[Snyk] Fix for 4 vulnerabilities #564
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| name: test | |
| on: [pull_request] #, push] | |
| jobs: | |
| # Runs the tests on combinations of the supported python/os matrix. | |
| test-code: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, windows-latest] | |
| python-version: ['3.8', '3.9', '3.10', '3.11'] | |
| fail-fast: false | |
| # continue-on-error: true | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Get conda env file | |
| shell: bash -l {0} | |
| run: | | |
| if [ "$RUNNER_OS" == "macOS" ]; then | |
| cp .github/test_conda_env_macOS.yml .github/test_conda_env.yml | |
| fi | |
| - name: Setup conda | |
| uses: conda-incubator/[email protected] | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: eqcorrscan-test | |
| use-mamba: true | |
| - name: Update Env | |
| run: mamba env update -n eqcorrscan-test -f .github/test_conda_env.yml | |
| - name: install eqcorrscan | |
| shell: bash -l {0} | |
| run: | | |
| pip install -v -e . --no-deps | |
| - name: print package info | |
| shell: bash -l {0} | |
| run: | | |
| conda info -a | |
| conda list | |
| # - name: run all tests | |
| # shell: bash -l {0} | |
| # run: | | |
| # py.test -n 2 -m "not serial and not network and not superslow" --cov-report=xml | |
| # export OMP_NUM_THREADS=2 | |
| # py.test -m "serial and not network" --cov-report=xml --cov-append | |
| # py.test -v -m "slow and not serial and not network" --cov-report=xml --cov-append | |
| - name: run main test suite | |
| shell: bash -l {0} | |
| run: | | |
| py.test -n 2 -m "not serial and not network and not superslow and not slow" --cov-report=xml --dist loadscope | |
| - name: run serial test | |
| if: always() | |
| shell: bash -l {0} | |
| run: | | |
| export OMP_NUM_THREADS=2 | |
| py.test -m "serial and not network" --cov-report=xml --cov-append | |
| - name: run slow tests | |
| if: always() | |
| shell: bash -l {0} | |
| run: | | |
| py.test -v -m "slow and not serial and not network" --cov-report=xml --cov-append | |
| - name: upload coverage | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| flags: unittests | |
| name: codecov-umbrella | |
| yml: ./codecov.yml | |
| fail_ci_if_error: true | |
| test-code-slow: | |
| runs-on: "ubuntu-latest" | |
| strategy: | |
| matrix: | |
| python-version: ['3.10'] | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Setup conda | |
| uses: conda-incubator/[email protected] | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: eqcorrscan-test | |
| use-mamba: true | |
| - name: Update Env | |
| run: mamba env update -n eqcorrscan-test -f .github/test_conda_env.yml | |
| - name: install eqcorrscan | |
| shell: bash -l {0} | |
| run: | | |
| pip install -e . --no-deps | |
| - name: print package info | |
| shell: bash -l {0} | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: run network tests | |
| shell: bash -l {0} | |
| run: | | |
| py.test -n 2 -m "network and not superslow" --cov-report=xml | |
| - name: run tutorials | |
| if: always() | |
| shell: bash -l {0} | |
| run: | | |
| py.test eqcorrscan/doc/tutorials/*.rst eqcorrscan/doc/submodules/*.rst --cov-report=xml --cov-append | |
| - name: run superslow tests | |
| if: always() | |
| shell: bash -l {0} | |
| run: | | |
| py.test -m "superslow" -s eqcorrscan/tests/tutorials_test.py eqcorrscan/tests/subspace_test.py --cov-report=xml --cov-append | |
| - name: upload coverage | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| flags: unittests | |
| name: codecov-umbrella | |
| yml: ./codecov.yml | |
| fail_ci_if_error: true | |
| test-code-fmf: | |
| runs-on: "ubuntu-latest" | |
| strategy: | |
| matrix: | |
| python-version: ['3.9'] | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Setup conda | |
| uses: conda-incubator/[email protected] | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: eqcorrscan-test | |
| use-mamba: true | |
| - name: Update Env | |
| run: mamba env update -n eqcorrscan-test -f .github/test_conda_env.yml | |
| - name: install fmf | |
| shell: bash -l {0} | |
| run: | | |
| cd .. | |
| git clone https://github.com/beridel/fast_matched_filter.git | |
| cd fast_matched_filter | |
| pip install -e . --no-deps | |
| cd ../EQcorrscan | |
| - name: install eqcorrscan | |
| shell: bash -l {0} | |
| run: | | |
| pip install -e . | |
| - name: print package info | |
| shell: bash -l {0} | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: run correlation test | |
| shell: bash -l {0} | |
| run: | | |
| export OMP_NUM_THREADS=2 | |
| py.test eqcorrscan/tests/correlate_test.py --cov-report=xml | |
| - name: upload coverage | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| flags: unittests | |
| name: codecov-umbrella | |
| yml: ./codecov.yml | |
| fail_ci_if_error: true | |
| # This is a very useful step for debugging, it allows you to ssh into the CI | |
| # machine (https://github.com/marketplace/actions/debugging-with-tmate). | |
| # Make sure to open the log before the job starts else you cant see the tmate | |
| # url. See https://github.com/mxschmitt/action-tmate/issues/1. | |
| # Also, the CI machine will close on a non-zero exit code (annoying). This can | |
| # be overcome by coalescing the null command like so: | |
| # $ some-command-that-can-fail || : | |
| # | |
| #- name: Setup tmate session | |
| # uses: mxschmitt/action-tmate@v1 |