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node: $Format:%H$ | ||
node-date: $Format:%cI$ | ||
describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$ | ||
ref-names: $Format:%D$ |
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.git_archival.txt export-subst |
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See the [Scientific Python Developer Guide][spc-dev-intro] for a detailed | ||
description of best practices for developing scientific packages. | ||
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[spc-dev-intro]: https://scientific-python-cookie.readthedocs.io/guide/intro | ||
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# Setting up a development environment manually | ||
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You can set up a development environment by running: | ||
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```bash | ||
python3 -m venv .venv | ||
source ./.venv/bin/activate | ||
pip install -v -e .[dev] | ||
``` | ||
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or just | ||
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```bash | ||
hatch shell | ||
``` | ||
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# Post setup | ||
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You should prepare pre-commit, which will help you by checking that commits pass | ||
required checks: | ||
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```bash | ||
pip install pre-commit # or brew install pre-commit on macOS | ||
pre-commit install # Will install a pre-commit hook into the git repo | ||
``` | ||
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You can also/alternatively run `pre-commit run` (changes only) or | ||
`pre-commit run --all-files` to check even without installing the hook. | ||
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This project uses pre-commit for all style checking. Install pre-commit and run: | ||
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```bash | ||
pre-commit run -a | ||
``` | ||
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to check all files. | ||
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# Testing | ||
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Use pytest to run the unit checks: | ||
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```bash | ||
pytest | ||
``` | ||
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# Coverage | ||
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Use pytest-cov to generate coverage reports: | ||
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```bash | ||
pytest --cov=dask-ngs | ||
``` | ||
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# Building docs | ||
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You can build the docs using: | ||
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```bash | ||
hatch docs | ||
``` |
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version: 2 | ||
updates: | ||
# Maintain dependencies for GitHub Actions | ||
- package-ecosystem: "github-actions" | ||
directory: "/" | ||
schedule: | ||
interval: "weekly" |
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name: CI | ||
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on: | ||
workflow_dispatch: | ||
pull_request: | ||
push: | ||
branches: | ||
- main | ||
release: | ||
types: | ||
- published | ||
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concurrency: | ||
group: ${{ github.workflow }}-${{ github.ref }} | ||
cancel-in-progress: true | ||
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env: | ||
FORCE_COLOR: 3 | ||
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jobs: | ||
pre-commit: | ||
name: Format | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: actions/checkout@v3 | ||
with: | ||
fetch-depth: 0 | ||
- uses: actions/setup-python@v4 | ||
with: | ||
python-version: "3.x" | ||
- uses: pre-commit/[email protected] | ||
with: | ||
extra_args: --hook-stage manual --all-files | ||
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checks: | ||
name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }} | ||
runs-on: ${{ matrix.runs-on }} | ||
needs: [pre-commit] | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
python-version: ["3.7", "3.11"] | ||
runs-on: [ubuntu-latest, macos-latest, windows-latest] | ||
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steps: | ||
- uses: actions/checkout@v3 | ||
with: | ||
fetch-depth: 0 | ||
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- uses: actions/setup-python@v4 | ||
with: | ||
python-version: ${{ matrix.python-version }} | ||
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- name: Install package | ||
run: python -m pip install .[test] | ||
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- name: Test package | ||
run: >- | ||
python -m pytest -ra --cov --cov-report=xml --cov-report=term | ||
--durations=20 | ||
- name: Upload coverage report | ||
uses: codecov/[email protected] | ||
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dist: | ||
needs: [pre-commit] | ||
name: Distribution build | ||
runs-on: ubuntu-latest | ||
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steps: | ||
- uses: actions/checkout@v3 | ||
with: | ||
fetch-depth: 0 | ||
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- name: Build sdist and wheel | ||
run: pipx run build | ||
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- uses: actions/upload-artifact@v3 | ||
with: | ||
path: dist | ||
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- name: Check products | ||
run: pipx run twine check dist/* | ||
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publish: | ||
needs: [dist] | ||
name: Publish to PyPI | ||
environment: pypi | ||
permissions: | ||
id-token: write | ||
runs-on: ubuntu-latest | ||
if: github.event_name == 'release' && github.event.action == 'published' | ||
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steps: | ||
- uses: actions/download-artifact@v3 | ||
with: | ||
name: artifact | ||
path: dist | ||
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- uses: pypa/gh-action-pypi-publish@release/v1 | ||
if: github.event_name == 'release' && github.event.action == 'published' | ||
with: | ||
# Remember to tell (test-)pypi about this repo before publishing | ||
# Remove this line to publish to PyPI | ||
repository-url: https://test.pypi.org/legacy/ |
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# Byte-compiled / optimized / DLL files | ||
__pycache__/ | ||
*.py[cod] | ||
*$py.class | ||
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# C extensions | ||
*.so | ||
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# Distribution / packaging | ||
.Python | ||
build/ | ||
develop-eggs/ | ||
dist/ | ||
downloads/ | ||
eggs/ | ||
.eggs/ | ||
lib/ | ||
lib64/ | ||
parts/ | ||
sdist/ | ||
var/ | ||
wheels/ | ||
share/python-wheels/ | ||
*.egg-info/ | ||
.installed.cfg | ||
*.egg | ||
MANIFEST | ||
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# 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 | ||
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# Installer logs | ||
pip-log.txt | ||
pip-delete-this-directory.txt | ||
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# Unit test / coverage reports | ||
htmlcov/ | ||
.tox/ | ||
.nox/ | ||
.coverage | ||
.coverage.* | ||
.cache | ||
nosetests.xml | ||
coverage.xml | ||
*.cover | ||
*.py,cover | ||
.hypothesis/ | ||
.pytest_cache/ | ||
cover/ | ||
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# Translations | ||
*.mo | ||
*.pot | ||
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# Django stuff: | ||
*.log | ||
local_settings.py | ||
db.sqlite3 | ||
db.sqlite3-journal | ||
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# Flask stuff: | ||
instance/ | ||
.webassets-cache | ||
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# Scrapy stuff: | ||
.scrapy | ||
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# Sphinx documentation | ||
docs/_build/ | ||
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# PyBuilder | ||
.pybuilder/ | ||
target/ | ||
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# Jupyter Notebook | ||
.ipynb_checkpoints | ||
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# IPython | ||
profile_default/ | ||
ipython_config.py | ||
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# pyenv | ||
# For a library or package, you might want to ignore these files since the code is | ||
# intended to run in multiple environments; otherwise, check them in: | ||
# .python-version | ||
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# pipenv | ||
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. | ||
# However, in case of collaboration, if having platform-specific dependencies or dependencies | ||
# having no cross-platform support, pipenv may install dependencies that don't work, or not | ||
# install all needed dependencies. | ||
#Pipfile.lock | ||
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow | ||
__pypackages__/ | ||
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# Celery stuff | ||
celerybeat-schedule | ||
celerybeat.pid | ||
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# SageMath parsed files | ||
*.sage.py | ||
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# Environments | ||
.env | ||
.venv | ||
env/ | ||
venv/ | ||
ENV/ | ||
env.bak/ | ||
venv.bak/ | ||
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# Spyder project settings | ||
.spyderproject | ||
.spyproject | ||
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# Rope project settings | ||
.ropeproject | ||
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# mkdocs documentation | ||
/site | ||
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# mypy | ||
.mypy_cache/ | ||
.dmypy.json | ||
dmypy.json | ||
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# Pyre type checker | ||
.pyre/ | ||
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# pytype static type analyzer | ||
.pytype/ | ||
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# Cython debug symbols | ||
cython_debug/ | ||
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# setuptools_scm | ||
src/*/_version.py | ||
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# ruff | ||
.ruff_cache/ | ||
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# OS specific stuff | ||
.DS_Store | ||
.DS_Store? | ||
._* | ||
.Spotlight-V100 | ||
.Trashes | ||
ehthumbs.db | ||
Thumbs.db | ||
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# Common editor files | ||
*~ | ||
*.swp |
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ci: | ||
autoupdate_commit_msg: "chore: update pre-commit hooks" | ||
autofix_commit_msg: "style: pre-commit fixes" | ||
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repos: | ||
- repo: https://github.com/psf/black | ||
rev: "23.3.0" | ||
hooks: | ||
- id: black-jupyter | ||
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- repo: https://github.com/pre-commit/pre-commit-hooks | ||
rev: "v4.4.0" | ||
hooks: | ||
- id: check-added-large-files | ||
- id: check-case-conflict | ||
- id: check-merge-conflict | ||
- id: check-symlinks | ||
- id: check-yaml | ||
- id: debug-statements | ||
- id: end-of-file-fixer | ||
- id: mixed-line-ending | ||
- id: name-tests-test | ||
args: ["--pytest-test-first"] | ||
- id: requirements-txt-fixer | ||
- id: trailing-whitespace | ||
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- repo: https://github.com/pre-commit/pygrep-hooks | ||
rev: "v1.10.0" | ||
hooks: | ||
- id: rst-backticks | ||
- id: rst-directive-colons | ||
- id: rst-inline-touching-normal | ||
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- repo: https://github.com/asottile/blacken-docs | ||
rev: "1.13.0" | ||
hooks: | ||
- id: blacken-docs | ||
additional_dependencies: [black==23.3.0] | ||
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- repo: https://github.com/charliermarsh/ruff-pre-commit | ||
rev: "v0.0.264" | ||
hooks: | ||
- id: ruff | ||
args: ["--fix", "--show-fixes"] | ||
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- repo: https://github.com/codespell-project/codespell | ||
rev: "v2.2.4" | ||
hooks: | ||
- id: codespell |
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