labdata 0.1.17__tar.gz → 0.1.19__tar.gz

{labdata-0.1.17 → labdata-0.1.19}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: labdata
-Version: 0.1.17
+Version: 0.1.19
 Summary: Package to manage data in experimental neuroscience labs
 Author-email: Joao Couto <jpcouto@gmail.com>
 Project-URL: Homepage, https://github.com/jcouto/labdata

{labdata-0.1.17 → labdata-0.1.19}/labdata/__init__.py

@@ -1,4 +1,4 @@
-VERSION = "0.1.17"
+VERSION = "0.1.19"
 
 from .utils import *
 from .copy import copy_to_upload_server

{labdata-0.1.17 → labdata-0.1.19}/labdata/cli.py

@@ -625,16 +625,21 @@ Available analysis are
             return
         from .compute import parse_analysis, run_analysis
         # parse analysis will check if the analysis is defined
-        jobids,obj = parse_analysis(analysis = args.analysis,
-                                    job_id = args.job, 
-                                    subject = args.subject,
-                                    session = args.session,
-                                    datatype = args.datatype,
-                                    secondary_args = secondary_args,
-                                    multisession = args.multisession,
-                                    force_submit = args.force_submit,
-                                    full_command = ' '.join(sys.argv[1:]),
-                                    project = args.project)
+        try:
+            jobids,obj = parse_analysis(analysis = args.analysis,
+                                        job_id = args.job, 
+                                        subject = args.subject,
+                                        session = args.session,
+                                        datatype = args.datatype,
+                                        secondary_args = secondary_args,
+                                        multisession = args.multisession,
+                                        force_submit = args.force_submit,
+                                        full_command = ' '.join(sys.argv[1:]),
+                                        project = args.project)
+        except (ValueError, NotImplementedError) as err:
+            # what the request asked for is not there: say what, and stop
+            print(f'{tcolor["r"]("Nothing to run:")} {err}')
+            sys.exit(1)
         if not len(jobids):
             print('Nothing to run.')
             return

{labdata-0.1.17 → labdata-0.1.19}/labdata/compute/__init__.py

@@ -6,6 +6,7 @@ Tasks can be scheduled and run on dedicated containers using job schedulers.
 Available compute tasks:
 - SpksCompute: Spike sorting using Kilosort/Phy via SPKS
 - DeeplabcutCompute: Animal pose estimation using DeepLabCut
+- LightningPoseCompute: Animal pose estimation using Lightning Pose
 
 Each compute task can be:
 - Scheduled to run on compute clusters via SLURM/PBS
@@ -24,6 +25,6 @@ The compute tasks handle:
 from .utils import *
 from .singularity import build_singularity_container
 from .ephys import SpksCompute
-from .pose import DeeplabcutCompute
+from .pose import DeeplabcutCompute, LightningPoseCompute
 from .caiman import CaimanCompute
 from .suite2p import Suite2pCompute