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V 0.1.6 (#31)
* update version * Make tutorial notebooks external and update with latest cookiecutter changes (#28) * Make tutorial notebooks external * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update .readthedocs.yaml with the latest version on scverse cookiecutter * Realign pyproject.toml with scverse cookiecutter * Realign pyproject.toml with scverse cookiecutter * Realign pyproject.toml with scverse cookiecutter * Realign pyproject.toml with scverse cookiecutter * Realign pyproject.toml with scverse cookiecutter * Realign pyproject.toml with scverse cookiecutter * Realign pyproject.toml with scverse cookiecutter * Realign pyproject.toml with scverse cookiecutter * Realign pyproject.toml with scverse cookiecutter * Realign pyproject.toml with scverse cookiecutter * Realign pyproject.toml with scverse cookiecutter * Realign pyproject.toml with scverse cookiecutter * Realign pyproject.toml with scverse cookiecutter * Realign pyproject.toml with scverse cookiecutter * Realign pyproject.toml with scverse cookiecutter * Realign pyproject.toml with scverse cookiecutter * Realign pyproject.toml with scverse cookiecutter * Realign pyproject.toml with scverse cookiecutter * Realign pyproject.toml with scverse cookiecutter * Realign pyproject.toml with scverse cookiecutter --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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‎.github/workflows/build.yaml

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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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defaults:
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run:
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# to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
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shell: bash -euo pipefail {0}
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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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- uses: actions/checkout@v4
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with:
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filter: blob:none
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fetch-depth: 0
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- name: Install uv
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uses: astral-sh/setup-uv@v5
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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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cache-dependency-glob: pyproject.toml
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- name: Build package
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run: python -m build
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run: uv build
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- name: Check package
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run: twine check --strict dist/*.whl
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run: uvx twine check --strict dist/*.whl

‎.github/workflows/release.yaml

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release:
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types: [published]
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defaults:
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run:
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# to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
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shell: bash -euo pipefail {0}
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# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
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jobs:
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release:
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with:
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filter: blob:none
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fetch-depth: 0
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- uses: actions/setup-python@v4
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- name: Install uv
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uses: astral-sh/setup-uv@v5
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with:
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python-version: "3.x"
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cache: "pip"
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- run: pip install build
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- run: python -m build
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cache-dependency-glob: pyproject.toml
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- name: Build package
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run: uv build
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- name: Publish package distributions to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1

‎.github/workflows/test.yaml

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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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defaults:
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run:
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# to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
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shell: bash -euo pipefail {0}
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jobs:
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# Get the test environment from hatch as defined in pyproject.toml.
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# This ensures that the pyproject.toml is the single point of truth for test definitions and the same tests are
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# run locally and on continuous integration.
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# Check [[tool.hatch.envs.hatch-test.matrix]] in pyproject.toml and https://hatch.pypa.io/latest/environment/ for
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# more details.
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get-environments:
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runs-on: ubuntu-latest
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outputs:
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envs: ${{ steps.get-envs.outputs.envs }}
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steps:
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- uses: actions/checkout@v4
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with:
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filter: blob:none
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fetch-depth: 0
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- name: Install uv
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uses: astral-sh/setup-uv@v5
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- name: Get test environments
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id: get-envs
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run: |
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ENVS_JSON=$(uvx hatch env show --json | jq -c 'to_entries
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| map(
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select(.key | startswith("hatch-test"))
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| {
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name: .key,
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label: (if (.key | contains("pre")) then .key + " (PRE-RELEASE DEPENDENCIES)" else .key end),
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python: .value.python
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}
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)')
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echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT
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# Run tests through hatch. Spawns a separate runner for each environment defined in the hatch matrix obtained above.
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test:
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runs-on: ${{ matrix.os }}
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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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needs: get-environments
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strategy:
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fail-fast: false
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matrix:
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include:
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- os: ubuntu-latest
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python: "3.10"
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- os: ubuntu-latest
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python: "3.12"
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- os: ubuntu-latest
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python: "3.12"
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pip-flags: "--pre"
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name: PRE-RELEASE DEPENDENCIES
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name: ${{ matrix.name }} Python ${{ matrix.python }}
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os: [ubuntu-latest]
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env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
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env:
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OS: ${{ matrix.os }}
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PYTHON: ${{ matrix.python }}
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name: ${{ matrix.env.label }}
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runs-on: ${{ matrix.os }}
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steps:
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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@v4
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- uses: actions/checkout@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: Install test dependencies
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run: |
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python -m pip install --upgrade pip wheel
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- name: Install dependencies
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run: |
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pip install ${{ matrix.pip-flags }} ".[dev,test]"
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- name: Test
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filter: blob:none
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fetch-depth: 0
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- name: Install uv
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uses: astral-sh/setup-uv@v5
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with:
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python-version: ${{ matrix.env.python }}
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cache-dependency-glob: pyproject.toml
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- name: create hatch environment
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run: uvx hatch env create ${{ matrix.env.name }}
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- name: run tests using hatch
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env:
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MPLBACKEND: agg
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PLATFORM: ${{ matrix.os }}
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DISPLAY: :42
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run: |
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coverage run -m pytest -v --color=yes
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- name: Report coverage
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run: |
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coverage report
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run: uvx hatch run ${{ matrix.env.name }}:run-cov
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- name: generate coverage report
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run: uvx hatch run ${{ matrix.env.name }}:coverage xml
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- name: Upload coverage
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uses: codecov/codecov-action@v3
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uses: codecov/codecov-action@v4
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# Check that all tests defined above pass. This makes it easy to set a single "required" test in branch
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# protection instead of having to update it frequently. See https://github.com/re-actors/alls-green#why.
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check:
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name: Tests pass in all hatch environments
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if: always()
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needs:
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- get-environments
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- test
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runs-on: ubuntu-latest
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steps:
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- uses: re-actors/alls-green@release/v1
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with:
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jobs: ${{ toJSON(needs) }}

‎.gitmodules

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[submodule "docs/tutorials/external"]
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path = docs/tutorials/external
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url = https://github.com/theislab/DRVI_tutorials.git

‎.readthedocs.yaml

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# https://docs.readthedocs.io/en/stable/config-file/v2.html
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version: 2
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build:
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os: ubuntu-20.04
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os: ubuntu-24.04
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tools:
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python: "3.10"
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sphinx:
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configuration: docs/conf.py
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# disable this for more lenient docs builds
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fail_on_warning: false
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python:
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install:
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- method: pip
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path: .
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extra_requirements:
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- doc
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jobs:
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create_environment:
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- asdf plugin add uv
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- asdf install uv latest
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- asdf global uv latest
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build:
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html:
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- uvx hatch run docs:build
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- mv docs/_build $READTHEDOCS_OUTPUT
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submodules:
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include: all

‎README.md

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Please refer to the [documentation][link-docs]. In particular, the
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- [Tutorials][link-tutorials], specially
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- [A demo](https://drvi.readthedocs.io/latest/notebooks/general_pipeline.html) of how to train DRVI and interpret the latent dimensions.
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- [A demo](https://drvi.readthedocs.io/latest/tutorials/external/general_pipeline.html) of how to train DRVI and interpret the latent dimensions.
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- [API documentation][link-api], specially
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- [DRVI Model](https://drvi.readthedocs.io/latest/api/generated/drvi.model.DRVI.html)
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- [DRVI utility functions (tools)](https://drvi.readthedocs.io/latest/api/tools.html)
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[issue-tracker]: https://github.com/theislab/drvi/issues
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[changelog]: https://drvi.readthedocs.io/latest/changelog.html
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[link-docs]: https://drvi.readthedocs.io
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[link-api]: https://drvi.readthedocs.io/latest/api/index.html
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[link-api]: https://drvi.readthedocs.io
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[link-tutorials]: https://drvi.readthedocs.io/latest/tutorials.html
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[link-pypi]: https://pypi.org/project/drvi-py

‎docs/api/index.md

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‎docs/api/metrics.md

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# Metrics
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We have implemented a user-friendly class for evaluation of disentanglement with respect to known discrete targets.
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```{eval-rst}
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.. module:: drvi.utils.metrics
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.. currentmodule:: drvi.utils
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.. autosummary::
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:nosignatures:
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:toctree: generated
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metrics.DiscreteDisentanglementBenchmark
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```
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The following functions represent the similarity functions used in benchmarking:
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```{eval-rst}
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.. module:: drvi.utils.metrics
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.. currentmodule:: drvi.utils
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metrics.nn_alignment_score
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metrics.local_mutual_info_score
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metrics.global_dim_mutual_info_score
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metrics.spearman_correlataion_score
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```
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The following functions represent the aggregation functions used in benchmarking:
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```{eval-rst}
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.. module:: drvi.utils.metrics
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.. currentmodule:: drvi.utils
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.. autosummary::
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:nosignatures:
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:toctree: generated
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metrics.most_similar_averaging_score
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metrics.latent_matching_score
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metrics.most_similar_gap_score

‎docs/conf.py

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"sphinx.ext.napoleon",
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"sphinxcontrib.bibtex",
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"sphinx_autodoc_typehints",
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"sphinx_tabs.tabs",
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"sphinx.ext.mathjax",
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"IPython.sphinxext.ipython_console_highlighting",
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"sphinxext.opengraph",
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}
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intersphinx_mapping = {
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# General
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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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"matplotlib": ("https://matplotlib.org/stable/", None),
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# Numerical
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"numpy": ("https://numpy.org/doc/stable/", None),
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"pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
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"scipy": ("https://docs.scipy.org/doc/scipy/", None),
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# Deep learning
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"torch": ("https://docs.pytorch.org/docs/main", None),
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"lightning": ("https://lightning.ai/docs/pytorch/stable/", None),
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# Special
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"anndata": ("https://anndata.readthedocs.io/en/stable/", None),
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"mudata": ("https://mudata.readthedocs.io/en/stable/", None),
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"scvi-tools": ("https://docs.scvi-tools.org/en/stable/", None),
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}
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# List of patterns, relative to source directory, that match files and

‎docs/index.md

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```
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```{toctree}
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:caption: 'API'
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:hidden: true
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:maxdepth: 1
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api/model
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api/tools
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api/plotting
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api/metrics
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```
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```{toctree}
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:caption: 'General'
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:hidden: true
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:maxdepth: 1
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api/index.md
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changelog.md
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contributing.md
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references.md
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tutorials.md
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```
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```{toctree}
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:caption: 'Usage'
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:hidden: true
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:maxdepth: 1
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tutorials/index.md
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```

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