np_codeocean 0.3.2__tar.gz → 0.3.3__tar.gz

{np_codeocean-0.3.2 → np_codeocean-0.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: np_codeocean
-Version: 0.3.2
+Version: 0.3.3
 Summary: Tools for uploading and interacting with Mindscope Neuropixels experiments on Code Ocean
 Author-Email: Ben Hardcastle <ben.hardcastle@alleninstitute.org>, Chris Mochizuki <chrism@alleninstitute.org>, Arjun Sridhar <arjun.sridhar@alleninstitute.org>
 License: MIT

{np_codeocean-0.3.2 → np_codeocean-0.3.3}/pyproject.toml

@@ -40,7 +40,7 @@ composite = [
 
 [project]
 name = "np_codeocean"
-version = "0.3.2"
+version = "0.3.3"
 description = "Tools for uploading and interacting with Mindscope Neuropixels experiments on Code Ocean"
 authors = [
     { name = "Ben Hardcastle", email = "ben.hardcastle@alleninstitute.org" },

{np_codeocean-0.3.2 → np_codeocean-0.3.3}/src/np_codeocean/np_session_utils.py

@@ -342,8 +342,11 @@ def upload_session(
     csv_content: dict = get_upload_csv_for_session(upload)
     utils.write_upload_csv(csv_content, upload.job)
     np_logging.web('np_codeocean').info(f'Submitting {upload.session} to hpc upload queue')
+    extra_BasicUploadJobConfigs_params = {}
+    if codeocean_configs is not None:
+        extra_BasicUploadJobConfigs_params['codeocean_configs'] = codeocean_configs
     utils.put_jobs_for_hpc_upload(
-        utils.get_job_models_from_csv(upload.job, codeocean_configs=codeocean_configs),
+        utils.get_job_models_from_csv(upload.job, **extra_BasicUploadJobConfigs_params),
         upload_service_url=utils.DEV_SERVICE if test else utils.AIND_DATA_TRANSFER_SERVICE,
         user_email=hpc_upload_job_email,
         dry_run=dry_run,

{np_codeocean-0.3.2 → np_codeocean-0.3.3}/src/np_codeocean/scripts/upload_dynamic_routing_ecephys.py

@@ -153,6 +153,7 @@ def write_metadata_and_upload(
             ignore_errors=True,
             skip_existing=not regenerate_metadata,
         )
+        
     pipelines = [
         aind_codeocean_pipeline_monitor.models.PipelineMonitorSettings(
             run_params=codeocean.computation.RunParams(
@@ -204,13 +205,12 @@ def parse_args() -> argparse.Namespace:
     parser.add_argument('--dry-run', action='store_true', help="Create upload job but do not submit to hpc upload queue.")
     parser.add_argument('--preserve-symlinks', dest='regenerate_symlinks', action='store_false', help="Existing symlink folders will not be deleted and regenerated - may result in additional data being uploaded")
     parser.add_argument('--regenerate-metadata', action='store_true', help="Regenerate metadata files (session.json and rig.json) even if they already exist")
-    parser.add_argument('--no-sync', dest="adjust_ephys_timestamps", action='store_false', help="(disabled) Skip adjustment of ephys timestamps.npy using sync data for sessions where no sync data is available")
+    parser.add_argument('--sync', dest="adjust_ephys_timestamps", action='store_true', help="Adjust ephys timestamps.npy prior to upload using sync data (if available)")
     return parser.parse_args()
 
 def main() -> None:
     args = parse_args()
     kwargs = vars(args)
-    kwargs |= {'adjust_ephys_timestamps':  False} # unnecessary while we have machinery in place for adjusting in npc_sessions (adds 5 GB of timestamps files for each upload)
     np_codeocean.utils.set_npc_lims_credentials()
     write_metadata_and_upload(**kwargs)
 

{np_codeocean-0.3.2 → np_codeocean-0.3.3}/src/np_codeocean/utils.py

@@ -308,7 +308,7 @@ def get_job_models_from_csv(
     path: pathlib.Path,
     ephys_slurm_settings: aind_slurm_rest.models.V0036JobProperties = DEFAULT_EPHYS_SLURM_SETTINGS,
     user_email: str = HPC_UPLOAD_JOB_EMAIL,
-    **extra_BasicUploadJobConfigs_params: Any,
+    **e: Any,
 ) -> tuple[aind_data_transfer_models.core.BasicUploadJobConfigs, ...]:
     jobs = pl.read_csv(path, eol_char='\r').with_columns(
         pl.col('subject-id').cast(str),