sl-shared-assets 1.0.0rc1__py3-none-any.whl

sl_shared_assets/__init__.py

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+"""A Python library that stores assets shared between multiple Sun (NeuroAI) lab data pipelines.
+
+See https://github.com/Sun-Lab-NBB/sl-shared-assets for more details.
+API documentation: https://sl-shared-assets-api-docs.netlify.app/
+Authors: Ivan Kondratyev (Inkaros), Kushaan Gupta, Yuantao Deng
+"""
+
+from .server import Server, ServerCredentials
+from .suite2p import (
+    Main,
+    FileIO,
+    Output,
+    Channel2,
+    NonRigid,
+    ROIDetection,
+    Registration,
+    Classification,
+    OnePRegistration,
+    SignalExtraction,
+    CellposeDetection,
+    SpikeDeconvolution,
+    Suite2PConfiguration,
+)
+from .data_classes import (
+    RawData,
+    DrugData,
+    ImplantData,
+    SessionData,
+    SubjectData,
+    SurgeryData,
+    Destinations,
+    InjectionData,
+    MesoscopeData,
+    ProcedureData,
+    ProcessedData,
+    PersistentData,
+    ZaberPositions,
+    ExperimentState,
+    MesoscopePositions,
+    ProjectConfiguration,
+    HardwareConfiguration,
+    RunTrainingDescriptor,
+    LickTrainingDescriptor,
+    ExperimentConfiguration,
+    MesoscopeExperimentDescriptor,
+    replace_root_path,
+)
+from .transfer_tools import transfer_directory
+from .packaging_tools import calculate_directory_checksum
+
+__all__ = [
+    # Server module
+    "Server",
+    "ServerCredentials",
+    # Suite2p module
+    "Main",
+    "FileIO",
+    "Output",
+    "Channel2",
+    "NonRigid",
+    "ROIDetection",
+    "Registration",
+    "Classification",
+    "OnePRegistration",
+    "SignalExtraction",
+    "CellposeDetection",
+    "SpikeDeconvolution",
+    "Suite2PConfiguration",
+    # Data classes module
+    "RawData",
+    "DrugData",
+    "ImplantData",
+    "SessionData",
+    "SubjectData",
+    "SurgeryData",
+    "Destinations",
+    "InjectionData",
+    "MesoscopeData",
+    "ProcedureData",
+    "ProcessedData",
+    "PersistentData",
+    "ZaberPositions",
+    "ExperimentState",
+    "MesoscopePositions",
+    "ProjectConfiguration",
+    "HardwareConfiguration",
+    "RunTrainingDescriptor",
+    "LickTrainingDescriptor",
+    "ExperimentConfiguration",
+    "MesoscopeExperimentDescriptor",
+    "replace_root_path",
+    # Transfer tools module
+    "transfer_directory",
+    # Packaging tools module
+    "calculate_directory_checksum",
+]

sl_shared_assets/__init__.pyi

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+from .server import (
+    Server as Server,
+    ServerCredentials as ServerCredentials,
+)
+from .suite2p import (
+    Main as Main,
+    FileIO as FileIO,
+    Output as Output,
+    Channel2 as Channel2,
+    NonRigid as NonRigid,
+    ROIDetection as ROIDetection,
+    Registration as Registration,
+    Classification as Classification,
+    OnePRegistration as OnePRegistration,
+    SignalExtraction as SignalExtraction,
+    CellposeDetection as CellposeDetection,
+    SpikeDeconvolution as SpikeDeconvolution,
+    Suite2PConfiguration as Suite2PConfiguration,
+)
+from .data_classes import (
+    RawData as RawData,
+    DrugData as DrugData,
+    ImplantData as ImplantData,
+    SessionData as SessionData,
+    SubjectData as SubjectData,
+    SurgeryData as SurgeryData,
+    Destinations as Destinations,
+    InjectionData as InjectionData,
+    MesoscopeData as MesoscopeData,
+    ProcedureData as ProcedureData,
+    ProcessedData as ProcessedData,
+    PersistentData as PersistentData,
+    ZaberPositions as ZaberPositions,
+    ExperimentState as ExperimentState,
+    MesoscopePositions as MesoscopePositions,
+    ProjectConfiguration as ProjectConfiguration,
+    HardwareConfiguration as HardwareConfiguration,
+    RunTrainingDescriptor as RunTrainingDescriptor,
+    LickTrainingDescriptor as LickTrainingDescriptor,
+    ExperimentConfiguration as ExperimentConfiguration,
+    MesoscopeExperimentDescriptor as MesoscopeExperimentDescriptor,
+    replace_root_path as replace_root_path,
+)
+from .transfer_tools import transfer_directory as transfer_directory
+from .packaging_tools import calculate_directory_checksum as calculate_directory_checksum
+
+__all__ = [
+    "Server",
+    "ServerCredentials",
+    "Main",
+    "FileIO",
+    "Output",
+    "Channel2",
+    "NonRigid",
+    "ROIDetection",
+    "Registration",
+    "Classification",
+    "OnePRegistration",
+    "SignalExtraction",
+    "CellposeDetection",
+    "SpikeDeconvolution",
+    "Suite2PConfiguration",
+    "RawData",
+    "DrugData",
+    "ImplantData",
+    "SessionData",
+    "SubjectData",
+    "SurgeryData",
+    "Destinations",
+    "InjectionData",
+    "MesoscopeData",
+    "ProcedureData",
+    "ProcessedData",
+    "PersistentData",
+    "ZaberPositions",
+    "ExperimentState",
+    "MesoscopePositions",
+    "ProjectConfiguration",
+    "HardwareConfiguration",
+    "RunTrainingDescriptor",
+    "LickTrainingDescriptor",
+    "ExperimentConfiguration",
+    "MesoscopeExperimentDescriptor",
+    "replace_root_path",
+    "transfer_directory",
+    "calculate_directory_checksum",
+]

sl_shared_assets/cli.py

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+"""This module stores the Command-Line Interfaces (CLIs) exposes by the library as part of the installation process.
+Primarily, these CLIs are used when setting up or reconfiguring the VRPC and other machines in the lab to work with
+sl-experiment and sl-forgery libraries."""
+
+from pathlib import Path
+
+import click
+
+from .server import generate_server_credentials
+from .data_classes import replace_root_path
+
+
+@click.command()
+@click.option(
+    "-p",
+    "--path",
+    type=click.Path(exists=True, file_okay=False, dir_okay=True, path_type=Path),
+    required=True,
+    prompt="Enter the path to the new local directory where to store all project subdirectories: ",
+    help="The path to the new local directory where to store all project subdirectories.",
+)
+def replace_local_root_directory(path: str) -> None:
+    """Replaces the root directory used to store all lab projects on the local PC with the specified directory.
+
+    To ensure all projects are saved in the same location, this library resolves and saves the absolute path to the
+    project directory when it is used for the first time. All future projects reuse the same 'root' path. Since this
+    information is stored in a typically hidden user directory, this CLI can be used to replace the local directory
+    path, if necessary.
+    """
+    replace_root_path(path=Path(path))
+
+
+@click.command()
+@click.option(
+    "-o",
+    "--output_directory",
+    type=click.Path(exists=True, file_okay=False, dir_okay=True, path_type=Path),
+    required=True,
+    prompt="Enter the path to the directory where to create the credentials file: ",
+    help="The path to the directory where to create the credentials file.",
+)
+@click.option(
+    "-h",
+    "--host",
+    type=str,
+    show_default=True,
+    required=True,
+    default="cbsuwsun.biohpc.cornell.edu",
+    help="The host name or IP address of the server to connect to.",
+)
+@click.option(
+    "-u",
+    "--username",
+    type=str,
+    required=True,
+    help="The username to use for server authentication.",
+)
+@click.option(
+    "-p",
+    "--password",
+    type=str,
+    required=True,
+    help="The password to use for server authentication.",
+)
+def generate_server_credentials_file(output_directory: str, host: str, username: str, password: str) -> None:
+    """Generates a new server_credentials.yaml file under the specified directory, using input information.
+
+    This CLI is used during the initial PC setup (typically, VRPC) to allow it to access the lab BioHPC server.
+    """
+    generate_server_credentials(
+        output_directory=Path(output_directory), username=username, password=password, host=host
+    )

sl_shared_assets/cli.pyi

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+from .server import generate_server_credentials as generate_server_credentials
+from .data_classes import replace_root_path as replace_root_path
+
+def replace_local_root_directory(path: str) -> None:
+    """Replaces the root directory used to store all lab projects on the local PC with the specified directory.
+
+    To ensure all projects are saved in the same location, this library resolves and saves the absolute path to the
+    project directory when it is used for the first time. All future projects reuse the same 'root' path. Since this
+    information is stored in a typically hidden user directory, this CLI can be used to replace the local directory
+    path, if necessary.
+    """
+
+def generate_server_credentials_file(output_directory: str, host: str, username: str, password: str) -> None:
+    """Generates a new server_credentials.yaml file under the specified directory, using input information.
+
+    This CLI is used during the initial PC setup (typically, VRPC) to allow it to access the lab BioHPC server.
+    """