do not attach PIPE file handle on STDIN of run_shell_cmd unless there are contents for it
#5547
Workflow file for this run
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| # 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 "[email protected]" | |
| 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 --exclude setup.py -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="${EASYBUILD_MODULE_SYNTAX}" | |
| eb --show-config | |
| # gather some useful info on test system | |
| eb --show-system-info | |
| # check GitHub configuration | |
| eb --check-github --github-user=easybuild_test | |
| # create file owned by root but writable by anyone (used by test_copy_file) | |
| sudo touch /tmp/file_to_overwrite_for_easybuild_test_copy_file.txt | |
| sudo chmod o+w /tmp/file_to_overwrite_for_easybuild_test_copy_file.txt | |
| # run test suite | |
| python -O -m test.framework.suite 2>&1 | tee test_framework_suite.log | |
| # try and make sure output of running tests is clean (no printed messages/warnings) | |
| IGNORE_PATTERNS="no GitHub token available" | |
| IGNORE_PATTERNS+="|skipping SvnRepository test" | |
| IGNORE_PATTERNS+="|requires Lmod as modules tool" | |
| IGNORE_PATTERNS+="|stty: 'standard input': Inappropriate ioctl for device" | |
| IGNORE_PATTERNS+="|CryptographyDeprecationWarning: Python 3.[567]" | |
| IGNORE_PATTERNS+="|from cryptography.* import " | |
| IGNORE_PATTERNS+="|CryptographyDeprecationWarning: Python 2" | |
| IGNORE_PATTERNS+="|Blowfish" | |
| IGNORE_PATTERNS+="|GC3Pie not available, skipping test" | |
| IGNORE_PATTERNS+="|CryptographyDeprecationWarning: TripleDES has been moved" | |
| IGNORE_PATTERNS+="|algorithms.TripleDES" | |
| # '|| true' is needed to avoid that GitHub Actions stops the job on non-zero exit of grep (i.e. when there are no matches) | |
| PRINTED_MSG=$(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 |