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GithubActionTests.yml
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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