feat: Update dependencies to latest versions #851
Workflow file for this run
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| name: PR Tests | |
| on: [pull_request] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test-linux: | |
| name: Linux tests | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| py_test_marker: | |
| - not long_running_1 and not long_running_2 | |
| - long_running_1 | |
| - long_running_2 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: set path | |
| run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
| - name: Install bioconda-utils | |
| run: | | |
| export BIOCONDA_DISABLE_BUILD_PREP=1 | |
| wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh | |
| bash install-and-set-up-conda.sh | |
| eval "$(conda shell.bash hook)" | |
| conda create -n bioconda --quiet --yes --file test-requirements.txt --file bioconda_utils/bioconda_utils-requirements.txt | |
| conda activate bioconda | |
| conda list | |
| python setup.py install | |
| - name: Build docker container | |
| run: | | |
| docker build -t quay.io/bioconda/bioconda-utils-build-env-cos7:latest ./ | |
| docker history quay.io/bioconda/bioconda-utils-build-env-cos7:latest | |
| docker run --rm -t quay.io/bioconda/bioconda-utils-build-env-cos7:latest sh -lec 'type -t conda && conda info --verbose && conda list' | |
| docker build -t quay.io/bioconda/bioconda-utils-test-env-cos7:latest -f ./Dockerfile.test ./ | |
| - name: Run tests '${{ matrix.py_test_marker }}' | |
| run: | | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| if git diff --name-only origin/master...HEAD | grep -vE ^docs; then | |
| py.test --durations=0 test/ -v --log-level=DEBUG --tb=native -m '${{ matrix.py_test_marker }}' | |
| else | |
| echo "Skipping pytest - only docs modified" | |
| fi | |
| test-macosx: | |
| name: OSX tests | |
| runs-on: macos-13 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: set path | |
| run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
| - name: Install bioconda-utils | |
| run: | | |
| export BIOCONDA_DISABLE_BUILD_PREP=1 | |
| wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh | |
| bash install-and-set-up-conda.sh | |
| eval "$(conda shell.bash hook)" | |
| conda create -n bioconda --quiet --yes --file test-requirements.txt --file bioconda_utils/bioconda_utils-requirements.txt | |
| conda list | |
| conda activate bioconda | |
| python setup.py install | |
| - name: Run tests | |
| run: | | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| if git diff --name-only origin/master...HEAD | grep -vE ^docs; then | |
| py.test --durations=0 test/ -v --log-level=DEBUG -k "not docker" --tb=native | |
| else | |
| echo "Skipping pytest - only docs modified" | |
| fi | |
| autobump-test: | |
| name: autobump test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: set path | |
| run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
| - name: Install bioconda-utils | |
| run: | | |
| export BIOCONDA_DISABLE_BUILD_PREP=1 | |
| wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh | |
| bash install-and-set-up-conda.sh | |
| eval "$(conda shell.bash hook)" | |
| conda create -n bioconda --quiet --yes --file test-requirements.txt --file bioconda_utils/bioconda_utils-requirements.txt | |
| conda activate bioconda | |
| conda list | |
| python setup.py install | |
| - name: Test autobump | |
| run: | | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| git clone --depth 1 https://github.com/bioconda/bioconda-recipes.git | |
| cd bioconda-recipes | |
| git config user.name Autobump | |
| git config user.email [email protected] | |
| mkdir /tmp/artifacts | |
| bioconda-utils autobump \ | |
| --packages "a*" \ | |
| --unparsed-urls /tmp/artifacts/unparsed_urls.txt \ | |
| --failed-urls /tmp/artifacts/failed_urls.txt \ | |
| --recipe-status /tmp/artifacts/status.txt \ | |
| --create-pr \ | |
| --no-check-pinnings \ | |
| --no-check-pending-deps \ | |
| --no-follow-graph \ | |
| --exclude bioconductor-* \ | |
| --commit-as BiocondaBot [email protected] \ | |
| --max-updates 5 \ | |
| --dry-run |