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Merge pull request #3052 from easybuilders/4.0.x
release EasyBuild v4.0.1
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‎.github/workflows/unit_tests.yml‎

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# documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
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name: EasyBuild framework unit tests
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on: [push, pull_request]
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jobs:
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build:
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runs-on: ubuntu-18.04
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strategy:
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matrix:
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python: [2.7, 3.5, 3.6, 3.7]
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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]
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module_syntax: [Lua, Tcl]
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# exclude some configuration for non-Lmod modules tool:
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# - don't test with Lua module syntax (only supported in Lmod)
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# - don't test with Python 3.5 and 3.7 (only with 2.7 and 3.6), to limit test configurations
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exclude:
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- modules_tool: modules-tcl-1.147
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module_syntax: Lua
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- modules_tool: modules-3.2.10
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module_syntax: Lua
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- modules_tool: modules-4.1.4
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module_syntax: Lua
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- modules_tool: modules-tcl-1.147
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python: 3.5
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- modules_tool: modules-tcl-1.147
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python: 3.7
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- modules_tool: modules-3.2.10
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python: 3.5
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- modules_tool: modules-3.2.10
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python: 3.7
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- modules_tool: modules-4.1.4
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python: 3.5
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- modules_tool: modules-4.1.4
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python: 3.7
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fail-fast: false
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steps:
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- uses: actions/checkout@v1
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- name: set up Python
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uses: actions/setup-python@v1
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with:
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python-version: ${{matrix.python}}
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architecture: x64
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- name: install OS & Python packages
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run: |
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# for modules tool
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sudo apt-get install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev
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# fix for lua-posix packaging issue, see https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082
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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
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# for GitPython, python-hglib
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sudo apt-get install git mercurial
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# dep for GC3Pie
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sudo apt-get install time
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# Python packages
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pip --version
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pip install --upgrade pip
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pip --version
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pip install -r requirements.txt
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# git config is required to make actual git commits (cfr. tests for GitRepository)
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git config --global user.name "Travis CI"
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git config --global user.email "[email protected]"
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git config --get-regexp 'user.*'
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- name: install GitHub token (if available)
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env:
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# see https://github.com/<username>/easybuild-framework/settings/secrets
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GITHUB_TOKEN: ${{secrets.TEST_GITHUB_TOKEN}}
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run: |
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if [ ! -z $GITHUB_TOKEN ]; then
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if [ "x${{matrix.python}}" == 'x2.6' ];
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then SET_KEYRING="keyring.set_keyring(keyring.backends.file.PlaintextKeyring())";
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else SET_KEYRING="import keyrings; keyring.set_keyring(keyrings.alt.file.PlaintextKeyring())";
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fi;
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python -c "import keyring; $SET_KEYRING; keyring.set_password('github_token', 'easybuild_test', '$GITHUB_TOKEN')";
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fi
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- name: install modules tool
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run: |
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# avoid downloading modules tool sources into easybuild-framework dir
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cd $HOME
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export INSTALL_DEP=$GITHUB_WORKSPACE/easybuild/scripts/install_eb_dep.sh
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# install Lmod
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source $INSTALL_DEP ${{matrix.modules_tool}} $HOME
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# changes in environment are not passed to other steps, so need to create files...
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echo $MOD_INIT > mod_init
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echo $PATH > path
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if [ ! -z $MODULESHOME ]; then echo $MODULESHOME > moduleshome; fi
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- name: check sources
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run: |
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# make sure there are no (top-level) "import setuptools" or "import pkg_resources" statements,
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# since EasyBuild should not have a runtime requirement on setuptools
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SETUPTOOLS_IMPORTS=$(egrep -RI '^(from|import)[ ]*pkg_resources|^(from|import)[ ]*setuptools' * || true)
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test "x$SETUPTOOLS_IMPORTS" = "x" || (echo "Found setuptools and/or pkg_resources imports in easybuild/:\n${SETUPTOOLS_IMPORTS}" && exit 1)
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- name: install sources
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run: |
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# install from source distribution tarball, to test release as published on PyPI
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python setup.py sdist
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ls dist
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export PREFIX=/tmp/$USER/$GITHUB_SHA
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pip install --prefix $PREFIX dist/easybuild-framework*tar.gz
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- name: run test suite & test bootstrap script
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env:
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EB_VERBOSE: 1
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EASYBUILD_MODULE_SYNTAX: ${{matrix.module_syntax}}
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TEST_EASYBUILD_MODULE_SYNTAX: ${{matrix.module_syntax}}
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run: |
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# initialize environment for modules tool
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if [ -f $HOME/moduleshome ]; then export MODULESHOME=$(cat $HOME/moduleshome); fi
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source $(cat $HOME/mod_init); type module
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# make sure 'eb' is available via $PATH, and that $PYTHONPATH is set (some tests expect that);
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# also pick up changes to $PATH set by sourcing $MOD_INIT
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export PREFIX=/tmp/$USER/$GITHUB_SHA
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export PATH=$PREFIX/bin:$(cat $HOME/path)
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export PYTHONPATH=$PREFIX/lib/python${{matrix.python}}/site-packages:$PYTHONPATH
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eb --version
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# tell EasyBuild which modules tool is available
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if [[ ${{matrix.modules_tool}} =~ ^modules-tcl- ]]; then
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export EASYBUILD_MODULES_TOOL=EnvironmentModulesTcl
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elif [[ ${{matrix.modules_tool}} =~ ^modules-3 ]]; then
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export EASYBUILD_MODULES_TOOL=EnvironmentModulesC
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elif [[ ${{matrix.modules_tool}} =~ ^modules-4 ]]; then
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export EASYBUILD_MODULES_TOOL=EnvironmentModules
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else
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export EASYBUILD_MODULES_TOOL=Lmod
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fi
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export TEST_EASYBUILD_MODULES_TOOL=$EASYBUILD_MODULES_TOOL
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eb --show-config
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# gather some useful info on test system
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eb --show-system-info
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# check GitHub configuration
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eb --check-github --github-user=easybuild_test
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# run test suite
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python -O -m test.framework.suite 2>&1 | tee test_framework_suite.log
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# try and make sure output of running tests is clean (no printed messages/warnings)
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IGNORE_PATTERNS="no GitHub token available|skipping SvnRepository test|requires Lmod as modules tool|stty: 'standard input': Inappropriate ioctl for device"
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# '|| true' is needed to avoid that Travis stops the job on non-zero exit of grep (i.e. when there are no matches)
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PRINTED_MSG=$(egrep -v "${IGNORE_PATTERNS}" test_framework_suite.log | grep '\.\n*[A-Za-z]' || true)
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test "x$PRINTED_MSG" = "x" || (echo "ERROR: Found printed messages in output of test suite\n${PRINTED_MSG}" && exit 1)
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# version and SHA256 checksum are hardcoded below to avoid forgetting to update the version in the script along with contents
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EB_BOOTSTRAP_VERSION=$(grep '^EB_BOOTSTRAP_VERSION' easybuild/scripts/bootstrap_eb.py | sed 's/[^0-9.]//g')
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EB_BOOTSTRAP_SHA256SUM=$(sha256sum easybuild/scripts/bootstrap_eb.py | cut -f1 -d' ')
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EB_BOOTSTRAP_FOUND="$EB_BOOTSTRAP_VERSION $EB_BOOTSTRAP_SHA256SUM"
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EB_BOOTSTRAP_EXPECTED="20190922.01 778762479d77df641c247aba33c13203c8c5b8275e47f59464bab93917aaaf22"
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test "$EB_BOOTSTRAP_FOUND" = "$EB_BOOTSTRAP_EXPECTED" || (echo "Version check on bootstrap script failed $EB_BOOTSTRAP_FOUND" && exit 1)
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# test bootstrap script (only compatible with Python 2 for now)
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if [[ ${{matrix.python}} =~ '2.' ]]; then
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export PREFIX=/tmp/$USER/$GITHUB_SHA/eb_bootstrap
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python easybuild/scripts/bootstrap_eb.py $PREFIX
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# unset $PYTHONPATH to avoid mixing two EasyBuild 'installations' when testing bootstrapped EasyBuild module
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unset PYTHONPATH
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# simple sanity check on bootstrapped EasyBuild module (skip when testing with Python 3, for now)
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module use $PREFIX/modules/all
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module load EasyBuild
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eb --version
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else
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echo "Testing of bootstrap script skipped when testing with Python ${{matrix.python}}"
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fi

‎.travis.yml‎

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# run test suite
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- python -O -m test.framework.suite 2>&1 | tee test_framework_suite.log
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# try and make sure output of running tests is clean (no printed messages/warnings)
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- IGNORE_PATTERNS="vsc\.install\.shared_setup|no GitHub token available|skipping SvnRepository test|lib/python2.6/site-packages|required Lmod as modules tool|GC3Pie not available, skipping test"
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- IGNORE_PATTERNS="no GitHub token available|skipping SvnRepository test|lib/python2.6/site-packages|requires Lmod as modules tool"
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# '|| true' is needed to avoid that Travis stops the job on non-zero exit of grep (i.e. when there are no matches)
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- PRINTED_MSG=$(egrep -v "${IGNORE_PATTERNS}" test_framework_suite.log | grep '\.\n*[A-Za-z]' || true)
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- test "x$PRINTED_MSG" = "x" || (echo "Found printed messages in output of test suite\n${PRINTED_MSG}" && exit 1)
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- EB_BOOTSTRAP_VERSION=$(grep '^EB_BOOTSTRAP_VERSION' $TRAVIS_BUILD_DIR/easybuild/scripts/bootstrap_eb.py | sed 's/[^0-9.]//g')
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- EB_BOOTSTRAP_SHA256SUM=$(sha256sum $TRAVIS_BUILD_DIR/easybuild/scripts/bootstrap_eb.py | cut -f1 -d' ')
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- EB_BOOTSTRAP_FOUND="$EB_BOOTSTRAP_VERSION $EB_BOOTSTRAP_SHA256SUM"
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- EB_BOOTSTRAP_EXPECTED="20190523.01 f419ce397246b722d8fa4862d56275badfc9062e965a6e45be9c1282c552352d"
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- EB_BOOTSTRAP_EXPECTED="20190922.01 778762479d77df641c247aba33c13203c8c5b8275e47f59464bab93917aaaf22"
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- test "$EB_BOOTSTRAP_FOUND" = "$EB_BOOTSTRAP_EXPECTED" || (echo "Version check on bootstrap script failed $EB_BOOTSTRAP_FOUND" && exit 1)
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# test bootstrap script (skip when testing with Python 3 for now, since latest EasyBuild release is not compatible with Python 3 yet)
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- if [ ! "x$TRAVIS_PYTHON_VERSION" =~ x3.[0-9] ]; then python $TRAVIS_BUILD_DIR/easybuild/scripts/bootstrap_eb.py /tmp/$TRAVIS_JOB_ID/eb_bootstrap; fi

‎RELEASE_NOTES‎

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These release notes can also be consulted at https://easybuild.readthedocs.io/en/latest/Release_notes.html.
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v4.0.1 (October 15th 2019)
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--------------------------
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update/bugfix release
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- various enhancements, including:
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- add 'parallel' to list of config templates (#3036)
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- add GitHub Actions workflow to run easybuild-framework test suite (#3039)
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- add 'retest' as a reason to --close-pr, to close/re-open PRs to trigger re-test in Travis (#3040)
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- define $EB_SCRIPT_PATH in 'eb' wrapper script, and consider it before location of 'eb' determined via $PATH in get_paths_for function (#3046)
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- add support for --remove-ghost-install-dirs configuration option, and warn about (potential) ghost install dirs by default when --force/--rebuild is used (#3050)
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- various bug fixes, including:
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- update bootstrap script to support installing EasyBuild v4.0 (#3017)
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- fix broken test_download_repo due to archiving of easyconfigs (#3019, #3023)
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- avoid that --inject-checksums introduces list of patches for extensions as a single long line (#3025, #3034)
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- enhance regex in fix_shebang method to fix more Python/Perl shebangs + avoid patching binary files (#3029)
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- delete test gist that is created by --check-github (#3031)
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- disable templates when defining easyconfig parameters in EasyConfig.set_keys() (#3037)
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- avoid setting GC3Pie's max_in_flight to None if --job-max-jobs is not specified (#3038)
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- fix use of obtain_file method for extensions (#3042)
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- error out if some GC3Pie job failed (#3044)
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v4.0.0 (September 20th 2019)
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----------------------------
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