Updated comments and documentation after recent fixes

Author: tieneupin

pyproject.toml

@@ -31,7 +31,7 @@ classifiers = [
 ]
 dependencies = [
     "defusedxml", # For safely parsing XML files
-    "pydantic<2", # Pip hops between installing v2.7 or v1.10 depending on which of the additional dependencies are requested
+    "pydantic<2", # Locked to <2 by zocalo
     "requests",
     "rich",
     "werkzeug",

src/murfey/client/analyser.py

@@ -1,3 +1,11 @@
+"""
+Contains functions for analysing the various types of files hauled by Murfey, and
+assigning to them the correct contexts (CLEM, SPA, tomography, etc.) for processing
+on the server side.
+
+Individual contexts can be found in murfey.client.contexts.
+"""
+
 from __future__ import annotations
 
 import logging
@@ -108,13 +116,15 @@ def _find_context(self, file_path: Path) -> bool:
         assigns the necessary context class to it for subsequent stages of processing
         """
 
-        # CLEM workflow check
-        # Look for LIF files
+        # CLEM workflow checks
+        # Look for LIF and XLIF files
         if file_path.suffix in (".lif", ".xlif"):
             self._role = "detector"
             self._context = CLEMContext("leica", self._basepath)
             return True
-
+        # Look for TIFF files associated with CLEM workflow
+        # Leica's autosave mode seems to name the TIFFs in the format
+        # PostionXX--ZXX-CXX.tif
         if (
             "--" in file_path.name
             and file_path.suffix in (".tiff", ".tif")
@@ -131,6 +141,7 @@ def _find_context(self, file_path: Path) -> bool:
                 self._context = CLEMContext("leica", self._basepath)
                 return True
 
+        # Checks for tomography and SPA workflows
         split_file_name = file_path.name.split("_")
         if split_file_name:
             # Files starting with "FoilHole" belong to the SPA workflow
@@ -226,7 +237,9 @@ def post_transfer(self, transferred_file: Path):
                     transferred_file, role=self._role, environment=self._environment
                 )
         except Exception as e:
-            logger.error(f"An exception was encountered post transfer: {e}")
+            logger.error(
+                f"An exception was encountered posting the file for transfer: {e}"
+            )
 
     def _analyse(self):
         logger.info("Analyser thread started")
@@ -328,6 +341,7 @@ def _analyse(self):
                                         ),
                                     }
                                 )
+                # If a file with a CLEM context is identified, immediately post it
                 elif isinstance(self._context, CLEMContext):
                     self.post_transfer(transferred_file)
                 elif not self._extension or self._unseen_xml:

src/murfey/client/contexts/clem.py

@@ -1,9 +1,6 @@
 """
-Add a CLEM class context (refer to src/murfey/client/contexts/fib.py)
-
-Provide a post transfer function to pass on:
-- File path on the DLS file system
-- Session ID (src/murfey/client/instance_environment.py)
+Provides instructions to the server side on how different file types associated with
+the CLEM workflow should be processed.
 """
 
 # import requests
@@ -32,9 +29,12 @@ def _file_transferred_to(
     machine_config = get_machine_config(
         str(environment.url.geturl()), demo=environment.demo
     )
+    # rsync basepath and modules are set in the microscope's configuration YAML file
     return (
         Path(machine_config.get("rsync_basepath", ""))
-        / (machine_config.get("rsync_module", "data") or "data")
+        / (
+            machine_config.get("rsync_module", "data") or "data"
+        )  # Add "data" if it wasn't set
         / str(datetime.now().year)
         / source.name
         / file_path.relative_to(source)
@@ -171,7 +171,7 @@ def post_transfer(
 
             # Post message if all files for the associated series have been collected
             if len(self._tiff_series[series_name]) == self._files_in_series.get(
-                series_name, 0
+                series_name, 0  # Return 0 if the key hasn't been generated yet
             ):
 
                 # Construct URL for Murfey server to communicate with