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junpenglaojunpenglao
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Merge branch 'main' into vi_dev
2 parents 40d8cfb + 17199c6 commit 7000b2f

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‎.github/workflows/benchmark.yml

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name: Benchmarks
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on:
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push:
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branches:
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- main
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jobs:
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benchmark:
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name: Run benchmarks
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [ '3.10' ]
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steps:
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- uses: actions/checkout@v1
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Set up benchmark environment
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run: |
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python -m pip install -U pip
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pip install .
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less requirements.txt | grep 'pytest\|chex' | xargs -i -t pip install {}
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- name: Run benchmarks
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run: |
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pytest -vv -m benchmark

‎.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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push:
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branches: [main]
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jobs:
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build_and_publish:
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name: Build source distribution
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name: Build and publish on PyPi
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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: "3.7"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install --upgrade build
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- name: Build the sdist
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run: python -m build
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env:
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BUILD_BLACKJAX_NIGHTLY: true
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- uses: pypa/gh-action-pypi-publish@v1.4.2
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with:
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user: __token__
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password: ${{ secrets.PYPI_NIGHTLY_TOKEN }}
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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: Update pyproject.toml
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# Taken from https://github.com/aesara-devs/aesara/pull/1375
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run: |
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curl -sSLf https://github.com/TomWright/dasel/releases/download/v2.0.2/dasel_linux_amd64 \
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-L -o /tmp/dasel && chmod +x /tmp/dasel
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/tmp/dasel put -f pyproject.toml project.name -v blackjax-nightly
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/tmp/dasel put -f pyproject.toml tool.setuptools_scm.version_scheme -v post-release
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/tmp/dasel put -f pyproject.toml tool.setuptools_scm.local_scheme -v no-local-version
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- name: Build the sdist and wheel
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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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python -m build
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- name: Check sdist install and imports
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run: |
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mkdir -p test-sdist
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cd test-sdist
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python -m venv venv-sdist
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venv-sdist/bin/python -m pip install ../dist/blackjax-nightly-*.tar.gz
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venv-sdist/bin/python -c "import blackjax"
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- name: Check wheel install and imports
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run: |
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mkdir -p test-wheel
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cd test-wheel
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python -m venv venv-wheel
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venv-wheel/bin/python -m pip install ../dist/blackjax_nightly-*.whl
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- name: Publish to PyPi
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uses: pypa/gh-action-pypi-publish@v1.4.2
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with:
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user: __token__
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password: ${{ secrets.PYPI_NIGHTLY_TOKEN }}

‎.github/workflows/release.yml

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jobs:
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release-job:
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name: Release on PyPi
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name: Build and publish on PyPi
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runs-on: ubuntu-latest
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env:
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PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
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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@v1
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uses: actions/setup-python@v2
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with:
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python-version: 3.7
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- name: Install release tooling
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python-version: 3.9
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- name: Build sdist and wheel
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run: |
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pip install twine wheel
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- name: Build package
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python -m pip install -U pip
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python -m pip install build
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python -m build
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- name: Check that the package version matches the Release name
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run: |
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python setup.py sdist bdist_wheel
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- name: Check that `blackjax.__version__` matches the Release name
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run: |
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echo "GITHUB_REF: ${GITHUB_REF}"
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# The GITHUB_REF should be something like "refs/tags/v3.x.x"
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# Make sure the package version is the same as the tag
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grep -Rq "^Version: ${GITHUB_REF:10}$" blackjax.egg-info/PKG-INFO
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- name: Publish to PyPi
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- name: Check sdist install and imports
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run: |
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twine check dist/*
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twine upload --repository pypi --username __token__ --password ${PYPI_TOKEN} dist/*
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mkdir -p test-sdist
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cd test-sdist
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python -m venv venv-sdist
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venv-sdist/bin/python -m pip install ../dist/blackjax-*.tar.gz
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venv-sdist/bin/python -c "import blackjax"
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- name: Check wheel install and imports
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run: |
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mkdir -p test-wheel
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cd test-wheel
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python -m venv venv-wheel
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venv-wheel/bin/python -m pip install ../dist/blackjax-*.whl
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venv-wheel/bin/python -c "import blackjax"
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- name: Publish to PyPi
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uses: pypa/gh-action-pypi-publish@v1.4.2
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with:
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user: __token__
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password: ${{ secrets.PYPI_TOKEN }}
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test-install-job:
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name: Test install from PyPi
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needs: release-job

‎.github/workflows/test.yml

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steps:
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- uses: actions/checkout@v2
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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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- uses: pre-commit/action@v2.0.0
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test:
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matrix:
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python-version: [ '3.7', '3.10']
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steps:
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- uses: actions/checkout@v1
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dev environment & blackjax
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run: |
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python -m pip install --upgrade pip
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pip install .
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less requirements.txt | grep 'pytest\|chex' | xargs -i -t pip install {}
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- name: Run the tests with pytest
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run: |
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pytest -n 4 -vv -m "not benchmark" --cov=blackjax --cov-report=xml --cov-report=term tests
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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
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benchmark:
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name: Run benchmarks
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needs: [test]
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [ '3.10' ]
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steps:
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- uses: actions/checkout@v1
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dev environment & blackjax
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run: |
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python -m pip install --upgrade pip
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pip install .
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less requirements.txt | grep 'pytest\|chex' | xargs -i -t pip install {}
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- name: Run the benchmarks with pytest-benchmark
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run: |
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pytest -n 4 -vv -m benchmark --cov=blackjax --cov-report=xml --cov-report=term tests
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- uses: actions/checkout@v1
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Set up test environment
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run: |
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python -m pip install --upgrade pip
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pip install .
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less requirements.txt | grep 'pytest\|chex' | xargs -i -t pip install {}
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- name: Run tests
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run: |
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pytest -n auto -vv -m "not benchmark" --cov=blackjax --cov-report=xml --cov-report=term tests
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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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.installed.cfg
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*.egg
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MANIFEST
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_version.py
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# Installer logs
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pip-log.txt

‎.gitlint

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[title-max-length]
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line-length=120
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[title-min-length]
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min-length=15
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[title-match-regex]
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# python-style regex that the commit-msg title must match
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# Note that the regex can contradict with other rules if not used correctly
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# (e.g. title-must-not-contain-word).
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regex=^[A-Z].*$
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[title-must-not-contain-word]
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# Comma-separated list of words that should not occur in the title. Matching is case
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# insensitive. It's fine if the keyword occurs as part of a larger word (so "WIPING"
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# will not cause a violation, but "WIP: my title" will.
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words=wip
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[body-max-line-length]
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line-length=72

‎.pre-commit-config.yaml

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exclude: |
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(?x)^(
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versioneer\.py|
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blackjax/_version\.py|
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)$
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repos:
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args: ['--profile=black']
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- id: nbqa-flake8
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args: ['--ignore=E501,E203,E302,E402,E731,W503']
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- repo: https://github.com/jorisroovers/gitlint
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rev: v0.18.0
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hooks:
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- id: gitlint
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- id: gitlint-ci

‎blackjax/__init__.py

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from blackjax._version import __version__
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from .diagnostics import effective_sample_size as ess
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from .diagnostics import potential_scale_reduction as rhat
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from .kernels import (
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from .optimizers import dual_averaging, lbfgs
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__all__ = [
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"__version__",
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"dual_averaging", # optimizers
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"lbfgs",
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"hmc", # mcmc
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"ess", # diagnostics
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"rhat",
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]
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from . import _version
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__version__ = _version.get_versions()["version"]

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