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MartinBubelMartinBubel
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Merge pull request SheffieldML#1061 from SheffieldML/1060-update-github-actions
1060 update GitHub actions
2 parents 27144e2 + b39ade5 commit 9260b09

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‎.github/workflows/actions.yml‎

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‎.github/workflows/test-and-deploy.yml‎

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name: "Test Python Lib"
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on:
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push:
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branches:
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- main
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- devel
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- deploy
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pull_request:
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permissions:
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contents: read
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pull-requests: read
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jobs:
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test-windows:
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strategy:
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matrix:
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os: [windows-latest]
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python: ['3.9', '3.10', '3.11', '3.12']
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runs-on: ${{ matrix.os }}
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Setup python
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python }}
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- name: Install dependencies
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run: |
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pip install setuptools
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pip install matplotlib
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pip install pytest
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- name: Install lib
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run: |
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python setup.py develop
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- name: pytest
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run: |
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pytest GPy/testing
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test-linux:
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strategy:
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matrix:
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os: [ubuntu-latest]
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python: ['3.9', '3.10', '3.11', '3.12']
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runs-on: ${{ matrix.os }}
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Setup python
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python }}
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- name: Install dependencies
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run: |
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pip install setuptools
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pip install matplotlib
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pip install pytest
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- name: Install lib
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run: |
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python setup.py develop
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- name: pytest
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run: |
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pytest GPy/testing
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test-macos:
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strategy:
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matrix:
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os: [macos-latest]
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python: ['3.10', '3.11', '3.12']
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runs-on: ${{ matrix.os }}
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Setup python
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python }}
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- name: Install dependencies
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run: |
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pip install setuptools
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pip install matplotlib
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pip install pytest
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- name: Install lib
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run: |
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python setup.py develop
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- name: pytest
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run: |
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pytest GPy/testing
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build-windows:
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if: github.event_name == 'release'
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strategy:
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matrix:
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os: [windows-latest]
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python: ['3.9', '3.10', '3.11', '3.12']
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runs-on: ${{ matrix.os }}
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Setup python
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python }}
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- name: Build lib
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run: |
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pip install setuptools
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pip install wheel
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python setup.py develop
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python setup.py bdist_wheel
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python setup.py sdist bdist_wheel
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- name: List contents of dist
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run: ls -R dist
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- name: Archive build artifacts
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uses: actions/upload-artifact@v3
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with:
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name: dist-artifacts-${{ matrix.os }}-${{ matrix.python }}
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path: dist
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build-macos:
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if: github.event_name == 'release'
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strategy:
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matrix:
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os: [macos-latest]
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python: ['3.10', '3.11', '3.12'] # 3.9 triggers scipy issues when installing
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runs-on: ${{ matrix.os }}
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Setup python
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python }}
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- name: Build lib
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run: |
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pip install setuptools
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pip install wheel
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python setup.py develop
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python setup.py bdist_wheel
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- name: List contents of dist
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run: ls -R dist
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- name: Archive build artifacts
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uses: actions/upload-artifact@v3
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with:
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name: dist-artifacts-${{ matrix.os }}-${{ matrix.python }}
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path: dist/*
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build-linux:
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if: github.event_name == 'release'
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strategy:
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matrix:
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python: ['cp39-cp39', 'cp310-cp310', 'cp311-cp311', 'cp312-cp312']
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runs-on: ubuntu-latest
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container:
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image: quay.io/pypa/manylinux2014_x86_64
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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- name: Compile c headers
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run: |
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/opt/python/${{ matrix.python }}/bin/python setup.py develop
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- name: Build wheel files
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run: |
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/opt/python/${{ matrix.python }}/bin/python setup.py bdist_wheel
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- name: Install auditwheel # this should be available?!
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run: |
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/opt/python/${{ matrix.python }}/bin/python -m pip install auditwheel
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- name: Repair wheel files
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run: |
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/opt/python/${{ matrix.python }}/bin/python -m auditwheel repair dist/*${{ matrix.python }}-linux_x86_64.whl
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- name: List contents of dist
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run: ls -R dist
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- name: List contests of wheelhouse
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run: ls -R wheelhouse
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- name: Move wheelhouse wheel files to dist
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run: |
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rm dist/*
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mv wheelhouse/* dist/
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rmdir wheelhouse
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- name: List contents of dist
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run: ls -R dist
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- name: Archive build artifacts
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uses: actions/upload-artifact@v3
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with:
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name: dist-artifacts-manylinux-${{ matrix.python }}
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path: dist/*
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deploy:
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runs-on: ubuntu-latest
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needs: [test-windows, test-linux, test-macos, build-linux, build-windows, build-macos]
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if: github.event_name == 'release'
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Setup python
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uses: actions/setup-python@v4
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with:
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python-version: '3.9'
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- name: Install twine
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run: |
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pip install --upgrade pip
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pip install twine
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- name: Download all artifacts to a specific directory
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uses: actions/download-artifact@v3
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with:
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path: dist
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- name: Create dist directory
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run: mkdir -p dist
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- name: Move files from subdirectories
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run: |
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for subdirectory in dist/*/; do
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dir_name=$(basename "$subdirectory")
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mv "$subdirectory"* dist/
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rm -r "$subdirectory"
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echo "Moved files from '$dir_name' to 'dist/'"
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done
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- name: Inspect wheel files
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run: |
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ls -R dist
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- name: Upload to PyPI using twine
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run: twine upload --skip-existing dist/*
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env:
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TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
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TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}

‎GPy/testing/test_model.py‎

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assert m.checkgrad()
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m.predict(m.X)
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@pytest.mark.skip(
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"numpy.linalg.LinAlgError: no not positive definite, even with jitter"
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) # TODO: fix
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def test_raw_predict_numerical_stability(self):
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"""
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Test whether the predicted variance of normal GP goes negative under numerical unstable situation.

‎GPy/testing/test_rv_transformation.py‎

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import GPy
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class TestModel(GPy.core.Model):
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class Model(GPy.core.Model):
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"""
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A simple GPy model with one parameter.
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"""
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def __init__(self, theta=1.0):
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super(TestModel, self).__init__("test_model")
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super(Model, self).__init__("test_model")
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theta = GPy.core.Param("theta", theta)
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self.link_parameter(theta)
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class TestRVTransformation:
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def _test_trans(self, trans):
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m = TestModel()
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m = Model()
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prior = GPy.priors.LogGaussian(0.5, 0.1)
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m.theta.set_prior(prior)
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m.theta.unconstrain()
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def _test_grad(self, trans):
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np.random.seed(1234)
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m = TestModel(np.random.uniform(0.5, 1.5, 20))
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m = Model(np.random.uniform(0.5, 1.5, 20))
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prior = GPy.priors.LogGaussian(0.5, 0.1)
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m.theta.set_prior(prior)
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m.theta.constrain(trans)

‎setup.py‎

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]
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# 'some-pkg @ git+ssh://[email protected]/someorgname/[email protected]#egg=some-pkg',
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matplotlib_version = "matplotlib==3.3.4"
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install_requirements += ["scipy>=1.3.0"]
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install_requirements += ["scipy>=1.3.0,<1.12.0"]
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setup(
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name="GPy",

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