Merge pull request #15 from gpetretto/develop

update shell io

src/qtoolkit/host/remote.py

@@ -161,6 +161,10 @@ def execute(self, command: str | list[str], workdir: str | Path | None = None):
         exit_code : int
             Exit code of the command.
         """
+
+        if isinstance(command, (list, tuple)):
+            command = " ".join(command)
+
         # TODO: check here if we use the context manager. What happens if we provide the
         #  connection from outside (not through a config) and we want to keep it alive ?
 

src/qtoolkit/io/__init__.py

@@ -3,4 +3,4 @@
 from qtoolkit.io.shell import ShellIO, ShellState
 from qtoolkit.io.slurm import SlurmIO, SlurmState
 
-scheduler_mapping = {"slurm": SlurmIO, "pbs": PBSIO}
+scheduler_mapping = {"slurm": SlurmIO, "pbs": PBSIO, "shell": ShellIO}

src/qtoolkit/io/shell.py

@@ -59,6 +59,10 @@ def qstate(self) -> QState:
 
 class ShellIO(BaseSchedulerIO):
     header_template: str = """
+exec > $${qout_path}
+exec 2> $${qerr_path}
+
+echo $${job_name}
 $${qverbatim}
 """
 
@@ -200,8 +204,10 @@ def parse_jobs_list_output(self, exit_code, stdout, stderr) -> list[QJob]:
         if isinstance(stderr, bytes):
             stderr = stderr.decode()
 
-        if exit_code != 0:
-            msg = f"command ps failed: {stderr}"
+        # if asking only for pid that are not running the exit code is != 0,
+        # so check also on stderr for failing
+        if exit_code != 0 and stderr.strip():
+            msg = f"command ps failed: stdout: {stdout}. stderr: {stderr}"
             raise CommandFailedError(msg)
 
         jobs_list = []