re-introduce looping over all lines in buffer before attempting QA

easybuild/tools/run.py

@@ -507,9 +507,7 @@ def to_cmd_str(cmd):
         stdin = stdin.encode()
 
     if stream_output or qa_patterns:
-        print_msg(f"(streaming) output for command '{cmd_str}':")
-
-        # make stdout, stderr, stdin non-blocking files
+        # enable non-blocking access to stdout, stderr, stdin
         channels = [channel for channel in (proc.stdout, proc.stdin, proc.stderr) if channel is not None]
         for channel in channels:
             os.set_blocking(channel.fileno(), False)
@@ -528,16 +526,14 @@ def to_cmd_str(cmd):
 
         while exit_code is None:
             # collect output line by line, while checking for questions to answer (if qa_patterns is provided)
-            more_stdout = proc.stdout.readline()
-            if more_stdout:
-                _log.debug(f"Obtained more stdout: {more_stdout.decode(errors='ignore').rstrip()}")
-                stdout += more_stdout
+            for line in iter(proc.stdout.readline, b''):
+                _log.debug(f"Captured stdout: {line.decode(errors='ignore').rstrip()}")
+                stdout += line
 
             # note: we assume that there won't be any questions in stderr output
             if split_stderr:
-                more_stderr = proc.stderr.readline()
-                if more_stderr:
-                    stderr += more_stderr
+                for line in iter(proc.stderr.readline, b''):
+                    stderr += line
 
             if qa_patterns:
                 # only check for question patterns if additional output is available
@@ -556,17 +552,16 @@ def to_cmd_str(cmd):
                         error_msg = "No matching questions found for current command output, "
                         error_msg += f"giving up after {qa_timeout} seconds!"
                         raise EasyBuildError(error_msg)
-                    else:
-                        _log.debug(f"{time_no_match:0.1f} seconds without match in output of interactive shell command")
+                    _log.debug(f"{time_no_match:0.1f} seconds without match in output of interactive shell command")
 
             time.sleep(check_interval_secs)
 
             exit_code = proc.poll()
 
         # collect last bit of output once processed has exited
-        more_stdout = proc.stdout.read() or b''
-        _log.debug(f"Obtained last stdout: {more_stdout.decode(errors='ignore').rstrip()}")
-        stdout += more_stdout
+        for line in iter(proc.stdout.readline, b''):
+            _log.debug(f"Captured stdout: {line.decode(errors='ignore').rstrip()}")
+            stdout += line
         if split_stderr:
             stderr += proc.stderr.read() or b''
     else: