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improve portability of reproducible tarballs by replacing external tar command with tarfile module from Python standard library #5515

improve portability of reproducible tarballs by replacing external tar command with tarfile module from Python standard library

improve portability of reproducible tarballs by replacing external tar command with tarfile module from Python standard library #5515

Workflow file for this run

# documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
name: EasyBuild framework unit tests
on: [push, pull_request]
permissions:
contents: read # to fetch code (actions/checkout)
concurrency:
group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}}
cancel-in-progress: true
jobs:
setup:
runs-on: ubuntu-20.04
outputs:
lmod8: Lmod-8.7.6
modules4: modules-4.5.3
modules5: modules-5.3.1
steps:
- run: "true"
build:
needs: setup
runs-on: ubuntu-20.04
strategy:
matrix:
python: [3.6]
modules_tool:
# use variables defined by 'setup' job above, see also
# https://docs.github.com/en/actions/reference/context-and-expression-syntax-for-github-actions#needs-context
- ${{needs.setup.outputs.lmod8}}
- ${{needs.setup.outputs.modules4}}
- ${{needs.setup.outputs.modules5}}
lc_all: [""]
include:
# Test different Python 3 versions with Lmod 8.x (with both Lua and Tcl module syntax)
- python: 3.7
modules_tool: ${{needs.setup.outputs.lmod8}}
- python: 3.8
modules_tool: ${{needs.setup.outputs.lmod8}}
- python: 3.9
modules_tool: ${{needs.setup.outputs.lmod8}}
- python: '3.10'
modules_tool: ${{needs.setup.outputs.lmod8}}
- python: '3.11'
modules_tool: ${{needs.setup.outputs.lmod8}}
- python: '3.12'
modules_tool: ${{needs.setup.outputs.lmod8}}
- python: '3.13'
modules_tool: ${{needs.setup.outputs.lmod8}}
# There may be encoding errors in Python 3 which are hidden when an UTF-8 encoding is set
# Hence run the tests (again) with LC_ALL=C and Python 3.6 (or any < 3.7)
- python: 3.6
modules_tool: ${{needs.setup.outputs.lmod8}}
lc_all: C
fail-fast: false
steps:
- uses: actions/checkout@v3
- name: set up Python
uses: actions/setup-python@v4
with:
python-version: ${{matrix.python}}
architecture: x64
- name: install OS & Python packages
run: |
# for modules tool
APT_PKGS="lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev"
# for GitPython, python-hglib
APT_PKGS+=" git mercurial"
# dep for GC3Pie
APT_PKGS+=" time"
# Avoid apt-get update, as we don't really need it,
# and it does more harm than good (it's fairly expensive, and it results in flaky test runs)
if ! sudo apt-get install $APT_PKGS; then
# Try to update cache, then try again to resolve 404s of old packages
sudo apt-get update -yqq || true
sudo apt-get install $APT_PKGS
fi
# fix for lua-posix packaging issue, see https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082
# needed for Ubuntu 18.04, but not for Ubuntu 20.04, so skipping symlinking if posix.so already exists
if [ ! -e /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so ] ; then
sudo ln -s /usr/lib/x86_64-linux-gnu/lua/5.2/posix_c.so /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so
fi
# Python packages
pip --version
pip install --upgrade pip
pip --version
pip install -r requirements.txt
if ! python -c "import distutils" 2> /dev/null; then
# we need setuptools for distutils in Python 3.12+, needed for python setup.py sdist
pip install --upgrade setuptools
fi
# git config is required to make actual git commits (cfr. tests for GitRepository)
git config --global user.name "Travis CI"
git config --global user.email "travis@travis-ci.org"
git config --get-regexp 'user.*'
- name: install GitHub token (if available)
env:
# token (owned by @boegelbot) with gist permissions (required for some of the tests for GitHub integration);
# this token is not available in pull requests, so tests that require it are skipped in PRs,
# and are only run after the PR gets merged
GITHUB_TOKEN: ${{secrets.CI_UNIT_TESTS_GITHUB_TOKEN}}
run: |
# only install GitHub token when testing with Lmod 8.x + Python 3.6 or 3.9, to avoid hitting GitHub rate limit
# tests that require a GitHub token are skipped automatically when no GitHub token is available
if [[ "${{matrix.modules_tool}}" =~ 'Lmod-8' ]] && [[ "${{matrix.python}}" =~ 3.[69] ]]; then
if [ ! -z $GITHUB_TOKEN ]; then
SET_KEYRING="import keyrings.alt.file; keyring.set_keyring(keyrings.alt.file.PlaintextKeyring())"
python -c "import keyring; $SET_KEYRING; keyring.set_password('github_token', 'easybuild_test', '$GITHUB_TOKEN')"
fi
echo "GitHub token installed!"
else
echo "Installation of GitHub token skipped!"
fi
- name: install modules tool
run: |
# avoid downloading modules tool sources into easybuild-framework dir
cd $HOME
export INSTALL_DEP=$GITHUB_WORKSPACE/easybuild/scripts/install_eb_dep.sh
# install Lmod
source $INSTALL_DEP ${{matrix.modules_tool}} $HOME
# changes in environment are not passed to other steps, so need to create files...
echo $MOD_INIT > mod_init
echo $PATH > path
if [ ! -z $MODULESHOME ]; then echo $MODULESHOME > moduleshome; fi
- name: check sources
run: |
# make sure there are no (top-level) "import setuptools" or "import pkg_resources" statements,
# since EasyBuild should not have a runtime requirement on setuptools
SETUPTOOLS_IMPORTS=$(egrep -RI '^(from|import)[ ]*pkg_resources|^(from|import)[ ]*setuptools' * || true)
test "x$SETUPTOOLS_IMPORTS" = "x" || (echo "Found setuptools and/or pkg_resources imports in easybuild/:\n${SETUPTOOLS_IMPORTS}" && exit 1)
- name: install sources
run: |
# install from source distribution tarball, to test release as published on PyPI
python setup.py sdist
ls dist
export PREFIX=/tmp/$USER/$GITHUB_SHA
pip install --prefix $PREFIX dist/easybuild[-_]framework*tar.gz
- name: run test suite
env:
EB_VERBOSE: 1
LC_ALL: ${{matrix.lc_all}}
run: |
# run tests *outside* of checked out easybuild-framework directory,
# to ensure we're testing installed version (see previous step)
cd $HOME
# initialize environment for modules tool
if [ -f $HOME/moduleshome ]; then export MODULESHOME=$(cat $HOME/moduleshome); fi
source $(cat $HOME/mod_init)
type module
module --version
# make sure 'eb' is available via $PATH, and that $PYTHONPATH is set (some tests expect that);
# also pick up changes to $PATH set by sourcing $MOD_INIT
export PREFIX=/tmp/$USER/$GITHUB_SHA
export PATH=$PREFIX/bin:$(cat $HOME/path)
export PYTHONPATH=$PREFIX/lib/python${{matrix.python}}/site-packages:$PYTHONPATH
eb --version
# tell EasyBuild which modules tool is available
if [[ ${{matrix.modules_tool}} =~ ^modules- ]]; then
export EASYBUILD_MODULES_TOOL=EnvironmentModules
else
export EASYBUILD_MODULES_TOOL=Lmod
fi
export TEST_EASYBUILD_MODULES_TOOL=${EASYBUILD_MODULES_TOOL}
# Run tests with LUA and Tcl module syntax (where supported)
for module_syntax in Lua Tcl; do
# Only Lmod supports Lua
if [[ "${module_syntax}" == "Lua" ]] && [[ "${EASYBUILD_MODULES_TOOL}" != "Lmod" ]]; then
echo "Not testing with '${module_syntax}' as module syntax with '${EASYBUILD_MODULES_TOOL}' as modules tool"
continue
fi
printf "\n\n=====================> Using $module_syntax module syntax <=====================\n\n"
export EASYBUILD_MODULE_SYNTAX="${module_syntax}"
export TEST_EASYBUILD_MODULE_SYNTAX="${EASYBUILD_MODULE_SYNTAX}"
eb --show-config
# gather some useful info on test system
eb --show-system-info
# check GitHub configuration
eb --check-github --github-user=easybuild_test
# create file owned by root but writable by anyone (used by test_copy_file)
sudo touch /tmp/file_to_overwrite_for_easybuild_test_copy_file.txt
sudo chmod o+w /tmp/file_to_overwrite_for_easybuild_test_copy_file.txt
# run test suite
python -O -m test.framework.suite 2>&1 | tee test_framework_suite.log
# try and make sure output of running tests is clean (no printed messages/warnings)
IGNORE_PATTERNS="no GitHub token available"
IGNORE_PATTERNS+="|skipping SvnRepository test"
IGNORE_PATTERNS+="|requires Lmod as modules tool"
IGNORE_PATTERNS+="|stty: 'standard input': Inappropriate ioctl for device"
IGNORE_PATTERNS+="|CryptographyDeprecationWarning: Python 3.[56]"
IGNORE_PATTERNS+="|from cryptography.* import "
IGNORE_PATTERNS+="|CryptographyDeprecationWarning: Python 2"
IGNORE_PATTERNS+="|Blowfish"
IGNORE_PATTERNS+="|GC3Pie not available, skipping test"
IGNORE_PATTERNS+="|CryptographyDeprecationWarning: TripleDES has been moved"
IGNORE_PATTERNS+="|algorithms.TripleDES"
# '|| true' is needed to avoid that GitHub Actions stops the job on non-zero exit of grep (i.e. when there are no matches)
PRINTED_MSG=$(egrep -v "${IGNORE_PATTERNS}" test_framework_suite.log | grep '\.\n*[A-Za-z]' || true)
test "x$PRINTED_MSG" = "x" || (echo "ERROR: Found printed messages in output of test suite" && echo "${PRINTED_MSG}" && exit 1)
done