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grstgrst
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template update
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‎.cruft.json

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{
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"template": "https://github.com/scverse/cookiecutter-scverse",
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"commit": "7cc5403b05e299d7a4bb169c2bd8c27a2a7676f3",
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"checkout": null,
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"context": {
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"cookiecutter": {
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"project_name": "sobolev_alignment",
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"package_name": "sobolev_alignment",
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"project_description": "Sobolev alignment of deep probabilistic models for comparing single cell profiles",
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"author_full_name": "Soufiane Mourragui",
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"author_email": "soufiane.mourragui@gmail.com",
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"github_user": "saroudant",
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"project_repo": "https://github.com/saroudant/sobolev_alignment",
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"license": "MIT 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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"template": "https://github.com/scverse/cookiecutter-scverse",
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"commit": "c21b82bf134f3a0f13db7482d4fb04ca1f562d59",
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"checkout": "main",
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"context": {
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"cookiecutter": {
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"project_name": "sobolev_alignment",
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"package_name": "sobolev_alignment",
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"project_description": "Sobolev alignment of deep probabilistic models for comparing single cell profiles",
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"author_full_name": "Soufiane Mourragui",
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"author_email": "soufiane.mourragui@gmail.com",
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"github_user": "saroudant",
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"project_repo": "https://github.com/saroudant/sobolev_alignment",
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"license": "MIT 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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}

‎.flake8

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This file was deleted.

‎.github/ISSUE_TEMPLATE/bug_report.yml

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**Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
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detailing how to provide the necessary information for us to reproduce your bug. In brief:
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* Please provide exact steps how to reproduce the bug in a clean Python environment.
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* In case it's not clear what's causing this bug, please provide the data or the data generation procecure.
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* Sometimes it is not possible to share the data but usually it is possible to replicate problems on publicly
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* In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
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* Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
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available datasets or to share a subset of your data.
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- type: textarea

‎.github/workflows/build.yaml

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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@v2
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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@v2
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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

‎.github/workflows/sync.yaml

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manually merge these changes.**
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For more information about the template sync, please refer to the
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[template documentation](https://cookiecutter-scverse-instance.readthedocs.io/en/latest/developer_docs.html#automated-template-sync).
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[template documentation](https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html#automated-template-sync).

‎.github/workflows/test.yaml

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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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test:
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runs-on: ${{ 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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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python }}
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uses: actions/setup-python@v2
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python }}
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cache: "pip"
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cache-dependency-path: "**/pyproject.toml"
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- name: Get pip cache dir
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id: pip-cache-dir
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run: |
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echo "::set-output name=dir::$(pip cache dir)"
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- name: Restore pip cache
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uses: actions/cache@v2
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with:
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path: ${{ steps.pip-cache-dir.outputs.dir }}
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key: pip-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml') }}
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restore-keys: |
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pip-${{ runner.os }}-${{ env.pythonLocation }}-
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- name: Install test dependencies
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run: |
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python -m pip install --upgrade pip wheel
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pip install codecov
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- name: Install dependencies
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run: |
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pip install ".[dev,test]"

‎.github/workflows/test.yaml.rej

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diff a/.github/workflows/test.yaml b/.github/workflows/test.yaml (rejected hunks)
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run: |
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pytest -v --cov --color=yes
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- name: Upload coverage
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- env:
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- CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
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- run: |
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- codecov --required --flags=unittests
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+ uses: codecov/codecov-action@v3

‎.gitignore

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# Temp files
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.DS_Store
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*~
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buck-out/
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# Compiled files
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.venv/
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__pycache__/
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.mypy_cache/
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.ruff_cache/
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# Distribution / packaging
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/build/

‎.pre-commit-config.yaml

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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: 23.3.0
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rev: "23.3.0"
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hooks:
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- id: black
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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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- 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/PyCQA/isort
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rev: 5.12.0
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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: isort
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- repo: https://github.com/asottile/yesqa
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rev: v1.4.0
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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: v0.0.261
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hooks:
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- id: yesqa
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additional_dependencies:
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- flake8-tidy-imports
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- flake8-docstrings
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- flake8-rst-docstrings
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- flake8-comprehensions
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- flake8-bugbear
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- flake8-blind-except
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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:

‎.pre-commit-config.yaml.rej

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diff a/.pre-commit-config.yaml b/.pre-commit-config.yaml (rejected hunks)
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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: https://github.com/myint/autoflake
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- rev: v2.0.2
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- hooks:
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- - id: autoflake
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- args:
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- - --in-place
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- - --remove-all-unused-imports
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- - --remove-unused-variable
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- - --ignore-init-module-imports
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- - repo: https://github.com/PyCQA/flake8
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- rev: 6.0.0
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- hooks:
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- - id: flake8
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- additional_dependencies:
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- - flake8-tidy-imports
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- - flake8-docstrings
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- - flake8-rst-docstrings
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- - flake8-comprehensions
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- - flake8-bugbear
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- - flake8-blind-except
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- - repo: https://github.com/asottile/pyupgrade
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- rev: v3.3.1
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- hooks:
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- - id: pyupgrade
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- args: [--py3-plus, --py38-plus, --keep-runtime-typing]
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- repo: local
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hooks:
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- id: forbid-to-commit

‎docs/conf.py

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napoleon_include_init_with_doc = False
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napoleon_use_rtype = True # having a separate entry generally helps readability
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napoleon_use_param = True
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myst_heading_anchors = 3 # create anchors for h1-h3
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myst_heading_anchors = 6 # create anchors for h1-h6
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myst_enable_extensions = [
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"amsmath",
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"colon_fence",
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}
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intersphinx_mapping = {
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"python": ("https://docs.python.org/3", None),
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"anndata": ("https://anndata.readthedocs.io/en/stable/", None),
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"numpy": ("https://numpy.org/doc/stable/", None),
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}

‎docs/conf.py.rej

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diff a/docs/conf.py b/docs/conf.py (rejected hunks)
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@@ -16,12 +16,15 @@ sys.path.insert(0, str(HERE / "extensions"))
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# -- Project information -----------------------------------------------------
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+# NOTE: If you installed your project in editable mode, this might be stale.
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+# If this is the case, reinstall it to refresh the metadata
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info = metadata("sobolev_alignment")
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project_name = info["Name"]
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author = info["Author"]
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copyright = f"{datetime.now():%Y}, {author}."
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version = info["Version"]
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-repository_url = f"https://github.com/saroudant/{project_name}"
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+urls = dict(pu.split(", ") for pu in info.get_all("Project-URL"))
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+repository_url = urls["Source"]
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# The full version, including alpha/beta/rc tags
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release = info["Version"]
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html_theme_options = {
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"repository_url": repository_url,
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"use_repository_button": True,
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+ "path_to_docs": "docs/",
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}
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pygments_style = "default"

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