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Merge branch 'pymc-devs:main' into debug_docs_and_function_helpers
2 parents eebac25 + 89f6fcf commit d4df94f

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‎.github/workflows/devcontainer-docker-image.yml‎

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steps:
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- name: Checkout source
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uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
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uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
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- name: Setup Docker buildx
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uses: docker/setup-buildx-action@v3.0.0
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uses: docker/setup-buildx-action@v3.2.0
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- name: Prepare metadata
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id: meta
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type=raw,value=latest
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- name: Log into registry ${{ env.REGISTRY }}
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uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d
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uses: docker/login-action@e92390c5fb421da1463c202d546fed0ec5c39f20
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with:
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registry: ${{ env.REGISTRY }}
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Build and push Docker image
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id: docker_build
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uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09
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uses: docker/build-push-action@2cdde995de11925a030ce8070c3d77a52ffcf1c0
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with:
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context: .
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file: scripts/dev.Dockerfile

‎.github/workflows/dispatched_pre-commit.yml‎

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runPreCommit:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
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- uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
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with:
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repository: ${{github.event.client_payload.pull_request.head.repo.full_name}}
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ref: ${{github.event.client_payload.pull_request.head.ref}}

‎.github/workflows/docker-image.yml‎

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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@b4ffde65f46336ab88eb53be808477a3936bae11
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uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
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- name: Login to Docker Hub
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uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d
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uses: docker/login-action@e92390c5fb421da1463c202d546fed0ec5c39f20
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with:
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username: ${{ secrets.DOCKERHUB_USERNAME }}
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password: ${{ secrets.DOCKERHUB_TOKEN }}
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type=semver,pattern={{major}}.{{minor}}
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- name: Build and load image
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uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09
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uses: docker/build-push-action@2cdde995de11925a030ce8070c3d77a52ffcf1c0
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with:
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context: .
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file: scripts/Dockerfile
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docker run --rm ${{ env.CONTAINER_NAME }} conda run -n pymc-dev python -c 'import pymc;print(pymc.__version__)'
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- name: Build and push
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uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09
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uses: docker/build-push-action@2cdde995de11925a030ce8070c3d77a52ffcf1c0
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with:
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push: true

‎.github/workflows/pre-commit.yml‎

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env:
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SKIP: no-commit-to-branch
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steps:
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- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
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- uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
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- uses: actions/setup-python@v5
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with:
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python-version: "3.9" # Run pre-commit on oldest supported Python version
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run:
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shell: bash -l {0}
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steps:
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- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
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- uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
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- name: Cache conda
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uses: actions/cache@v4
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env:

‎.github/workflows/release.yml‎

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env:
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PYPI_TOKEN: ${{ secrets.PYPI_TOKEN_PYMC }}
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steps:
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- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
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- uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
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- name: Set up Python
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uses: actions/setup-python@v5
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‎.github/workflows/tests.yml‎

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outputs:
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changes: ${{ steps.changes.outputs.src }}
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steps:
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- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
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- uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
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with:
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fetch-depth: 0
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- uses: dorny/paths-filter@v3
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matrix:
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python-version: ["3.11"]
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python-version: ["3.12"]
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- |
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tests/test_util.py
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tests/distributions/test_multivariate.py
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- |
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tests/distributions/test_bound.py
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tests/distributions/test_censored.py
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tests/distributions/test_simulator.py
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tests/sampling/test_forward.py
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shell: bash -l {0}
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steps:
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- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
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- uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
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- name: Cache conda
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uses: actions/cache@v4
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env:
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conda activate pymc-test
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python -m pytest -vv --cov=pymc --cov-report=xml --no-cov-on-fail --cov-report term --durations=50 $TEST_SUBSET
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v3
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uses: codecov/codecov-action@v4
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token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
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env_vars: TEST_SUBSET
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- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
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- uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
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- name: Cache conda
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conda activate pymc-test &&
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python -m pytest -vv --cov=pymc --cov-report=xml --no-cov-on-fail --cov-report term --durations=50 %TEST_SUBSET%
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v3
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uses: codecov/codecov-action@v4
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token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
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env_vars: TEST_SUBSET
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python-version: ["3.10"]
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- |
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tests/sampling/test_parallel.py
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shell: bash -l {0}
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- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
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- uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
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- name: Cache conda
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env:
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python -m pytest -vv --cov=pymc --cov-report=xml --no-cov-on-fail --cov-report term --durations=50 $TEST_SUBSET
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v3
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uses: codecov/codecov-action@v4
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with:
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token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
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env_vars: TEST_SUBSET
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os: [ubuntu-20.04]
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python-version: ["3.11"]
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python-version: ["3.12"]
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test-subset:
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- tests/sampling/test_jax.py tests/sampling/test_mcmc_external.py
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fail-fast: false
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shell: bash -l {0}
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- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
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- uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
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- name: Cache conda
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python -m pytest -vv --cov=pymc --cov-report=xml --no-cov-on-fail --cov-report term --durations=50 $TEST_SUBSET
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v3
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uses: codecov/codecov-action@v4
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token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
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env_vars: TEST_SUBSET
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floatx: [float32]
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python-version: ["3.11"]
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python-version: ["3.12"]
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test-subset:
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- tests/sampling/test_mcmc.py tests/ode/test_ode.py tests/ode/test_utils.py tests/distributions/test_transform.py
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fail-fast: false
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shell: cmd
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- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
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- uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633
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- name: Cache conda
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env:
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conda activate pymc-test &&
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python -m pytest -vv --cov=pymc --cov-report=xml --no-cov-on-fail --cov-report term --durations=50 %TEST_SUBSET%
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v3
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uses: codecov/codecov-action@v4
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‎.pre-commit-config.yaml‎

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- --exclude=binder/
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- --exclude=versioneer.py
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.2.1
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rev: v0.3.4
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hooks:
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- id: ruff
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args: ["--fix", "--output-format=full"]

‎codecov.yml‎

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require_ci_to_pass: yes
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notify:
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after_n_builds: 15 # This should be updated if number of test jobs changes
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precision: 2

‎conda-envs/environment-dev.yml‎

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- pandas>=0.24.0
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- pip
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- pytensor>=2.18.1,<2.19
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- pytensor>=2.19,<2.20
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- python-graphviz
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- networkx
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- scipy>=1.4.1

‎conda-envs/environment-docs.yml‎

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- pip
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- pytensor>=2.18.1,<2.19
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- pytensor>=2.19,<2.20
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- python-graphviz
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- scipy>=1.4.1
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- typing-extensions>=3.7.4
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- sphinx-copybutton
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- sphinx-design
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- sphinx-notfound-page
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- sphinx-sitemap
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- sphinx>=5
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- sphinxext-rediraffe
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- watermark

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