From b3d5a7ddda47dae9f2252254e28e669aff5eb14d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 2 Mar 2025 16:03:28 +0100
Subject: [PATCH 1/4] stop using Ubuntu 20.4 in GitHub Actions workflows, use
 Ubuntu 22.04 instead

---
 .github/workflows/container_tests.yml         |  6 +-
 .../workflows/container_tests_apptainer.yml   | 14 +---
 .github/workflows/eb_command.yml              | 16 ++--
 .github/workflows/end2end.yml                 |  9 +-
 .github/workflows/linting.yml                 |  8 +-
 .github/workflows/unit_tests.yml              | 42 ++++------
 .github/workflows/unit_tests_python36.yml     | 82 +++++++++++++++++++
 7 files changed, 118 insertions(+), 59 deletions(-)
 create mode 100644 .github/workflows/unit_tests_python36.yml

diff --git a/.github/workflows/container_tests.yml b/.github/workflows/container_tests.yml
index 85e9198855..4521186580 100644
--- a/.github/workflows/container_tests.yml
+++ b/.github/workflows/container_tests.yml
@@ -17,10 +17,10 @@ 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
@@ -28,7 +28,7 @@ jobs:
     - 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"
 
diff --git a/.github/workflows/container_tests_apptainer.yml b/.github/workflows/container_tests_apptainer.yml
index 4f9df0df9a..1f8417ea7d 100644
--- a/.github/workflows/container_tests_apptainer.yml
+++ b/.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
diff --git a/.github/workflows/eb_command.yml b/.github/workflows/eb_command.yml
index 625206b870..e1c3f87996 100644
--- a/.github/workflows/eb_command.yml
+++ b/.github/workflows/eb_command.yml
@@ -11,16 +11,16 @@ concurrency:
 
 jobs:
   test-eb:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python: [3.6, 3.7, 3.8, 3.9, '3.10', '3.11', '3.12', '3.13']
+        python: [3.7, 3.8, 3.9, '3.10', '3.11', '3.12', '3.13']
       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
@@ -38,7 +38,7 @@ jobs:
         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)
@@ -48,12 +48,6 @@ 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
diff --git a/.github/workflows/end2end.yml b/.github/workflows/end2end.yml
index dedbcaa8d9..3ebce2ccc6 100644
--- a/.github/workflows/end2end.yml
+++ b/.github/workflows/end2end.yml
@@ -8,12 +8,13 @@ jobs:
       matrix:
         container:
           - 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
@@ -27,7 +28,7 @@ jobs:
           curl -LO https://unofficial-builds.nodejs.org/download/release/v20.9.0/node-v20.9.0-linux-x64-glibc-217.tar.xz
           tar -xf node-v20.9.0-linux-x64-glibc-217.tar.xz --strip-components 1 -C /node20217
       - name: Check out the repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
 
       - name: download and unpack easyblocks and easyconfigs repositories
         run: |
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 9dba1ed474..faff6f75a9 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -10,15 +10,15 @@ concurrency:
 
 jobs:
   python-linting:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9, '3.10', '3.11', '3.12', '3.13']
+        python-version: [3.7, 3.8, 3.9, '3.10', '3.11', '3.12', '3.13']
     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 }}
 
diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml
index d39994361d..a2409daeae 100644
--- a/.github/workflows/unit_tests.yml
+++ b/.github/workflows/unit_tests.yml
@@ -11,9 +11,9 @@ concurrency:
 
 jobs:
   setup:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     outputs:
-        lmod8: Lmod-8.7.6
+        lmod8: Lmod-8.7.58
         modules4: modules-4.5.3
         modules5: modules-5.3.1
     steps:
@@ -23,7 +23,8 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python: [3.6]
+        # Python 3.10 is default in Ubuntu 22.04
+        python: ['3.10']
         modules_tool:
           # use variables defined by 'setup' job above, see also
           # https://docs.github.com/en/actions/reference/context-and-expression-syntax-for-github-actions#needs-context
@@ -33,13 +34,11 @@ jobs:
         lc_all: [""]
         include:
           # Test different Python 3 versions with Lmod 8.x (with both Lua and Tcl module syntax)
-          - python: 3.7
-            modules_tool: ${{needs.setup.outputs.lmod8}}
-          - python: 3.8
+          - python: '3.7'
             modules_tool: ${{needs.setup.outputs.lmod8}}
-          - python: 3.9
+          - python: '3.8'
             modules_tool: ${{needs.setup.outputs.lmod8}}
-          - python: '3.10'
+          - python: '3.9'
             modules_tool: ${{needs.setup.outputs.lmod8}}
           - python: '3.11'
             modules_tool: ${{needs.setup.outputs.lmod8}}
@@ -47,17 +46,12 @@ jobs:
             modules_tool: ${{needs.setup.outputs.lmod8}}
           - python: '3.13'
             modules_tool: ${{needs.setup.outputs.lmod8}}
-          # There may be encoding errors in Python 3 which are hidden when an UTF-8 encoding is set
-          # Hence run the tests (again) with LC_ALL=C and Python 3.6 (or any < 3.7)
-          - python: 3.6
-            modules_tool: ${{needs.setup.outputs.lmod8}}
-            lc_all: C
       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
@@ -65,7 +59,7 @@ jobs:
     - 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 GitPython, python-hglib
         APT_PKGS+=" git mercurial"
         # dep for GC3Pie
@@ -79,11 +73,6 @@ 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
         # Python packages
         pip --version
         pip install --upgrade pip
@@ -94,8 +83,8 @@ jobs:
             pip install --upgrade setuptools
         fi
         # git config is required to make actual git commits (cfr. tests for GitRepository)
-        git config --global user.name "Travis CI"
-        git config --global user.email "travis@travis-ci.org"
+        git config --global user.name "Github Actions"
+        git config --global user.email "actions@github.com"
         git config --get-regexp 'user.*'
 
     - name: install GitHub token (if available)
@@ -105,9 +94,9 @@ jobs:
         # and are only run after the PR gets merged
         GITHUB_TOKEN: ${{secrets.CI_UNIT_TESTS_GITHUB_TOKEN}}
       run: |
-        # only install GitHub token when testing with Lmod 8.x + Python 3.6 or 3.9, to avoid hitting GitHub rate limit
+        # only install GitHub token when testing with Lmod 8.x + Python 3.9, to avoid hitting GitHub rate limit
         # tests that require a GitHub token are skipped automatically when no GitHub token is available
-        if [[ "${{matrix.modules_tool}}" =~ 'Lmod-8' ]] && [[ "${{matrix.python}}" =~ 3.[69] ]]; then
+        if [[ "${{matrix.modules_tool}}" =~ 'Lmod-8' ]] && [[ "${{matrix.python}}" =~ 3.9 ]]; then
           if [ ! -z $GITHUB_TOKEN ]; then
             SET_KEYRING="import keyrings.alt.file; keyring.set_keyring(keyrings.alt.file.PlaintextKeyring())"
             python -c "import keyring; $SET_KEYRING; keyring.set_password('github_token', 'easybuild_test', '$GITHUB_TOKEN')"
@@ -197,9 +186,8 @@ jobs:
             IGNORE_PATTERNS+="|skipping SvnRepository test"
             IGNORE_PATTERNS+="|requires Lmod as modules tool"
             IGNORE_PATTERNS+="|stty: 'standard input': Inappropriate ioctl for device"
-            IGNORE_PATTERNS+="|CryptographyDeprecationWarning: Python 3.[567]"
+            IGNORE_PATTERNS+="|CryptographyDeprecationWarning: Python 3.7"
             IGNORE_PATTERNS+="|from cryptography.* import "
-            IGNORE_PATTERNS+="|CryptographyDeprecationWarning: Python 2"
             IGNORE_PATTERNS+="|Blowfish"
             IGNORE_PATTERNS+="|GC3Pie not available, skipping test"
             IGNORE_PATTERNS+="|CryptographyDeprecationWarning: TripleDES has been moved"
diff --git a/.github/workflows/unit_tests_python36.yml b/.github/workflows/unit_tests_python36.yml
new file mode 100644
index 0000000000..061cc3c0c7
--- /dev/null
+++ b/.github/workflows/unit_tests_python36.yml
@@ -0,0 +1,82 @@
+# documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
+name: EasyBuild framework unit tests (Python 3.6)
+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:
+  test_python36:
+    runs-on: ubuntu-22.04
+    container:
+      # Ubuntu 20.04 container that already includes Lmod & co,
+      # see https://github.com/easybuilders/easybuild-containers
+      image: ghcr.io/easybuilders/ubuntu-20.04-amd64
+    steps:
+    - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
+
+    - name: install Python packages
+      run: |
+        # Python packages
+        python3 -V
+        python3 -m pip --version
+        python3 -m pip install --upgrade pip
+        python3 -m pip --version
+        python3 -m pip install -r requirements.txt
+        # git config is required to make actual git commits (cfr. tests for GitRepository)
+        sudo -u easybuild git config --global user.name "GitHub Actions"
+        sudo -u easybuild git config --global user.email "actions@github.com"
+        sudo -u easybuild git config --get-regexp 'user.*'
+
+    - name: install GitHub token (if available)
+      env:
+        # 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: |
+        # tests that require a GitHub token are skipped automatically when no GitHub token is available
+        if [ ! -z $GITHUB_TOKEN ]; then
+          sudo -u easybuild python3 -c "import keyring; import keyrings.alt.file; keyring.set_keyring(keyrings.alt.file.PlaintextKeyring()); keyring.set_password('github_token', 'easybuild_test', '$GITHUB_TOKEN')";
+          echo "GitHub token installed!"
+        else
+          echo "Installation of GitHub token skipped!"
+        fi
+
+    - name: install sources
+      run: |
+          # install from source distribution tarball, to test release as published on PyPI
+          python3 setup.py sdist
+          ls dist
+          export PREFIX=/tmp/$USER/$GITHUB_SHA
+          python3 -m pip install --prefix $PREFIX dist/easybuild-framework*tar.gz
+
+    - name: run test suite
+      run: |
+          # run tests *outside* of checked out easybuild-framework directory,
+          # to ensure we're testing installed version (see previous step)
+          cd $HOME
+          # make sure 'eb' is available via $PATH, and that $PYTHONPATH is set (some tests expect that)
+          export PREFIX=/tmp/$USER/$GITHUB_SHA
+          ENV_CMDS="export PATH=$PREFIX/bin:$PATH; export PYTHONPATH=$PREFIX/lib/python3.6/site-packages:$PYTHONPATH"
+          ENV_CMDS="${ENV_CMDS}; export EB_VERBOSE=1; export EB_PYTHON=python3"
+          # run EasyBuild command via (non-root) easybuild user + login shell
+          sudo -u easybuild bash -l -c "${ENV_CMDS}; module --version; eb --version"
+          # show active EasyBuild configuration
+          sudo -u easybuild bash -l -c "${ENV_CMDS}; eb --show-config"
+          # gather some useful info on test system
+          sudo -u easybuild bash -l -c "${ENV_CMDS}; eb --show-system-info"
+          # check GitHub configuration
+          sudo -u easybuild bash -l -c "${ENV_CMDS}; eb --check-github --github-user=easybuild_test"
+          # create file owned by root but writable by anyone (used by test_copy_file)
+          sudo touch /tmp/file_to_overwrite_for_easybuild_test_copy_file.txt
+          sudo chmod o+w /tmp/file_to_overwrite_for_easybuild_test_copy_file.txt
+          # run test suite (via easybuild user + login shell)
+          sudo -u easybuild bash -l -c "${ENV_CMDS}; python3 -O -m test.framework.suite"
+          # There may be encoding errors in Python 3 which are hidden when an UTF-8 encoding is set
+          # Hence run the tests (again) with LC_ALL=C and Python 3.6 (or any < 3.7)
+          sudo -u easybuild bash -l -c "${ENV_CMDS}; export LC_ALL=C; python3 -O -m test.framework.suite"

From 8516e1cd3a185ce3ac9de14e11b58320b1f2a186 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 3 Mar 2025 18:41:54 +0100
Subject: [PATCH 2/4] use python3.6 command instead of python3 in workflow to
 run tests with Python 3.6 in Ubuntu 20.04 container

---
 .github/workflows/unit_tests_python36.yml | 26 +++++++++++------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/unit_tests_python36.yml b/.github/workflows/unit_tests_python36.yml
index 061cc3c0c7..0fc842c934 100644
--- a/.github/workflows/unit_tests_python36.yml
+++ b/.github/workflows/unit_tests_python36.yml
@@ -13,20 +13,20 @@ jobs:
   test_python36:
     runs-on: ubuntu-22.04
     container:
-      # Ubuntu 20.04 container that already includes Lmod & co,
+      # Ubuntu 20.04 container that already includes Python 3.6 + Lmod & co,
       # see https://github.com/easybuilders/easybuild-containers
-      image: ghcr.io/easybuilders/ubuntu-20.04-amd64
+      image: ghcr.io/easybuilders/ubuntu-20.04-python36-amd64
     steps:
     - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
 
     - name: install Python packages
       run: |
         # Python packages
-        python3 -V
-        python3 -m pip --version
-        python3 -m pip install --upgrade pip
-        python3 -m pip --version
-        python3 -m pip install -r requirements.txt
+        python3.6 -V
+        python3.6 -m pip --version
+        python3.6 -m pip install --upgrade pip
+        python3.6 -m pip --version
+        python3.6 -m pip install -r requirements.txt
         # git config is required to make actual git commits (cfr. tests for GitRepository)
         sudo -u easybuild git config --global user.name "GitHub Actions"
         sudo -u easybuild git config --global user.email "actions@github.com"
@@ -41,7 +41,7 @@ jobs:
       run: |
         # tests that require a GitHub token are skipped automatically when no GitHub token is available
         if [ ! -z $GITHUB_TOKEN ]; then
-          sudo -u easybuild python3 -c "import keyring; import keyrings.alt.file; keyring.set_keyring(keyrings.alt.file.PlaintextKeyring()); keyring.set_password('github_token', 'easybuild_test', '$GITHUB_TOKEN')";
+          sudo -u easybuild python3.6 -c "import keyring; import keyrings.alt.file; keyring.set_keyring(keyrings.alt.file.PlaintextKeyring()); keyring.set_password('github_token', 'easybuild_test', '$GITHUB_TOKEN')";
           echo "GitHub token installed!"
         else
           echo "Installation of GitHub token skipped!"
@@ -50,10 +50,10 @@ jobs:
     - name: install sources
       run: |
           # install from source distribution tarball, to test release as published on PyPI
-          python3 setup.py sdist
+          python3.6 setup.py sdist
           ls dist
           export PREFIX=/tmp/$USER/$GITHUB_SHA
-          python3 -m pip install --prefix $PREFIX dist/easybuild-framework*tar.gz
+          python3.6 -m pip install --prefix $PREFIX dist/easybuild-framework*tar.gz
 
     - name: run test suite
       run: |
@@ -63,7 +63,7 @@ jobs:
           # make sure 'eb' is available via $PATH, and that $PYTHONPATH is set (some tests expect that)
           export PREFIX=/tmp/$USER/$GITHUB_SHA
           ENV_CMDS="export PATH=$PREFIX/bin:$PATH; export PYTHONPATH=$PREFIX/lib/python3.6/site-packages:$PYTHONPATH"
-          ENV_CMDS="${ENV_CMDS}; export EB_VERBOSE=1; export EB_PYTHON=python3"
+          ENV_CMDS="${ENV_CMDS}; export EB_VERBOSE=1; export EB_PYTHON=python3.6"
           # run EasyBuild command via (non-root) easybuild user + login shell
           sudo -u easybuild bash -l -c "${ENV_CMDS}; module --version; eb --version"
           # show active EasyBuild configuration
@@ -76,7 +76,7 @@ jobs:
           sudo touch /tmp/file_to_overwrite_for_easybuild_test_copy_file.txt
           sudo chmod o+w /tmp/file_to_overwrite_for_easybuild_test_copy_file.txt
           # run test suite (via easybuild user + login shell)
-          sudo -u easybuild bash -l -c "${ENV_CMDS}; python3 -O -m test.framework.suite"
+          sudo -u easybuild bash -l -c "${ENV_CMDS}; python3.6 -O -m test.framework.suite"
           # There may be encoding errors in Python 3 which are hidden when an UTF-8 encoding is set
           # Hence run the tests (again) with LC_ALL=C and Python 3.6 (or any < 3.7)
-          sudo -u easybuild bash -l -c "${ENV_CMDS}; export LC_ALL=C; python3 -O -m test.framework.suite"
+          sudo -u easybuild bash -l -c "${ENV_CMDS}; export LC_ALL=C; python3.6 -O -m test.framework.suite"

From 796df9a9225c4f13abfea4017b72a27b6a810092 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 3 Mar 2025 20:30:48 +0100
Subject: [PATCH 3/4] use --filter-deps in end2end test in fedora-41 or
 ubuntu-24.04 container + remove workarounds that were only needed in
 centos-7.9 container

---
 .github/workflows/end2end.yml | 14 +++++---------
 1 file changed, 5 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/end2end.yml b/.github/workflows/end2end.yml
index 3ebce2ccc6..b2bf320d94 100644
--- a/.github/workflows/end2end.yml
+++ b/.github/workflows/end2end.yml
@@ -18,15 +18,7 @@ jobs:
       fail-fast: false
     container:
       image: ghcr.io/easybuilders/${{ matrix.container }}-amd64
-      volumes:
-        - /node20217:/node20217:rw,rshared
-        - ${{ matrix.container == 'centos-7.9' && '/node20217:/__e/node20:ro,rshared' || ' ' }}
     steps:
-      - name: install nodejs20glibc2.17
-        if: ${{ matrix.container == 'centos-7.9' }}
-        run: |
-          curl -LO https://unofficial-builds.nodejs.org/download/release/v20.9.0/node-v20.9.0-linux-x64-glibc-217.tar.xz
-          tar -xf node-v20.9.0-linux-x64-glibc-217.tar.xz --strip-components 1 -C /node20217
       - name: Check out the repo
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
 
@@ -67,4 +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}"

From ccd481a40c59d69d7785c6fc95a874b4c1db085e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 4 Mar 2025 20:22:34 +0100
Subject: [PATCH 4/4] remove custom workflow for running test suite with Python
 3.6, will be added via a separate PR

---
 .github/workflows/unit_tests_python36.yml | 82 -----------------------
 1 file changed, 82 deletions(-)
 delete mode 100644 .github/workflows/unit_tests_python36.yml

diff --git a/.github/workflows/unit_tests_python36.yml b/.github/workflows/unit_tests_python36.yml
deleted file mode 100644
index 0fc842c934..0000000000
--- a/.github/workflows/unit_tests_python36.yml
+++ /dev/null
@@ -1,82 +0,0 @@
-# documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
-name: EasyBuild framework unit tests (Python 3.6)
-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:
-  test_python36:
-    runs-on: ubuntu-22.04
-    container:
-      # Ubuntu 20.04 container that already includes Python 3.6 + Lmod & co,
-      # see https://github.com/easybuilders/easybuild-containers
-      image: ghcr.io/easybuilders/ubuntu-20.04-python36-amd64
-    steps:
-    - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
-
-    - name: install Python packages
-      run: |
-        # Python packages
-        python3.6 -V
-        python3.6 -m pip --version
-        python3.6 -m pip install --upgrade pip
-        python3.6 -m pip --version
-        python3.6 -m pip install -r requirements.txt
-        # git config is required to make actual git commits (cfr. tests for GitRepository)
-        sudo -u easybuild git config --global user.name "GitHub Actions"
-        sudo -u easybuild git config --global user.email "actions@github.com"
-        sudo -u easybuild git config --get-regexp 'user.*'
-
-    - name: install GitHub token (if available)
-      env:
-        # 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: |
-        # tests that require a GitHub token are skipped automatically when no GitHub token is available
-        if [ ! -z $GITHUB_TOKEN ]; then
-          sudo -u easybuild python3.6 -c "import keyring; import keyrings.alt.file; keyring.set_keyring(keyrings.alt.file.PlaintextKeyring()); keyring.set_password('github_token', 'easybuild_test', '$GITHUB_TOKEN')";
-          echo "GitHub token installed!"
-        else
-          echo "Installation of GitHub token skipped!"
-        fi
-
-    - name: install sources
-      run: |
-          # install from source distribution tarball, to test release as published on PyPI
-          python3.6 setup.py sdist
-          ls dist
-          export PREFIX=/tmp/$USER/$GITHUB_SHA
-          python3.6 -m pip install --prefix $PREFIX dist/easybuild-framework*tar.gz
-
-    - name: run test suite
-      run: |
-          # run tests *outside* of checked out easybuild-framework directory,
-          # to ensure we're testing installed version (see previous step)
-          cd $HOME
-          # make sure 'eb' is available via $PATH, and that $PYTHONPATH is set (some tests expect that)
-          export PREFIX=/tmp/$USER/$GITHUB_SHA
-          ENV_CMDS="export PATH=$PREFIX/bin:$PATH; export PYTHONPATH=$PREFIX/lib/python3.6/site-packages:$PYTHONPATH"
-          ENV_CMDS="${ENV_CMDS}; export EB_VERBOSE=1; export EB_PYTHON=python3.6"
-          # run EasyBuild command via (non-root) easybuild user + login shell
-          sudo -u easybuild bash -l -c "${ENV_CMDS}; module --version; eb --version"
-          # show active EasyBuild configuration
-          sudo -u easybuild bash -l -c "${ENV_CMDS}; eb --show-config"
-          # gather some useful info on test system
-          sudo -u easybuild bash -l -c "${ENV_CMDS}; eb --show-system-info"
-          # check GitHub configuration
-          sudo -u easybuild bash -l -c "${ENV_CMDS}; eb --check-github --github-user=easybuild_test"
-          # create file owned by root but writable by anyone (used by test_copy_file)
-          sudo touch /tmp/file_to_overwrite_for_easybuild_test_copy_file.txt
-          sudo chmod o+w /tmp/file_to_overwrite_for_easybuild_test_copy_file.txt
-          # run test suite (via easybuild user + login shell)
-          sudo -u easybuild bash -l -c "${ENV_CMDS}; python3.6 -O -m test.framework.suite"
-          # There may be encoding errors in Python 3 which are hidden when an UTF-8 encoding is set
-          # Hence run the tests (again) with LC_ALL=C and Python 3.6 (or any < 3.7)
-          sudo -u easybuild bash -l -c "${ENV_CMDS}; export LC_ALL=C; python3.6 -O -m test.framework.suite"