Convert Ensembl/ensembl-production to GitHub Actions #12
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name: Ensembl/ensembl-production | |
on: | |
push: | |
branches: | |
- "**/*" | |
pull_request: | |
schedule: | |
- cron: "0 0 * * 1" | |
jobs: | |
test: | |
runs-on: ubuntu-latest | |
steps: | |
- name: checkout | |
uses: actions/[email protected] | |
- uses: shogo82148/[email protected] | |
with: | |
perl-version: "${{ matrix.perl }}" | |
- run: apt-get update && apt-get -y install unzip sendmail graphviz emboss | |
- run: git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git | |
- run: export PATH=$PATH:$PWD/ensembl-git-tools/bin | |
- run: export ENSEMBL_BRANCH=master | |
- run: export SECONDARY_BRANCH=main | |
- run: echo "TRAVIS_BRANCH=${{ github.ref }}" | |
- run: if [[ ${{ github.ref }} =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=${{ github.ref }}; export SECONDARY_BRANCH=${{ github.ref }}; fi | |
- run: echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH" | |
- run: echo "SECONDARY_BRANCH=$SECONDARY_BRANCH" | |
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test | |
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl | |
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-compara | |
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck | |
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation | |
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-metadata | |
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen | |
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-hive | |
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-orm | |
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-taxonomy | |
- run: git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git | |
- run: git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git | |
- run: cd htslib | |
- run: make | |
- run: export HTSLIB_DIR=$(pwd -P) | |
- run: cd .. | |
- run: cpanm --sudo -v --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile . | |
- run: cpanm --sudo -v --installdeps --notest --cpanfile ensembl-hive/cpanfile . | |
- run: cpanm --sudo -v --installdeps --notest --cpanfile ensembl-datacheck/cpanfile . | |
- run: export PERL5LIB=$PERL5LIB:$PWD/bioperl-live | |
- run: cpanm --sudo -v --installdeps --notest . | |
- run: cpanm --sudo -n Devel::Cover::Report::Coveralls | |
- run: cp travisci/MultiTestDB.conf.travisci modules/t/MultiTestDB.conf | |
- run: mysql -u root -h localhost -e 'GRANT ALL PRIVILEGES ON *.* TO "travis"@"%"' | |
- run: "./travisci/harness.sh" | |
- uses: rtCamp/[email protected] | |
env: | |
SLACK_WEBHOOK: "${{ secrets.SLACK_WEBHOOK }}" | |
strategy: | |
matrix: | |
perl: | |
- '5.14' | |
- '5.26.2' | |
include: | |
- COVERALLS: 'true' | |
DB: mysql | |
services: | |
mysql: | |
image: mysql | |
env: | |
COVERALLS: "${{ matrix.COVERALLS }}" | |
DB: "${{ matrix.DB }}" | |
MYSQL_ROOT_PASSWORD: "ensembl" | |
test_2: | |
runs-on: ubuntu-latest | |
env: | |
COVERALLS: 'true' | |
DB: mysql | |
MYSQL_ROOT_PASSWORD: "ensembl" | |
MYSQL_ALLOW_EMPTY_PASSWORD: 'true' | |
steps: | |
- name: checkout | |
uses: actions/[email protected] | |
- uses: actions/[email protected] | |
with: | |
python-version: 3.7.6 | |
- run: apt-get update && apt-get -y install unzip sendmail graphviz emboss | |
- run: git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git | |
- run: export PATH=$PATH:$PWD/ensembl-git-tools/bin | |
- run: export ENSEMBL_BRANCH=master | |
- run: export SECONDARY_BRANCH=main | |
- run: echo "TRAVIS_BRANCH=${{ github.ref }}" | |
- run: if [[ ${{ github.ref }} =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=${{ github.ref }}; export SECONDARY_BRANCH=${{ github.ref }}; fi | |
- run: echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH" | |
- run: echo "SECONDARY_BRANCH=$SECONDARY_BRANCH" | |
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test | |
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl | |
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-compara | |
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck | |
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation | |
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-metadata | |
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen | |
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-hive | |
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-orm | |
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-taxonomy | |
- run: git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git | |
- run: git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git | |
- run: cd htslib | |
- run: make | |
- run: export HTSLIB_DIR=$(pwd -P) | |
- run: cd .. | |
- run: pip install -r requirements-test.txt | |
- run: pip install -e . | |
- run: pytest src/python/test | |
- uses: rtCamp/[email protected] | |
env: | |
SLACK_WEBHOOK: "${{ secrets.SLACK_WEBHOOK }}" | |
services: | |
mysql: | |
image: mysql | |
test_3: | |
runs-on: ubuntu-latest | |
env: | |
COVERALLS: 'true' | |
DB: mysql | |
MYSQL_ROOT_PASSWORD: "ensembl" | |
MYSQL_ALLOW_EMPTY_PASSWORD: 'true' | |
steps: | |
- name: checkout | |
uses: actions/[email protected] | |
- uses: actions/[email protected] | |
with: | |
python-version: 3.8 | |
- run: apt-get update && apt-get -y install unzip sendmail graphviz emboss | |
- run: git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git | |
- run: export PATH=$PATH:$PWD/ensembl-git-tools/bin | |
- run: export ENSEMBL_BRANCH=master | |
- run: export SECONDARY_BRANCH=main | |
- run: echo "TRAVIS_BRANCH=${{ github.ref }}" | |
- run: if [[ ${{ github.ref }} =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=${{ github.ref }}; export SECONDARY_BRANCH=${{ github.ref }}; fi | |
- run: echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH" | |
- run: echo "SECONDARY_BRANCH=$SECONDARY_BRANCH" | |
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test | |
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl | |
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-compara | |
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck | |
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation | |
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-metadata | |
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen | |
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-hive | |
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-orm | |
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-taxonomy | |
- run: git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git | |
- run: git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git | |
- run: cd htslib | |
- run: make | |
- run: export HTSLIB_DIR=$(pwd -P) | |
- run: cd .. | |
- run: pip install -r requirements-test.txt | |
- run: pip install -e . | |
- run: pytest src/python/test | |
- uses: rtCamp/[email protected] | |
env: | |
SLACK_WEBHOOK: "${{ secrets.SLACK_WEBHOOK }}" | |
services: | |
mysql: | |
image: mysql |