Merge pull request #4662 from Micket/declare

also defined functions in interactive shell session created by `cmd.sh` script that is produced by `run_shell_cmd`

Author: boegel

.github/workflows/unit_tests.yml

@@ -152,7 +152,9 @@ 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

easybuild/tools/run.py

@@ -208,6 +208,11 @@ def create_cmd_scripts(cmd_str, work_dir, env, tmpdir, out_file, err_file):
     if env is None:
         env = os.environ.copy()
 
+    # Decode any declared bash functions
+    proc = subprocess.Popen('declare -f', stdout=subprocess.PIPE, stderr=subprocess.DEVNULL,
+                            env=env, shell=True, executable='bash')
+    (bash_functions, _) = proc.communicate()
+
     env_fp = os.path.join(tmpdir, 'env.sh')
     with open(env_fp, 'w') as fid:
         # unset all environment variables in current environment first to start from a clean slate;
@@ -219,6 +224,8 @@ def create_cmd_scripts(cmd_str, work_dir, env, tmpdir, out_file, err_file):
         fid.write('\n'.join(f'export {key}={shlex.quote(value)}' for key, value in sorted(env.items())
                             if not key.endswith('%')) + '\n')
 
+        fid.write(bash_functions.decode(errors='ignore') + '\n')
+
         fid.write('\n\nPS1="eb-shell> "')
 
         # define $EB_CMD_OUT_FILE to contain path to file with command output

test/framework/run.py

@@ -52,6 +52,7 @@
 from easybuild.tools.build_log import EasyBuildError, init_logging, stop_logging
 from easybuild.tools.config import update_build_option
 from easybuild.tools.filetools import adjust_permissions, change_dir, mkdir, read_file, remove_dir, write_file
+from easybuild.tools.modules import EnvironmentModules, Lmod
 from easybuild.tools.run import RunShellCmdResult, RunShellCmdError, check_async_cmd, check_log_for_errors
 from easybuild.tools.run import complete_cmd, fileprefix_from_cmd, get_output_from_process, parse_log_for_error
 from easybuild.tools.run import run_cmd, run_cmd_qa, run_shell_cmd, subprocess_terminate
@@ -233,6 +234,20 @@ def test_run_shell_cmd_basic(self):
         pwd = res[0].strip()[5:]
         self.assertTrue(os.path.samefile(pwd, self.test_prefix))
 
+        cmd = f"{cmd_script} -c 'module --version'"
+        with self.mocked_stdout_stderr():
+            res = run_shell_cmd(cmd, fail_on_error=False)
+        self.assertEqual(res.exit_code, 0)
+
+        if isinstance(self.modtool, Lmod):
+            regex = re.compile("^Modules based on Lua: Version [0-9]", re.M)
+        elif isinstance(self.modtool, EnvironmentModules):
+            regex = re.compile("^Modules Release [0-9]", re.M)
+        else:
+            self.fail("Unknown modules tool used!")
+
+        self.assertTrue(regex.search(res.output), f"Pattern '{regex.pattern}' should be found in {res.output}")
+
         # test running command that emits non-UTF-8 characters
         # this is constructed to reproduce errors like:
         # UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe2