Merge pull request #4823 from easybuilders/5.0.x

release EasyBuild v5.0.0

Author: boegel

.github/workflows/container_tests.yml

@@ -17,18 +17,18 @@ jobs:
         python: [3.7]
       fail-fast: false
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
 
     - name: set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0
       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"
+        APT_PKGS="lua5.3 liblua5.3-dev lua-filesystem lua-posix tcl tcl-dev"
         # for building Singularity images
         APT_PKGS+=" rpm dnf"
 
@@ -74,7 +74,7 @@ jobs:
           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
+          pip install --prefix $PREFIX https://github.com/easybuilders/easybuild-easyblocks/archive/5.0.x.tar.gz
 
     - name: run test
       run: |
@@ -95,7 +95,7 @@ jobs:
           echo '%_dbpath %{_var}/lib/rpm' >> $HOME/.rpmmacros
           # build CentOS 7 container image for bzip2 1.0.8 using EasyBuild;
           # see https://docs.easybuild.io/en/latest/Containers.html
-          curl -OL https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/develop/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb
+          curl -OL https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/5.0.x/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb
           export EASYBUILD_CONTAINERPATH=$PWD
           export EASYBUILD_CONTAINER_CONFIG='bootstrap=docker,from=ghcr.io/easybuilders/centos-7.9-python3-amd64'
           eb bzip2-1.0.8.eb --containerize --experimental --container-build-image

.github/workflows/container_tests_apptainer.yml

@@ -15,13 +15,13 @@ jobs:
     strategy:
       matrix:
         python: [3.7]
-        apptainer: [1.0.0, 1.1.7]
+        apptainer: [1.0.0, 1.1.7, 1.3.6]
       fail-fast: false
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
 
     - name: set up Python
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0
       with:
         python-version: ${{matrix.python}}
         architecture: x64
@@ -31,7 +31,7 @@ jobs:
         # for building CentOS 7 container images
         APT_PKGS="rpm dnf"
         # for modules tool
-        APT_PKGS+=" lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev"
+        APT_PKGS+=" lua5.3 liblua5.3-dev lua-filesystem lua-posix tcl tcl-dev"
 
         # 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 +41,6 @@ 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
@@ -74,7 +68,7 @@ jobs:
           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
+          pip install --prefix $PREFIX https://github.com/easybuilders/easybuild-easyblocks/archive/5.0.x.tar.gz
 
     - name: run test
       run: |
@@ -95,7 +89,7 @@ jobs:
           echo '%_dbpath %{_var}/lib/rpm' >> $HOME/.rpmmacros
           # build CentOS 7 container image for bzip2 1.0.8 using EasyBuild;
           # see https://docs.easybuild.io/en/latest/Containers.html
-          curl -OL https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/develop/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb
+          curl -OL https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/5.0.x/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb
           export EASYBUILD_CONTAINERPATH=$PWD
           export EASYBUILD_CONTAINER_CONFIG='bootstrap=docker,from=ghcr.io/easybuilders/centos-7.9-python3-amd64'
           export EASYBUILD_CONTAINER_TYPE='apptainer'

.github/workflows/eb_command.yml

@@ -11,16 +11,19 @@ concurrency:
 
 jobs:
   test-eb:
-    runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python: [3.6, 3.7, 3.8, 3.9, '3.10', '3.11']
+        python: [3.8, 3.9, '3.10', '3.11', '3.12', '3.13']
+        include:
+          - python: 3.7
+            os: ubuntu-22.04
       fail-fast: false
+    runs-on: ${{matrix.os || 'ubuntu-24.04'}}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
 
     - name: set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0
       with:
         python-version: ${{matrix.python}}
         architecture: x64
@@ -32,9 +35,13 @@ jobs:
         # update to latest pip, check version
         pip install --upgrade pip
         pip --version
+        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
 
         # for modules tool
-        APT_PKGS="lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev"
+        APT_PKGS="lua5.3 liblua5.3-dev lua-filesystem lua-posix tcl tcl-dev"
 
         # 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)
@@ -44,12 +51,6 @@ 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 modules tool
       run: |
           # avoid downloading modules tool sources into easybuild-framework dir
@@ -91,7 +92,7 @@ jobs:
           pymajver=$(python -c 'import sys; print(sys.version_info[0])')
           pymajminver=$(python -c 'import sys; print(".".join(str(x) for x in sys.version_info[:2]))')
           # check patterns in verbose output
-          for pattern in "^>> Considering .python.\.\.\." "^>> .python. version: ${pymajminver}\.[0-9]\+, which matches Python ${pymajver} version requirement" "^>> 'python' is able to import 'easybuild.framework', so retaining it" "^>> Selected Python command: python \(.*/bin/python\)" "^This is EasyBuild 4\.[0-9.]\+"; do
+          for pattern in "^>> Considering .python3.\.\.\." "^>> .python3. version: ${pymajminver}\.[0-9]\+, which matches Python ${pymajver} version requirement" "^>> 'python3' is able to import 'easybuild.framework', so retaining it" "^>> Selected Python command: python3 \(.*/bin/python3\)" "^This is EasyBuild 5\.[0-9.]\+"; do
               echo "Looking for pattern \"${pattern}\" in eb_version.out..."
               grep "$pattern" eb_version.out
           done
@@ -103,7 +104,7 @@ jobs:
           for eb_python in "python${pymajver}" "python${pymajminver}"; do
               export EB_PYTHON="${eb_python}"
               eb --version | tee eb_version.out 2>&1
-              for pattern in "^>> Considering .${eb_python}.\.\.\." "^>> .${eb_python}. version: ${pymajminver}\.[0-9]\+, which matches Python ${pymajver} version requirement" "^>> '${eb_python}' is able to import 'easybuild.framework', so retaining it" "^>> Selected Python command: ${eb_python} \(.*/bin/${eb_python}\)" "^This is EasyBuild 4\.[0-9.]\+"; do
+              for pattern in "^>> Considering .${eb_python}.\.\.\." "^>> .${eb_python}. version: ${pymajminver}\.[0-9]\+, which matches Python ${pymajver} version requirement" "^>> '${eb_python}' is able to import 'easybuild.framework', so retaining it" "^>> Selected Python command: ${eb_python} \(.*/bin/${eb_python}\)" "^This is EasyBuild 5\.[0-9.]\+"; do
                   echo "Looking for pattern \"${pattern}\" in eb_version.out..."
                   grep "$pattern" eb_version.out
               done

.github/workflows/end2end.yml

@@ -7,37 +7,36 @@ jobs:
     strategy:
       matrix:
         container:
-          - centos-7.9
           - centos-8.5
-          - fedora-36
+          - fedora-41
           - opensuse-15.4
-          - rockylinux-8.8
-          - rockylinux-9.2
+          - rockylinux-8.10
+          - rockylinux-9.5
           - ubuntu-20.04
           - ubuntu-22.04
+          - ubuntu-24.04
       fail-fast: false
     container:
       image: ghcr.io/easybuilders/${{ matrix.container }}-amd64
-    env: {ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION: true} # Allow using Node16 actions
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
 
       - name: download and unpack easyblocks and easyconfigs repositories
         run: |
           cd $HOME
           for pkg in easyblocks easyconfigs; do
-              curl -OL https://github.com/easybuilders/easybuild-${pkg}/archive/develop.tar.gz
-              tar xfz develop.tar.gz
-              rm -f develop.tar.gz
+              curl -OL https://github.com/easybuilders/easybuild-${pkg}/archive/5.0.x.tar.gz
+              tar xfz 5.0.x.tar.gz
+              rm -f 5.0.x.tar.gz
           done
 
       - name: Set up environment
         shell: bash
         run: |
           # collect environment variables to be set in subsequent steps in script that can be sourced
           echo "export PATH=$PWD:$PATH" > /tmp/eb_env
-          echo "export PYTHONPATH=$PWD:$HOME/easybuild-easyblocks-develop:$HOME/easybuild-easyconfigs-develop" >> /tmp/eb_env
+          echo "export PYTHONPATH=$PWD:$HOME/easybuild-easyblocks-5.0.x:$HOME/easybuild-easyconfigs-5.0.x" >> /tmp/eb_env
 
       - name: Run commands to check test environment
         shell: bash
@@ -50,6 +49,7 @@ jobs:
             "eb --show-system-info"
             "eb --check-eb-deps"
             "eb --show-config"
+            "eb -x bzip2-1.0.8.eb"
           )
           for cmd in "${cmds[@]}"; do
               echo ">>> $cmd"
@@ -59,4 +59,8 @@ jobs:
       - name: End-to-end test of installing bzip2 with EasyBuild
         shell: bash
         run: |
-          sudo -u easybuild bash -l -c "source /tmp/eb_env; eb bzip2-1.0.8.eb --trace --robot"
+          EB_ARGS=''
+          if [[ "${{ matrix.container }}" == "fedora-41" ]] || [[ "${{ matrix.container }}" == "ubuntu-24.04" ]]; then
+              EB_ARGS='--filter-deps=binutils'
+          fi
+          sudo -u easybuild bash -l -c "source /tmp/eb_env; eb bzip2-1.0.8.eb --trace --robot ${EB_ARGS}"

.github/workflows/linting.yml

@@ -10,16 +10,19 @@ concurrency:
 
 jobs:
   python-linting:
-    runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9, '3.10', '3.11']
-        
+        python: [3.8, 3.9, '3.10', '3.11', '3.12', '3.13']
+        include:
+          - python: 3.7
+            os: ubuntu-22.04
+      fail-fast: false
+    runs-on: ${{matrix.os || 'ubuntu-24.04'}}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
 
     - name: set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -30,10 +33,4 @@ jobs:
 
     - name: Run flake8 to verify PEP8-compliance of Python code
       run: |
-        # don't check py2vs3/py3.py when testing with Python 2, and vice versa
-        if [[ "${{ matrix.python-version }}" =~ "2." ]]; then
-            py_excl=py3
-        else
-            py_excl=py2
-        fi
-        flake8 --exclude ./easybuild/tools/py2vs3/${py_excl}.py
+        flake8