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Merge pull request #7 from theislab/feat/update_package
update dependences
2 parents f831275 + 9223303 commit a985186

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‎.editorconfig

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# http://editorconfig.org
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root = true
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[*]
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indent_style = space
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indent_size = 4
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trim_trailing_whitespace = true
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insert_final_newline = true
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charset = utf-8
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end_of_line = lf
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[*.bat]
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indent_style = tab
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end_of_line = crlf
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[LICENSE]
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insert_final_newline = false
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[Makefile]
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indent_style = tab

‎.github/workflows/release.yml

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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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# will use ref/SHA that triggered it
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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: "3.9"
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- name: Install poetry
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uses: abatilo/actions-poetry@v2.0.0
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with:
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poetry-version: 1.4.2
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- name: Build project for distribution
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run: poetry build
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- name: Check Version
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id: check-version
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run: |
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[[ "$(poetry version --short)" =~ ^[0-9]+\.[0-9]+\.[0-9]+$ ]] \
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|| echo ::set-output name=prerelease::true
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- name: Publish to PyPI
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env:
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POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
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run: poetry publish

‎.github/workflows/test.yml

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# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
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# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
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name: regvelo
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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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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.9", "3.10", "3.11"]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Cache pip
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uses: actions/cache@v2
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
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restore-keys: |
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${{ runner.os }}-pip-
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- name: Install dependencies
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run: |
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pip install pytest-cov
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pip install .[dev]
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- name: Test with pytest
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run: |
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pytest --cov-report=xml --cov=velovi
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- name: After success
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run: |
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bash <(curl -s https://codecov.io/bash)
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pip list

‎.gitignore

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# DS_Store
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.DS_Store
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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pip-wheel-metadata/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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.python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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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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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# vscode
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.vscode/settings.json
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docs/api/reference/
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*.h5ad

‎.pre-commit-config.yaml

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fail_fast: false
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default_language_version:
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python: python3
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default_stages:
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- commit
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- push
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minimum_pre_commit_version: 2.16.0
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repos:
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- repo: https://github.com/psf/black
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rev: "23.1.0"
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hooks:
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- id: black
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- repo: https://github.com/asottile/blacken-docs
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rev: 1.13.0
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hooks:
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- id: blacken-docs
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- repo: https://github.com/pre-commit/mirrors-prettier
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rev: v3.0.0-alpha.6
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hooks:
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- id: prettier
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# Newer versions of node don't work on systems that have an older version of GLIBC
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# (in particular Ubuntu 18.04 and Centos 7)
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# EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
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# See https://github.com/scverse/cookiecutter-scverse/issues/143 and
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# https://github.com/jupyterlab/jupyterlab/issues/12675
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language_version: "17.9.1"
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- repo: https://github.com/charliermarsh/ruff-pre-commit
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rev: v0.0.254
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hooks:
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- id: ruff
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args: [--fix, --exit-non-zero-on-fix]
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.4.0
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hooks:
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- id: detect-private-key
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- id: check-ast
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- id: end-of-file-fixer
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- id: mixed-line-ending
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args: [--fix=lf]
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- id: trailing-whitespace
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- id: check-case-conflict
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- repo: local
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hooks:
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- id: forbid-to-commit
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name: Don't commit rej files
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entry: |
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Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
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Fix the merge conflicts manually and remove the .rej files.
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language: fail
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files: '.*\.rej$'

‎docs/conf.py

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author = info["Weixu Wang"]
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copyright = f"{datetime.now():%Y}, {author}."
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version = info["Version"]
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repository_url = "https://github.com/theislab/RegVelo_repo"
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repository_url = "https://github.com/theislab/RegVelo"
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# The full version, including alpha/beta/rc tags
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release = info["Version"]

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