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.travis.yml
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.travis.yml
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os: linux
language: generic
env:
global:
# yamllint disable-line rule:line-length
- secure: bGSZASCtRCcE2VZ3u4hdvjh6CDHe+Uo3MR7B4eobSFFhZVjIN3/DKaGrQYprEeSIB/vb75rveyTheO3qe3lHwq71e18cBk2ulQA6/L0eUJYsoR3u2y7d9whu8dS97IoLzize6hItxJFP8TmRaJBtWqOixyWHNW72X/fKF1a192E=
addons:
apt:
packages:
- graphviz
services:
- mysql
cache:
pip: true
directories:
- $HOME/deps
# Clone all repositories, setup the directory structure and the environment
before_install:
# yamllint disable-line rule:indentation
- cpanm -nq local::lib
- eval "$(perl -Mlocal::lib=${HOME}/deps)"
- export ENSEMBL_BRANCH='release/113'
- export SECONDARY_BRANCH='main'
# yamllint disable rule:line-length
- git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git
- export PATH=$PATH:$PWD/ensembl-git-tools/bin
- git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test
- git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-rest
- git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen
- git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation
- git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-io
- git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl
- git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck
# yamllint enable rule:line-length
- git-ensembl --clone --branch main --depth 1 ensembl-hive
- git-ensembl --clone --branch main --depth 1 ensembl-taxonomy
- ln -s . ensembl-compara
- git clone --branch v1.6.x --depth 1 https://github.com/bioperl/bioperl-live
- git clone --branch release-1-6-9 --depth 1 https://github.com/bioperl/bioperl-run
- sed -i '/Bio::DB::HTS/d' ensembl-rest/cpanfile
# Setup the environment variables
- export ENSEMBL_ROOT_DIR=$PWD
- export EHIVE_ROOT_DIR=$PWD/ensembl-hive
- export PERL5LIB=$PERL5LIB:$PWD/bioperl-live
- export PERL5LIB=$PERL5LIB:$PWD/bioperl-run/lib
- export PERL5LIB=$PERL5LIB:$PWD/modules
- export PERL5LIB=$PERL5LIB:$PWD/travisci/fake_libs/
- export PERL5LIB=$PERL5LIB:$PWD/ensembl/modules
- export PERL5LIB=$PERL5LIB:$PWD/ensembl-rest/lib
- export PERL5LIB=$PERL5LIB:$PWD/ensembl-hive/modules
- export PERL5LIB=$PERL5LIB:$PWD/ensembl-test/modules
- export PERL5LIB=$PERL5LIB:$PWD/ensembl-funcgen/modules
- export PERL5LIB=$PERL5LIB:$PWD/ensembl-variation/modules
- export PERL5LIB=$PERL5LIB:$PWD/ensembl-taxonomy/modules
- export PERL5LIB=$PERL5LIB:$PWD/ensembl-io/modules
- export PERL5LIB=$PERL5LIB:$PWD/ensembl-datacheck/lib
- cp -f travisci/MultiTestDB.conf.travisci modules/t/MultiTestDB.conf
- cp -f ensembl-rest/travisci/MultiTestDB.conf.travisci ensembl-rest/t/MultiTestDB.conf
- cp -f ensembl/travisci/MultiTestDB.conf.travisci.mysql ensembl/modules/t/MultiTestDB.conf
- mysql -u root -h localhost -e 'GRANT ALL PRIVILEGES ON *.* TO "travis"@"%"'
# What jobs to run and in which order
jobs:
include:
- language: perl
perl: 5.30
name: "Housekeeping (all languages)"
install:
- sudo apt-get -y install shellcheck
# --user is required on Perl VMs because it's the system pip/python
- pip install --user yamllint
- cpanm --quiet --installdeps --notest --cpanfile ensembl/cpanfile .
- cpanm --quiet --installdeps --notest .
- yamllint --version
- shellcheck --version
script: prove -rv ./travisci/all-housekeeping/
- language: perl
perl: 5.30
name: "SQL unit tests"
install:
- cpanm --quiet --installdeps --notest --cpanfile ensembl/cpanfile .
script: prove -r ./travisci/sql-unittest/
- language: perl
perl: 5.26
name: "Perl unit tests on the minimum version"
env:
- COVERAGE=true
install:
- cpanm --quiet --installdeps --notest --cpanfile ensembl/cpanfile .
- cpanm --quiet --installdeps --notest --cpanfile ensembl-hive/cpanfile .
- cpanm --quiet --installdeps --notest --cpanfile ensembl-rest/cpanfile .
- cpanm --quiet --installdeps --notest .
- cpanm --quiet --notest Devel::Cover::Report::Codecov
script: ./travisci/perl-unittest_harness.sh
- language: perl
perl: 5.30
name: "Perl unit tests on the latest version, with code coverage"
env:
- COVERAGE=true
install:
- cpanm --quiet --installdeps --notest --cpanfile ensembl/cpanfile .
- cpanm --quiet --installdeps --notest --cpanfile ensembl-hive/cpanfile .
- cpanm --quiet --installdeps --notest --cpanfile ensembl-rest/cpanfile .
- cpanm --quiet --installdeps --notest .
- cpanm --quiet --notest Devel::Cover::Report::Codecov
script: ./travisci/perl-unittest_harness.sh
after_success:
- cover --nosummary -report codecov
- language: perl
perl: 5.30
name: "Perl external unit tests on the latest version, with code coverage"
env:
- COVERAGE=true
install:
- cpanm --quiet --installdeps --notest --cpanfile ensembl/cpanfile .
# 8.43 is the last version compatible with Perl 5.14
- cpanm --quiet --notest [email protected]
- cpanm --quiet --installdeps --notest --cpanfile ensembl-rest/cpanfile .
- cpanm --quiet --installdeps --notest --cpanfile ensembl-hive/cpanfile .
- cpanm --quiet --installdeps --notest .
- cpanm --quiet --notest Devel::Cover::Report::Codecov
script: ./travisci/perl-external_unittest_harness.sh
after_success:
- cover --nosummary -report codecov
- language: perl
perl: 5.30
name: "Perl linter"
install:
- cpanm --quiet --installdeps --notest --cpanfile ensembl/cpanfile .
script: ./travisci/perl-linter_harness.sh
- language: python
python: 3.9
name: "Python unit tests on the minimum version"
install:
- pip install --upgrade pip
- pip install .[test]
script:
- pytest --server=mysql://[email protected]:3306/
- language: python
python: 3.9
name: "Python unit tests on the latest version, with code coverage"
install:
- pip install codecov
- pip install .[test]
script:
# yamllint disable rule:line-length
- pytest --cov=./ --cov-report=term-missing --server=mysql://[email protected]:3306/
# yamllint enable rule:line-length
after_success:
- codecov
- language: python
python: 3.9
name: "Python linter"
install:
- pip uninstall dataclasses -y
- pip install .[test]
script: ./travisci/python-linter_harness.sh