Update configparser SafeConfigParser and readfp, new in python 3.12 #1
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| name: CI | |
| on: | |
| push: | |
| paths-ignore: | |
| - "README.md" | |
| - "**/docs/**" | |
| - ".github/workflows/docs.yml" | |
| pull_request: | |
| branches: | |
| - master | |
| - dev | |
| schedule: | |
| - cron: "0 11 * * *" | |
| jobs: | |
| skip_duplicate: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| should_skip: ${{ steps.skip_check.outputs.should_skip }} | |
| steps: | |
| - id: skip_check | |
| uses: fkirc/skip-duplicate-actions@master | |
| with: | |
| github_token: ${{ github.token }} | |
| concurrent_skipping: never | |
| skip_after_successful_duplicate: true | |
| paths_ignore: '["**/README.md", "**/docs/**"]' | |
| do_not_skip: '["pull_request", "schedule"]' | |
| test-pip: | |
| name: Test on Pip | |
| needs: skip_duplicate | |
| if: ${{ needs.skip_duplicate.outputs.should_skip == 'false' }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.9","3.10","3.11"] | |
| os: ["ubuntu-latest", "macos-latest", "macos-12"] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip wheel setuptools numpy | |
| # Temp fix due to speclite not supporting the latest version | |
| pip install "matplotlib<3.9" | |
| if [[ ${{matrix.os}} == macos-latest ]]; | |
| then | |
| brew update | |
| brew install hdf5 | |
| fi | |
| if [[ "${ISDEV}" == "true" ]]; then | |
| pip install --upgrade --pre astromodels | |
| else | |
| pip install --upgrade astromodels | |
| fi | |
| pip install --upgrade flake8 coverage pytest-cov cython | |
| pip install -e . | |
| env: | |
| ISDEV: ${{contains(github.ref, 'dev') || contains(github.base_ref, 'dev')}} | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test pip on ${{ matrix.python-version }} | |
| run: | | |
| python -m pytest -vv --cov=threeML --cov-report=xml | |
| env: | |
| PYTEST_ADDOPTS: "--color=yes" | |
| OMP_NUM_THREADS: 1 | |
| MKL_NUM_THREADS: 1 | |
| NUMEXPR_NUM_THREADS: 1 | |
| MPLBACKEND: "Agg" | |
| test-dev: | |
| name: Test on Pip against astromodels-dev | |
| needs: skip_duplicate | |
| if: ${{ needs.skip_duplicate.outputs.should_skip == 'false' }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.9","3.10","3.11"] | |
| os: [ "ubuntu-latest", "macos-latest", "macos-12"] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip wheel | |
| # Temp fix due to speclite not supporting the latest version | |
| pip install "matplotlib<3.9" | |
| if [[ ${{matrix.os}} == macos-latest ]]; | |
| then | |
| brew update | |
| brew install hdf5 | |
| fi | |
| git clone https://github.com/threeML/astromodels | |
| cd astromodels | |
| git checkout dev | |
| python -m pip install -e . | |
| cd .. | |
| pip install --upgrade flake8 coverage pytest-cov cython | |
| pip install -e . | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test pip on ${{ matrix.python-version }} | |
| run: | | |
| python -m pytest -vv --cov=threeML --cov-report=xml | |
| env: | |
| PYTEST_ADDOPTS: "--color=yes" | |
| OMP_NUM_THREADS: 1 | |
| MKL_NUM_THREADS: 1 | |
| NUMEXPR_NUM_THREADS: 1 | |
| MPLBACKEND: "Agg" | |
| test-conda: | |
| name: Test on Conda | |
| needs: skip_duplicate | |
| if: ${{ needs.skip_duplicate.outputs.should_skip == 'false' }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest", "macos-12"] | |
| python-version: [3.9] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: XCode | |
| uses: maxim-lobanov/setup-xcode@v1 | |
| with: | |
| xcode-version: latest | |
| if: runner.os == 'macOS' | |
| #- name: Cache conda | |
| # uses: actions/cache@v2 | |
| # env: | |
| # Increase this value to reset cache if etc/example-environment.yml has not changed | |
| # CACHE_NUMBER: 0 | |
| # with: | |
| # path: ~/conda_pkgs_dir | |
| # key: conda-${{ matrix.os }}-python-${{ matrix.python-version }}-${{ hashFiles('ci/environment.yml') }} | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| #miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| activate-environment: test_env | |
| python-version: ${{ matrix.python-version }} | |
| channels: conda-forge, xspecmodels, threeml, fermi, defaults | |
| environment-file: ci/environment.yml | |
| use-only-tar-bz2: true | |
| - name: Init Env | |
| shell: bash -l {0} | |
| run: | | |
| export PKG_VERSION=$(python -c "import versioneer;print(versioneer.get_version())") | |
| echo "HOME= ${HOME}" | |
| echo "Building ${PKG_VERSION} ..." | |
| echo "Python version: ${{matrix.python-version}}" | |
| echo "Running on development branch: ${ISDEV} " | |
| if [[ "${ISDEV}" == "true" ]]; then | |
| mamba install -c conda-forge -c threeml/label/dev "threeml/label/dev::astromodels" | |
| fi | |
| pip install --upgrade speclite | |
| pip install fermipy "matplotlib<3.9" | |
| env: | |
| ISDEV: ${{contains(github.ref, 'dev') || contains(github.base_ref, 'dev')}} | |
| - name: Conda list | |
| shell: bash -l {0} | |
| run: | | |
| conda list | |
| - name: install it | |
| shell: bash -l {0} | |
| run: | | |
| pip install -e . | |
| - name: Lint with flake8 | |
| shell: bash -l {0} | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: test it | |
| shell: bash -l {0} | |
| run: | | |
| wget https://raw.githubusercontent.com/fermi-lat/pyBurstAnalysisGUI/master/python/GtBurst/updater.py -O $CONDA_PREFIX/lib/python${{ matrix.python-version }}/site-packages/fermitools/GtBurst/updater.py | |
| python $CONDA_PREFIX/lib/python${{ matrix.python-version }}/site-packages/fermitools/GtBurst/updater.py | |
| python -m pytest -vv --cov=threeML --cov-report=xml | |
| env: | |
| PYTEST_ADDOPTS: "--color=yes" | |
| OMP_NUM_THREADS: 1 | |
| MKL_NUM_THREADS: 1 | |
| NUMEXPR_NUM_THREADS: 1 | |
| MPLBACKEND: "Agg" | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v1 | |
| with: | |
| file: ./coverage.xml | |
| files: ./coverage1.xml,./coverage2.xml | |
| Directory: ./coverage/reports/ | |
| publish-pypi: | |
| name: Publish to PyPi | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
| runs-on: ubuntu-latest | |
| permissions: | |
| # IMPORTANT: this permission is mandatory for trusted publishing | |
| id-token: write | |
| steps: | |
| - name: Checkout source | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: 3.9 | |
| - name: Build package | |
| run: | | |
| pip install wheel setuptools -U | |
| python setup.py sdist bdist_wheel | |
| - name: Publish | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| skip-existing: true | |
| test-publish-pypi: | |
| name: Build & verify package | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.9 | |
| - name: Install twine | |
| run: | | |
| python -m pip install twine | |
| pip install wheel setuptools -U | |
| - name: Build package | |
| run: | | |
| python setup.py sdist bdist_wheel | |
| - name: List result | |
| run: | | |
| ls -lh dist | |
| - name: Check long_description | |
| run: | | |
| python -m twine check dist/* |