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Switch to scverse cookiecutter template (#402)
* Add tests for databases and fix IEDB Despite sticking to v3 version number, IEDB have updated their file format * BCR and TCR are now in separate files * the csv header has changed. Names are different, and there are now *two* rows representing the header. * rename to src * update readme * WIP * update pyproject.toml * add changelog * fix tests * apply pre-commit autofixes * update pre-commit file * clean up sphinx modules * Switch to ipynb tutorials for now * WIP docs * WIP docs * WIP docs * update CI * update conda deps * Add action to test notebook * add RTD config * clean up imports in ddatasets * add dependency for coverage * CI * CI * doc fixes * CI * CI * get rid of raw cells in IO tutorial * CI * convert raw cells in 3k tutorial * bump tutorials * debug rtd * Revert "debug rtd" This reverts commit 3b5ef86. * debug rtd * debug rtd * fix spacing * exclude a few ruff warnings * update editorconfig * fix blacken-docs pre-commit * Add cruft.json * update target versions for black/ruff * update README * sphinx fail on warning * debug rtd * debug rtd * debug rtd * debug RTD
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Diff for: ‎.conda/meta.yaml

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requirements:
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host:
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- python >=3.8
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- pip!=22.1 # https://github.com/pypa/pip/issues/11110
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- flit
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- setuptools_scm
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- pytoml
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- importlib_metadata
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- python >=3.9
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- hatchling
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- hatch-vcs
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run:
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- python >=3.8
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- python >=3.9
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- anndata >=0.9
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- awkward >=2.1.0
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- mudata >=0.2.2
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- scirpy
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commands:
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- pytest --pyargs scirpy -m "not extra"
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- cd docs && jupytext --execute tutorials/tutorial_3k_tcr.md
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about:
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home: https://scverse.org/scirpy

Diff for: ‎.cruft.json

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{
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"template": "https://github.com/scverse/cookiecutter-scverse",
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"commit": "6a4338030e0c83a9034d607ed66abeff83e18840",
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"checkout": null,
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"context": {
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"cookiecutter": {
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"project_name": "scirpy",
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"package_name": "scirpy",
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"project_description": "A very interesting piece of code",
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"author_full_name": "Gregor Sturm",
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"author_email": "[email protected]",
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"github_user": "grst",
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"project_repo": "https://github.com/scverse/scirpy",
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"license": "BSD 3-Clause License",
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"_copy_without_render": [
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".github/workflows/**.yaml",
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"docs/_templates/autosummary/**.rst"
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],
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"_template": "https://github.com/scverse/cookiecutter-scverse"
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}
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},
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"directory": null
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}

Diff for: ‎.editorconfig

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root = true
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[*]
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charset = utf-8
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indent_style = space
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indent_size = 4
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end_of_line = lf
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insert_final_newline = true
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charset = utf-8
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trim_trailing_whitespace = true
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max_line_length = 88
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insert_final_newline = true
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[*.py]
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indent_size = 4
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indent_style = space
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[*.{yml,yaml}]
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indent_size = 2
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[.cruft.json]
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indent_size = 2
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[Makefile]
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indent_style = tab

Diff for: ‎.gitattributes

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# Pickle files (for testing) should always have UNIX line endings.
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# Pickle files (for testing) should always have UNIX line endings.
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*.pkl text eol=lf

Diff for: ‎.github/ISSUE_TEMPLATE/bug_report.md

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**System**
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- OS: [e.g. Windows 10]
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- Python version [e.g. 3.9]
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- Versions of libraries involved [e.g. AnnData 0.8.0, Scirpy 0.12.0]
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- OS: [e.g. Windows 10]
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- Python version [e.g. 3.9]
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- Versions of libraries involved [e.g. AnnData 0.8.0, Scirpy 0.12.0]
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**Additional context**
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Add any other context about the problem here.

Diff for: ‎.github/ISSUE_TEMPLATE/config.yml

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blank_issues_enabled: true
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contact_links:
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- name: Scverse Community Forum
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url: https://discourse.scverse.org/
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about: If you have questions about “How to do X”, please ask them here.
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blank_issues_enabled: true
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contact_links:
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- name: Scverse Community Forum
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url: https://discourse.scverse.org/
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about: If you have questions about “How to do X”, please ask them here.

Diff for: ‎.github/workflows/build.yaml

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name: Check Build
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on:
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push:
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branches: [main]
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pull_request:
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branches: [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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jobs:
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package:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python 3.10
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uses: actions/setup-python@v4
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with:
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python-version: "3.10"
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cache: "pip"
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cache-dependency-path: "**/pyproject.toml"
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- name: Install build dependencies
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run: python -m pip install --upgrade pip wheel twine build
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- name: Build package
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run: python -m build
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- name: Check package
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run: twine check --strict dist/*.whl

Diff for: ‎.github/workflows/conda.yml renamed to ‎.github/workflows/conda.yaml

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branches: [main]
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jobs:
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if: "!contains(github.event.head_commit.message, 'skip ci')"
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test:
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defaults:
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run:
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shell: bash -e {0} # -e to fail on error
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matrix:
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python-version: ["3.8", "3.9", "3.10"]
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os: ["ubuntu-latest", "macos-latest"]
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include:
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- os: ubuntu-latest
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python: "3.9"
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env:
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OS: ${{ matrix.os }}
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PYTHON: ${{ matrix.python }}
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0 # required for setuptools-scm
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- uses: actions/checkout@v3
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Diff for: ‎.github/workflows/docs.yml

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Diff for: ‎.github/workflows/pythonpublish.yml

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Diff for: ‎.github/workflows/release.yaml

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name: Release
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on:
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push:
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tags:
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- "*.*.*"
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jobs:
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release:
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name: Release
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runs-on: ubuntu-latest
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steps:
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- name: Checkout code
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uses: actions/checkout@v3
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- name: Set up Python 3.10
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uses: actions/setup-python@v4
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with:
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python-version: "3.10"
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- name: Install hatch
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run: pip install hatch
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- name: Build project for distribution
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run: hatch build
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- name: Publish a Python distribution to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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password: ${{ secrets.PYPI_API_TOKEN }}

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