Merge branch 'main' into flush-test

Author: stephen-riggs

.bumpclient.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "0.16.5"
+current_version = "0.16.6"
 commit = true
 tag = false
 

.bumpversion.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "0.16.5"
+current_version = "0.16.6"
 commit = true
 tag = true
 

pyproject.toml

@@ -7,7 +7,7 @@ requires = [
 
 [project]
 name = "murfey"
-version = "0.16.5"
+version = "0.16.6"
 description = "Client-Server architecture hauling Cryo-EM data"
 readme = "README.md"
 keywords = [
@@ -36,6 +36,7 @@ dependencies = [
     "requests",
     "rich",
     "werkzeug",
+    "xmltodict",
 ]
 [project.optional-dependencies]
 cicd = [
@@ -44,7 +45,6 @@ cicd = [
 client = [
     "textual==0.42.0",
     "websocket-client",
-    "xmltodict",
 ]
 developer = [
     "bump-my-version<0.11.0", # Version control

src/murfey/__init__.py

@@ -1,4 +1,4 @@
 from __future__ import annotations
 
-__version__ = "0.16.5"
-__supported_client_version__ = "0.16.5"
+__version__ = "0.16.6"
+__supported_client_version__ = "0.16.6"

src/murfey/client/contexts/spa_metadata.py

@@ -162,8 +162,7 @@ def post_transfer(
                 }
                 capture_post(url, json=dcg_data)
                 gs_pix_positions = get_grid_square_atlas_positions(
-                    _atlas_destination(environment, source, transferred_file)
-                    / environment.samples[source].atlas
+                    source_visit_dir / environment.visit / partial_path
                 )
                 for gs, pos_data in gs_pix_positions.items():
                     if pos_data:

src/murfey/util/spa_metadata.py

@@ -157,6 +157,8 @@ def foil_hole_data(xml_path: Path, foil_hole: int, grid_square: int) -> FoilHole
         serialization_array = data["TargetLocations"]["TargetLocationsEfficient"][
             "a:m_serializationArray"
         ]
+        if len(serialization_array.keys()) == 0:
+            return FoilHoleInfo(id=foil_hole, grid_square_id=grid_square)
         for key in serialization_array.keys():
             if key.startswith("b:KeyValuePairOfintTargetLocation"):
                 required_key = key

src/murfey/workflows/spa/flush_spa_preprocess.py

@@ -352,7 +352,7 @@ def flush_spa_preprocess(message: dict, murfey_db: Session, demo: bool = False)
             # Register grid square and foil hole if not present
             try:
                 foil_hole_id = _flush_position_analysis(
-                    movie_path=f.file_path,
+                    movie_path=Path(f.file_path),
                     dcg_id=collected_ids[0].id,
                     session_id=session_id,
                     murfey_db=murfey_db,