Improvements/python linter harness #751
Merged
Travis CI / Travis CI - Pull Request
succeeded
Mar 15, 2024 in 17m 39s
Build Passed
Details
This is a pull request build.
It is running a build against the merge commit, after merging #751 Improvements/python linter harness.
Any changes that have been made to the release/111 branch before the build ran are also included.
Jobs and Stages
This build has nine jobs, running in parallel.
| Job | Perl | Python | ENV | OS | State |
|---|---|---|---|---|---|
| 15841.1 Housekeeping (all languages) |
5.30 | AUTH_TOKEN=[secure] | Linux | passed | |
| 15841.2 SQL unit tests |
5.30 | AUTH_TOKEN=[secure] | Linux | passed | |
| 15841.3 Perl unit tests on the minimum version |
5.26 | AUTH_TOKEN=[secure] | Linux | passed | |
| 15841.4 Perl unit tests on the latest version, with code coverage |
5.30 | AUTH_TOKEN=[secure] | Linux | passed | |
| 15841.5 Perl external unit tests on the latest version, with code coverage |
5.30 | AUTH_TOKEN=[secure] | Linux | passed | |
| 15841.6 Perl linter |
5.30 | AUTH_TOKEN=[secure] | Linux | passed | |
| 15841.7 Python unit tests on the minimum version |
3.8 | AUTH_TOKEN=[secure] | Linux | passed | |
| 15841.8 Python unit tests on the latest version, with code coverage |
3.9 | AUTH_TOKEN=[secure] | Linux | passed | |
| 15841.9 Python linter |
3.9 | AUTH_TOKEN=[secure] | Linux | passed |
Build Configuration
| Build Option | Setting |
|---|---|
| Language | Generic |
| Operating System | Linux (Xenial) |
Build Configuration
{
"language": "generic",
"os": [
"linux"
],
"dist": "xenial",
"env": [
"global=AUTH_TOKEN=[secure]"
],
"addons": {
"apt": {
"packages": [
"graphviz"
]
}
},
"services": [
"mysql"
],
"cache": {
"pip": true,
"directories": [
"$HOME/deps"
]
},
"before_install": [
"cpanm -nq local::lib",
"eval \"$(perl -Mlocal::lib=${HOME}/deps)\"",
"export ENSEMBL_BRANCH='release/111'",
"export SECONDARY_BRANCH='main'",
"git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git",
"export PATH=$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 $SECONDARY_BRANCH --depth 1 ensembl-datacheck",
"git-ensembl --clone --branch main --depth 1 ensembl-hive",
"git-ensembl --clone --branch main --depth 1 ensembl-taxonomy",
"ln -s . ensembl-compara",
"git clone --branch v1.6.x --depth 1 https://github.com/bioperl/bioperl-live",
"git clone --branch release-1-6-9 --depth 1 https://github.com/bioperl/bioperl-run",
"sed -i '/Bio::DB::HTS/d' ensembl-rest/cpanfile",
"export ENSEMBL_ROOT_DIR=$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\"@\"%\"'"
],
"jobs": {
"include": [
{
"language": "perl",
"perl": "5.30",
"name": "Housekeeping (all languages)",
"install": [
"sudo apt-get -y install shellcheck",
"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 .",
"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": "3.8",
"name": "Python unit tests on the minimum version",
"install": [
"pip install -r requirements.txt -r requirements-test.txt",
"pip install ."
],
"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 -r requirements.txt -r requirements-test.txt",
"pip install ."
],
"script": [
"pytest --cov=./ --cov-report=term-missing --server=mysql://[email protected]:3306/"
],
"after_success": [
"codecov"
]
},
{
"language": "python",
"python": "3.9",
"name": "Python linter",
"install": [
"pip freeze | grep -v -f requirements.txt - | grep -v '^#' | xargs pip uninstall -y",
"pip install pylint mypy",
"pip install -r requirements.txt",
"pip install ."
],
"script": [
"./travisci/python-linter_harness.sh"
]
}
]
}
}
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