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Merge branch 'pymc-devs:main' into main
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‎.coveragerc

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‎.github/PULL_REQUEST_TEMPLATE.md

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@@ -5,6 +5,6 @@ Depending on what your PR does, here are a few things you might want to address
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+ [ ] what are the (breaking) changes that this PR makes?
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+ [ ] important background, or details about the implementation
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+ [ ] are the changes—especially new features—covered by tests and docstrings?
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+ [ ] [linting/style checks have been run](https://github.com/pymc-devs/pymc3/wiki/PyMC3-Python-Code-Style)
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+ [ ] [linting/style checks have been run](https://docs.pymc.io/en/latest/contributing/python_style.html)
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+ [ ] [consider adding/updating relevant example notebooks](https://github.com/pymc-devs/pymc-examples)
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+ [ ] right before it's ready to merge, mention the PR in the RELEASE-NOTES.md

‎.github/workflows/arviz_compat.yml

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pull_request:
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push:
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branches: [main]
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paths:
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- ".github/workflows/*"
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- "pymc/**"
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- "setup.py"
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- "pyproject.toml"
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- "buildosx"
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- "conda-envs/**"
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- "codecov.yml"
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jobs:
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pytest:
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os: [ubuntu-latest, macos-latest]
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floatx: [float64]
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test-subset:
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- pymc/tests/test_distributions.py
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- pymc/tests/test_distributions_random.py
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- pymc/tests/test_sampling.py
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- |
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pymc/tests/test_parallel_sampling.py
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pymc/tests/test_posteriors.py
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pymc/tests/test_sampling.py
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- |
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pymc/tests/test_data_container.py
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pymc/tests/test_idata_conversion.py
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pymc/tests/test_missing.py
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pymc/tests/test_model.py
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pymc/tests/test_shape_handling.py
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pymc/tests/test_shared.py
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fail-fast: false
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runs-on: ${{ matrix.os }}
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env:
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- name: Cache conda
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uses: actions/cache@v1
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env:
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# Increase this value to reset cache if environment-dev-py39.yml has not changed
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# Increase this value to reset cache if environment-test-py39.yml has not changed
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CACHE_NUMBER: 0
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with:
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path: ~/conda_pkgs_dir
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key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
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hashFiles('conda-envs/environment-dev-py39.yml') }}
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hashFiles('conda-envs/environment-test-py39.yml') }}
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- name: Cache multiple paths
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uses: actions/cache@v2
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env:
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hashFiles('requirements.txt') }}
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- uses: conda-incubator/setup-miniconda@v2
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with:
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activate-environment: pymc-dev-py39
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miniforge-variant: Mambaforge
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miniforge-version: latest
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mamba-version: "*"
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activate-environment: pymc-test-py39
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channel-priority: strict
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environment-file: conda-envs/environment-dev-py39.yml
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environment-file: conda-envs/environment-test-py39.yml
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use-mamba: true
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use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
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- name: Install pymc
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run: |
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conda activate pymc-dev-py39
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conda activate pymc-test-py39
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pip install -e .
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python --version
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- name: Install latest arviz
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conda activate pymc-dev-py39
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conda activate pymc-test-py39
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pip uninstall arviz -y
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pip install git+git://github.com/arviz-devs/arviz.git
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pip install git+https://github.com/arviz-devs/arviz
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- name: Run tests
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python -m pytest -vv --cov=pymc --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET

‎.github/workflows/jaxtests.yml

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pull_request:
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push:
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branches: [main]
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paths:
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- ".github/workflows/*"
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- "pymc/**"
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- "setup.py"
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- "pyproject.toml"
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- "buildosx"
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- "conda-envs/**"
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- "codecov.yml"
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- name: Cache conda
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uses: actions/cache@v1
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env:
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# Increase this value to reset cache if environment-dev-py39.yml has not changed
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# Increase this value to reset cache if environment-test-py39.yml has not changed
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CACHE_NUMBER: 0
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with:
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path: ~/conda_pkgs_dir
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key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
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hashFiles('conda-envs/environment-dev-py39.yml') }}
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hashFiles('conda-envs/environment-test-py39.yml') }}
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- name: Cache multiple paths
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hashFiles('requirements.txt') }}
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- uses: conda-incubator/setup-miniconda@v2
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with:
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activate-environment: pymc-dev-py39
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miniforge-variant: Mambaforge
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miniforge-version: latest
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mamba-version: "*"
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activate-environment: pymc-test-py39
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channel-priority: strict
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environment-file: conda-envs/environment-dev-py39.yml
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environment-file: conda-envs/environment-test-py39.yml
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use-mamba: true
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use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
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- name: Install pymc
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conda activate pymc-dev-py39
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conda activate pymc-test-py39
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pip install -e .
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python --version
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conda activate pymc-dev-py39
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conda activate pymc-test-py39
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pip install "numpyro>=0.8.0"
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pip install git+https://github.com/blackjax-devs/blackjax.git@main
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python -m pytest -vv --cov=pymc --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET

‎.github/workflows/nightly.yml

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name: nightly
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on:
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schedule:
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- cron: "0 0 * * *"
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jobs:
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build-and-publish-nightly:
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name: Build source distribution
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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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with:
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fetch-depth: 0
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- uses: actions/setup-python@v2
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with:
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python-version: 3.9
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- name: Install dependencies
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run: |
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python -m pip install -U pip
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python -m pip install build
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- name: Build the sdist
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run: python -m build --sdist .
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env:
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BUILD_PYMC_NIGHTLY: true
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- name: Publish to PyPI
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uses: pypa/[email protected]
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with:
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user: __token__
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password: ${{ secrets.PYPI_TOKEN_PYMC_NIGHTLY }}
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test-install-job:
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needs: build-and-publish-nightly
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: 3.9
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- name: Give PyPI a chance to update the index
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run: sleep 240
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- name: Install from PyPI
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pip install pymc-nightly==$(grep 'version' pymc/__init__.py | awk '{print $3}' | tr -d '"').dev$(date +"%Y%m%d")

‎.github/workflows/pytest.yml

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branches: [main]
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paths:
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- ".github/workflows/*"
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- "pymc/**"
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- "setup.py"
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- "pyproject.toml"
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- "buildosx"
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- "conda-envs/**"
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- "codecov.yml"
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--ignore=pymc/tests/test_distributions_timeseries.py
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--ignore=pymc/tests/test_initial_point.py
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--ignore=pymc/tests/test_mixture.py
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--ignore=pymc/tests/test_model_graph.py
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--ignore=pymc/tests/test_modelcontext.py
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--ignore=pymc/tests/test_step.py
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--ignore=pymc/tests/test_tuning.py
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--ignore=pymc/tests/test_transforms.py
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--ignore=pymc/tests/test_variational_inference.py
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--ignore=pymc/tests/test_sampling_jax.py
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--ignore=pymc/tests/test_dist_math.py
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--ignore=pymc/tests/test_minibatches.py
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--ignore=pymc/tests/test_pickling.py
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--ignore=pymc/tests/test_updates.py
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--ignore=pymc/tests/test_gp.py
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--ignore=pymc/tests/test_model.py
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--ignore=pymc/tests/test_model_func.py
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--ignore=pymc/tests/test_ode.py
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--ignore=pymc/tests/test_posdef_sym.py
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--ignore=pymc/tests/test_quadpotential.py
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--ignore=pymc/tests/test_shape_handling.py
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--ignore=pymc/tests/test_distributions.py
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--ignore=pymc/tests/test_distributions_random.py
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--ignore=pymc/tests/test_idata_conversion.py
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--ignore=pymc/tests/test_smc.py
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--ignore=pymc/tests/test_missing.py
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pymc/tests/test_pickling.py
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pymc/tests/test_transforms.py
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pymc/tests/test_smc.py
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pymc/tests/test_mixture.py
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pymc/tests/test_step.py
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pymc/tests/test_profile.py
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pymc/tests/test_step.py
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pymc/tests/test_missing.py
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- uses: conda-incubator/setup-miniconda@v2
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with:
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miniforge-variant: Mambaforge
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miniforge-version: latest
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mamba-version: "*"
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activate-environment: pymc-test-py37
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use-mamba: true
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- name: Install-pymc
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pymc/tests/test_distributions_random.py
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pymc/tests/test_distributions_timeseries.py
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pymc/tests/test_variational_inference.py
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pymc/tests/test_parallel_sampling.py
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pymc/tests/test_model.py
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pymc/tests/test_modelcontext.py
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pymc/tests/test_model_graph.py
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- uses: conda-incubator/setup-miniconda@v2
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miniforge-variant: Mambaforge
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miniforge-version: latest
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mamba-version: "*"
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activate-environment: pymc-test-py38
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use-mamba: true
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- name: Install-pymc
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‎.github/workflows/release.yml

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twine check dist/*
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twine upload --repository pypi --username __token__ --password ${PYPI_TOKEN_PYMC} dist/*
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twine upload --repository pypi --username __token__ --password ${PYPI_TOKEN} dist/*
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test-install-job:
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needs: release-job
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runs-on: ubuntu-latest

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