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Merge branch 'master' into fix-4206
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‎.codecov.yml

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# basic
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target: auto
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threshold: 1%
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base: auto
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base: auto
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patch:
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default:
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# basic
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target: 50%
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threshold: 1%
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base: auto
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base: auto
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comment:
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layout: "reach, diff, flags, files"

‎.github/ISSUE_TEMPLATE.md

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If you have questions about a specific use case, or you are not sure whether this is a bug or not, please post it to our discourse channel: https://discourse.pymc.io
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If you have questions about a specific use case, or you are not sure whether this is a bug or not, please post it to our discourse channel: https://discourse.pymc.io
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## Description of your problem
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‎.github/workflows/arviz_compat.yml

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pytest:
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strategy:
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matrix:
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python-version: ["3.8"]
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os: [ubuntu-18.04]
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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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- pymc3/tests/test_distributions_random.py
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- pymc3/tests/test_sampling.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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TEST_SUBSET: ${{ matrix.test-subset }}
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THEANO_FLAGS: floatX=${{ matrix.floatx }},gcc.cxxflags='-march=native'
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THEANO_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=native'
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defaults:
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run:
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shell: bash -l {0}
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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.yml has not changed
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# Increase this value to reset cache if environment-dev-py38.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 }}-${{
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hashFiles('environment-dev.yml') }}
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hashFiles('conda-envs/environment-dev-py38.yml') }}
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- name: Cache multiple paths
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uses: actions/cache@v2
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env:
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# Increase this value to reset cache if requirements.txt has not changed
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CACHE_NUMBER: 0
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with:
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path: |
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~/.cache/pip
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$RUNNER_TOOL_CACHE/Python/*
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~\AppData\Local\pip\Cache
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key: ${{ runner.os }}-build-${{ matrix.python-version }}-${{
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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: testenv
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activate-environment: pymc3-dev-py38
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channel-priority: strict
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environment-file: environment-dev.yml
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environment-file: conda-envs/environment-dev-py38.yml
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use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
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- run: |
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conda activate testenv
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conda remove arviz -y
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- name: Install pymc3
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run: |
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conda activate pymc3-dev-py38
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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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run: |
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conda activate pymc3-dev-py38
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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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python -m pytest -v --cov=pymc3 --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET -n auto
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- name: Run tests
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run: |
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python -m pytest -vv --cov=pymc3 --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET

‎.github/workflows/autoupdate-pre-commit-config.yml

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name: "Update pre-commit config"
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on:
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schedule:
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- cron: "0 7 * * 1" # At 07:00 on each Monday.
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workflow_dispatch:
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jobs:
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update-pre-commit:
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if: github.repository_owner == 'pymc-devs'
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name: Autoupdate pre-commit config
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runs-on: ubuntu-latest
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steps:
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- name: Set up Python
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uses: actions/setup-python@v2
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- name: Cache multiple paths
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uses: actions/cache@v2
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with:
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path: |
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~/.cache/pre-commit
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~/.cache/pip
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key: pre-commit-autoupdate-${{ runner.os }}-build
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- name: Update pre-commit config packages
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uses: technote-space/create-pr-action@v2
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with:
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GITHUB_TOKEN: ${{ secrets.ACTION_TRIGGER_TOKEN }}
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EXECUTE_COMMANDS: |
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pip install pre-commit
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pre-commit autoupdate || (exit 0);
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pre-commit run -a || (exit 0);
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COMMIT_MESSAGE: "⬆️ UPGRADE: Autoupdate pre-commit config"
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PR_BRANCH_NAME: "pre-commit-config-update-${PR_ID}"
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PR_TITLE: "⬆️ UPGRADE: Autoupdate pre-commit config"

‎.github/workflows/pre-commit.yml

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jobs:
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pre-commit:
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runs-on: ubuntu-latest
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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@v2
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- uses: actions/setup-python@v2

‎.github/workflows/pytest.yml

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pytest:
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strategy:
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matrix:
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python-version: ["3.6"]
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os: [ubuntu-18.04]
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floatx: [float32, float64]
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test-subset:
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--ignore=pymc3/tests/test_distributions_timeseries.py
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--ignore=pymc3/tests/test_examples.py
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--ignore=pymc3/tests/test_gp.py
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--ignore=pymc3/tests/test_mixture.py
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--ignore=pymc3/tests/test_ode.py
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--ignore=pymc3/tests/test_parallel_sampling.py
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--ignore=pymc3/tests/test_posteriors.py
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--ignore=pymc3/tests/test_quadpotential.py
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--ignore=pymc3/tests/test_random.py
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--ignore=pymc3/tests/test_sampling.py
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--ignore=pymc3/tests/test_shape_handling
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--ignore=pymc3/tests/test_shape_handling.py
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--ignore=pymc3/tests/test_shared.py
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--ignore=pymc3/tests/test_smc.py
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--ignore=pymc3/tests/test_step.py
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--ignore=pymc3/tests/test_updates.py
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--ignore=pymc3/tests/test_variational_inference.py
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- |
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pymc3/tests/test_dist_math.py
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pymc3/tests/test_distribution_defaults.py
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pymc3/tests/test_distributions_random.py
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pymc3/tests/test_distributions_timeseries.py
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pymc3/tests/test_parallel_sampling.py
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pymc3/tests/test_random.py
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pymc3/tests/test_sampling.py
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pymc3/tests/test_shared.py
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pymc3/tests/test_smc.py
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- |
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pymc3/tests/test_examples.py
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pymc3/tests/test_gp.py
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pymc3/tests/test_mixture.py
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pymc3/tests/test_ode.py
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pymc3/tests/test_posteriors.py
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pymc3/tests/test_quadpotential.py
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- |
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pymc3/tests/test_distributions_timeseries.py
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pymc3/tests/test_shape_handling.py
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pymc3/tests/test_step.py
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pymc3/tests/test_updates.py
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pymc3/tests/test_variational_inference.py
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- |
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pymc3/tests/test_distributions.py
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pymc3/tests/test_gp.py
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pymc3/tests/test_sampling.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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TEST_SUBSET: ${{ matrix.test-subset }}
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THEANO_FLAGS: floatX=${{ matrix.floatx }},gcc.cxxflags='-march=native'
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THEANO_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=native'
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defaults:
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run:
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shell: bash -l {0}
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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.yml has not changed
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# Increase this value to reset cache if environment-dev-py36.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 }}-${{
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hashFiles('environment-dev.yml') }}
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hashFiles('conda-envs/environment-dev-py36.yml') }}
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- name: Cache multiple paths
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uses: actions/cache@v2
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env:
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# Increase this value to reset cache if requirements.txt has not changed
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CACHE_NUMBER: 0
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with:
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path: |
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~/.cache/pip
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$RUNNER_TOOL_CACHE/Python/*
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~\AppData\Local\pip\Cache
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key: ${{ runner.os }}-build-${{ matrix.python-version }}-${{
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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: testenv
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activate-environment: pymc3-dev-py36
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channel-priority: strict
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environment-file: environment-dev.yml
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environment-file: conda-envs/environment-dev-py36.yml
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use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
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- run: |
80-
conda activate testenv
81-
python -m pytest -v --cov=pymc3 --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET -n auto
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- name: Install-pymc3
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run: |
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conda activate pymc3-dev-py36
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pip install -e .
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python --version
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- name: Run tests
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run: |
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conda activate pymc3-dev-py36
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python -m pytest -vv --cov=pymc3 --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v1
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with:

‎.github/workflows/windows.yml

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name: windows
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on:
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pull_request:
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push:
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branches: [master]
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jobs:
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pytest:
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strategy:
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matrix:
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os: [windows-latest]
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floatx: [float64]
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test-subset:
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- pymc3/tests/test_distributions_random.py
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- pymc3/tests/test_sampling.py
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runs-on: ${{ matrix.os }}
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env:
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TEST_SUBSET: ${{ matrix.test-subset }}
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THEANO_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=core2'
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defaults:
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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@v2
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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 conda-envs/environment-dev-py37.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 }}-${{
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hashFiles('conda-envs/environment-dev-py37.yml') }}
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- name: Cache multiple paths
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uses: actions/cache@v2
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env:
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# Increase this value to reset cache if requirements.txt has not changed
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CACHE_NUMBER: 0
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with:
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path: |
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~/.cache/pip
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$RUNNER_TOOL_CACHE/Python/*
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~\AppData\Local\pip\Cache
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key: ${{ runner.os }}-build-${{ matrix.python-version }}-${{
46+
hashFiles('requirements.txt') }}
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- uses: conda-incubator/setup-miniconda@v2
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with:
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activate-environment: pymc3-dev-py37
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channel-priority: strict
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environment-file: conda-envs/environment-dev-py37.yml
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use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
53+
- name: Install-pymc3
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run: |
55+
conda activate pymc3-dev-py37
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pip install -e .
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python --version
58+
- run: |
59+
conda activate pymc3-dev-py37
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python -m pytest -vv --cov=pymc3 --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET

‎.pre-commit-config.yaml

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exclude: ^(docs/logos|pymc3/examples/data)/
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
34
rev: v3.3.0
45
hooks:
5-
- id: end-of-file-fixer
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- id: check-merge-conflict
67
- id: check-toml
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- id: check-yaml
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- id: debug-statements
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- id: end-of-file-fixer
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- id: no-commit-to-branch
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args: [--branch, master]
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- id: requirements-txt-fixer
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exclude: ^requirements-dev\.txt$
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- id: trailing-whitespace
716
- repo: https://github.com/nbQA-dev/nbQA
8-
rev: 0.4.1
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rev: 0.5.4
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hooks:
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- id: nbqa-black
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additional_dependencies: [black==20.8b1]
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- id: nbqa-isort
1322
additional_dependencies: [isort==5.6.4]
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- id: nbqa-pyupgrade
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additional_dependencies: [pyupgrade==2.7.4]
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- repo: https://github.com/PyCQA/isort
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rev: 5.6.4
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hooks:
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- id: isort
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name: isort
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- repo: https://github.com/asottile/pyupgrade
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rev: v2.7.4
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hooks:
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- repo: local
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hooks:
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- id: watermark
34-
name: Check notebooks have watermark (see Jupyter style guide from PyMC3 Wiki)
35-
types: [jupyter]
48+
args: [--negate, --multiline]
3649
entry: '%load_ext watermark.*%watermark -n -u -v -iv -w'
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language: pygrep
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args: [--negate, --multiline]
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minimum_pre_commit_version: 2.8.0
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name: Check notebooks have watermark (see Jupyter style guide from PyMC3 Wiki)
53+
types: [jupyter]
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- id: check-toc
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entry: python scripts/check_toc_is_complete.py
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language: python
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name: Check all notebooks appear in table of contents
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types: [jupyter]
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entry: python scripts/check_toc_is_complete.py
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- id: check-no-tests-are-ignored
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entry: python scripts/check_all_tests_are_covered.py
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files: ^\.github/workflows/pytest\.yml$
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language: python
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name: Check no tests are ignored
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pass_filenames: false
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- id: conda-env-sort
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additional_dependencies: [pyyaml]
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entry: python scripts/sort_conda_envs.py
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files: ^conda-envs/
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language: python
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name: Sort dependencies in conda envs
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types: [yaml]
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- id: pip-from-conda
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additional_dependencies: [pyyaml]
74+
entry: python scripts/generate_pip_deps_from_conda.py
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files: ^conda-envs/
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language: python
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name: Generate pip dependency from conda
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- id: no-relative-imports
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name: No relative imports
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entry: from \.[\.\w]* import
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types: [python]
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language: pygrep

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