sl-shared-assets 3.0.0rc4__py3-none-any.whl → 3.0.0rc5__py3-none-any.whl

sl_shared_assets/__init__.py

@@ -20,7 +20,6 @@ from .data_classes import (
     SessionData,
     SubjectData,
     SurgeryData,
-    VersionData,
     InjectionData,
     ProcedureData,
     ProcessedData,
@@ -31,7 +30,6 @@ from .data_classes import (
     TrialCueSequence,
     ProcessingTracker,
     MesoscopePositions,
-    ProjectConfiguration,
     RunTrainingDescriptor,
     LickTrainingDescriptor,
     MesoscopeHardwareState,
@@ -59,7 +57,6 @@ __all__ = [
     "ImplantData",
     "SessionData",
     "RawData",
-    "VersionData",
     "ProcessedData",
     "SubjectData",
     "SurgeryData",
@@ -69,7 +66,6 @@ __all__ = [
     "ZaberPositions",
     "ExperimentState",
     "MesoscopePositions",
-    "ProjectConfiguration",
     "MesoscopeHardwareState",
     "RunTrainingDescriptor",
     "LickTrainingDescriptor",

sl_shared_assets/__init__.pyi

@@ -16,7 +16,6 @@ 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,
@@ -27,7 +26,6 @@ from .data_classes import (
     TrialCueSequence as TrialCueSequence,
     ProcessingTracker as ProcessingTracker,
     MesoscopePositions as MesoscopePositions,
-    ProjectConfiguration as ProjectConfiguration,
     RunTrainingDescriptor as RunTrainingDescriptor,
     LickTrainingDescriptor as LickTrainingDescriptor,
     MesoscopeHardwareState as MesoscopeHardwareState,
@@ -49,7 +47,6 @@ __all__ = [
     "ImplantData",
     "SessionData",
     "RawData",
-    "VersionData",
     "ProcessedData",
     "SubjectData",
     "SurgeryData",
@@ -59,7 +56,6 @@ __all__ = [
     "ZaberPositions",
     "ExperimentState",
     "MesoscopePositions",
-    "ProjectConfiguration",
     "MesoscopeHardwareState",
     "RunTrainingDescriptor",
     "LickTrainingDescriptor",

sl_shared_assets/data_classes/__init__.py

@@ -11,7 +11,7 @@ from .runtime_data import (
     MesoscopeHardwareState,
     MesoscopeExperimentDescriptor,
 )
-from .session_data import RawData, SessionData, VersionData, ProcessedData, ProcessingTracker, ProjectConfiguration
+from .session_data import RawData, SessionData, ProcessedData, ProcessingTracker
 from .surgery_data import (
     DrugData,
     ImplantData,
@@ -38,7 +38,6 @@ __all__ = [
     "ImplantData",
     "SessionData",
     "RawData",
-    "VersionData",
     "ProcessedData",
     "SubjectData",
     "SurgeryData",
@@ -47,7 +46,6 @@ __all__ = [
     "ZaberPositions",
     "ExperimentState",
     "MesoscopePositions",
-    "ProjectConfiguration",
     "MesoscopeHardwareState",
     "RunTrainingDescriptor",
     "LickTrainingDescriptor",

sl_shared_assets/data_classes/__init__.pyi

@@ -9,10 +9,8 @@ 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,
 )
 from .surgery_data import (
     DrugData as DrugData,
@@ -40,7 +38,6 @@ __all__ = [
     "ImplantData",
     "SessionData",
     "RawData",
-    "VersionData",
     "ProcessedData",
     "SubjectData",
     "SurgeryData",
@@ -49,7 +46,6 @@ __all__ = [
     "ZaberPositions",
     "ExperimentState",
     "MesoscopePositions",
-    "ProjectConfiguration",
     "MesoscopeHardwareState",
     "RunTrainingDescriptor",
     "LickTrainingDescriptor",

sl_shared_assets/data_classes/configuration_data.py

@@ -66,7 +66,7 @@ class TrialCueSequence:
     during behavior data parsing to assign trial information to data collected from various sources.
     """
 
-    cue_sequence: tuple[int, ...]
+    cue_sequence: list[int]
     """Specifies the sequence of wall cues experienced by the animal while running this trial."""
     trial_length_unity_unit: float
     """The length of the trial cue sequence, in Unity units."""
@@ -131,7 +131,7 @@ class MesoscopeExperimentConfiguration(YamlConfig):
     trial_structures: dict[str, TrialCueSequence] = field(
         default_factory=lambda: {
             "circular 4 cue": TrialCueSequence(
-                cue_sequence=(0, 1, 0, 2, 0, 3, 0, 4), trial_length_unity_unit=24.0, trial_length_cm=240.0
+                cue_sequence=[0, 1, 0, 2, 0, 3, 0, 4], trial_length_unity_unit=24.0, trial_length_cm=240.0
             )
         }
     )
@@ -176,6 +176,22 @@ class MesoscopePaths:
     """The path to the GeniCam CTI file used to connect to Harvesters-managed cameras."""
 
 
+@dataclass()
+class MesoscopeSheets:
+    """Stores the IDs of Google Sheets used by the Mesoscope-VR data acquisition system."""
+
+    surgery_sheet_id: str = ""
+    """The ID of the Google Sheet file that stores information about surgical interventions performed on all animals 
+    participating in each lab project. This log sheet is used to parse and write the surgical intervention data for 
+    each animal into every runtime session raw_data folder, so that the surgery data is always kept together with the 
+    rest of the training and experiment data."""
+    water_log_sheet_id: str = ""
+    """The ID of the Google Sheet file that stores information about water restriction (and behavior tracker) 
+    information for all animals participating in the managed project. This is used to synchronize the information 
+    inside the water restriction log with the state of the animal at the end of each training or experiment session.
+    """
+
+
 @dataclass()
 class MesoscopeCameras:
     """Stores the configuration parameters for the cameras used by the Mesoscope-VR system to record behavior videos."""
@@ -226,7 +242,7 @@ class MesoscopeMicroControllers:
     at maximum voltage (break is fully engaged)."""
     wheel_diameter_cm: float = 15.0333
     """The diameter of the running wheel connected to the break and torque sensor, in centimeters."""
-    lick_threshold_adc: int = 500
+    lick_threshold_adc: int = 850
     """The threshold voltage, in raw analog units recorded by a 12-bit Analog-to-Digital-Converter (ADC), interpreted 
     as the animal's tongue contacting the sensor. Note, 12-bit ADC only supports values between 0 and 4095, so setting 
     the threshold above 4095 will result in no licks being reported to Unity."""
@@ -255,10 +271,10 @@ class MesoscopeMicroControllers:
     torque_report_ccw: bool = True
     """Determines whether the sensor should report torque in the Counter-Clockwise (CCW) direction. This direction 
     corresponds to the animal trying to move the wheel forward."""
-    torque_signal_threshold_adc: int = 300
+    torque_signal_threshold_adc: int = 100
     """The minimum voltage, in raw analog units recorded by a 12-bit Analog-to-Digital-Converter (ADC), reported to the
     PC as a non-zero value. Voltages below this level are interpreted as noise and are always pulled to 0."""
-    torque_delta_threshold_adc: int = 300
+    torque_delta_threshold_adc: int = 70
     """The minimum absolute difference in raw analog units recorded by a 12-bit Analog-to-Digital-Converter (ADC) for 
     the change to be reported to the PC. This is used to prevent reporting repeated static torque readouts to the 
     PC, conserving communication bandwidth."""
@@ -293,10 +309,10 @@ class MesoscopeMicroControllers:
     encoder uses a dedicated parameter, as the encoder needs to be sampled at a higher frequency than all other sensors.
     """
     valve_calibration_data: dict[int | float, int | float] | tuple[tuple[int | float, int | float], ...] = (
-        (15000, 1.75),
-        (30000, 3.85),
-        (45000, 7.95),
-        (60000, 12.65),
+        (15000, 1.10),
+        (30000, 3.00),
+        (45000, 6.25),
+        (60000, 10.90),
     )
     """A tuple of tuples that maps water delivery solenoid valve open times, in microseconds, to the dispensed volume 
     of water, in microliters. During training and experiment runtimes, this data is used by the ValveModule to translate
@@ -341,6 +357,8 @@ class MesoscopeSystemConfiguration(YamlConfig):
     """Stores the descriptive name of the data acquisition system."""
     paths: MesoscopePaths = field(default_factory=MesoscopePaths)
     """Stores the filesystem configuration parameters for the Mesoscope-VR data acquisition system."""
+    sheets: MesoscopeSheets = field(default_factory=MesoscopeSheets)
+    """Stores the IDs of Google Sheets used by the Mesoscope-VR data acquisition system."""
     cameras: MesoscopeCameras = field(default_factory=MesoscopeCameras)
     """Stores the configuration parameters for the cameras used by the Mesoscope-VR system to record behavior videos."""
     microcontrollers: MesoscopeMicroControllers = field(default_factory=MesoscopeMicroControllers)

sl_shared_assets/data_classes/configuration_data.pyi

@@ -38,7 +38,7 @@ class TrialCueSequence:
     during behavior data parsing to assign trial information to data collected from various sources.
     """
 
-    cue_sequence: tuple[int, ...]
+    cue_sequence: list[int]
     trial_length_unity_unit: float
     trial_length_cm: float
 
@@ -78,6 +78,13 @@ class MesoscopePaths:
     mesoscope_directory: Path = ...
     harvesters_cti_path: Path = ...
 
+@dataclass()
+class MesoscopeSheets:
+    """Stores the IDs of Google Sheets used by the Mesoscope-VR data acquisition system."""
+
+    surgery_sheet_id: str = ...
+    water_log_sheet_id: str = ...
+
 @dataclass()
 class MesoscopeCameras:
     """Stores the configuration parameters for the cameras used by the Mesoscope-VR system to record behavior videos."""
@@ -155,6 +162,7 @@ class MesoscopeSystemConfiguration(YamlConfig):
 
     name: str = ...
     paths: MesoscopePaths = field(default_factory=MesoscopePaths)
+    sheets: MesoscopeSheets = field(default_factory=MesoscopeSheets)
     cameras: MesoscopeCameras = field(default_factory=MesoscopeCameras)
     microcontrollers: MesoscopeMicroControllers = field(default_factory=MesoscopeMicroControllers)
     additional_firmware: MesoscopeAdditionalFirmware = field(default_factory=MesoscopeAdditionalFirmware)

sl_shared_assets/data_classes/runtime_data.py

@@ -4,7 +4,7 @@ restore the data acquisition and runtime management system to the same state acr
 the same animal.
 """
 
-from dataclasses import field, dataclass
+from dataclasses import dataclass
 
 from ataraxis_data_structures import YamlConfig
 
@@ -76,6 +76,9 @@ class MesoscopeHardwareState(YamlConfig):
     recorded_mesoscope_ttl: bool | None = None
     """TTLInterface instance property. A boolean flag that determines whether the processed session recorded brain 
     activity data with the mesoscope."""
+    system_state_codes: dict[str, int] | None = None
+    """A MesoscopeVRSystem property. A dictionary that maps integer state-codes used by the Mesoscope-VR system to 
+    communicate its states to human-readable state names."""
 
 
 @dataclass()
@@ -87,7 +90,8 @@ class LickTrainingDescriptor(YamlConfig):
     mouse_weight_g: float
     """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."""
+    """Stores the total water volume, in milliliters, dispensed during runtime. This excludes the water volume 
+    dispensed during the paused (idle) state."""
     minimum_reward_delay_s: int
     """Stores the minimum delay, in seconds, that can separate the delivery of two consecutive water rewards."""
     maximum_reward_delay_s: int
@@ -100,11 +104,8 @@ class LickTrainingDescriptor(YamlConfig):
     """Stores the maximum number of consecutive rewards that can be delivered without the animal consuming them. If 
     the animal receives this many rewards without licking (consuming) them, reward delivery is paused until the animal 
     consumes the rewards."""
-    system_state_codes: dict[str, int] = field(
-        default_factory=lambda: {"idle": 0, "rest": 1, "run": 2, "lick training": 3, "run training": 4}
-    )
-    """Maps integer state-codes used by the acquisition system to communicate its states to human-readable state 
-    names."""
+    pause_dispensed_water_volume_ml: float = 0.0
+    """Stores the total water volume, in milliliters, dispensed during the paused (idle) state."""
     experimenter_notes: str = "Replace this with your notes."
     """This field is not set during runtime. It is expected that each experimenter replaces this field with their 
     notes made during runtime."""
@@ -155,11 +156,8 @@ class RunTrainingDescriptor(YamlConfig):
     """Stores the maximum time, in seconds, the animal can dip below the running speed threshold to still receive the 
     reward. This allows animals that 'run' by taking a series of large steps, briefly dipping below speed threshold at 
     the end of each step, to still get water rewards."""
-    system_state_codes: dict[str, int] = field(
-        default_factory=lambda: {"idle": 0, "rest": 1, "run": 2, "lick training": 3, "run training": 4}
-    )
-    """Maps integer state-codes used by the acquisition system to communicate its states to human-readable state 
-    names."""
+    pause_dispensed_water_volume_ml: float = 0.0
+    """Stores the total water volume, in milliliters, dispensed during the paused (idle) state."""
     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."""
@@ -185,14 +183,11 @@ class MesoscopeExperimentDescriptor(YamlConfig):
     """Stores the maximum number of consecutive rewards that can be delivered without the animal consuming them. If 
     the animal receives this many rewards without licking (consuming) them, reward delivery is paused until the animal 
     consumes the rewards."""
-    system_state_codes: dict[str, int] = field(
-        default_factory=lambda: {"idle": 0, "rest": 1, "run": 2, "lick training": 3, "run training": 4}
-    )
-    """Maps integer state-codes used by the acquisition system to communicate its states to human-readable state 
-    names."""
     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."""
+    pause_dispensed_water_volume_ml: float = 0.0
+    """Stores the total water volume, in milliliters, dispensed during the paused (idle) state."""
     experimenter_given_water_volume_ml: float = 0.0
     """The additional volume of water, in milliliters, administered by the experimenter to the animal after the session.
     """
@@ -229,15 +224,15 @@ class ZaberPositions(YamlConfig):
     """The absolute position, in native motor units, of the HeadBar pitch-axis motor."""
     headbar_roll: int = 0
     """The absolute position, in native motor units, of the HeadBar roll-axis motor."""
-    wheel_x: int = 0
-    """The absolute position, in native motor units, of the running wheel platform x-axis motor. Although this motor is
-    not itself part of the HeadBar assembly, it is controlled through the HeadBar controller port."""
     lickport_z: int = 0
     """The absolute position, in native motor units, of the LickPort z-axis motor."""
     lickport_x: int = 0
     """The absolute position, in native motor units, of the LickPort x-axis motor."""
     lickport_y: int = 0
     """The absolute position, in native motor units, of the LickPort y-axis motor."""
+    wheel_x: int = 0
+    """The absolute position, in native motor units, of the running wheel platform x-axis motor. Although this motor is
+    not itself part of the HeadBar assembly, it is controlled through the HeadBar controller port."""
 
 
 @dataclass()

sl_shared_assets/data_classes/runtime_data.pyi

@@ -1,6 +1,5 @@
-from dataclasses import field, dataclass
+from dataclasses import dataclass
 
-from _typeshed import Incomplete
 from ataraxis_data_structures import YamlConfig
 
 @dataclass()
@@ -43,6 +42,7 @@ class MesoscopeHardwareState(YamlConfig):
     torque_per_adc_unit: float | None = ...
     screens_initially_on: bool | None = ...
     recorded_mesoscope_ttl: bool | None = ...
+    system_state_codes: dict[str, int] | None = ...
 
 @dataclass()
 class LickTrainingDescriptor(YamlConfig):
@@ -56,7 +56,7 @@ class LickTrainingDescriptor(YamlConfig):
     maximum_water_volume_ml: float
     maximum_training_time_m: int
     maximum_unconsumed_rewards: int = ...
-    system_state_codes: dict[str, int] = field(default_factory=Incomplete)
+    pause_dispensed_water_volume_ml: float = ...
     experimenter_notes: str = ...
     experimenter_given_water_volume_ml: float = ...
     incomplete: bool = ...
@@ -79,7 +79,7 @@ class RunTrainingDescriptor(YamlConfig):
     maximum_training_time_m: int
     maximum_unconsumed_rewards: int = ...
     maximum_idle_time_s: float = ...
-    system_state_codes: dict[str, int] = field(default_factory=Incomplete)
+    pause_dispensed_water_volume_ml: float = ...
     experimenter_notes: str = ...
     experimenter_given_water_volume_ml: float = ...
     incomplete: bool = ...
@@ -92,8 +92,8 @@ class MesoscopeExperimentDescriptor(YamlConfig):
     mouse_weight_g: float
     dispensed_water_volume_ml: float
     maximum_unconsumed_rewards: int = ...
-    system_state_codes: dict[str, int] = field(default_factory=Incomplete)
     experimenter_notes: str = ...
+    pause_dispensed_water_volume_ml: float = ...
     experimenter_given_water_volume_ml: float = ...
     incomplete: bool = ...
 
@@ -122,10 +122,10 @@ class ZaberPositions(YamlConfig):
     headbar_z: int = ...
     headbar_pitch: int = ...
     headbar_roll: int = ...
-    wheel_x: int = ...
     lickport_z: int = ...
     lickport_x: int = ...
     lickport_y: int = ...
+    wheel_x: int = ...
 
 @dataclass()
 class MesoscopePositions(YamlConfig):

sl_shared_assets/data_classes/session_data.py

@@ -5,7 +5,6 @@ classes, which are also stored as .yaml files inside each session's raw_data and
 these classes contain all necessary information to restore the data hierarchy on any machine. All other Sun lab
 libraries use these classes to work with all lab-generated data."""
 
-import re
 import copy
 import shutil as sh
 from pathlib import Path
@@ -22,127 +21,6 @@ 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
-    sessions.
-
-    An instance of this class is generated and saved as a .yaml file in the 'configuration' directory of each project
-    when it is created. After that, the stored data is reused for every runtime (training or experiment session) carried
-    out for each animal of the project. Additionally, a copy of the most actual configuration file is saved inside each
-    runtime session's 'raw_data' folder, providing seamless integration between the managed data and various Sun lab
-    (sl-) libraries.
-
-    Notes:
-        Together with SessionData, this class forms the entry point for all interactions with the data acquired in the
-        Sun lab. The fields of this class are used to flexibly configure the runtime behavior of major data acquisition
-        (sl-experiment) and processing (sl-forgery) libraries, adapting them for any project in the lab.
-    """
-
-    project_name: str = ""
-    """Stores the descriptive name of the project. This name is used to create the root directory for the project and 
-    to initialize SessionData instances each time any Sun lab library interacts with the session's data."""
-    surgery_sheet_id: str = ""
-    """The ID of the Google Sheet file that stores information about surgical interventions performed on all animals 
-    participating in the managed project. This log sheet is used to parse and write the surgical intervention data for 
-    each animal into every runtime session raw_data folder, so that the surgery data is always kept together with the 
-    rest of the training and experiment data."""
-    water_log_sheet_id: str = ""
-    """The ID of the Google Sheet file that stores information about water restriction (and behavior tracker) 
-    information for all animals participating in the managed project. This is used to synchronize the information 
-    inside the water restriction log with the state of the animal at the end of each training or experiment session.
-    """
-
-    @classmethod
-    def load(cls, configuration_path: Path) -> "ProjectConfiguration":
-        """Loads the project configuration parameters from the specified project_configuration.yaml file.
-
-        This method is called during each interaction with any runtime session's data, including the creation of a new
-        session.
-
-        Args:
-            configuration_path: The path to the project_configuration.yaml file from which to load the data.
-
-        Returns:
-            The initialized ProjectConfiguration instance that stores the configuration data for the target project.
-
-        Raise:
-            FileNotFoundError: If the specified configuration file does not exist or is not a valid YAML file.
-        """
-
-        # Prevents loading non-existent files.
-        if configuration_path.suffix != ".yaml" or not configuration_path.exists():
-            message = (
-                f"Unable to load the project configuration data from the specified path: {configuration_path}. Valid "
-                f"configuration file paths should use the '.yaml' extension and point to an existing file."
-            )
-            console.error(message=message, error=FileNotFoundError)
-
-        # Loads the data from the YAML file and initializes the class instance.
-        instance: ProjectConfiguration = cls.from_yaml(file_path=configuration_path)  # type: ignore
-
-        # Verifies the loaded data. Most importantly, this step does not allow proceeding if the user did not
-        # replace the surgery log and water restriction log placeholders with valid ID values.
-        instance._verify_data()
-
-        # Returns the initialized class instance to caller
-        return instance
-
-    def save(self, path: Path) -> None:
-        """Saves class instance data to disk as a project_configuration.yaml file.
-
-        This method is automatically called from the 'sl_experiment' library when a new project is created. After this
-        method's runtime, all future project initialization calls will use the load() method to reuse configuration data
-        saved to the .yaml file created by this method.
-
-        Args:
-            path: The path to the .yaml file to save the data to.
-        """
-
-        # Saves the data to the YAML file
-        self.to_yaml(file_path=path)
-
-    def _verify_data(self) -> None:
-        """Verifies the user-modified data loaded from the project_configuration.yaml file.
-
-        Since this class is explicitly designed to be modified by the user, this verification step is carried out to
-        ensure that the loaded data matches expectations. This reduces the potential for user errors to impact the
-        runtime behavior of the libraries using this class. This internal method is automatically called by the load()
-        method.
-
-        Raises:
-            ValueError: If the loaded data does not match expected formats or values.
-        """
-
-        # Verifies Google Sheet ID formatting. Google Sheet IDs are usually 44 characters long, containing letters,
-        # numbers, hyphens, and underscores
-        pattern = r"^[a-zA-Z0-9_-]{44}$"
-        if not re.match(pattern, self.surgery_sheet_id):
-            message = (
-                f"Unable to verify the surgery_sheet_id field loaded from the 'project_configuration.yaml' file. "
-                f"Expected a string with 44 characters, using letters, numbers, hyphens, and underscores, but found: "
-                f"{self.surgery_sheet_id}."
-            )
-            console.error(message=message, error=ValueError)
-        if not re.match(pattern, self.water_log_sheet_id):
-            message = (
-                f"Unable to verify the surgery_sheet_id field loaded from the 'project_configuration.yaml' file. "
-                f"Expected a string with 44 characters, using letters, numbers, hyphens, and underscores, but found: "
-                f"{self.water_log_sheet_id}."
-            )
-            console.error(message=message, error=ValueError)
-
-
 @dataclass()
 class RawData:
     """Stores the paths to the directories and files that make up the 'raw_data' session-specific directory.
@@ -384,6 +262,10 @@ class SessionData(YamlConfig):
     field is not None (null), it communicates the specific experiment configuration used by the session. During runtime,
     the name stored here is used to load the specific experiment configuration data stored in a .yaml file with the 
     same name. If the session is not an experiment session, this field is ignored."""
+    python_version: str = "3.11.13"
+    """Stores the Python version used to acquire raw session data."""
+    sl_experiment_version: str = "2.0.0"
+    """Stores the version of the sl-experiment library that was used to acquire the raw session data."""
     raw_data: RawData = field(default_factory=lambda: RawData())
     """Stores the paths to all subfolders and files found under the /project/animal/session/raw_data directory of any 
     PC used to work with Sun lab data."""

sl_shared_assets/data_classes/session_data.pyi

@@ -8,71 +8,6 @@ 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
-    sessions.
-
-    An instance of this class is generated and saved as a .yaml file in the 'configuration' directory of each project
-    when it is created. After that, the stored data is reused for every runtime (training or experiment session) carried
-    out for each animal of the project. Additionally, a copy of the most actual configuration file is saved inside each
-    runtime session's 'raw_data' folder, providing seamless integration between the managed data and various Sun lab
-    (sl-) libraries.
-
-    Notes:
-        Together with SessionData, this class forms the entry point for all interactions with the data acquired in the
-        Sun lab. The fields of this class are used to flexibly configure the runtime behavior of major data acquisition
-        (sl-experiment) and processing (sl-forgery) libraries, adapting them for any project in the lab.
-    """
-
-    project_name: str = ...
-    surgery_sheet_id: str = ...
-    water_log_sheet_id: str = ...
-    @classmethod
-    def load(cls, configuration_path: Path) -> ProjectConfiguration:
-        """Loads the project configuration parameters from the specified project_configuration.yaml file.
-
-        This method is called during each interaction with any runtime session's data, including the creation of a new
-        session.
-
-        Args:
-            configuration_path: The path to the project_configuration.yaml file from which to load the data.
-
-        Returns:
-            The initialized ProjectConfiguration instance that stores the configuration data for the target project.
-
-        Raise:
-            FileNotFoundError: If the specified configuration file does not exist or is not a valid YAML file.
-        """
-    def save(self, path: Path) -> None:
-        """Saves class instance data to disk as a project_configuration.yaml file.
-
-        This method is automatically called from the 'sl_experiment' library when a new project is created. After this
-        method's runtime, all future project initialization calls will use the load() method to reuse configuration data
-        saved to the .yaml file created by this method.
-
-        Args:
-            path: The path to the .yaml file to save the data to.
-        """
-    def _verify_data(self) -> None:
-        """Verifies the user-modified data loaded from the project_configuration.yaml file.
-
-        Since this class is explicitly designed to be modified by the user, this verification step is carried out to
-        ensure that the loaded data matches expectations. This reduces the potential for user errors to impact the
-        runtime behavior of the libraries using this class. This internal method is automatically called by the load()
-        method.
-
-        Raises:
-            ValueError: If the loaded data does not match expected formats or values.
-        """
-
 @dataclass()
 class RawData:
     """Stores the paths to the directories and files that make up the 'raw_data' session-specific directory.
@@ -178,6 +113,8 @@ class SessionData(YamlConfig):
     session_type: str
     acquisition_system: str
     experiment_name: str | None
+    python_version: str = ...
+    sl_experiment_version: str = ...
     raw_data: RawData = field(default_factory=Incomplete)
     processed_data: ProcessedData = field(default_factory=Incomplete)
     def __post_init__(self) -> None:

sl_shared_assets/tools/ascension_tools.py

@@ -7,10 +7,10 @@ from pathlib import Path
 import datetime
 
 import numpy as np
-from ataraxis_base_utilities import LogLevel, console, ensure_directory_exists
+from ataraxis_base_utilities import LogLevel, console
 from ataraxis_time.time_helpers import extract_timestamp_from_bytes
 
-from ..data_classes import SessionData, ProjectConfiguration, get_system_configuration_data
+from ..data_classes import SessionData, get_system_configuration_data
 from .transfer_tools import transfer_directory
 from .packaging_tools import calculate_directory_checksum
 
@@ -194,26 +194,12 @@ def ascend_tyche_data(root_directory: Path) -> None:
         root_directory: The directory that stores one or more Tyche animal folders. This can be conceptualized as the
             root directory for the Tyche project.
     """
-    # Generates a (shared) project configuration file.
-    project_configuration = ProjectConfiguration()
-
     # The acquisition system config resolves most paths and filesystem configuration arguments
     acquisition_system = get_system_configuration_data()
-    output_root_directory = acquisition_system.paths.root_directory
     server_root_directory = acquisition_system.paths.server_storage_directory
 
     # Statically defines project name and local root paths
     project_name = "Tyche"
-    project_configuration.project_name = project_name
-
-    # Uses nonsensical google sheet IDs. Tyche project did not use Google Sheet processing like our modern projects do.
-    project_configuration.water_log_sheet_id = "1xFh9Q2zT7pL3mVkJdR8bN6yXoE4wS5aG0cHu2Kf7D3v"
-    project_configuration.surgery_sheet_id = "1xFh9Q2zT7pL3mVkJdR8bN6yXoE4wS5aG0cHu2Kf7D3v"
-
-    # Dumps project configuration into the 'configuration' subfolder of the Tyche project.
-    configuration_path = output_root_directory.joinpath("Tyche", "configuration", "project_configuration.yaml")
-    ensure_directory_exists(configuration_path)
-    project_configuration.save(path=configuration_path)
 
     # Assumes that root directory stores all animal folders to be processed
     for animal_folder in root_directory.iterdir():
@@ -230,11 +216,10 @@ def ascend_tyche_data(root_directory: Path) -> None:
                 # This procedure generates timestamp-based session names, analogous to how our modern pipeline does it.
                 session_name = _generate_session_name(acquisition_path=acquisition_folder)
 
-                # Uses derived session name and the statically created project configuration file to create the
-                # session data hierarchy using the output root. This generates a 'standard' Sun lab directory structure
-                # for the Tyche data.
+                # Uses derived session name and the derived project name to create the session data hierarchy using the
+                # output root. This generates a 'standard' Sun lab directory structure for the Tyche data.
                 session_data = SessionData.create(
-                    project_name=project_configuration.project_name,
+                    project_name=project_name,
                     session_name=session_name,
                     animal_id=animal_name,
                     session_type="mesoscope experiment",

sl_shared_assets/tools/ascension_tools.pyi

@@ -2,7 +2,6 @@ from pathlib import Path
 
 from ..data_classes import (
     SessionData as SessionData,
-    ProjectConfiguration as ProjectConfiguration,
     get_system_configuration_data as get_system_configuration_data,
 )
 from .transfer_tools import transfer_directory as transfer_directory

{sl_shared_assets-3.0.0rc4.dist-info → sl_shared_assets-3.0.0rc5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sl-shared-assets
-Version: 3.0.0rc4
+Version: 3.0.0rc5
 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-3.0.0rc4.dist-info → sl_shared_assets-3.0.0rc5.dist-info}/RECORD

@@ -1,16 +1,16 @@
-sl_shared_assets/__init__.py,sha256=0v_te6XWwWEsxfq5RWfLecsNoTx1XVJj0D5OWu1OJtk,2289
-sl_shared_assets/__init__.pyi,sha256=wE_YjwirUFaRql_RVCdbNbvR3tDlyuyq0JF2nQLUO1U,2531
+sl_shared_assets/__init__.py,sha256=tNLUHtKWe-yn7LfvDv4kOqr2NLRf5BFD1MCyuVwdU6M,2199
+sl_shared_assets/__init__.pyi,sha256=WhQ5s5_vvTbMEtZ9F_8jYC0dJar2XAUzYnDqKsm6zNk,2402
 sl_shared_assets/cli.py,sha256=R_h_Dlla48mG1LpFDDE9flZ_NyDC9UguRUAYZL6gA9s,18383
 sl_shared_assets/cli.pyi,sha256=8ZJK56_jh2QlF3XCN6c7fI6Z022XtehB0eCrQDJbAsU,5515
 sl_shared_assets/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sl_shared_assets/data_classes/__init__.py,sha256=1NusIC_gUoQDFuHtvnpPj4RJQ2pCzZhjfVzgFThG8Ws,1936
-sl_shared_assets/data_classes/__init__.pyi,sha256=gdCYkXzyoZRURR5e5C0kd_frFURHEu_UI_d0QJ0RRwA,2154
-sl_shared_assets/data_classes/configuration_data.py,sha256=a8MDzSJ0T3P3MGz0JyfpJ4bmlIuzXTYUVb-EG4UhyWQ,32683
-sl_shared_assets/data_classes/configuration_data.pyi,sha256=anjl32Z-OgVgy96T7s7y1XN5HM_FfnztOvUFWTUjQfw,10462
-sl_shared_assets/data_classes/runtime_data.py,sha256=V98VSUHBFiqRngHAYtH6r6X_zDht65wi9TpdbbYAhS8,16656
-sl_shared_assets/data_classes/runtime_data.pyi,sha256=zATWUIP0whD0iRpxkvt78cLL_Ajr-d_9C6goHdTLnSw,6927
-sl_shared_assets/data_classes/session_data.py,sha256=0dNv_49WJeUf5IYgbGMWnMwX3aAYPIv7u8OJM5itIJA,50673
-sl_shared_assets/data_classes/session_data.pyi,sha256=8EqaQbydl2fwDFBMDh77fbSd7os2t0x9GwDJYYsPtLY,16400
+sl_shared_assets/data_classes/__init__.py,sha256=B-kR3bGEUwuAk1q3DmwiYi1w-OeiBl9uI0K3PW4Z3RQ,1854
+sl_shared_assets/data_classes/__init__.pyi,sha256=YKK9Dx5RtylJLfVjgw5grLLH0FNr5FcnKrEZIMfTk0Q,2025
+sl_shared_assets/data_classes/configuration_data.py,sha256=CHoKs4wgg_qMNbvZHxfJJHLkeNbnUCevNG1PfiKu9kk,33786
+sl_shared_assets/data_classes/configuration_data.pyi,sha256=SpVnTcAVmR7uDSECbmR4wDmNdTEtavRn8gjI9Lhi5dI,10721
+sl_shared_assets/data_classes/runtime_data.py,sha256=O98BZg7i7cEUlpIE16JswKOwQNRsS5RxVdBzXYvAw00,16543
+sl_shared_assets/data_classes/runtime_data.pyi,sha256=i8CuZd9p0Nu43xhpE62pB07AiovZIgtMZYN5wQjz-r0,6861
+sl_shared_assets/data_classes/session_data.py,sha256=Ethlbf1rF1KJ3fWe5DkMUEZatIPxPYlZYmFtA1MZ1hw,44408
+sl_shared_assets/data_classes/session_data.pyi,sha256=ku8wvXkkCUSvC1ZQpRmU6DxuNz253OfDCi8AAp4G_WY,13246
 sl_shared_assets/data_classes/surgery_data.py,sha256=qsMj3NkjhylAT9b_wHBY-1XwTu2xsZcZatdECmkA7Bs,7437
 sl_shared_assets/data_classes/surgery_data.pyi,sha256=rf59lJ3tGSYKHQlEGXg75MnjajBwl0DYhL4TClAO4SM,2605
 sl_shared_assets/server/__init__.py,sha256=w7y73RXXjBrWQsjU5g1QNCv_gsXDYnHos3NpOoR2AHA,452
@@ -21,16 +21,16 @@ sl_shared_assets/server/server.py,sha256=MGk1v49aEFeIChMDsiR7CXjVkWwDpD9kA1TK0fw
 sl_shared_assets/server/server.pyi,sha256=5Yxq4txhjtd9w-6U9fPehzMeIZL5GcprVCHd9mPP6FI,15113
 sl_shared_assets/tools/__init__.py,sha256=NktXk62E_HHOrO_93z_MVmSd6-Oir3mE4xE9Yr8Qa7U,682
 sl_shared_assets/tools/__init__.pyi,sha256=0UXorfCXXmHQOP5z7hODpsqEX0DAkOta5VZqN6FSS-w,623
-sl_shared_assets/tools/ascension_tools.py,sha256=kIqYGX9F8lRao_LaVOacIiT8J9SypTvarb9mgaI9ZPs,15387
-sl_shared_assets/tools/ascension_tools.pyi,sha256=tQCDdWZ20ZjUjpMs8aGIN0yBg5ff3j6spi62b3Han4o,3755
+sl_shared_assets/tools/ascension_tools.py,sha256=o5R-M0VCJg1RwH6-2fYjMK-9yBgzJ22YVLQee17Mmw0,14431
+sl_shared_assets/tools/ascension_tools.pyi,sha256=c-SI9TYJ1vmJXMV2pSW9Nri4mlySF8MtXqrvRvz5C8s,3705
 sl_shared_assets/tools/packaging_tools.py,sha256=QikjeaE_A8FyVJi3cnWLeW-hUXy1-FF1N23muA5VfT4,7526
 sl_shared_assets/tools/packaging_tools.pyi,sha256=vgGbAQCExwg-0A5F72MzEhzHxu97Nqg1yuz-5P89ycU,3118
 sl_shared_assets/tools/project_management_tools.py,sha256=Z_U0R26w9Le1O-u66gyF5CG8M_YaLFNpH9diQeH1AZQ,29381
 sl_shared_assets/tools/project_management_tools.pyi,sha256=4kok98nOZ4KnT-Sg-ZCZYg-WIM5qZqiyK8g1XiiDjHM,10375
 sl_shared_assets/tools/transfer_tools.py,sha256=J26kwOp_NpPSY0-xu5FTw9udte-rm_mW1FJyaTNoqQI,6606
 sl_shared_assets/tools/transfer_tools.pyi,sha256=FoH7eYZe7guGHfPr0MK5ggO62uXKwD2aJ7h1Bu7PaEE,3294
-sl_shared_assets-3.0.0rc4.dist-info/METADATA,sha256=35CAPKPkE-DLPvdQ5WuGnsn77wggdxEZDRQGV1e45Ls,49309
-sl_shared_assets-3.0.0rc4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-sl_shared_assets-3.0.0rc4.dist-info/entry_points.txt,sha256=UmO1rl7ly9N7HWPwWyP9E0b5KBUStpBo4TRoqNtizDY,430
-sl_shared_assets-3.0.0rc4.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-sl_shared_assets-3.0.0rc4.dist-info/RECORD,,
+sl_shared_assets-3.0.0rc5.dist-info/METADATA,sha256=STS00DFD8iiTx7LzSGoGziBUwLQfivCPY0rTXOEtGss,49309
+sl_shared_assets-3.0.0rc5.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+sl_shared_assets-3.0.0rc5.dist-info/entry_points.txt,sha256=UmO1rl7ly9N7HWPwWyP9E0b5KBUStpBo4TRoqNtizDY,430
+sl_shared_assets-3.0.0rc5.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+sl_shared_assets-3.0.0rc5.dist-info/RECORD,,