Close file handles for run_shell_cmd

The stdin/stdout/stderr handles need be closed by calling `communicate`.
Otherwise the handles will be leaked and e.g.
`test_run_shell_cmd_qa_trace` fails because it may capture a related
warning.

Author: Flamefire

easybuild/tools/run.py

@@ -570,11 +570,12 @@ def to_cmd_str(cmd):
             exit_code = proc.poll()
 
         # collect last bit of output once processed has exited
-        for line in iter(proc.stdout.readline, b''):
-            _log.debug(f"Captured stdout: {line.decode(errors='ignore').rstrip()}")
-            stdout += line
+        last_stdout, last_stderr = proc.communicate()
+        if last_stdout:
+            _log.debug(f"Captured stdout: {last_stdout.decode(errors='ignore').rstrip()}")
+            stdout += last_stdout
         if split_stderr:
-            stderr += proc.stderr.read() or b''
+            stderr += last_stderr or b''
     else:
         (stdout, stderr) = proc.communicate(input=stdin)