Sync PR#4248 with 5.0.x

.github/workflows/container_tests_apptainer.yml

@@ -29,10 +29,18 @@ jobs:
     - name: install OS & Python packages
       run: |
         # for building CentOS 7 container images
-        sudo apt-get install rpm
-        sudo apt-get install dnf
+        APT_PKGS="rpm dnf"
         # for modules tool
-        sudo apt-get install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev
+        APT_PKGS+=" lua5.2 liblua5.2-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)
+        if ! sudo apt-get install $APT_PKGS; then
+          # Try to update cache, then try again to resolve 404s of old packages
+          sudo apt-get update -yqq || true
+          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

.github/workflows/unit_tests.yml

@@ -166,7 +166,7 @@ jobs:
               echo "Not testing with '${module_syntax}' as module syntax with '${EASYBUILD_MODULES_TOOL}' as modules tool"
               continue
             fi
-            printf '\n\n=====================> Using $module_syntax module syntax <=====================\n\n'
+            printf "\n\n=====================> Using $module_syntax module syntax <=====================\n\n"
             export EASYBUILD_MODULE_SYNTAX="${module_syntax}"
             export TEST_EASYBUILD_MODULE_SYNTAX="${EASYBUILD_MODULE_SYNTAX}"
 

easybuild/tools/filetools.py

@@ -162,7 +162,7 @@
     # tar.Z: using compress (LZW), but can be handled with gzip so use 'z'
     '.tar.z': "tar xzf %(filepath)s",
     # shell scripts don't need to be unpacked, just copy there
-    '.sh': "cp -a %(filepath)s .",
+    '.sh': "cp -dR %(filepath)s .",
 }
 
 ZIPPED_PATCH_EXTS = ('.bz2', '.gz', '.xz')

easybuild/tools/github.py

@@ -1371,8 +1371,7 @@ def close_pr(pr, motivation_msg=None):
     if not reopen:
         msg += "\nPlease don't hesitate to reopen this PR or add a comment if you feel this contribution is still "
         msg += "relevant.\nFor more information on our policy w.r.t. closing PRs, see "
-        msg += "https://easybuild.readthedocs.io/en/latest/Contributing.html"
-        msg += "#why-a-pull-request-may-be-closed-by-a-maintainer"
+        msg += "https://docs.easybuild.io/contributing/#contributing_review_process_why_pr_closed_by_maintainer"
     post_comment_in_issue(pr, msg, account=pr_target_account, repo=pr_target_repo, github_user=github_user)
 
     if dry_run:

easybuild/tools/options.py

@@ -353,7 +353,8 @@ def override_options(self):
                                             None, 'store_true', False),
             'allow-use-as-root-and-accept-consequences': ("Allow using of EasyBuild as root (NOT RECOMMENDED!)",
                                                           None, 'store_true', False),
-            'backup-modules': ("Back up an existing module file, if any. Only works when using --module-only",
+            'backup-modules': ("Back up an existing module file, if any. "
+                               "Auto-enabled when using --module-only or --skip",
                                None, 'store_true', None),  # default None to allow auto-enabling if not disabled
             'backup-patched-files': ("Create a backup (*.orig) file when applying a patch",
                                      None, 'store_true', False),

test/framework/filetools.py

@@ -106,7 +106,7 @@ def test_extract_cmd(self):
             ('test.txz', "unset TAPE; unxz test.txz --stdout | tar x"),
             ('test.iso', "7z x test.iso"),
             ('test.tar.Z', "tar xzf test.tar.Z"),
-            ('test.foo.bar.sh', "cp -a test.foo.bar.sh ."),
+            ('test.foo.bar.sh', "cp -dR test.foo.bar.sh ."),
             # check whether extension is stripped correct to determine name of target file
             # cfr. https://github.com/easybuilders/easybuild-framework/pull/3705
             ('testbz2.bz2', "bunzip2 -c testbz2.bz2 > testbz2"),

test/framework/options.py

@@ -4905,26 +4905,29 @@ def test_github_merge_pr(self):
         self.assertEqual(stderr.strip(), expected_stderr)
         self.assertTrue(stdout.strip().endswith(expected_stdout), "'%s' ends with '%s'" % (stdout, expected_stdout))
 
-        # full eligible merged PR, default target branch
+        # full eligible merged PR, default target branch;
+        # note: we frequently need to change to a more recent PR here,
+        #       to avoid that this test starts failing because commit status is set to None for old commits
         del args[-1]
-        args[1] = '17065'
+        # easyconfig PR for EasyBuild v4.8.2
+        args[1] = '19105'
 
         stdout, stderr = self._run_mock_eb(args, do_build=True, raise_error=True, testing=False)
 
         expected_stdout = '\n'.join([
-            "Checking eligibility of easybuilders/easybuild-easyconfigs PR #17065 for merging...",
+            "Checking eligibility of easybuilders/easybuild-easyconfigs PR #19105 for merging...",
             "* targets develop branch: OK",
             "* test suite passes: OK",
             "* last test report is successful: OK",
             "* no pending change requests: OK",
             "* approved review: OK (by SebastianAchilles)",
-            "* milestone is set: OK (4.7.1)",
+            "* milestone is set: OK (4.9.0)",
             "* mergeable state is clean: PR is already merged",
             '',
             "Review OK, merging pull request!",
             '',
-            "[DRY RUN] Adding comment to easybuild-easyconfigs issue #17065: 'Going in, thanks @boegel!'",
-            "[DRY RUN] Merged easybuilders/easybuild-easyconfigs pull request #17065",
+            "[DRY RUN] Adding comment to easybuild-easyconfigs issue #19105: 'Going in, thanks @boegel!'",
+            "[DRY RUN] Merged easybuilders/easybuild-easyconfigs pull request #19105",
         ])
         expected_stderr = ''
         self.assertEqual(stderr.strip(), expected_stderr)

test/framework/sandbox/easybuild/easyblocks/generic/toy_extension.py

@@ -93,7 +93,7 @@ def run_async(self, thread_pool):
             cmd = f"echo 'no sources for {self.name}'"
 
         return thread_pool.submit(run_shell_cmd, cmd, asynchronous=True, env=os.environ.copy(),
-                                  fail_on_error=False, task_id=task_id)
+                                  fail_on_error=False, task_id=task_id, work_dir=os.getcwd())
 
     def postrun(self):
         """

test/framework/sandbox/easybuild/easyblocks/t/toy.py

@@ -170,7 +170,7 @@ def run_async(self, thread_pool):
         cmd = compose_toy_build_cmd(self.cfg, self.name, self.cfg['prebuildopts'], self.cfg['buildopts'])
         task_id = f'ext_{self.name}_{self.version}'
         return thread_pool.submit(run_shell_cmd, cmd, asynchronous=True, env=os.environ.copy(),
-                                  fail_on_error=False, task_id=task_id)
+                                  fail_on_error=False, task_id=task_id, work_dir=os.getcwd())
 
     def postrun(self):
         """