sl-shared-assets 1.1.2__tar.gz → 1.2.0rc2__tar.gz

{sl_shared_assets-1.1.2 → sl_shared_assets-1.2.0rc2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sl-shared-assets
-Version: 1.1.2
+Version: 1.2.0rc2
 Summary: Stores assets shared between multiple Sun (NeuroAI) lab data pipelines.
 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-1.1.2 → sl_shared_assets-1.2.0rc2}/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 = "1.1.2"
+version = "1.2.0rc2"
 description = "Stores assets shared between multiple Sun (NeuroAI) lab data pipelines."
 readme = "README.md"
 license = { file = "LICENSE" }

{sl_shared_assets-1.1.2 → sl_shared_assets-1.2.0rc2}/src/sl_shared_assets/__init__.py

@@ -16,6 +16,7 @@ from .data_classes import (
     SessionData,
     SubjectData,
     SurgeryData,
+    VersionData,
     InjectionData,
     ProcedureData,
     ProcessedData,
@@ -52,6 +53,7 @@ __all__ = [
     "ImplantData",
     "SessionData",
     "RawData",
+    "VersionData",
     "ProcessedData",
     "SubjectData",
     "SurgeryData",

{sl_shared_assets-1.1.2 → sl_shared_assets-1.2.0rc2}/src/sl_shared_assets/__init__.pyi

@@ -16,6 +16,7 @@ from .data_classes import (
     SessionData as SessionData,
     SubjectData as SubjectData,
     SurgeryData as SurgeryData,
+    VersionData as VersionData,
     InjectionData as InjectionData,
     ProcedureData as ProcedureData,
     ProcessedData as ProcessedData,
@@ -46,6 +47,7 @@ __all__ = [
     "ImplantData",
     "SessionData",
     "RawData",
+    "VersionData",
     "ProcessedData",
     "SubjectData",
     "SurgeryData",

{sl_shared_assets-1.1.2 → sl_shared_assets-1.2.0rc2}/src/sl_shared_assets/data_classes/__init__.py

@@ -11,13 +11,7 @@ from .runtime_data import (
     MesoscopeHardwareState,
     MesoscopeExperimentDescriptor,
 )
-from .session_data import (
-    RawData,
-    SessionData,
-    ProcessedData,
-    ProcessingTracker,
-    ProjectConfiguration,
-)
+from .session_data import RawData, SessionData, VersionData, ProcessedData, ProcessingTracker, ProjectConfiguration
 from .surgery_data import (
     DrugData,
     ImplantData,
@@ -43,6 +37,7 @@ __all__ = [
     "ImplantData",
     "SessionData",
     "RawData",
+    "VersionData",
     "ProcessedData",
     "SubjectData",
     "SurgeryData",

{sl_shared_assets-1.1.2 → sl_shared_assets-1.2.0rc2}/src/sl_shared_assets/data_classes/__init__.pyi

@@ -9,6 +9,7 @@ from .runtime_data import (
 from .session_data import (
     RawData as RawData,
     SessionData as SessionData,
+    VersionData as VersionData,
     ProcessedData as ProcessedData,
     ProcessingTracker as ProcessingTracker,
     ProjectConfiguration as ProjectConfiguration,
@@ -38,6 +39,7 @@ __all__ = [
     "ImplantData",
     "SessionData",
     "RawData",
+    "VersionData",
     "ProcessedData",
     "SubjectData",
     "SurgeryData",

{sl_shared_assets-1.1.2 → sl_shared_assets-1.2.0rc2}/src/sl_shared_assets/data_classes/runtime_data.py

@@ -171,6 +171,9 @@ class MesoscopeExperimentDescriptor(YamlConfig):
     """The weight of the animal, in grams, at the beginning of the session."""
     dispensed_water_volume_ml: float
     """Stores the total water volume, in milliliters, dispensed during runtime."""
+    is_guided: bool = False
+    """Determines whether the animal has to lick in the reward zone to receive water rewards. If this is set to False, 
+    the system automatically dispenses water when the animal enters the reward zone."""
     experimenter_notes: str = "Replace this with your notes."
     """This field is not set during runtime. It is expected that each experimenter will replace this field with their 
     notes made during runtime."""

{sl_shared_assets-1.1.2 → sl_shared_assets-1.2.0rc2}/src/sl_shared_assets/data_classes/runtime_data.pyi

@@ -88,6 +88,7 @@ class MesoscopeExperimentDescriptor(YamlConfig):
     experimenter: str
     mouse_weight_g: float
     dispensed_water_volume_ml: float
+    is_guided: bool = ...
     experimenter_notes: str = ...
     experimenter_given_water_volume_ml: float = ...
     incomplete: bool = ...

{sl_shared_assets-1.1.2 → sl_shared_assets-1.2.0rc2}/src/sl_shared_assets/data_classes/session_data.py

@@ -22,6 +22,16 @@ from .configuration_data import get_system_configuration_data
 _valid_session_types = {"lick training", "run training", "mesoscope experiment", "window checking"}
 
 
+@dataclass()
+class VersionData(YamlConfig):
+    """Stores information about the versions of important Sun lab libraries used to acquire the session's data."""
+
+    python_version: str = ""
+    """Stores the Python version used by the environment that acquired the data."""
+    sl_experiment_version: str = ""
+    """Stores the version of the sl-experiment library that was used to acquire the data."""
+
+
 @dataclass()
 class ProjectConfiguration(YamlConfig):
     """Stores the project-specific configuration parameters that do not change between different animals and runtime
@@ -223,6 +233,9 @@ class RawData:
     'verify-session' CLI command to indicate whether the session data inside the folder marked by the file has been 
     verified for integrity. Primarily, this is used when the data is moved to the long-term storage destination (BioHPC
     server) to ensure it is safe to remove any local copies of the data stored on the acquisition system machine(s)."""
+    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.
@@ -255,6 +268,7 @@ 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."""
@@ -676,7 +690,6 @@ class ProcessingTracker(YamlConfig):
         """Saves the current processing state stored inside instance attributes to the specified .YAML file."""
         # Resets the _lock and file_path to None before dumping the data to .YAML to avoid issues with loading it
         # back.
-        console.echo(message=f"{self.file_path}")
         original = copy.deepcopy(self)
         original.file_path = None  # type: ignore
         original._lock_path = None  # type: ignore

{sl_shared_assets-1.1.2 → sl_shared_assets-1.2.0rc2}/src/sl_shared_assets/data_classes/session_data.pyi

@@ -8,6 +8,13 @@ from .configuration_data import get_system_configuration_data as get_system_conf
 
 _valid_session_types: Incomplete
 
+@dataclass()
+class VersionData(YamlConfig):
+    """Stores information about the versions of important Sun lab libraries used to acquire the session's data."""
+
+    python_version: str = ...
+    sl_experiment_version: str = ...
+
 @dataclass()
 class ProjectConfiguration(YamlConfig):
     """Stores the project-specific configuration parameters that do not change between different animals and runtime
@@ -97,6 +104,7 @@ 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.