Merge branch '5.0.x' into search_path_lib

Author: lexming

.github/workflows/eb_command.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python: [3.6, 3.7, 3.8, 3.9, '3.10', '3.11', '3.12']
+        python: [3.6, 3.7, 3.8, 3.9, '3.10', '3.11', '3.12', '3.13']
       fail-fast: false
     steps:
     - uses: actions/checkout@v3

.github/workflows/linting.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9, '3.10', '3.11', '3.12']
+        python-version: [3.6, 3.7, 3.8, 3.9, '3.10', '3.11', '3.12', '3.13']
     steps:
     - uses: actions/checkout@v3
 

.github/workflows/unit_tests.yml

@@ -45,6 +45,8 @@ jobs:
             modules_tool: ${{needs.setup.outputs.lmod8}}
           - python: '3.12'
             modules_tool: ${{needs.setup.outputs.lmod8}}
+          - python: '3.13'
+            modules_tool: ${{needs.setup.outputs.lmod8}}
           # There may be encoding errors in Python 3 which are hidden when an UTF-8 encoding is set
           # Hence run the tests (again) with LC_ALL=C and Python 3.6 (or any < 3.7)
           - python: 3.6
@@ -131,7 +133,7 @@ jobs:
       run: |
           # make sure there are no (top-level) "import setuptools" or "import pkg_resources" statements,
           # since EasyBuild should not have a runtime requirement on setuptools
-          SETUPTOOLS_IMPORTS=$(egrep -RI '^(from|import)[ ]*pkg_resources|^(from|import)[ ]*setuptools' * || true)
+          SETUPTOOLS_IMPORTS=$(egrep --exclude setup.py -RI '^(from|import)[ ]*pkg_resources|^(from|import)[ ]*setuptools' * || true)
           test "x$SETUPTOOLS_IMPORTS" = "x" || (echo "Found setuptools and/or pkg_resources imports in easybuild/:\n${SETUPTOOLS_IMPORTS}" && exit 1)
 
     - name: install sources
@@ -152,7 +154,9 @@ jobs:
           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
+          source $(cat $HOME/mod_init)
+          type module
+          module --version
           # 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

RELEASE_NOTES

@@ -4,6 +4,18 @@ 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.
 
 
+v4.9.4 (22 September 2024)
+--------------------------
+
+update/bugfix release
+
+- various enhancements, including:
+  - set $LMOD_TERSE_DECORATIONS to 'no' to avoid additional info in output produced by 'ml --terse avail' (#4648)
+- various bug fixes, including:
+  - implement workaround for permission error when copying read-only files that have extended attributes set and using Python 3.6 (#4642)
+  - take into account alternate sysroot for /bin/bash used by run_cmd (#4646)
+
+
 v4.9.3 (14 September 2024)
 --------------------------
 

easybuild/_deprecated.py

@@ -131,7 +131,7 @@ def get_output_from_process(proc, read_size=None, asynchronous=False, print_depr
 @run_cmd_cache
 def run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True, log_output=False, path=None,
             force_in_dry_run=False, verbose=True, shell=None, trace=True, stream_output=None, asynchronous=False,
-            with_hooks=True):
+            with_hooks=True, with_sysroot=True):
     """
     Run specified command (in a subshell)
     :param cmd: command to run
@@ -149,6 +149,7 @@ def run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True
     :param stream_output: enable streaming command output to stdout
     :param asynchronous: run command asynchronously (returns subprocess.Popen instance if set to True)
     :param with_hooks: trigger pre/post run_shell_cmd hooks (if defined)
+    :param with_sysroot: prepend sysroot to exec_cmd (if defined)
     """
 
     _log.deprecated("run_cmd is deprecated, use run_shell_cmd from easybuild.tools.run instead", '6.0')
@@ -228,6 +229,16 @@ def run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True
 
     exec_cmd = "/bin/bash"
 
+    # if EasyBuild is configured to use an alternate sysroot,
+    # we should also run shell commands using the bash shell provided in there,
+    # since /bin/bash may not be compatible with the alternate sysroot
+    if with_sysroot:
+        sysroot = build_option('sysroot')
+        if sysroot:
+            sysroot_bin_bash = os.path.join(sysroot, 'bin', 'bash')
+            if os.path.exists(sysroot_bin_bash):
+                exec_cmd = sysroot_bin_bash
+
     if not shell:
         if isinstance(cmd, list):
             exec_cmd = None
@@ -237,6 +248,8 @@ def run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True
         else:
             raise EasyBuildError("Don't know how to prefix with /usr/bin/env for commands of type %s", type(cmd))
 
+    _log.info("Using %s as shell for running cmd: %s", exec_cmd, cmd)
+
     if with_hooks:
         hooks = load_hooks(build_option('hooks'))
         hook_res = run_hook(RUN_SHELL_CMD, hooks, pre_step_hook=True, args=[cmd], kwargs={'work_dir': os.getcwd()})