Merge pull request #54 from fmi-basel/dev-enrico

Print scMultipleX version at the beginning of the run and fix typo.

Author: nrepina

scripts/prefect/00_build_experiment.py

@@ -169,7 +169,7 @@ def get_config_params(config_file_path):
 
 def main():
     parser = argparse.ArgumentParser()
-    parser.add_argument("--config")
+    parser.add_argument("--config", required = True)
     parser.add_argument("--cpus", type=int, default=get_core_count())
     args = parser.parse_args()
     cpus = args.cpus

scripts/prefect/01_feature_extraction.py

@@ -91,7 +91,7 @@ def get_organoids(
 
 
 @task()
-def organioid_feature_extraction_and_linking_task(
+def organoid_feature_extraction_and_linking_task(
     organoid, nuc_ending: str, mem_ending: str, mask_ending: str, spacing: List[float], org_seg_ch, nuc_seg_ch, mem_seg_ch, ovr_channel, iop_cutoff
     ):
     set_spacing(spacing)
@@ -142,7 +142,7 @@ def run_flow(r_params, cpus):
 
         organoids = get_organoids(exp, mask_ending, excluded_plates, excluded_wells, upstream_tasks = [wfeo_t])
 
-        organioid_feature_extraction_and_linking_task.map(
+        organoid_feature_extraction_and_linking_task.map(
             organoids,
             unmapped(nuc_ending),
             unmapped(mem_ending),
@@ -229,7 +229,7 @@ def get_config_params(config_file_path):
 
 def main():
     parser = argparse.ArgumentParser()
-    parser.add_argument("--config")
+    parser.add_argument("--config", required = True)
     parser.add_argument("--cpus", type=int, default=get_core_count())
     args = parser.parse_args()
     cpus = args.cpus

scripts/prefect/02_organoid_multiplex.py

@@ -174,7 +174,7 @@ def get_config_params(config_file_path):
 
 def main():
     parser = argparse.ArgumentParser()
-    parser.add_argument("--config")
+    parser.add_argument("--config", required = True)
     parser.add_argument("--cpus", type=int, default=get_core_count())
     args = parser.parse_args()
     cpus = args.cpus

scripts/prefect/03_nuclear_multiplex.py

@@ -186,7 +186,7 @@ def get_config_params(config_file_path):
 
 def main():
     parser = argparse.ArgumentParser()
-    parser.add_argument("--config")
+    parser.add_argument("--config", required = True)
     parser.add_argument("--cpus", type=int, default=get_core_count())
     args = parser.parse_args()
     cpus = args.cpus

scripts/prefect/04_aggregate_features.py

@@ -100,7 +100,7 @@ def get_config_params(config_file_path):
 
 def main():
     parser = argparse.ArgumentParser()
-    parser.add_argument("--config")
+    parser.add_argument("--config", required = True)
     parser.add_argument("--cpus", type=int, default=get_core_count())
     args = parser.parse_args()
     cpus = args.cpus

scripts/prefect/05_combine_nuc_mem_features.py

@@ -89,7 +89,7 @@ def get_config_params(config_file_path):
 
 def main():
     parser = argparse.ArgumentParser()
-    parser.add_argument("--config")
+    parser.add_argument("--config", required = True)
     parser.add_argument("--cpus", type=int, default=get_core_count())
     args = parser.parse_args()
     cpus = args.cpus

scripts/prefect/06_aggregate_organoid_multiplex.py

@@ -93,7 +93,7 @@ def get_config_params(config_file_path):
 
 def main():
     parser = argparse.ArgumentParser()
-    parser.add_argument("--config")
+    parser.add_argument("--config", required = True)
     parser.add_argument("--cpus", type=int, default=get_core_count())
     args = parser.parse_args()
     cpus = args.cpus

scripts/prefect/07_aggregate_nuclear_multiplex.py

@@ -90,7 +90,7 @@ def get_config_params(config_file_path):
 
 def main():
     parser = argparse.ArgumentParser()
-    parser.add_argument("--config")
+    parser.add_argument("--config", required = True)
     parser.add_argument("--cpus", type=int, default=get_core_count())
     args = parser.parse_args()
     cpus = args.cpus

scripts/prefect/run_scmultiplex

@@ -25,6 +25,7 @@ from traceback import format_exc
 
 from scmultiplex.config import get_workflow_params
 from scmultiplex.utils import get_core_count
+from scmultiplex import version
 
 try:
 	from os import waitstatus_to_exitcode
@@ -132,9 +133,13 @@ def main(args):
 
 	save_dir = get_config_params(config_path)['save_dir']
 	logfile_name = 'scmultiplex-%s.log' % datetime.now().strftime(log_time_format)
+	logfile_path = os.path.join(save_dir, logfile_name)
+	print('scMultipleX version %s' % version)
+	with open(logfile_path, 'a') as logfile:
+		logfile.write('scMultipleX version %s' % version)
 
 	for task in task_list:
-		run_task(task, config_path, os.path.join(save_dir, logfile_name), cpus)
+		run_task(task, config_path, logfile_path, cpus)
 
 if __name__ == '__main__':
 	# workaround terminal width detection bug

src/scmultiplex/__init__.py

@@ -0,0 +1,6 @@
+from ._version import (
+	version,
+	version_tuple,
+	__version__,
+	__version_tuple__,
+	)