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MarcoGorelliMarcoGorelli
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Merge remote-tracking branch 'upstream/master' into extend-plot_posterior_predictive_glm
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‎.codecov.yml

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codecov:
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require_ci_to_pass: no
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notify:
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after_n_builds: 7
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after_n_builds: 9
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coverage:
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precision: 2
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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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name: arviz-compatibility
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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: [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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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 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 }}-${{
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hashFiles('conda-envs/environment-dev-py38.yml') }}
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- name: Cache multiple paths
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uses: actions/cache@v2
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env:
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# Increase this value to reset cache if requirements.txt has not changed
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CACHE_NUMBER: 0
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with:
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path: |
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~/.cache/pip
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$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: pymc3-dev-py38
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channel-priority: strict
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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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- 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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- 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/dispatched_pre-commit.yml

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name: run pre-commit
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on:
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repository_dispatch:
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types: [pre-commit-run-command]
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jobs:
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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@v2
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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}}
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token: ${{ secrets.ACTION_TRIGGER_TOKEN }}
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- name: Cache multiple paths
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uses: actions/cache@v2
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with:
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path: |
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~/.cache/pre-commit
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~/.cache/pip
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key: pre-commit-dispatched-${{ runner.os }}-build
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- uses: actions/setup-python@v2
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with:
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python-version: 3.8
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- name: install-pre-commit
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run: python -m pip install --upgrade pre-commit
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- name: Slash Command Dispatch
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run: pre-commit run --all-files || (exit 0)
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- run: |
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git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
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git config --local user.name "github-actions[bot]"
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git commit -m "Run pre-commit" -a
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git push

‎.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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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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- |
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--ignore=pymc3/tests/test_examples.py
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--ignore=pymc3/tests/test_distributions_random.py
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--ignore=pymc3/tests/test_variational_inference.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_updates.py
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--ignore=pymc3/tests/test_posteriors.py
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--ignore=pymc3/tests/test_sampling.py
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--ignore=pymc3/tests/test_parallel_sampling.py
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--ignore=pymc3/tests/test_dist_math.py
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--ignore=pymc3/tests/test_distribution_defaults.py
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--ignore=pymc3/tests/test_distributions.py
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--ignore=pymc3/tests/test_distributions_random.py
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--ignore=pymc3/tests/test_distributions_timeseries.py
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--ignore=pymc3/tests/test_random.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_shape_handling
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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.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_distributions_random.py
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pymc3/tests/test_shared.py
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pymc3/tests/test_smc.py
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pymc3/tests/test_sampling.py
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pymc3/tests/test_parallel_sampling.py
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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_timeseries.py
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pymc3/tests/test_distributions_random.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_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_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_gp.py
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pymc3/tests/test_quadpotential.py
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- |
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pymc3/tests/test_variational_inference.py
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pymc3/tests/test_updates.py
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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-py39.yml has not changed
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CACHE_NUMBER: 0
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with:
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key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
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hashFiles('environment-dev.yml') }}
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hashFiles('conda-envs/environment-dev-py39.yml') }}
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- name: Cache multiple paths
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uses: actions/cache@v2
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env:
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# Increase this value to reset cache if requirements.txt has not changed
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CACHE_NUMBER: 0
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with:
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path: |
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~/.cache/pip
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$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-py39
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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-py39.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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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-py39
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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-py39
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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/slash_dispatch.yml

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name: Slash Command Dispatch
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on:
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issue_comment:
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types: [created]
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jobs:
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slashCommandDispatch:
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runs-on: ubuntu-latest
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steps:
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- name: Slash Command Dispatch
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uses: peter-evans/slash-command-dispatch@v2
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with:
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token: ${{ secrets.ACTION_TRIGGER_TOKEN }}
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issue-type: pull-request
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commands: |
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pre-commit-run

‎.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 }}-${{
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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: 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!
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- name: Install-pymc3
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run: |
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conda activate pymc3-dev-py37
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pip install -e .
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python --version
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- run: |
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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

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