From c2791e6e1121e4cc7906e13cbf3a8970775560f3 Mon Sep 17 00:00:00 2001
From: Guido Petretto <g.petretto@gmail.com>
Date: Wed, 28 Jun 2023 13:55:04 +0200
Subject: [PATCH 1/2] update shell io

---
 src/qtoolkit/io/__init__.py |  2 +-
 src/qtoolkit/io/shell.py    | 10 ++++++++--
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/src/qtoolkit/io/__init__.py b/src/qtoolkit/io/__init__.py
index a4d31ea..cc9080d 100644
--- a/src/qtoolkit/io/__init__.py
+++ b/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}
diff --git a/src/qtoolkit/io/shell.py b/src/qtoolkit/io/shell.py
index d3fc6cd..727bc39 100644
--- a/src/qtoolkit/io/shell.py
+++ b/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}
 """
 
@@ -178,8 +182,10 @@ 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 = []

From f0a9e77e952fa6c15e228bad466e28157c942901 Mon Sep 17 00:00:00 2001
From: Guido Petretto <g.petretto@gmail.com>
Date: Wed, 28 Jun 2023 17:24:41 +0200
Subject: [PATCH 2/2] fix remote host

---
 src/qtoolkit/host/remote.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/qtoolkit/host/remote.py b/src/qtoolkit/host/remote.py
index 362e043..9fc6080 100644
--- a/src/qtoolkit/host/remote.py
+++ b/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 ?