Merge branch 'main' into fix-LLVMhookForBundles

Author: casparvl

.github/workflows/modules/append_module.lua

@@ -0,0 +1,3 @@
+setenv("INSIDE_GITHUB_ACTIONS", "true")
+-- Interfere with PATH so Lmod keeps a record
+prepend_path("PATH", "/snap/bin")

.github/workflows/modules/prepend_module.lua

@@ -0,0 +1,3 @@
+setenv("INSIDE_GITHUB_ACTIONS", "true")
+-- Interfere with PATH so Lmod keeps a record
+prepend_path("PATH", "/snap/bin")

.github/workflows/scripts/test_init_scripts.sh

@@ -11,11 +11,17 @@ if [ -z ${EXPECTED_EASYBUILD_VERSION} ]; then
   exit 1
 fi
 
+if [ -z ${EESSI_SOFTWARE_SUBDIR_OVERRIDE} ]; then
+  echo "\$EESSI_SOFTWARE_SUBDIR_OVERRIDE has to be set (e.g., x86_64/intel/haswell) so we can do well defined string comparison for the architecture."
+  exit 1
+fi
+
 # initialize assert framework
 if [ ! -d assert.sh ]; then
   echo "assert.sh not cloned."
   echo ""
   echo "run \`git clone https://github.com/lehmannro/assert.sh.git\`"
+  echo "(see workflow file that calls this script for how to only clone specific commit if you are worried about security)"
   exit 1
 fi
 . assert.sh/assert.sh
@@ -28,12 +34,16 @@ for shell in ${SHELLS[@]}; do
   echo  RUNNING TESTS FOR SHELL: $shell
   echo = | awk 'NF += (OFS = $_) + 100'
   if [[ ! " ${TEST_SHELLS[*]} " =~ [[:space:]]${shell}[[:space:]] ]]; then
-    ### EXCEPTION FOR CSH ###
     echo -e "\033[33mWe don't now how to test the shell '$shell', PRs are Welcome.\033[0m" 
   else
+    if [ "$shell" = "csh" ]; then
+      # make sure our .cshrc is empty before we begin as we will clobber it
+      [ -f ~/.cshrc ] && mv ~/.cshrc ~/.cshrc_orig
+    fi
+
     # TEST 1: Source Script and check Module Output
-    expected="Module for EESSI/$EESSI_VERSION loaded successfully"
-    assert "$shell -c 'source init/lmod/$shell' 2>&1 " "${expected}"
+    expected_pattern=".*EESSI has selected $EESSI_SOFTWARE_SUBDIR_OVERRIDE as the compatible CPU target for EESSI/$EESSI_VERSION.*"
+    assert_raises "$shell -c 'source init/lmod/$shell' 2>&1 | grep -E \"${expected_pattern}\""
 
     # TEST 2: Check if module overviews first section is the loaded EESSI module
     if [ "$shell" = "csh" ]; then
@@ -43,21 +53,22 @@ for shell in ${SHELLS[@]}; do
       echo "source init/lmod/$shell" > ~/.cshrc
       MODULE_SECTIONS=($($shell -c "module ov" 2>&1 | grep -e '---'))
     else
-      MODULE_SECTIONS=($($shell -c "source init/lmod/$shell 2>/dev/null; module ov 2>&1 | grep -e '---'"))
+      MODULE_SECTIONS=($($shell -c "source init/lmod/$shell >/dev/null 2>&1; module ov 2>&1 | grep -e '---'"))
     fi
-    PATTERN="/cvmfs/software\.eessi\.io/versions/$EESSI_VERSION/software/linux/x86_64/(intel/haswell|amd/zen3)/modules/all"
+    PATTERN="/cvmfs/software\.eessi\.io/versions/$EESSI_VERSION/software/linux/$EESSI_SOFTWARE_SUBDIR_OVERRIDE/modules/all"
     assert_raises 'echo "${MODULE_SECTIONS[1]}" | grep -E "$PATTERN"'
+    # echo "${MODULE_SECTIONS[1]}" "$PATTERN"
 
     # TEST 3: Check if module overviews second section is the EESSI init module
-    assert "echo ${MODULE_SECTIONS[4]}" "/cvmfs/software.eessi.io/versions/$EESSI_VERSION/init/modules"
+    assert "echo ${MODULE_SECTIONS[4]}" "/cvmfs/software.eessi.io/init/modules"
 
     # TEST 4: Load EasyBuild module and check version
     # eb --version outputs: "This is EasyBuild 5.1.1 (framework: 5.1.1, easyblocks: 5.1.1) on host ..."
     if [ "$shell" = "csh" ]; then
       echo "source init/lmod/$shell" > ~/.cshrc
-      command="$shell -c 'module load EasyBuild/${EXPECTED_EASYBUILD_VERSION}; eb --version' | cut -d \" \" -f4"
+      command="$shell -c 'module load EasyBuild/${EXPECTED_EASYBUILD_VERSION}; eb --version' | tail -n 1 | awk '{print \$4}'"
     else
-      command="$shell -c 'source init/lmod/$shell 2>/dev/null; module load EasyBuild/${EXPECTED_EASYBUILD_VERSION}; eb --version | cut -d \" \" -f4'"
+      command="$shell -c 'source init/lmod/$shell >/dev/null 2>&1; module load EasyBuild/${EXPECTED_EASYBUILD_VERSION}; eb --version' | tail -n 1 | awk '{print \$4}'"
     fi
     assert "$command" "$EXPECTED_EASYBUILD_VERSION"
 
@@ -69,12 +80,82 @@ for shell in ${SHELLS[@]}; do
       EASYBUILD_PATH=$($shell -c "source init/lmod/$shell 2>/dev/null; module load EasyBuild/${EXPECTED_EASYBUILD_VERSION}; which eb")
     fi
     # escape the dots in ${EASYBUILD_VERSION}
-    PATTERN="/cvmfs/software\.eessi\.io/versions/$EESSI_VERSION/software/linux/x86_64/(intel/haswell|amd/zen3)/software/EasyBuild/${EXPECTED_EASYBUILD_VERSION//./\\.}/bin/eb"
-    echo "$EASYBUILD_PATH" | grep -E "$PATTERN"
+    PATTERN="/cvmfs/software\.eessi\.io/versions/$EESSI_VERSION/software/linux/$EESSI_SOFTWARE_SUBDIR_OVERRIDE/software/EasyBuild/${EXPECTED_EASYBUILD_VERSION//./\\.}/bin/eb"
+    # echo "$EASYBUILD_PATH" | grep -E "$PATTERN"
     assert_raises 'echo "$EASYBUILD_PATH" | grep -E "$PATTERN"'
+    # echo "$EASYBUILD_PATH" "$PATTERN"
+
+    # TEST 6 and 7: Check the various options (EESSI_DEFAULT_MODULES_APPEND, EESSI_DEFAULT_MODULES_APPEND, EESSI_EXTRA_MODULEPATH) all work
+    if [ "$shell" = "csh" ]; then
+      echo "setenv EESSI_DEFAULT_MODULES_APPEND append_module" > ~/.cshrc
+      echo "setenv EESSI_DEFAULT_MODULES_PREPEND prepend_module" >> ~/.cshrc
+      echo "setenv EESSI_EXTRA_MODULEPATH .github/workflows/modules" >> ~/.cshrc
+      echo "source init/lmod/$shell" >> ~/.cshrc
+      TEST_LMOD_SYSTEM_DEFAULT_MODULES=$($shell -c 'echo $LMOD_SYSTEM_DEFAULT_MODULES')
+      TEST_MODULEPATH=$($shell -c 'echo $MODULEPATH')
+    elif [ "$shell" = "fish" ]; then
+      TEST_LMOD_SYSTEM_DEFAULT_MODULES=$($shell -c 'set -x EESSI_DEFAULT_MODULES_APPEND append_module ; set -x EESSI_DEFAULT_MODULES_PREPEND prepend_module ; set -x EESSI_EXTRA_MODULEPATH .github/workflows/modules ; source init/lmod/'"$shell"' 2>/dev/null; echo $LMOD_SYSTEM_DEFAULT_MODULES')
+      TEST_MODULEPATH=$($shell -c 'set -x EESSI_DEFAULT_MODULES_APPEND append_module ; set -x EESSI_DEFAULT_MODULES_PREPEND prepend_module ; set -x EESSI_EXTRA_MODULEPATH .github/workflows/modules ; source init/lmod/'"$shell"' 2>/dev/null; echo $MODULEPATH')
+    else
+      TEST_LMOD_SYSTEM_DEFAULT_MODULES=$($shell -c 'export EESSI_DEFAULT_MODULES_APPEND=append_module ; export EESSI_DEFAULT_MODULES_PREPEND=prepend_module ; export EESSI_EXTRA_MODULEPATH=.github/workflows/modules ; source init/lmod/'"$shell"' ; echo $LMOD_SYSTEM_DEFAULT_MODULES')
+      TEST_MODULEPATH=$($shell -c 'export EESSI_DEFAULT_MODULES_APPEND=append_module ; export EESSI_DEFAULT_MODULES_PREPEND=prepend_module ; export EESSI_EXTRA_MODULEPATH=.github/workflows/modules ; source init/lmod/'"$shell"' 2>/dev/null; echo $MODULEPATH')
+    fi
+    LMOD_SYSTEM_DEFAULT_MODULES_PATTERN='^prepend_module:.*:append_module$'
+    # echo "$TEST_LMOD_SYSTEM_DEFAULT_MODULES" AND "$LMOD_SYSTEM_DEFAULT_MODULES_PATTERN"
+    assert_raises 'echo "$TEST_LMOD_SYSTEM_DEFAULT_MODULES" | grep -E "$LMOD_SYSTEM_DEFAULT_MODULES_PATTERN"'
+    if [ "$shell" = "fish" ]; then
+      MODULEPATH_PATTERN='\.github/workflows/modules$'
+    else
+      MODULEPATH_PATTERN=':\.github/workflows/modules$'
+    fi
+    # echo "$TEST_MODULEPATH" AND "$MODULEPATH_PATTERN"
+    assert_raises 'echo "$TEST_MODULEPATH" | grep -E "$MODULEPATH_PATTERN"'
+
+    # TEST 8 and 9: Add a conditional test depending on whether we have the Lmod command is available locally or not (Ubuntu-based location for CI)
+    if [ -d "$LMOD_PKG/init" ]; then
+        echo "Running check for locally available Lmod with purge"
+        if [ "$shell" = "csh" ]; then
+          echo "source $LMOD_PKG/init/$shell" > ~/.cshrc
+          echo "source init/lmod/$shell" >> ~/.cshrc
+          TEST_EESSI_WITH_PURGE=$($shell -c 'echo')
+          echo "source $LMOD_PKG/init/$shell" > ~/.cshrc
+          echo "setenv EESSI_NO_MODULE_PURGE_ON_INIT 1" >> ~/.cshrc
+          echo "source init/lmod/$shell" >> ~/.cshrc
+          TEST_EESSI_WITHOUT_PURGE=$($shell -c 'echo $EESSI_NO_MODULE_PURGE_ON_INIT')
+        elif [ "$shell" = "fish" ]; then
+          TEST_EESSI_WITH_PURGE=$($shell -c "source $LMOD_PKG/init/$shell 2>/dev/null ; source init/lmod/$shell 2>/dev/null")
+          TEST_EESSI_WITHOUT_PURGE=$($shell -c "set -x EESSI_NO_MODULE_PURGE_ON_INIT 1 ; source $LMOD_PKG/init/$shell 2>/dev/null ; source init/lmod/$shell 2>/dev/null")
+        else
+          TEST_EESSI_WITH_PURGE=$($shell -c "source $LMOD_PKG/init/$shell 2>/dev/null ; source init/lmod/$shell 2>/dev/null")
+          TEST_EESSI_WITHOUT_PURGE=$($shell -c "export EESSI_NO_MODULE_PURGE_ON_INIT=1 ; source $LMOD_PKG/init/$shell 2>/dev/null ; source init/lmod/$shell 2>/dev/null")
+        fi
+        # In the first case we should have the test and in the second case we shouldn't
+        pattern="Modules purged before initialising EESSI"
+        echo $TEST_EESSI_WITH_PURGE
+        assert_raises 'echo "$TEST_EESSI_WITH_PURGE" | grep "$pattern"'
+        # this case should raise 1
+        echo $TEST_EESSI_WITHOUT_PURGE
+        assert_raises 'echo "$TEST_EESSI_WITHOUT_PURGE" | grep "$pattern"' 1
+    fi
+
+    # Optional test 10, check if the prompt has been updated
+    if [ "$shell" = "bash" ] || [ "$shell" = "ksh" ] || [ "$shell" = "zsh" ]; then
+        # Typically this is a non-interactive shell, so manually unset PS1 and reset to a non-exported variable when testing
+        TEST_EESSI_PS1_UPDATE=$($shell -c "unset PS1 ; PS1='$ ' ; source init/lmod/$shell 2>/dev/null ; echo \"\$PS1\"")
+        TEST_EESSI_NO_PS1_UPDATE=$($shell -c "unset PS1 ; source init/lmod/$shell 2>/dev/null ; echo \"\$PS1\"")
+        pattern="{EESSI/${EESSI_VERSION}} "
+        assert_raises 'echo "$TEST_EESSI_PS1_UPDATE" | grep "$pattern"'
+        assert_raises 'echo "$TEST_EESSI_NO_PS1_UPDATE" | grep "$pattern"' 1
+    fi
 
     # End Test Suite
     assert_end "source_eessi_$shell"
+
+    if [ "$shell" = "csh" ]; then
+      # Restore our .cshrc
+      [ -f ~/.cshrc_orig ] && mv ~/.cshrc_orig ~/.cshrc
+    fi
+
   fi
 done
 

.github/workflows/test_eessi_container_script.yml

@@ -17,6 +17,8 @@ jobs:
         - help
         - listrepos_default
         - listrepos_custom
+        - no_cvmfs_mounts
+        - exec
         - run
         - shell
         - container
@@ -70,14 +72,33 @@ jobs:
                 ./eessi_container.sh --verbose --list-repos | tee ${outfile2}
                 grep "EESSI/20AB.CD" ${outfile2}
 
-              # test use of --mode run
+              # test use of --repository None
+              elif [[ ${{matrix.SCRIPT_TEST}} == 'no_cvmfs_mounts' ]]; then
+                outfile=out_nocvmfs.txt
+                ./eessi_container.sh --verbose --repository None --mode exec mount | tee ${outfile}
+                # make sure that there are no CVMFS mounts in the container, i.e. mount does not have any lines line:
+                # cvmfs2 on /cvmfs/...
+                ! grep "^cvmfs" ${outfile}
+
+              # test use of --mode exec
+              elif [[ ${{matrix.SCRIPT_TEST}} == 'exec' ]]; then
+                outfile=out_exec.txt
+                echo "${test_cmd}" > test_script.sh
+                chmod u+x test_script.sh
+                export SINGULARITY_BIND="$PWD:/test"
+                ./eessi_container.sh --verbose --mode exec /test/test_script.sh | tee ${outfile}
+                grep "${out_pattern}" ${outfile}
+
+              # test use of --mode run, which should now print a warning
               elif [[ ${{matrix.SCRIPT_TEST}} == 'run' ]]; then
                 outfile=out_run.txt
                 echo "${test_cmd}" > test_script.sh
                 chmod u+x test_script.sh
                 export SINGULARITY_BIND="$PWD:/test"
                 ./eessi_container.sh --verbose --mode run /test/test_script.sh | tee ${outfile}
                 grep "${out_pattern}" ${outfile}
+                warn_message="Note: the behaviour of the run mode has changed."
+                grep "${warn_message}" ${outfile}
 
               # test use of --mode shell
               elif [[ ${{matrix.SCRIPT_TEST}} == 'shell' ]]; then
@@ -100,7 +121,7 @@ jobs:
                 echo "touch /cvmfs/software.eessi.io/${fn}" > test_script.sh
                 chmod u+x test_script.sh
                 export SINGULARITY_BIND="$PWD:/test"
-                ./eessi_container.sh --verbose --access rw --mode run /test/test_script.sh > ${outfile}
+                ./eessi_container.sh --verbose --access rw --mode exec /test/test_script.sh > ${outfile}
 
                 tmpdir=$(grep "\-\-resume" ${outfile} | sed "s/.*--resume \([^']*\).*/\1/g")
                 # note: must use '--access rw' again here, since touched file is in overlay upper dir
@@ -143,7 +164,7 @@ jobs:
                 export SINGULARITY_BIND="$PWD:/test"
                 echo 'ls -ld /cvmfs*/software.eessi.io/*' > test_script.sh
                 chmod u+x test_script.sh
-                ./eessi_container.sh --verbose --container ${container} --access rw --overlay-tool unionfs --mode run /test/test_script.sh 2>&1 | tee ${outfile}
+                ./eessi_container.sh --verbose --container ${container} --access rw --overlay-tool unionfs --mode exec /test/test_script.sh 2>&1 | tee ${outfile}
                 for pattern in "/cvmfs/software.eessi.io/versions" "/cvmfs_ro/software.eessi.io/versions"; do
                   grep "${pattern}" ${outfile} || (echo "Pattern '${pattern}' not found in ${outfile}"; exit 1)
                 done

.github/workflows/test_licenses.yml

@@ -109,11 +109,11 @@ jobs:
           # First do (and undo) the Lmod initialisation
           export MODULEPATH=init/modules
           # Turn on debug output in case we want to take a look
-          export EESSI_DEBUG_INIT=true
+          export EESSI_MODULE_DEBUG_INIT=true
           CPU_ARCH=$(./init/eessi_archdetect.sh -a cpupath)
           module load EESSI/${{matrix.EESSI_VERSION}}
-          # EESSI_DEBUG_INIT/EESSI_ARCHDETECT_OPTIONS only relevant for Lmod init
-          unset EESSI_DEBUG_INIT
+          # EESSI_MODULE_DEBUG_INIT/EESSI_ARCHDETECT_OPTIONS only relevant for Lmod init
+          unset EESSI_MODULE_DEBUG_INIT
           # Store all relevant environment variables
           env | grep -E '(^EESSI_|^LMOD_RC|^LMOD_PACKAGE_PATH|^MODULEPATH)' | grep -v EESSI_ARCHDETECT_OPTIONS | sort > "${moduleoutfile}"
           module unload EESSI/${{matrix.EESSI_VERSION}}
@@ -200,7 +200,7 @@ jobs:
           fi
 
           # Turn on debug output in case we want to take a look
-          export EESSI_DEBUG_INIT=true
+          export EESSI_MODULE_DEBUG_INIT=true
 
           initial_env_file="initial_env.txt"
           module_cycled_file="load_unload_cycle.txt"
@@ -315,3 +315,45 @@ jobs:
           module load "EESSI/${{matrix.EESSI_VERSION}}"
           GREP_PATTERN="Lmod is automatically replacing \"EESSI/${{matrix.EESSI_VERSION}}\" with \"${LOCAL_STACK_NAME}/${LOCAL_STACK_VERSION}\"."
           module load "${LOCAL_STACK_NAME}/${LOCAL_STACK_VERSION}" |& grep "${GREP_PATTERN}"
+
+  check_PS1_update_eessi_module:
+    runs-on: ubuntu-24.04
+    strategy:
+      fail-fast: false
+      matrix:
+        EESSI_VERSION:
+          - '2023.06'
+          - '2025.06'
+
+    steps:
+      - name: Check out software-layer repository
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+
+      - name: Mount EESSI CernVM-FS repository
+        uses: cvmfs-contrib/github-action-cvmfs@55899ca74cf78ab874bdf47f5a804e47c198743c # v4.0
+        with:
+          cvmfs_config_package: https://github.com/EESSI/filesystem-layer/releases/download/latest/cvmfs-config-eessi_latest_all.deb
+          cvmfs_http_proxy: DIRECT
+          cvmfs_repositories: software.eessi.io
+
+      - name: Make sure we can use EESSI_UPDATE_PS1 to update PS1 in the EESSI module
+        run: |
+          # Initialise Lmod
+          . /cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}/compat/linux/$(uname -m)/usr/share/Lmod/init/bash
+
+          export MODULEPATH=init/modules
+          # Set the relevant environment variable, load the EESSI module, and grep for what we expect in PS1
+          export EESSI_MODULE_UPDATE_PS1=1
+          # Need to set PS1 manually as we are in a non-interactive shell
+          export PS1="mytest $"
+          echo $PS1
+          module load "EESSI/${{matrix.EESSI_VERSION}}"
+          GREP_PATTERN="{EESSI/${{matrix.EESSI_VERSION}}} "
+          # Pipe the PS1 variable into grep to check for the pattern
+          echo "$PS1"
+          echo "$PS1" | grep "$GREP_PATTERN"
+
+          # Let's also check that quiet mode works
+          module load "EESSI/${{matrix.EESSI_VERSION}}" |& grep -q "Module for EESSI/${{matrix.EESSI_VERSION}} loaded successfully"
+          export EESSI_MODULE_QUIET_LOAD=1
+          ! module load "EESSI/${{matrix.EESSI_VERSION}}" |& grep -q "Module for EESSI/${{matrix.EESSI_VERSION}} loaded successfully"

.github/workflows/tests_eessi_module.yml

@@ -46,18 +46,34 @@ jobs:
             sed -i "s/__EESSI_VERSION_DEFAULT__/${{matrix.EESSI_VERSION}}/g" init/lmod/${shell}
           done
 
-      - name: Clone assert.sh script
-        run: git clone https://github.com/lehmannro/assert.sh.git
+      - name: Clone assert.sh at pinned commit
+        run: |
+          ASSERT_COMMIT_SHA=fe359e341670f1e8e86a3804ca00e5a3ebc30fa4
+          git clone --no-checkout https://github.com/lehmannro/assert.sh.git
+          cd assert.sh
+          git fetch --depth 1 origin $ASSERT_COMMIT_SHA
+          git checkout $ASSERT_COMMIT_SHA
 
       - name: Install missing shells
         run: |
           sudo apt update
           sudo apt install zsh ksh fish tcsh
           echo "# INIT ZSH" > ~/.zshrc
 
-      - name: Run tests for available shells
+      - name: Run tests for available shells without system Lmod
         run: |
+          export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
+          export EESSI_VERSION=${{matrix.EESSI_VERSION}}
+          export EXPECTED_EASYBUILD_VERSION=${{matrix.EXPECTED_EASYBUILD_VERSION}}
+          .github/workflows/scripts/test_init_scripts.sh "bash" "zsh" "ksh" "fish" "csh"
+      - name: Run tests for available shells with system Lmod
+        run: |
+          # We also want to perform the same test when there is an Lmod version available on the system
+          sudo apt install lmod
+          source /usr/share/lmod/lmod/init/bash
+          export MODULEPATH=/usr/share/lmod/lmod/modulefiles
+          module avail
+          export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
           export EESSI_VERSION=${{matrix.EESSI_VERSION}}
           export EXPECTED_EASYBUILD_VERSION=${{matrix.EXPECTED_EASYBUILD_VERSION}}
           .github/workflows/scripts/test_init_scripts.sh "bash" "zsh" "ksh" "fish" "csh"
-