Merge pull request #4265 from easybuilders/4.7.x

release EasyBuild v4.7.2

.github/workflows/container_tests.yml

@@ -1,5 +1,5 @@
 # documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
-name: Tests for container support
+name: Tests for Singularity container support
 on: [push, pull_request]
 
 permissions:
@@ -11,11 +11,10 @@ concurrency:
 
 jobs:
   build:
-    # stick to Ubuntu 18.04, where we can still easily install yum via 'apt install'
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python: [2.7, 3.6]
+        python: [2.7, 3.7]
       fail-fast: false
     steps:
     - uses: actions/checkout@v3
@@ -31,7 +30,7 @@ jobs:
         # for modules tool
         APT_PKGS="lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev"
         # for building Singularity images
-        APT_PKGS+=" rpm yum"
+        APT_PKGS+=" rpm dnf"
 
         # 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)
@@ -41,12 +40,6 @@ jobs:
           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
-
     - name: install Lmod
       run: |
           # avoid downloading modules tool sources into easybuild-framework dir
@@ -104,7 +97,7 @@ jobs:
           # see https://docs.easybuild.io/en/latest/Containers.html
           curl -OL https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/develop/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb
           export EASYBUILD_CONTAINERPATH=$PWD
-          export EASYBUILD_CONTAINER_CONFIG='bootstrap=yum,osversion=7'
+          export EASYBUILD_CONTAINER_CONFIG='bootstrap=docker,from=ghcr.io/easybuilders/centos-7.9-python3-amd64'
           eb bzip2-1.0.8.eb --containerize --experimental --container-build-image
           singularity exec bzip2-1.0.8.sif command -v bzip2 | grep '/app/software/bzip2/1.0.8/bin/bzip2' || (echo "Path to bzip2 '$which_bzip2' is not correct" && exit 1)
           singularity exec bzip2-1.0.8.sif bzip2 --help

.github/workflows/container_tests_apptainer.yml

@@ -0,0 +1,96 @@
+# documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
+name: Tests for Apptainer container support
+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-22.04
+    strategy:
+      matrix:
+        python: [2.7, 3.7]
+        apptainer: [1.0.0, 1.1.7]
+      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: |
+        # for building CentOS 7 container images
+        sudo apt-get install rpm
+        sudo apt-get install dnf
+        # 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
+
+    - name: install Lmod
+      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 Lmod-8.4.27 $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 $MODULESHOME > moduleshome; fi
+
+    - name: install Apptainer
+      run: |
+        curl -OL https://github.com/apptainer/apptainer/releases/download/v${{matrix.apptainer}}/apptainer_${{matrix.apptainer}}_amd64.deb
+        sudo apt install ./apptainer*.deb
+        # Apptainer provides both apptainer and singularity commands
+        apptainer --version
+        singularity --version
+
+    - name: install sources
+      run: |
+          # install from source distribution tarball, to test release as published on PyPI
+          python setup.py sdist
+          ls dist
+          export PREFIX=/tmp/$USER/$GITHUB_SHA
+          pip install --prefix $PREFIX dist/easybuild-framework*tar.gz
+          pip install --prefix $PREFIX https://github.com/easybuilders/easybuild-easyblocks/archive/develop.tar.gz
+
+    - name: run test
+      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
+          # 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
+          # create $HOME/.rpmmacros, see also https://github.com/apptainer/singularity/issues/241
+          echo '%_var /var' > $HOME/.rpmmacros
+          echo '%_dbpath %{_var}/lib/rpm' >> $HOME/.rpmmacros
+          # build CentOS 7 container image for bzip2 1.0.8 using EasyBuild;
+          # see https://docs.easybuild.io/en/latest/Containers.html
+          curl -OL https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/develop/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb
+          export EASYBUILD_CONTAINERPATH=$PWD
+          export EASYBUILD_CONTAINER_CONFIG='bootstrap=docker,from=ghcr.io/easybuilders/centos-7.9-python3-amd64'
+          export EASYBUILD_CONTAINER_TYPE='apptainer'
+          eb bzip2-1.0.8.eb --containerize --experimental --container-build-image
+          apptainer exec bzip2-1.0.8.sif command -v bzip2 | grep '/app/software/bzip2/1.0.8/bin/bzip2' || (echo "Path to bzip2 '$which_bzip2' is not correct" && exit 1)
+          apptainer exec bzip2-1.0.8.sif bzip2 --help

.github/workflows/unit_tests.yml

@@ -120,14 +120,16 @@ jobs:
 
     - name: install GitHub token (if available)
       env:
-        # see https://github.com/<username>/easybuild-framework/settings/secrets
-        GITHUB_TOKEN: ${{secrets.TEST_GITHUB_TOKEN}}
+        # 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: ${{secrets.CI_UNIT_TESTS_GITHUB_TOKEN}}
       run: |
         # don't install GitHub token when testing with Lmod 7.x or non-Lmod module tools,
         # and only when testing with Lua as module syntax,
         # to avoid hitting GitHub rate limit;
         # tests that require a GitHub token are skipped automatically when no GitHub token is available
-        if [[ ! "${{matrix.modules_tool}}" =~ 'Lmod-7' ]] && [[ ! "${{matrix.modules_tool}}" =~ 'modules-' ]] && [[ "${{matrix.modules_syntax}}" == 'Lua' ]]; then
+        if [[ ! "${{matrix.modules_tool}}" =~ 'Lmod-7' ]] && [[ ! "${{matrix.modules_tool}}" =~ 'modules-' ]] && [[ "${{matrix.module_syntax}}" == 'Lua' ]]; then
           if [ ! -z $GITHUB_TOKEN ]; then
             if [ "x${{matrix.python}}" == 'x2.6' ];
               then SET_KEYRING="keyring.set_keyring(keyring.backends.file.PlaintextKeyring())";

RELEASE_NOTES

@@ -4,6 +4,27 @@ For more detailed information, please see the git log.
 These release notes can also be consulted at https://easybuild.readthedocs.io/en/latest/Release_notes.html.
 
 
+v4.7.2 (27 May 2023)
+--------------------
+
+update/bugfix release
+
+- various enhancements, including:
+  - extend (experimental) support for generating container images with Apptainer (#3975)
+  - add default download timeout (#4226)
+  - make the RPATH section check with `readelf -d` in sanity check optional  (#4249)
+- various bug fixes, including:
+  - add `make_extension_string` and `_make_extension_list` methods to `EasyBlock` class, so easyblocks can customize them (#3697)
+  - fix typo in condition guarding installation of GitHub token in CI workflow to run unit tests + fix broken tests related to GitHub integration features (#4216)
+  - fix --check-github as gist url now includes username (#4231)
+  - switch to Ubuntu 22.04 in GitHub Actions workflow to run container tests (#4238)
+  - use "/usr/bin/env python" in test_run_cmd_script (#4241)
+- other changes:
+  - print potential errors after running a command only once (#4065)
+  - change github_* template descriptions to be somewhat clearer (#4251)
+  - remove workflow to test bootstrap script (#4255)
+
+
 v4.7.1 (March 20th 2023)
 ------------------------