From ebfc3ab0a211868753cc79e34371f76fcea81450 Mon Sep 17 00:00:00 2001
From: Kiarash Jamali <kjamali@mrc-lmb.cam.ac.uk>
Date: Thu, 28 Sep 2023 14:09:45 +0100
Subject: [PATCH 1/3] WIP test relion pipeline-control

---
 model_angelo/apps/build.py        | 3 ++-
 model_angelo/apps/build_no_seq.py | 3 ++-
 model_angelo/apps/hmm_search.py   | 3 ++-
 model_angelo/apps/refine.py       | 3 ++-
 model_angelo/utils/misc_utils.py  | 4 ++--
 5 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/model_angelo/apps/build.py b/model_angelo/apps/build.py
index a5659af..7e6abca 100644
--- a/model_angelo/apps/build.py
+++ b/model_angelo/apps/build.py
@@ -129,7 +129,8 @@ def add_args(parser):
     parser.add_argument(
         "--pipeline-control",
         "--pipeline_control",
-        action="store_true",
+        type=str,
+        default="",
         help=argparse.SUPPRESS,
     )
 
diff --git a/model_angelo/apps/build_no_seq.py b/model_angelo/apps/build_no_seq.py
index e55b1c5..ece968e 100644
--- a/model_angelo/apps/build_no_seq.py
+++ b/model_angelo/apps/build_no_seq.py
@@ -105,7 +105,8 @@ def add_args(parser):
     parser.add_argument(
         "--pipeline-control",
         "--pipeline_control",
-        action="store_true",
+        type=str,
+        default="",
         help=argparse.SUPPRESS,
     )
 
diff --git a/model_angelo/apps/hmm_search.py b/model_angelo/apps/hmm_search.py
index 308ad7c..7a4b04d 100644
--- a/model_angelo/apps/hmm_search.py
+++ b/model_angelo/apps/hmm_search.py
@@ -106,7 +106,8 @@ def add_args(parser):
     parser.add_argument(
         "--pipeline-control",
         "--pipeline_control",
-        action="store_true",
+        type=str,
+        default="",
         help=argparse.SUPPRESS,
     )
 
diff --git a/model_angelo/apps/refine.py b/model_angelo/apps/refine.py
index 0e2c34c..d4fd2b0 100644
--- a/model_angelo/apps/refine.py
+++ b/model_angelo/apps/refine.py
@@ -99,7 +99,8 @@ def add_args(parser):
     parser.add_argument(
         "--pipeline-control",
         "--pipeline_control",
-        action="store_true",
+        type=str,
+        default="",
         help=argparse.SUPPRESS,
     )
 
diff --git a/model_angelo/utils/misc_utils.py b/model_angelo/utils/misc_utils.py
index 00ab8b3..2366cda 100644
--- a/model_angelo/utils/misc_utils.py
+++ b/model_angelo/utils/misc_utils.py
@@ -129,9 +129,9 @@ def is_relion_abort(directory: str) -> bool:
 
 
 def write_relion_job_exit_status(
-    directory: str, status: str, pipeline_control: bool = False,
+    directory: str, status: str, pipeline_control: str = "",
 ):
-    if pipeline_control:
+    if pipeline_control != "":
         open(os.path.join(directory, f"RELION_JOB_EXIT_{status}"), "a").close()
     elif status == "FAILURE":
         sys.exit(1)

From 9f6a688564c8d3fca778ede8a0b0900f5e2fa422 Mon Sep 17 00:00:00 2001
From: Kiarash Jamali <kjamali@mrc-lmb.cam.ac.uk>
Date: Thu, 28 Sep 2023 14:25:14 +0100
Subject: [PATCH 2/3] Errors should propagate to stderr

---
 model_angelo/utils/misc_utils.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/model_angelo/utils/misc_utils.py b/model_angelo/utils/misc_utils.py
index 2366cda..694fcfd 100644
--- a/model_angelo/utils/misc_utils.py
+++ b/model_angelo/utils/misc_utils.py
@@ -71,6 +71,14 @@ def setup_logger(log_path: str):
         enqueue=True,
         diagnose=True,
     )
+    logger.add(
+        sys.stderr,
+        format="{time:YYYY-MM-DD at HH:mm:ss} | {level} | {message}",
+        enqueue=True,
+        level="ERROR",
+        backtrace=False,
+        diagnose=False,
+    )
     return logger
 
 

From 7c2d69fa3139bd0041ee8471b76e611ed9078a7f Mon Sep 17 00:00:00 2001
From: Kiarash Jamali <kjamali@mrc-lmb.cam.ac.uk>
Date: Thu, 28 Sep 2023 14:25:51 +0100
Subject: [PATCH 3/3] Bump version

---
 model_angelo/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/model_angelo/__init__.py b/model_angelo/__init__.py
index 1dd50dd..5617bc1 100644
--- a/model_angelo/__init__.py
+++ b/model_angelo/__init__.py
@@ -5,4 +5,4 @@
 """
 
 
-__version__ = "1.0.3"
+__version__ = "1.0.4"