sl-shared-assets 3.0.0rc5__tar.gz → 3.0.0rc7__tar.gz

{sl_shared_assets-3.0.0rc5 → sl_shared_assets-3.0.0rc7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sl-shared-assets
-Version: 3.0.0rc5
+Version: 3.0.0rc7
 Summary: Provides data acquisition and processing assets shared between Sun (NeuroAI) lab libraries.
 Project-URL: Homepage, https://github.com/Sun-Lab-NBB/sl-shared-assets
 Project-URL: Documentation, https://sl-shared-assets-api-docs.netlify.app/

{sl_shared_assets-3.0.0rc5 → sl_shared_assets-3.0.0rc7}/pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "hatchling.build"
 # Project metdata section. Provides the genral ID information about the project.
 [project]
 name = "sl-shared-assets"
-version = "3.0.0rc5"
+version = "3.0.0rc7"
 description = "Provides data acquisition and processing assets shared between Sun (NeuroAI) lab libraries."
 readme = "README.md"
 license = { file = "LICENSE" }

{sl_shared_assets-3.0.0rc5 → sl_shared_assets-3.0.0rc7}/src/sl_shared_assets/data_classes/session_data.py

@@ -68,9 +68,6 @@ class RawData:
     surgery_metadata_path: Path = Path()
     """Stores the path to the surgery_metadata.yaml file. This file contains the most actual information about the 
     surgical intervention(s) performed on the animal prior to the session."""
-    project_configuration_path: Path = Path()
-    """Stores the path to the project_configuration.yaml file. This file contains the snapshot of the configuration 
-    parameters for the session's project."""
     session_data_path: Path = Path()
     """Stores the path to the session_data.yaml file. This path is used by the SessionData instance to save itself to 
     disk as a .yaml file. The file contains the paths to all raw and processed data directories used during data 
@@ -110,9 +107,6 @@ class RawData:
     """Stores the path to the integrity_verification.yaml tracker file. This file stores the current state of the data 
     integrity verification pipeline. It prevents more than one instance of the pipeline from working with the data 
     at a given time and communicates the outcome (success or failure) of the most recent pipeline runtime."""
-    version_data_path: Path = Path()
-    """Stores the path to the version_data.yaml file. This file contains the snapshot of Python and sl-experiment 
-    library versions that were used when the data was acquired."""
 
     def resolve_paths(self, root_directory_path: Path) -> None:
         """Resolves all paths managed by the class instance based on the input root directory path.
@@ -135,7 +129,6 @@ class RawData:
         self.session_descriptor_path = self.raw_data_path.joinpath("session_descriptor.yaml")
         self.hardware_state_path = self.raw_data_path.joinpath("hardware_state.yaml")
         self.surgery_metadata_path = self.raw_data_path.joinpath("surgery_metadata.yaml")
-        self.project_configuration_path = self.raw_data_path.joinpath("project_configuration.yaml")
         self.session_data_path = self.raw_data_path.joinpath("session_data.yaml")
         self.experiment_configuration_path = self.raw_data_path.joinpath("experiment_configuration.yaml")
         self.mesoscope_positions_path = self.raw_data_path.joinpath("mesoscope_positions.yaml")
@@ -145,7 +138,6 @@ class RawData:
         self.telomere_path = self.raw_data_path.joinpath("telomere.bin")
         self.ubiquitin_path = self.raw_data_path.joinpath("ubiquitin.bin")
         self.integrity_verification_tracker_path = self.raw_data_path.joinpath("integrity_verification_tracker.yaml")
-        self.version_data_path = self.raw_data_path.joinpath("version_data.yaml")
 
     def make_directories(self) -> None:
         """Ensures that all major subdirectories and the root directory exist, creating any missing directories."""
@@ -289,6 +281,8 @@ class SessionData(YamlConfig):
         session_type: str,
         experiment_name: str | None = None,
         session_name: str | None = None,
+        python_version: str = "3.11.13",
+        sl_experiment_version: str = "2.0.0",
     ) -> "SessionData":
         """Creates a new SessionData object and generates the new session's data structure on the local PC.
 
@@ -300,9 +294,9 @@ class SessionData(YamlConfig):
 
             This method automatically dumps the data of the created SessionData instance into the session_data.yaml file
             inside the root raw_data directory of the created hierarchy. It also finds and dumps other configuration
-            files, such as project_configuration.yaml, experiment_configuration.yaml, and system_configuration.yaml into
-            the same raw_data directory. This ensures that if the session's runtime is interrupted unexpectedly, the
-            acquired data can still be processed.
+            files, such as experiment_configuration.yaml and system_configuration.yaml into the same raw_data directory.
+            This ensures that if the session's runtime is interrupted unexpectedly, the acquired data can still be
+            processed.
 
         Args:
             project_name: The name of the project for which the data is acquired.
@@ -315,6 +309,10 @@ class SessionData(YamlConfig):
                 sessions. When provided, the method uses this name instead of generating a new timestamp-based name.
                 This is only used during the 'ascension' runtime to convert old data structures to the modern
                 lab standards.
+            python_version: The string that specifies the Python version used to collect raw session data. Has to be
+                specified using the major.minor.patch version format.
+            sl_experiment_version: The string that specifies the version of the sl-experiment library used to collect
+                raw session data. Has to be specified using the major.minor.patch version format.
 
         Returns:
             An initialized SessionData instance that stores the layout of the newly created session's data.
@@ -387,20 +385,16 @@ class SessionData(YamlConfig):
             raw_data=raw_data,
             processed_data=processed_data,
             experiment_name=experiment_name,
+            python_version=python_version,
+            sl_experiment_version=sl_experiment_version,
         )
 
         # Saves the configured instance data to the session's folder, so that it can be reused during processing or
         # preprocessing.
         instance._save()
 
-        # Also saves the ProjectConfiguration, SystemConfiguration, and ExperimentConfiguration instances to the same
-        # folder using the paths resolved for the RawData instance above.
-
-        # Copies the project_configuration.yaml file to session's folder
-        project_configuration_path = acquisition_system.paths.root_directory.joinpath(
-            project_name, "configuration", "project_configuration.yaml"
-        )
-        sh.copy2(project_configuration_path, instance.raw_data.project_configuration_path)
+        # Also saves the SystemConfiguration and ExperimentConfiguration instances to the same folder using the paths
+        # resolved for the RawData instance above.
 
         # Dumps the acquisition system's configuration data to session's folder
         acquisition_system.save(path=instance.raw_data.system_configuration_path)

{sl_shared_assets-3.0.0rc5 → sl_shared_assets-3.0.0rc7}/src/sl_shared_assets/data_classes/session_data.pyi

@@ -29,7 +29,6 @@ class RawData:
     session_descriptor_path: Path = ...
     hardware_state_path: Path = ...
     surgery_metadata_path: Path = ...
-    project_configuration_path: Path = ...
     session_data_path: Path = ...
     experiment_configuration_path: Path = ...
     mesoscope_positions_path: Path = ...
@@ -39,7 +38,6 @@ class RawData:
     telomere_path: Path = ...
     ubiquitin_path: Path = ...
     integrity_verification_tracker_path: Path = ...
-    version_data_path: Path = ...
     def resolve_paths(self, root_directory_path: Path) -> None:
         """Resolves all paths managed by the class instance based on the input root directory path.
 
@@ -127,6 +125,8 @@ class SessionData(YamlConfig):
         session_type: str,
         experiment_name: str | None = None,
         session_name: str | None = None,
+        python_version: str = "3.11.13",
+        sl_experiment_version: str = "2.0.0",
     ) -> SessionData:
         """Creates a new SessionData object and generates the new session's data structure on the local PC.
 
@@ -138,9 +138,9 @@ class SessionData(YamlConfig):
 
             This method automatically dumps the data of the created SessionData instance into the session_data.yaml file
             inside the root raw_data directory of the created hierarchy. It also finds and dumps other configuration
-            files, such as project_configuration.yaml, experiment_configuration.yaml, and system_configuration.yaml into
-            the same raw_data directory. This ensures that if the session's runtime is interrupted unexpectedly, the
-            acquired data can still be processed.
+            files, such as experiment_configuration.yaml and system_configuration.yaml into the same raw_data directory.
+            This ensures that if the session's runtime is interrupted unexpectedly, the acquired data can still be
+            processed.
 
         Args:
             project_name: The name of the project for which the data is acquired.
@@ -153,6 +153,10 @@ class SessionData(YamlConfig):
                 sessions. When provided, the method uses this name instead of generating a new timestamp-based name.
                 This is only used during the 'ascension' runtime to convert old data structures to the modern
                 lab standards.
+            python_version: The string that specifies the Python version used to collect raw session data. Has to be
+                specified using the major.minor.patch version format.
+            sl_experiment_version: The string that specifies the version of the sl-experiment library used to collect
+                raw session data. Has to be specified using the major.minor.patch version format.
 
         Returns:
             An initialized SessionData instance that stores the layout of the newly created session's data.