fix unsetting of current environment in env.sh script produced by run…

…_shell_cmd

easybuild/tools/run.py

@@ -210,13 +210,15 @@ def create_cmd_scripts(cmd_str, work_dir, env, tmpdir):
 
     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;
+        # we need to be careful to filter out functions definitions, so first undefine those
+        fid.write("unset -f $(env | grep '%=' | cut -f1 -d'%' | sed 's/BASH_FUNC_//g')\n")
+        fid.write("unset $(env | cut -f1 -d=)\n")
+
         # excludes bash functions (environment variables ending with %)
         fid.write('\n'.join(f'export {key}={shlex.quote(value)}' for key, value in sorted(env.items())
                             if not key.endswith('%')) + '\n')
 
-        # unset environment variables in current environment if they're not defined in environment used to run command
-        fid.write('\n'.join(f'unset {key}' for key in os.environ if key not in env and not key.endswith('%')))
-
         fid.write('\n\nPS1="eb-shell> "')
 
         # also change to working directory (to ensure that working directory is correct for interactive bash shell)

test/framework/run.py

@@ -209,9 +209,10 @@ def test_run_shell_cmd_basic(self):
         self.assertIn("history -s 'echo hello'", env_script_txt)
 
         with self.mocked_stdout_stderr():
-            res = run_shell_cmd(f"source {env_script}; echo $FOOBAR; history")
+            res = run_shell_cmd(f"source {env_script}; echo $USER; echo $FOOBAR; history")
         self.assertEqual(res.exit_code, 0)
-        self.assertTrue(res.output.startswith('foobar\n'))
+        user = os.getenv('USER')
+        self.assertTrue(res.output.startswith(f'{user}\nfoobar\n'))
         self.assertTrue(res.output.endswith("echo hello\n"))
 
         # check on cmd.sh script that can be used to create interactive shell environment for command
@@ -268,18 +269,23 @@ def test_run_shell_cmd_env(self):
         self.assertEqual(len(paths), 1)
         cmd_tmpdir = paths[0]
 
+        # set environment variable in current environment,
+        # this should not be set in shell environment produced by scripts
+        os.environ['TEST123'] = 'test123'
+
         env_script = os.path.join(cmd_tmpdir, 'env.sh')
         self.assertExists(env_script)
         env_script_txt = read_file(env_script)
-        self.assertTrue(env_script_txt.startswith('export FOOBAR=foobar\nexport PATH'))
+        self.assertTrue(env_script_txt.startswith('unset -f $('))
+        self.assertIn('\nexport FOOBAR=foobar\nexport PATH', env_script_txt)
 
         cmd_script = os.path.join(cmd_tmpdir, 'cmd.sh')
         self.assertExists(cmd_script)
 
         with self.mocked_stdout_stderr():
-            res = run_shell_cmd(f"{cmd_script} -c 'echo $FOOBAR'", fail_on_error=False)
+            res = run_shell_cmd(f"{cmd_script} -c 'echo $FOOBAR; echo TEST123:$TEST123'", fail_on_error=False)
         self.assertEqual(res.exit_code, 0)
-        self.assertTrue(res.output.endswith('\nfoobar\n'))
+        self.assertTrue(res.output.endswith('\nfoobar\nTEST123:\n'))
 
     def test_fileprefix_from_cmd(self):
         """test simplifications from fileprefix_from_cmd."""