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‎.codecov.yml

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codecov:
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require_ci_to_pass: yes
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require_ci_to_pass: no
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notify:
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after_n_builds: 9
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coverage:
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precision: 2
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round: down
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range: "70...100"
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status:
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project: yes
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patch: yes
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changes: no
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project:
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default:
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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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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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comment:
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layout: "reach, diff, flags, files"

‎.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-18.04]
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floatx: [float64]
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test-subset:
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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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- 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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conda remove 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/pytest.yml

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name: pytest
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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-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_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_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_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_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_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_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_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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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-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('conda-envs/environment-dev-py36.yml') }}
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- uses: conda-incubator/setup-miniconda@v2
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with:
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activate-environment: pymc3-dev-py36
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channel-priority: strict
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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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- 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:
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env_vars: OS,PYTHON
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name: codecov-umbrella
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fail_ci_if_error: false

‎.gitignore

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# Merge tool
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*.orig
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# Test artifacts
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mcmc.sqlite
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# Docker development
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# notebooks/
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pytestdebug.log
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.dir-locals.el
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.pycheckers
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# Codespaces
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pythonenv*

‎.pre-commit-config.yaml

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- id: end-of-file-fixer
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- id: check-toml
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- repo: https://github.com/nbQA-dev/nbQA
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rev: 0.3.5
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rev: 0.4.1
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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
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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/asottile/pyupgrade
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rev: v2.7.3
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rev: v2.7.4
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hooks:
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- id: pyupgrade
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args: [--py36-plus]
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- repo: https://github.com/psf/black
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rev: 20.8b1
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hooks:
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- id: black
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- repo: https://github.com/PyCQA/pylint
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rev: pylint-2.6.0
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hooks:
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- id: pylint
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args: [--rcfile=.pylintrc]
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files: ^pymc3/
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- repo: local
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hooks:
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- id: watermark
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name: Check notebooks have watermark (see Jupyter style guide from PyMC3 Uncyclo)
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types: [jupyter]
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args: [--negate, --multiline]
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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 Uncyclo)
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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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pass_filenames: false
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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

‎.pylintrc

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# Enable the message, report, category or checker with the given id(s). You can
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# either give multiple identifier separated by comma (,) or put this option
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# multiple time. See also the "--disable" option for examples.
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enable=import-error,
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import-self,
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enable=import-self,
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reimported,
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wildcard-import,
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misplaced-future,

‎.travis.yml

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This file was deleted.

‎CONTRIBUTING.md

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3. Create a ``feature`` branch to hold your development changes:
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```bash
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$ git checkout -b my-feature
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$ git switch -c my-feature
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```
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Always use a ``feature`` branch. It's good practice to never routinely work on the ``master`` branch of any repository.
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4. Project requirements are in ``requirements.txt``, and libraries used for development are in ``requirements-dev.txt``. To set up a development environment, you may (probably in a [virtual environment](https://docs.python-guide.org/dev/virtualenvs/)) run:
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4. Project requirements are in ``requirements.txt``, and libraries used for development are in ``requirements-dev.txt``. The easiest (and recommended) way to set up a development environment is via [miniconda](https://docs.conda.io/en/latest/miniconda.html):
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```bash
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$ pip install -r requirements.txt
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$ conda env create -f conda-envs/environment-dev-py36.yml # or py37 or py38
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$ conda activate pymc3-dev-py36
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$ pip install -e .
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```
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_Alternatively_ you may (probably in a [virtual environment](https://docs.python-guide.org/dev/virtualenvs/)) run:
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```bash
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$ pip install -e .
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$ pip install -r requirements-dev.txt
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```
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Alternatively, there is a script to create a docker environment for development. See: [Developing in Docker](#Developing-in-Docker).
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Yet another alternative is to create a docker environment for development. See: [Developing in Docker](#Developing-in-Docker).
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5. Develop the feature on your feature branch. Add changed files using ``git add`` and then ``git commit`` files:
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$ pytest --cov=pymc3 pymc3/tests/<name of test>.py
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```
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* No `pyflakes` warnings, check with:
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```bash
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$ pip install pyflakes
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$ pyflakes path/to/module.py
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```
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* No PEP8 warnings, check with:
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```bash
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$ pip install pycodestyle
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$ pycodestyle path/to/module.py
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```
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* AutoPEP8 can help you fix some of the easy redundant errors:
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```bash
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$ pip install autopep8
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$ autopep8 path/to/pep8.py
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```
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* No `pre-commit` errors: see the [Python code style](https://github.com/pymc-devs/pymc3/wiki/PyMC3-Python-Code-Style) and [Jupyter Notebook style](https://github.com/pymc-devs/pymc3/wiki/PyMC's-Jupyter-Notebook-Style) page from our Uncyclo on how to install and run it.
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## Developing in Docker
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‎README.rst

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- **Variational inference**: `ADVI <http://www.jmlr.org/papers/v18/16-107.html>`__
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for fast approximate posterior estimation as well as mini-batch ADVI
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for large data sets.
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- Relies on `Theano <http://deeplearning.net/software/theano/>`__ which provides:
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- Relies on `Theano <https://theano-pymc.readthedocs.io/en/latest/>`__ which provides:
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* Computation optimization and dynamic C compilation
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* Numpy broadcasting and advanced indexing
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* Linear algebra operators

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