https://github.com/biocommons/biocommons.example/issues" +Homepage = "https://biocommons.github.io/python-package/" +Issues = "https://github.com/biocommons/python-package/issues" +Repository = "https://github.com/biocommons/python-package" +Documentation = "https://biocommons.github.io/python-package/" +[tool.coverage] -[build-system] -requires = ["setuptools >= 70.1", "setuptools_scm[toml] ~= 8.1"] -build-backend = "setuptools.build_meta" - - -[tool.setuptools] -include-package-data = true - -[tool.setuptools.packages.find] -where = ["src"] -exclude = ["__pycache__", "*.pyc"] -namespaces = true - -[tool.setuptools.package-data] -"*" = ["*.gz", "*.json", "*.yaml"] - - -[tool.setuptools_scm] +[tool.coverage.report] +show_missing = true +skip_empty = true +exclude_lines = [ + # Have to re-enable the standard pragma + "pragma: no cover", + # Don't complain about missing debug-only code: + "def __repr__", + "if self.debug", + # Don't complain if tests don't hit defensive assertion code: + "raise AssertionError", + "raise NotImplementedError", + # Don't complain if non-runnable code isn't run: + "if __name__ == .__main__.:" +] +[tool.coverage.run] +branch = true +omit = ["*_test.py", "*/test/*", "*/tests/*"] +source = ["src"] # https://docs.pytest.org/en/6.2.x/customize.html#pyproject-toml [tool.pytest.ini_options] addopts = "-s -v -x --strict-markers -m 'not extra' --doctest-modules --cov=src" doctest_optionflags = [ - "ALLOW_BYTES", - "ALLOW_UNICODE", - "ELLIPSIS", - "IGNORE_EXCEPTION_DETAIL", - "NORMALIZE_WHITESPACE", + "ALLOW_BYTES", + "ALLOW_UNICODE", + "ELLIPSIS", + "IGNORE_EXCEPTION_DETAIL", + "NORMALIZE_WHITESPACE" ] markers = [ - "network: tests that require network connectivity", - "slow: slow tests that should be run infrequently", -] - - -[tool.coverage.run] -branch = true -source = ["biocommons.example"] -omit = ["*_test.py", "*/test/*", "*/tests/*"] - - -[tool.coverage.report] -show_missing = true -exclude_lines = [ - # Have to re-enable the standard pragma - "pragma: no cover", - - # Don't complain about missing debug-only code: - "def __repr__", - "if self.debug", - - # Don't complain if tests don't hit defensive assertion code: - "raise AssertionError", - "raise NotImplementedError", - - # Don't complain if non-runnable code isn't run: - "if __name__ == .__main__.:", + "network: tests that require network connectivity", + "slow: slow tests that should be run infrequently" ] [tool.ruff] @@ -107,60 +89,73 @@ line-length = 100 [tool.ruff.lint] select = [ - "F", # https://docs.astral.sh/ruff/rules/#pyflakes-f - "E", - "W", # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w - "I", # https://docs.astral.sh/ruff/rules/#isort-i - "N", # https://docs.astral.sh/ruff/rules/#pep8-naming-n - "UP", # https://docs.astral.sh/ruff/rules/#pyupgrade-up - "YTT", # https://docs.astral.sh/ruff/rules/#flake8-2020-ytt - "S", # https://docs.astral.sh/ruff/rules/#flake8-bandit-s - "B", # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b - "A", # https://docs.astral.sh/ruff/rules/#flake8-builtins-a - "C4", # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4 - "DTZ", # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz - "EM", # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em - "LOG", # https://docs.astral.sh/ruff/rules/#flake8-logging-log - "G", # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g - "PIE", # https://docs.astral.sh/ruff/rules/#flake8-pie-pie - "PT", # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt - "RSE", # https://docs.astral.sh/ruff/rules/#flake8-raise-rse - "RET", # https://docs.astral.sh/ruff/rules/#flake8-return-ret - "SIM", # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim - "ARG", # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg - "PTH", # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth - "PL", # https://docs.astral.sh/ruff/rules/#pylint-pl - "TRY", # https://docs.astral.sh/ruff/rules/#tryceratops-try - "PERF", # https://docs.astral.sh/ruff/rules/#perflint-perf - "RUF", # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf + "F", # https://docs.astral.sh/ruff/rules/#pyflakes-f + "E", + "W", # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w + "I", # https://docs.astral.sh/ruff/rules/#isort-i + "N", # https://docs.astral.sh/ruff/rules/#pep8-naming-n + "UP", # https://docs.astral.sh/ruff/rules/#pyupgrade-up + "YTT", # https://docs.astral.sh/ruff/rules/#flake8-2020-ytt + "S", # https://docs.astral.sh/ruff/rules/#flake8-bandit-s + "B", # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b + "A", # https://docs.astral.sh/ruff/rules/#flake8-builtins-a + "C4", # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4 + "DTZ", # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz + "EM", # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em + "LOG", # https://docs.astral.sh/ruff/rules/#flake8-logging-log + "G", # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g + "PIE", # https://docs.astral.sh/ruff/rules/#flake8-pie-pie + "PT", # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt + "RSE", # https://docs.astral.sh/ruff/rules/#flake8-raise-rse + "RET", # https://docs.astral.sh/ruff/rules/#flake8-return-ret + "SIM", # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim + "ARG", # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg + "PTH", # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth + "PL", # https://docs.astral.sh/ruff/rules/#pylint-pl + "TRY", # https://docs.astral.sh/ruff/rules/#tryceratops-try + "PERF", # https://docs.astral.sh/ruff/rules/#perflint-perf + "RUF" # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf ] fixable = [ - "F401", - "F541", - "I", - "D", - "UP", - "B", - "C4", - "EM", - "PIE", - "PT", - "RSE", - "RET", - "SIM", - "PERF", - "RUF", + "F401", + "F541", + "I", + "D", + "UP", + "B", + "C4", + "EM", + "PIE", + "PT", + "RSE", + "RET", + "SIM", + "PERF", + "RUF" ] ignore = [ - # ignore for compatibility with formatter - "W191", - "E111", - "E114", - "E117", - "S321", - # other - "PLR0913", + # ignore for compatibility with formatter + "W191", + "E111", + "E114", + "E117", + "S321", + # other + "PLR0913" ] [tool.ruff.lint.per-file-ignores] "tests/*" = ["S101"] + +[tool.setuptools] +include-package-data = true + +[tool.setuptools.package-data] +"*" = ["*.gz", "*.json", "*.yaml"] + +[tool.setuptools.packages.find] +where = ["src"] +exclude = ["__pycache__", "*.pyc"] +namespaces = true + +[tool.setuptools_scm] diff --git a/src/biocommons/example/__main__.py b/src/biocommons/example/__main__.py index 24dcdf9..f8dc29b 100644 --- a/src/biocommons/example/__main__.py +++ b/src/biocommons/example/__main__.py @@ -10,7 +10,7 @@ def main(): # pragma: no cover """marvin.example main""" - import coloredlogs + import coloredlogs # noqa: PLC0415 logging.Formatter.converter = time.gmtime coloredlogs.install( diff --git a/src/biocommons/example/quotes.yaml b/src/biocommons/example/quotes.yaml index 16b23f6..e85be62 100644 --- a/src/biocommons/example/quotes.yaml +++ b/src/biocommons/example/quotes.yaml @@ -12,15 +12,15 @@ quotes: fifty thousand times more intelligent than you and even I don't know the answer. It gives me a headache just trying to think down to your level. - + - >- There's only one life-form as intelligent as me within thirty parsecs of here and that's me. - + - >- I wish you'd just tell me rather trying to engage my enthusiasm because I haven't got one. - + - >- And then, of course, I've got this terrible pain in all the diodes down my left side. diff --git a/src/biocommons/example/tests/__init__.py b/src/biocommons/example/tests/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/src/biocommons/example/tests/conftest.py b/src/biocommons/example/tests/conftest.py deleted file mode 100644 index 79d7cd9..0000000 --- a/src/biocommons/example/tests/conftest.py +++ /dev/null @@ -1,10 +0,0 @@ -import importlib.resources - -import pytest -import yaml - - -@pytest.fixture() -def all_quotes(): - quotes_stream = importlib.resources.files("example").joinpath("quotes.yaml").read_text() - return yaml.load(quotes_stream, Loader=yaml.SafeLoader)["quotes"] diff --git a/src/biocommons/example/tests/marvin_subdir_test.py b/src/biocommons/example/tests/marvin_subdir_test.py deleted file mode 100644 index ff94067..0000000 --- a/src/biocommons/example/tests/marvin_subdir_test.py +++ /dev/null @@ -1,9 +0,0 @@ -"""biocommons.example test, within tests directory adjacent to source""" - -from ..marvin import get_quote - - -def test_get_quote(all_quotes): - """test get_quote""" - # NB: all_quotes argument is a test fixture; see ./conftest.py - assert get_quote() in all_quotes # noqa: S101 diff --git a/tox.ini b/tox.ini index 6890940..e9293f7 100644 --- a/tox.ini +++ b/tox.ini @@ -1,11 +1,19 @@ [tox] -requires = - tox >= 4 -env_list = py{310,311,312} -isolated_build = True +skipsdist = true +envlist = py39, py310, py311, py312, py313 -[gh] +[gh-actions] python = - 3.10 = py310 - 3.11 = py311 - 3.12 = py312 + 3.9: py39 + 3.10: py310 + 3.11: py311 + 3.12: py312 + 3.13: py313 + +[testenv] +passenv = PYTHON_VERSION +allowlist_externals = uv +commands = + uv sync 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