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Convert Ensembl/ensembl-production to GitHub Actions #894

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Convert Ensembl/ensembl-production to GitHub Actions #894

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43711ee
Add workflow Ensembl/ensembl-production
marcoooo Mar 18, 2024
0e3b3aa
Updated schedule
marcoooo Mar 18, 2024
68cfadd
Removed unwanted keys
marcoooo Mar 18, 2024
523ec95
Added MYSQL_ROOT_PASSWORD
marcoooo Mar 18, 2024
6b443a1
Fixed typo
marcoooo Mar 18, 2024
c676ff5
Moved env per job
marcoooo Mar 18, 2024
18fc62c
Allowed empty password
marcoooo Mar 18, 2024
1c30153
Moved env to another place in config
marcoooo Mar 18, 2024
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168 changes: 168 additions & 0 deletions .github/workflows/ensembl-production.yml
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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/checkout@v4.1.0
- uses: shogo82148/actions-setup-perl@v1.27.0
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/action-slack-notify@v2.2.1
env:
SLACK_WEBHOOK: "${{ secrets.SLACK_WEBHOOK }}"
strategy:
matrix:
perl:
- '5.14'
- '5.26.2'
include:
- COVERALLS: 'true'
DB: mysql
services:
mysql:
image: mysql
env:
MYSQL_ROOT_PASSWORD: "ensembl"
MYSQL_ALLOW_EMPTY_PASSWORD: 'true'
env:
COVERALLS: "${{ matrix.COVERALLS }}"
DB: "${{ matrix.DB }}"
MYSQL_ROOT_PASSWORD: "ensembl"
test_2:
runs-on: ubuntu-latest
env:
COVERALLS: 'true'
DB: mysql
steps:
- name: checkout
uses: actions/checkout@v4.1.0
- uses: actions/setup-python@v5.0.0
with:
python-version: 3.7.6
- run: apt-get update && apt-get -y install unzip sendmail graphviz emboss
- run: git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git
- run: export PATH=$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/action-slack-notify@v2.2.1
env:
SLACK_WEBHOOK: "${{ secrets.SLACK_WEBHOOK }}"
services:
mysql:
image: mysql
env:
MYSQL_ROOT_PASSWORD: "ensembl"
MYSQL_ALLOW_EMPTY_PASSWORD: 'true'
test_3:
runs-on: ubuntu-latest
env:
COVERALLS: 'true'
DB: mysql
steps:
- name: checkout
uses: actions/checkout@v4.1.0
- uses: actions/setup-python@v5.0.0
with:
python-version: 3.8
- run: apt-get update && apt-get -y install unzip sendmail graphviz emboss
- run: git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git
- run: export PATH=$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/action-slack-notify@v2.2.1
env:
SLACK_WEBHOOK: "${{ secrets.SLACK_WEBHOOK }}"
services:
mysql:
image: mysql
env:
MYSQL_ROOT_PASSWORD: "ensembl"
MYSQL_ALLOW_EMPTY_PASSWORD: 'true'
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