Update namd.py for NAMD 3 #402
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| name: easyblocks 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: | |
| build: | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| matrix: | |
| python: [2.7, 3.5, 3.6, 3.7, 3.8, 3.9, '3.10', '3.11'] | |
| modules_tool: [Lmod-6.6.3, Lmod-7.8.22, Lmod-8.1.14, modules-tcl-1.147, modules-3.2.10, modules-4.1.4] | |
| module_syntax: [Lua, Tcl] | |
| # exclude some configuration for non-Lmod modules tool: | |
| # - don't test with Lua module syntax (only supported in Lmod) | |
| # - don't test with Python 3.5 and 3.7+ (only with 2.7 and 3.6), to limit test configurations | |
| exclude: | |
| - modules_tool: modules-tcl-1.147 | |
| module_syntax: Lua | |
| - modules_tool: modules-3.2.10 | |
| module_syntax: Lua | |
| - modules_tool: modules-4.1.4 | |
| module_syntax: Lua | |
| - modules_tool: modules-tcl-1.147 | |
| python: 3.5 | |
| - modules_tool: modules-tcl-1.147 | |
| python: 3.7 | |
| - modules_tool: modules-tcl-1.147 | |
| python: 3.8 | |
| - modules_tool: modules-tcl-1.147 | |
| python: 3.9 | |
| - modules_tool: modules-tcl-1.147 | |
| python: '3.10' | |
| - modules_tool: modules-3.2.10 | |
| python: 3.5 | |
| - modules_tool: modules-3.2.10 | |
| python: 3.7 | |
| - modules_tool: modules-3.2.10 | |
| python: 3.8 | |
| - modules_tool: modules-3.2.10 | |
| python: 3.9 | |
| - modules_tool: modules-3.2.10 | |
| python: '3.10' | |
| - modules_tool: modules-4.1.4 | |
| python: 3.5 | |
| - modules_tool: modules-4.1.4 | |
| python: 3.7 | |
| - modules_tool: modules-4.1.4 | |
| python: 3.8 | |
| - modules_tool: modules-4.1.4 | |
| python: 3.9 | |
| - modules_tool: modules-4.1.4 | |
| python: '3.10' | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{matrix.python}} | |
| architecture: x64 | |
| - name: install OS & Python packages | |
| run: | | |
| # disable apt-get update, we don't really need it, | |
| # and it does more harm than good (it's fairly expensive, and it results in flaky test runs) | |
| # sudo apt-get update | |
| # for modules tool | |
| sudo apt-get install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev | |
| # fix for lua-posix packaging issue, see https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082 | |
| # needed for Ubuntu 18.04, but not for Ubuntu 20.04, so skipping symlinking if posix.so already exists | |
| if [ ! -e /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so ] ; then | |
| sudo ln -s /usr/lib/x86_64-linux-gnu/lua/5.2/posix_c.so /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so | |
| fi | |
| # for testing OpenMPI-system*eb we need to have Open MPI installed | |
| sudo apt-get install libopenmpi-dev openmpi-bin | |
| - name: install EasyBuild framework | |
| run: | | |
| # first determine which branch of easybuild-framework repo to install | |
| BRANCH=develop | |
| if [ "x$GITHUB_BASE_REF" = 'xmain' ]; then BRANCH=main; fi | |
| if [ "x$GITHUB_BASE_REF" = 'x4.x' ]; then BRANCH=4.x; fi | |
| echo "Using easybuild-framework branch $BRANCH (\$GITHUB_BASE_REF $GITHUB_BASE_REF)" | |
| git clone -b $BRANCH --depth 10 --single-branch https://github.com/easybuilders/easybuild-framework.git | |
| cd easybuild-framework; git log -n 1; cd - | |
| pip install $PWD/easybuild-framework | |
| - name: install modules tool | |
| run: | | |
| cd $HOME | |
| # use install_eb_dep.sh script provided with easybuild-framework | |
| export INSTALL_DEP=$(which install_eb_dep.sh) | |
| echo "Found install_eb_dep.sh script: $INSTALL_DEP" | |
| # install modules tool | |
| 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 $MODULESHOME > moduleshome; fi | |
| - name: install sources | |
| run: | | |
| # install from source distribution tarball, to test release as published on PyPI | |
| python setup.py sdist | |
| ls dist | |
| export PREFIX=/tmp/$USER/$GITHUB_SHA | |
| pip install --prefix $PREFIX dist/easybuild-easyblocks*tar.gz | |
| - name: run test suite | |
| env: | |
| EB_VERBOSE: 1 | |
| EASYBUILD_MODULE_SYNTAX: ${{matrix.module_syntax}} | |
| run: | | |
| # initialize environment for modules tool | |
| if [ -f $HOME/moduleshome ]; then export MODULESHOME=$(cat $HOME/moduleshome); fi | |
| source $(cat $HOME/mod_init); type module | |
| # 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 | |
| # tell EasyBuild which modules tool is available | |
| if [[ ${{matrix.modules_tool}} =~ ^modules-tcl- ]]; then | |
| export EASYBUILD_MODULES_TOOL=EnvironmentModulesTcl | |
| elif [[ ${{matrix.modules_tool}} =~ ^modules-3 ]]; then | |
| export EASYBUILD_MODULES_TOOL=EnvironmentModulesC | |
| elif [[ ${{matrix.modules_tool}} =~ ^modules-4 ]]; then | |
| export EASYBUILD_MODULES_TOOL=EnvironmentModules | |
| else | |
| export EASYBUILD_MODULES_TOOL=Lmod | |
| fi | |
| eb --version | |
| eb --show-config | |
| # gather some useful info on test system | |
| eb --show-system-info | |
| # actively break "import setuptools" and "import pkg_resources", | |
| # since EasyBuild should not have a runtime requirement on setuptools | |
| echo 'raise ImportError("setuptools should no longer be relied on")' > $PREFIX/setuptools.py | |
| echo 'raise ImportError("setuptools should no longer be relied on")' > $PREFIX/pkg_resources.py | |
| export PYTHONPATH=$PREFIX:$PYTHONPATH | |
| # run test suite | |
| python -O -m test.easyblocks.suite | |
| # check output of --list-easyblocks | |
| eb --list-easyblocks > eb_list_easyblocks.out | |
| grep 'ConfigureMake\>' eb_list_easyblocks.out | |
| grep EB_GCC eb_list_easyblocks.out |