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‎.copier-answers.yml‎

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# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
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_commit: 2024.01.24
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_src_path: gh:scientific-python/cookie
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backend: hatch
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email: [email protected]
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full_name: Davis Vann Bennett
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license: MIT
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org: zarr-developers
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project_name: n5py
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project_short_description: The N5 file format implemented in Python
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url: https://github.com/zarr-developers/n5py
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vcs: true

‎.git_archival.txt‎

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node: $Format:%H$
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node-date: $Format:%cI$
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describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
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ref-names: $Format:%D$

‎.gitattributes‎

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.git_archival.txt export-subst

‎.github/CONTRIBUTING.md‎

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See the [Scientific Python Developer Guide][spc-dev-intro] for a detailed
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description of best practices for developing scientific packages.
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[spc-dev-intro]: https://learn.scientific-python.org/development/
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# Quick development
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The fastest way to start with development is to use nox. If you don't have nox,
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you can use `pipx run nox` to run it without installing, or `pipx install nox`.
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If you don't have pipx (pip for applications), then you can install with
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`pip install pipx` (the only case were installing an application with regular
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pip is reasonable). If you use macOS, then pipx and nox are both in brew, use
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`brew install pipx nox`.
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To use, run `nox`. This will lint and test using every installed version of
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Python on your system, skipping ones that are not installed. You can also run
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specific jobs:
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```console
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$ nox -s lint # Lint only
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$ nox -s tests # Python tests
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$ nox -s docs -- --serve # Build and serve the docs
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$ nox -s build # Make an SDist and wheel
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```
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Nox handles everything for you, including setting up an temporary virtual
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environment for each run.
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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
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python3 -m venv .venv
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source ./.venv/bin/activate
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pip install -v -e .[dev]
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```
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If you have the
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[Python Launcher for Unix](https://github.com/brettcannon/python-launcher), you
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can instead do:
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```bash
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py -m venv .venv
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py -m install -v -e .[dev]
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```
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# Post setup
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You should prepare pre-commit, which will help you by checking that commits pass
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required checks:
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```bash
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pip install pre-commit # or brew install pre-commit on macOS
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pre-commit install # Will install a pre-commit hook into the git repo
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```
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You can also/alternatively run `pre-commit run` (changes only) or
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`pre-commit run --all-files` to check even without installing the hook.
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# Testing
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Use pytest to run the unit checks:
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```bash
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pytest
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```
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# Coverage
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Use pytest-cov to generate coverage reports:
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```bash
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pytest --cov=n5py
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```
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# Building docs
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You can build the docs using:
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```bash
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nox -s docs
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```
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You can see a preview with:
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```bash
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nox -s docs -- --serve
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```
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# Pre-commit
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This project uses pre-commit for all style checking. While you can run it with
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nox, this is such an important tool that it deserves to be installed on its own.
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Install pre-commit and run:
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```bash
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pre-commit run -a
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```
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to check all files.

‎.github/dependabot.yml‎

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version: 2
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updates:
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# Maintain dependencies for GitHub Actions
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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interval: "weekly"
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groups:
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actions:
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patterns:
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- "*"

‎.github/matchers/pylint.json‎

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{
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"problemMatcher": [
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{
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"severity": "warning",
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"pattern": [
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{
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"regexp": "^([^:]+):(\\d+):(\\d+): ([A-DF-Z]\\d+): \\033\\[[\\d;]+m([^\\033]+).*$",
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"file": 1,
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"line": 2,
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"column": 3,
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"code": 4,
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"message": 5
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}
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],
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"owner": "pylint-warning"
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},
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{
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"severity": "error",
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"pattern": [
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{
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"regexp": "^([^:]+):(\\d+):(\\d+): (E\\d+): \\033\\[[\\d;]+m([^\\033]+).*$",
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"file": 1,
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"line": 2,
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"column": 3,
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"code": 4,
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"message": 5
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}
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],
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"owner": "pylint-error"
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}
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]
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}

‎.github/workflows/cd.yml‎

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name: CD
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on:
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workflow_dispatch:
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pull_request:
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push:
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branches:
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- main
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release:
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types:
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- published
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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env:
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FORCE_COLOR: 3
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jobs:
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dist:
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name: Distribution build
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- uses: hynek/build-and-inspect-python-package@v2
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publish:
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needs: [dist]
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name: Publish to PyPI
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environment: pypi
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permissions:
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id-token: write
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runs-on: ubuntu-latest
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if: github.event_name == 'release' && github.event.action == 'published'
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steps:
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- uses: actions/download-artifact@v4
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with:
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name: Packages
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path: dist
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- uses: pypa/gh-action-pypi-publish@release/v1
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if: github.event_name == 'release' && github.event.action == 'published'
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with:
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# Remember to tell (test-)pypi about this repo before publishing
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# Remove this line to publish to PyPI
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repository-url: https://test.pypi.org/legacy/

‎.github/workflows/ci.yml‎

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name: CI
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on:
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workflow_dispatch:
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pull_request:
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push:
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branches:
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- main
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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env:
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FORCE_COLOR: 3
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jobs:
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pre-commit:
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name: Format
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- uses: actions/setup-python@v5
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with:
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python-version: "3.x"
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- uses: pre-commit/[email protected]
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with:
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extra_args: --hook-stage manual --all-files
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- name: Run PyLint
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run: |
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echo "::add-matcher::$GITHUB_WORKSPACE/.github/matchers/pylint.json"
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pipx run nox -s pylint
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checks:
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name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
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runs-on: ${{ matrix.runs-on }}
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needs: [pre-commit]
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.8", "3.12"]
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runs-on: [ubuntu-latest, macos-latest, windows-latest]
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include:
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- python-version: pypy-3.10
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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allow-prereleases: true
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- name: Install package
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run: python -m pip install .[test]
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- name: Test package
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run: >-
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python -m pytest -ra --cov --cov-report=xml --cov-report=term
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--durations=20
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- name: Upload coverage report
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uses: codecov/[email protected]

‎.gitignore‎

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# install all needed dependencies.
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#Pipfile.lock
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# poetry
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# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
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# This is especially recommended for binary packages to ensure reproducibility, and is more
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# commonly ignored for libraries.
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# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
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#poetry.lock
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# pdm
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# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
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#pdm.lock
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# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
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# in version control.
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# https://pdm.fming.dev/#use-with-ide
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.pdm.toml
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow
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__pypackages__/
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# Celery stuff
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# Cython debug symbols
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cython_debug/
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# PyCharm
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# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
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# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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#.idea/
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# setuptools_scm
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src/*/_version.py
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# ruff
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.ruff_cache/
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# OS specific stuff
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.DS_Store
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.DS_Store?
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._*
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.Spotlight-V100
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.Trashes
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ehthumbs.db
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Thumbs.db
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# Common editor files
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*~
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*.swp

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