sl-shared-assets 5.1.0__tar.gz → 5.1.2__tar.gz

{sl_shared_assets-5.1.0 → sl_shared_assets-5.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sl-shared-assets
-Version: 5.1.0
+Version: 5.1.2
 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-5.1.0 → sl_shared_assets-5.1.2}/envs/slsa_dev_lin.yml

@@ -6,7 +6,7 @@ dependencies:
   - _openmp_mutex=4.5=2_gnu
   - bzip2=1.0.8=h4bc722e_7
   - ca-certificates=2025.8.3=hbd8a1cb_0
-  - cachetools=6.1.0=pyhd8ed1ab_0
+  - cachetools=6.2.0=pyhd8ed1ab_0
   - chardet=5.2.0=pyhd8ed1ab_3
   - colorama=0.4.6=pyhd8ed1ab_1
   - distlib=0.4.0=pyhd8ed1ab_0

{sl_shared_assets-5.1.0 → sl_shared_assets-5.1.2}/envs/slsa_dev_lin_spec.txt

@@ -1,10 +1,10 @@
-List of packages in environment: "/home/cybermouse/miniforge3/envs/slsa_dev_lin"
+List of packages in environment: "/home/cyberaxolotl/miniforge3/envs/slsa_dev_lin"
 
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda
 https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda
-https://conda.anaconda.org/conda-forge/noarch/cachetools-6.1.0-pyhd8ed1ab_0.conda
+https://conda.anaconda.org/conda-forge/noarch/cachetools-6.2.0-pyhd8ed1ab_0.conda
 https://conda.anaconda.org/conda-forge/noarch/chardet-5.2.0-pyhd8ed1ab_3.conda
 https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_1.conda
 https://conda.anaconda.org/conda-forge/noarch/distlib-0.4.0-pyhd8ed1ab_0.conda

{sl_shared_assets-5.1.0 → sl_shared_assets-5.1.2}/pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "hatchling.build"
 # Project metdata section. Provides the genral ID information about the project.
 [project]
 name = "sl-shared-assets"
-version = "5.1.0"
+version = "5.1.2"
 description = "Provides data acquisition and processing assets shared between Sun (NeuroAI) lab libraries."
 readme = "README.md"
 license = { file = "LICENSE" }

{sl_shared_assets-5.1.0 → sl_shared_assets-5.1.2}/src/sl_shared_assets/__init__.py

@@ -8,7 +8,6 @@ Authors: Ivan Kondratyev (Inkaros), Kushaan Gupta, Natalie Yeung
 from ataraxis_base_utilities import console
 
 from .tools import (
-    ProjectManifest,
     acquire_lock,
     release_lock,
     delete_directory,
@@ -86,8 +85,10 @@ __all__ = [
     "MesoscopeSystemConfiguration",
     "ProcedureData",
     "ProcessedData",
+    "ProcessingPipeline",
+    "ProcessingPipelines",
+    "ProcessingStatus",
     "ProcessingTracker",
-    "ProjectManifest",
     "RawData",
     "RunTrainingDescriptor",
     "Server",

{sl_shared_assets-5.1.0 → sl_shared_assets-5.1.2}/src/sl_shared_assets/command_line_interfaces/manage.py

@@ -37,8 +37,10 @@ def manage() -> None:
     "--session-path",
     type=click.Path(exists=True, file_okay=False, dir_okay=True, path_type=Path),
     required=True,
-    help="The absolute path to the root session directory to process. This directory must contain the 'raw_data' "
-    "subdirectory.",
+    help=(
+        "The absolute path to the root session directory to process. This directory must contain the 'raw_data' "
+        "subdirectory."
+    ),
 )
 @click.option(
     "-pdr",

{sl_shared_assets-5.1.0 → sl_shared_assets-5.1.2}/src/sl_shared_assets/tools/__init__.py

@@ -4,7 +4,6 @@ integrity of the data. The tools from this package are used by most other data p
 from .transfer_tools import delete_directory, transfer_directory
 from .packaging_tools import calculate_directory_checksum
 from .project_management_tools import (
-    ProjectManifest,
     acquire_lock,
     release_lock,
     archive_session,
@@ -14,7 +13,6 @@ from .project_management_tools import (
 )
 
 __all__ = [
-    "ProjectManifest",
     "acquire_lock",
     "archive_session",
     "calculate_directory_checksum",

{sl_shared_assets-5.1.0 → sl_shared_assets-5.1.2}/src/sl_shared_assets/tools/project_management_tools.py

@@ -661,236 +661,3 @@ def generate_project_manifest(
             # If the tracker indicates that the processing is still running, the runtime has encountered an error.
             if runtime_tracker.is_running:
                 tracker.error(manager_id=manager_id)
-
-
-class ProjectManifest:
-    """Wraps the contents of a Sun lab project manifest .feather file and exposes methods for visualizing and
-    working with the data stored inside the file.
-
-    This class functions as a high-level API for working with Sun lab projects. It is used both to visualize the
-    current state of various projects and during automated data processing to determine which processing steps to
-    apply to different sessions.
-
-    Args:
-        manifest_file: The path to the .feather manifest file that stores the target project's state data.
-
-    Attributes:
-        _data: Stores the manifest data as a Polars DataFrame.
-        _animal_string: Determines whether animal IDs are stored as strings or unsigned integers.
-    """
-
-    def __init__(self, manifest_file: Path):
-        # Reads the data from the target manifest file into the class attribute
-        self._data: pl.DataFrame = pl.read_ipc(source=manifest_file, use_pyarrow=True)
-
-        # Determines whether animal IDs are stored as strings or as numbers
-        self._animal_string = False
-        schema = self._data.collect_schema()
-        if isinstance(schema["animal"], pl.String):
-            self._animal_string = True
-
-    def print_data(self) -> None:
-        """Prints the entire contents of the manifest file to the terminal."""
-        with pl.Config(
-            set_tbl_rows=-1,  # Displays all rows (-1 means unlimited)
-            set_tbl_cols=-1,  # Displays all columns (-1 means unlimited)
-            set_tbl_hide_column_data_types=True,
-            set_tbl_cell_alignment="LEFT",
-            set_tbl_width_chars=250,  # Sets table width to 200 characters
-            set_fmt_str_lengths=600,  # Allows longer strings to display properly (default is 32)
-        ):
-            print(self._data)
-
-    def print_summary(self, animal: str | int | None = None) -> None:
-        """Prints a summary view of the manifest file to the terminal, excluding the 'experimenter notes' data for
-        each session.
-
-        This data view is optimized for tracking which processing steps have been applied to each session inside the
-        project.
-
-        Args:
-            animal: The ID of the animal for which to display the data. If an ID is provided, this method will only
-                display the data for that animal. Otherwise, it will display the data for all animals.
-        """
-        summary_cols = [
-            "animal",
-            "date",
-            "session",
-            "type",
-            "system",
-            "complete",
-            "integrity",
-            "prepared",
-            "suite2p",
-            "behavior",
-            "video",
-            "archived",
-        ]
-
-        # Retrieves the data
-        df = self._data.select(summary_cols)
-
-        # Optionally filters the data for the target animal
-        if animal is not None:
-            # Ensures that the 'animal' argument has the same type as the data inside the DataFrame.
-            if self._animal_string:
-                animal = str(animal)
-            else:
-                animal = int(animal)
-            df = df.filter(pl.col("animal") == animal)
-
-        # Ensures the data displays properly
-        with pl.Config(
-            set_tbl_rows=-1,
-            set_tbl_cols=-1,
-            set_tbl_width_chars=250,
-            set_tbl_hide_column_data_types=True,
-            set_tbl_cell_alignment="CENTER",
-        ):
-            print(df)
-
-    def print_notes(self, animal: str | int | None = None) -> None:
-        """Prints only animal, session, and notes data from the manifest file.
-
-        This data view is optimized for experimenters to check what sessions have been recorded for each animal in the
-        project and refresh their memory on the outcomes of each session using experimenter notes.
-
-        Args:
-            animal: The ID of the animal for which to display the data. If an ID is provided, this method will only
-                display the data for that animal. Otherwise, it will display the data for all animals.
-        """
-
-        # Pre-selects the columns to display
-        df = self._data.select(["animal", "date", "session", "type", "system", "notes"])
-
-        # Optionally filters the data for the target animal
-        if animal is not None:
-            # Ensures that the 'animal' argument has the same type as the data inside the DataFrame.
-            if self._animal_string:
-                animal = str(animal)
-            else:
-                animal = int(animal)
-
-            df = df.filter(pl.col("animal") == animal)
-
-        #  Prints the extracted data
-        with pl.Config(
-            set_tbl_rows=-1,
-            set_tbl_cols=-1,
-            set_tbl_hide_column_data_types=True,
-            set_tbl_cell_alignment="LEFT",
-            set_tbl_width_chars=100,  # Wider columns for notes
-            set_fmt_str_lengths=800,  # Allows very long strings for notes
-        ):
-            print(df)
-
-    @property
-    def animals(self) -> tuple[str, ...]:
-        """Returns all unique animal IDs stored inside the manifest file.
-
-        This provides a tuple of all animal IDs participating in the target project.
-        """
-
-        # If animal IDs are stored as integers, converts them to string to support consistent return types.
-        return tuple(
-            [str(animal) for animal in self._data.select("animal").unique().sort("animal").to_series().to_list()]
-        )
-
-    def _get_filtered_sessions(
-        self,
-        animal: str | int | None = None,
-        exclude_incomplete: bool = True,
-    ) -> tuple[str, ...]:
-        """This worker method is used to get a list of sessions with optional filtering.
-
-        User-facing methods call this worker under-the-hood to fetch the filtered tuple of sessions.
-
-        Args:
-            animal: An optional animal ID to filter the sessions. If set to None, the method returns sessions for all
-                animals.
-            exclude_incomplete: Determines whether to exclude sessions not marked as 'complete' from the output
-                list.
-
-        Returns:
-            The tuple of session IDs matching the filter criteria.
-
-        Raises:
-            ValueError: If the specified animal is not found in the manifest file.
-        """
-        data = self._data
-
-        # Filter by animal if specified
-        if animal is not None:
-            # Ensures that the 'animal' argument has the same type as the data inside the DataFrame.
-            if self._animal_string:
-                animal = str(animal)
-            else:
-                animal = int(animal)
-
-            if animal not in self.animals:
-                message = f"Animal ID '{animal}' not found in the project manifest. Available animals: {self.animals}."
-                console.error(message=message, error=ValueError)
-
-            data = data.filter(pl.col("animal") == animal)
-
-        # Optionally filters out incomplete sessions
-        if exclude_incomplete:
-            data = data.filter(pl.col("complete") == 1)
-
-        # Formats and returns session IDs to the caller
-        sessions = data.select("session").sort("session").to_series().to_list()
-        return tuple(sessions)
-
-    @property
-    def sessions(self) -> tuple[str, ...]:
-        """Returns all session IDs stored inside the manifest file.
-
-        This property provides a tuple of all sessions, independent of the participating animal, that were recorded as
-        part of the target project. Use the get_sessions() method to get the list of session tuples with filtering.
-        """
-        return self._get_filtered_sessions(animal=None, exclude_incomplete=False)
-
-    def get_sessions(
-        self,
-        animal: str | int | None = None,
-        exclude_incomplete: bool = True,
-    ) -> tuple[str, ...]:
-        """Returns requested session IDs based on selected filtering criteria.
-
-        This method provides a tuple of sessions based on the specified filters. If no animal is specified, returns
-        sessions for all animals in the project.
-
-        Args:
-            animal: An optional animal ID to filter the sessions. If set to None, the method returns sessions for all
-                animals.
-            exclude_incomplete: Determines whether to exclude sessions not marked as 'complete' from the output
-                list.
-
-        Returns:
-            The tuple of session IDs matching the filter criteria.
-
-        Raises:
-            ValueError: If the specified animal is not found in the manifest file.
-        """
-        return self._get_filtered_sessions(
-            animal=animal,
-            exclude_incomplete=exclude_incomplete,
-        )
-
-    def get_session_info(self, session: str) -> pl.DataFrame:
-        """Returns a Polars DataFrame that stores detailed information for the specified session.
-
-        Since session IDs are unique, it is expected that filtering by session ID is enough to get the requested
-        information.
-
-        Args:
-            session: The ID of the session for which to retrieve the data.
-
-        Returns:
-            A Polars DataFrame with the following columns: 'animal', 'date', 'notes', 'session', 'type', 'system',
-            'complete', 'integrity', 'suite2p', 'behavior', 'video', 'archived'.
-        """
-
-        df = self._data
-        df = df.filter(pl.col("session").eq(session))
-        return df