Merge pull request #4378 from boegel/run_shell_cmd_use_bash

rename `shell` option in `run_shell_cmd` to `use_bash`

easybuild/tools/modules.py

@@ -820,7 +820,7 @@ def run_module(self, *args, **kwargs):
         cmd_list = self.compose_cmd_list(args)
         cmd = ' '.join(cmd_list)
         # note: module commands are always run in dry mode, and are kept hidden in trace and dry run output
-        res = run_shell_cmd(cmd_list, env=environ, fail_on_error=False, shell=False, split_stderr=True,
+        res = run_shell_cmd(cmd_list, env=environ, fail_on_error=False, use_bash=False, split_stderr=True,
                             hidden=True, in_dry_run=True, output_file=False)
 
         # stdout will contain python code (to change environment etc)
@@ -1422,7 +1422,7 @@ def update(self):
             cmd = ' '.join(cmd_list)
             self.log.debug("Running command '%s'...", cmd)
 
-            res = run_shell_cmd(cmd_list, env=os.environ, fail_on_error=False, shell=False, split_stderr=True,
+            res = run_shell_cmd(cmd_list, env=os.environ, fail_on_error=False, use_bash=False, split_stderr=True,
                                 hidden=True)
             stdout, stderr = res.output, res.stderr
 

easybuild/tools/run.py

@@ -180,7 +180,7 @@ def cache_aware_func(cmd, *args, **kwargs):
 
 @run_shell_cmd_cache
 def run_shell_cmd(cmd, fail_on_error=True, split_stderr=False, stdin=None, env=None,
-                  hidden=False, in_dry_run=False, verbose_dry_run=False, work_dir=None, shell=True,
+                  hidden=False, in_dry_run=False, verbose_dry_run=False, work_dir=None, use_bash=True,
                   output_file=True, stream_output=False, asynchronous=False, with_hooks=True,
                   qa_patterns=None, qa_wait_patterns=None):
     """
@@ -194,7 +194,7 @@ def run_shell_cmd(cmd, fail_on_error=True, split_stderr=False, stdin=None, env=N
     :param in_dry_run: also run command in dry run mode
     :param verbose_dry_run: show that command is run in dry run mode (overrules 'hidden')
     :param work_dir: working directory to run command in (current working directory if None)
-    :param shell: execute command through bash shell (enabled by default)
+    :param use_bash: execute command through bash shell (enabled by default)
     :param output_file: collect command output in temporary output file
     :param stream_output: stream command output to stdout
     :param asynchronous: run command asynchronously
@@ -270,7 +270,10 @@ def to_cmd_str(cmd):
     # use bash as shell instead of the default /bin/sh used by subprocess.run
     # (which could be dash instead of bash, like on Ubuntu, see https://wiki.ubuntu.com/DashAsBinSh)
     # stick to None (default value) when not running command via a shell
-    executable = '/bin/bash' if shell else None
+    if use_bash:
+        executable, shell = '/bin/bash', True
+    else:
+        executable, shell = None, False
 
     stderr = subprocess.PIPE if split_stderr else subprocess.STDOUT
 

test/framework/run.py

@@ -1066,6 +1066,25 @@ def test_run_cmd_script(self):
         self.assertEqual(ec, 0)
         self.assertEqual(out, "hello\n")
 
+    def test_run_shell_cmd_no_bash(self):
+        """Testing use of run_shell_cmd with use_bash=False to call external scripts"""
+        py_test_script = os.path.join(self.test_prefix, 'test.py')
+        write_file(py_test_script, '\n'.join([
+            '#!%s' % sys.executable,
+            'print("hello")',
+        ]))
+        adjust_permissions(py_test_script, stat.S_IXUSR)
+
+        with self.mocked_stdout_stderr():
+            res = run_shell_cmd(py_test_script)
+        self.assertEqual(res.exit_code, 0)
+        self.assertEqual(res.output, "hello\n")
+
+        with self.mocked_stdout_stderr():
+            res = run_shell_cmd([py_test_script], use_bash=False)
+        self.assertEqual(res.exit_code, 0)
+        self.assertEqual(res.output, "hello\n")
+
     def test_run_cmd_stream(self):
         """Test use of run_cmd with streaming output."""
         self.mock_stdout(True)