fix: test_package for .tar.bz2 and .conda #821
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 | |
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 }}' -k test_pkg_test_conda_package_format | |
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 -k test_pkg_test_conda_package_format | |
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 |