sl-shared-assets 1.0.0rc8__py3-none-any.whl → 1.0.0rc9__py3-none-any.whl

sl_shared_assets/packaging_tools.pyi

@@ -1,52 +0,0 @@
-from pathlib import Path
-
-def _calculate_file_checksum(base_directory: Path, file_path: Path) -> tuple[str, bytes]:
-    """Calculates xxHash3-128 checksum for a single file and its path relative to the base directory.
-
-    This function is passed to parallel workers used by the calculate_directory_hash() method that iteratively
-    calculates the checksum for all files inside a directory. Each call to this function returns the checksum for the
-    target file, which includes both the contents of the file and its path relative to the base directory.
-
-    Args:
-        base_directory: The path to the base (root) directory which is being checksummed by the main
-            'calculate_directory_checksum' function.
-        file_path: The absolute path to the target file.
-
-    Returns:
-        A tuple with two elements. The first element is the path to the file relative to the base directory. The second
-        element is the xxHash3-128 checksum that covers the relative path and the contents of the file.
-    """
-
-def calculate_directory_checksum(
-    directory: Path, num_processes: int | None = None, batch: bool = False, save_checksum: bool = True
-) -> str:
-    """Calculates xxHash3-128 checksum for the input directory, which includes the data of all contained files and
-    the directory structure information.
-
-    This function is used to generate a checksum for the raw_data directory of each experiment or training session.
-    Checksums are used to verify the session data integrity during transmission between the PC that acquired the data
-    and long-term storage locations, such as the Synology NAS or the BioHPC server. The function can be configured to
-    write the generated checksum as a hexadecimal string to the ax_checksum.txt file stored at the highest level of the
-    input directory.
-
-    Note:
-        This method uses multiprocessing to efficiently parallelize checksum calculation for multiple files. In
-        combination with xxHash3, this achieves a significant speedup over more common checksums, such as MD5 and
-        SHA256. Note that xxHash3 is not suitable for security purposes and is only used to ensure data integrity.
-
-        The method notifies the user about the checksum calculation process via the terminal.
-
-        The returned checksum accounts for both the contents of each file and the layout of the input directory
-        structure.
-
-    Args:
-        directory: The Path to the directory to be checksummed.
-        num_processes: The number of CPU processes to use for parallelizing checksum calculation. If set to None, the
-            function defaults to using (logical CPU count - 4).
-        batch: Determines whether the function is called as part of batch-processing multiple directories. This is used
-            to optimize progress reporting to avoid cluttering the terminal.
-        save_checksum: Determines whether the checksum should be saved (written to) a .txt file.
-
-    Returns:
-        The xxHash3-128 checksum for the input directory as a hexadecimal string.
-    """

sl_shared_assets/server.pyi

@@ -1,112 +0,0 @@
-from pathlib import Path
-from dataclasses import dataclass
-
-from simple_slurm import Slurm
-from paramiko.client import SSHClient as SSHClient
-from ataraxis_data_structures import YamlConfig
-
-def generate_server_credentials(
-    output_directory: Path, username: str, password: str, host: str = "cbsuwsun.biohpc.cornell.edu"
-) -> None:
-    """Generates a new server_credentials.yaml file under the specified directory, using input information.
-
-    This function provides a convenience interface for generating new BioHPC server credential files. Generally, this is
-    only used when setting up new host-computers in the lab.
-    """
-@dataclass()
-class ServerCredentials(YamlConfig):
-    """This class stores the hostname and credentials used to log into the BioHPC cluster to run Sun lab processing
-    pipelines.
-
-    Primarily, this is used as part of the sl-experiment library runtime to start data processing once it is
-    transferred to the BioHPC server during preprocessing.
-    """
-
-    username: str = ...
-    password: str = ...
-    host: str = ...
-
-class Server:
-    """Encapsulates access to the Sun lab BioHPC processing server.
-
-    This class provides the API that allows accessing the BioHPC server and creating and submitting various
-    SLURM-managed jobs to the server. It functions as the central interface used by all processing pipelines in the
-    lab to execute costly data processing on the server.
-
-    Notes:
-        All lab processing pipelines expect the data to be stored on the server and all processing logic to be packaged
-        and installed into dedicated conda environments on the server.
-
-    Args:
-        credentials_path: The path to the.yaml file containing the server hostname and access credentials.
-
-        Attributes:
-            _open: Tracks whether the connection to the server is open or not.
-            _client: Stores the initialized SSHClient instance used to interface with the server.
-    """
-
-    _open: bool
-    _credentials: ServerCredentials
-    _client: SSHClient
-    def __init__(self, credentials_path: Path) -> None: ...
-    def __del__(self) -> None:
-        """If the instance is connected to the server, terminates the connection before the instance is destroyed."""
-    @staticmethod
-    def generate_slurm_header(
-        job_name: str, output_log: Path, error_log: Path, cpus_to_use: int = 20, ram_gb: int = 4, time_limit: int = 60
-    ) -> Slurm:
-        """Creates a SLURM command object and fills it with initial job configuration data.
-
-        This method is used to generate the initial SLURM command object and fill it with job (SLURM) configuration and
-        (general!) conda initialization data. It is used by all processing pipelines in the lab as the initial
-        configuration point when writing job shell scripts.
-
-        Notes:
-            The command header generated by this method does not contain the command to initialize the specific conda
-            environment to be used during processing. This has to be provided as part of the additional command
-            configuration, typically by adding the "source activate {ENV_NAME}" subcommand to the end of the header
-            returned by this method.
-
-        Args:
-            job_name: The descriptive name of the SLURM job to be created.
-            output_log: The path to the .txt file on the processing server, where to store the standard output of the
-                job.
-            error_log: The path to the .txt file on the processing server, where to store the standard error of the
-                job.
-            cpus_to_use: The number of CPUs to use for the job.
-            ram_gb: The amount of RAM to allocate for the job in Gigabytes.
-            time_limit: The maximum time limit for the job, in minutes. It is highly advised to set an adequate maximum
-                runtime limit to prevent jobs from hogging the server for a long period of time.
-        """
-    def submit_job(self, slurm_command: Slurm, working_directory: Path) -> str:
-        """Submits the input SLURM command to the managed BioHPC server via the shell script.
-
-        This method submits various commands for execution via SLURM-managed BioHPC cluster. As part of its runtime, the
-        method translates the Slurm object into the shell script, moves the script to the target working directory on
-        the server, and instructs the server to execute the shell script (via SLURM).
-
-        Args:
-            slurm_command: The Slurm (command) object containing the job configuration and individual commands to run
-                as part of the processing pipeline.
-            working_directory: The path to the working directory on the server where the shell script is moved
-                and executed.
-
-        Returns:
-            The job ID assigned to the job by SLURM manager if the command submission is successful.
-
-        Raises:
-            RuntimeError: If the command submission to the server fails.
-        """
-    def job_complete(self, job_id: str) -> bool:
-        """Returns True if the job with the given ID has been completed or terminated its runtime due to an error.
-
-        If the job is still running or is waiting inside the execution queue, returns False.
-
-        Args:
-            job_id: The numeric ID of the job to check, assigned by SLURM.
-        """
-    def close(self) -> None:
-        """Closes the SSH connection to the server.
-
-        This method has to be called before destroying the class instance to ensure proper resource cleanup.
-        """

sl_shared_assets/suite2p.pyi

@@ -1,188 +0,0 @@
-from typing import Any
-from dataclasses import field, dataclass
-
-from _typeshed import Incomplete
-from ataraxis_data_structures import YamlConfig
-
-@dataclass
-class Main:
-    """Stores global settings used to broadly define the suite2p processing configuration."""
-
-    nplanes: int = ...
-    nchannels: int = ...
-    functional_chan: int = ...
-    tau: float = ...
-    force_sktiff: bool = ...
-    fs: float = ...
-    do_bidiphase: bool = ...
-    bidiphase: int = ...
-    bidi_corrected: bool = ...
-    frames_include: int = ...
-    multiplane_parallel: bool = ...
-    ignore_flyback: list[int] = field(default_factory=list)
-
-@dataclass
-class FileIO:
-    """Stores I/O settings used to specify input data file locations, formats, and output storage options."""
-
-    fast_disk: list[str] = field(default_factory=list)
-    delete_bin: bool = ...
-    mesoscan: bool = ...
-    bruker: bool = ...
-    bruker_bidirectional: bool = ...
-    h5py: list[str] = field(default_factory=list)
-    h5py_key: str = ...
-    nwb_file: str = ...
-    nwb_driver: str = ...
-    nwb_series: str = ...
-    save_path0: list[str] = field(default_factory=list)
-    save_folder: list[str] = field(default_factory=list)
-    look_one_level_down: bool = ...
-    subfolders: list[str] = field(default_factory=list)
-    move_bin: bool = ...
-
-@dataclass
-class Output:
-    """Stores I/O settings used to define the output format and organization of the processing results."""
-
-    preclassify: float = ...
-    save_nwb: bool = ...
-    save_mat: bool = ...
-    combined: bool = ...
-    aspect: float = ...
-    report_time: bool = ...
-
-@dataclass
-class Registration:
-    """Stores rigid registration settings used for correcting motion artifacts between frames."""
-
-    do_registration: bool = ...
-    align_by_chan: int = ...
-    nimg_init: int = ...
-    batch_size: int = ...
-    maxregshift: float = ...
-    smooth_sigma: float = ...
-    smooth_sigma_time: float = ...
-    keep_movie_raw: bool = ...
-    two_step_registration: bool = ...
-    reg_tif: bool = ...
-    reg_tif_chan2: bool = ...
-    subpixel: int = ...
-    th_badframes: float = ...
-    norm_frames: bool = ...
-    force_refImg: bool = ...
-    pad_fft: bool = ...
-
-@dataclass
-class OnePRegistration:
-    """Stores additional pre-registration processing settings used to improve the registration of 1-photon datasets."""
-
-    one_p_reg: bool = ...
-    spatial_hp_reg: int = ...
-    pre_smooth: float = ...
-    spatial_taper: float = ...
-
-@dataclass
-class NonRigid:
-    """Stores non-rigid registration settings used to improve motion registration in complex datasets."""
-
-    nonrigid: bool = ...
-    block_size: list[int] = field(default_factory=Incomplete)
-    snr_thresh: float = ...
-    maxregshiftNR: float = ...
-
-@dataclass
-class ROIDetection:
-    """Stores ROI detection and extraction settings used to identify cells and their activity signals."""
-
-    roidetect: bool = ...
-    sparse_mode: bool = ...
-    spatial_scale: int = ...
-    connected: bool = ...
-    threshold_scaling: float = ...
-    spatial_hp_detect: int = ...
-    max_overlap: float = ...
-    high_pass: int = ...
-    smooth_masks: bool = ...
-    max_iterations: int = ...
-    nbinned: int = ...
-    denoise: bool = ...
-
-@dataclass
-class CellposeDetection:
-    """Stores Cellpose algorithm settings used for cell detection."""
-
-    anatomical_only: int = ...
-    diameter: int = ...
-    cellprob_threshold: float = ...
-    flow_threshold: float = ...
-    spatial_hp_cp: int = ...
-    pretrained_model: str = ...
-
-@dataclass
-class SignalExtraction:
-    """Stores settings used to extract fluorescence signals from ROIs and surrounding neuropil regions."""
-
-    neuropil_extract: bool = ...
-    allow_overlap: bool = ...
-    min_neuropil_pixels: int = ...
-    inner_neuropil_radius: int = ...
-    lam_percentile: int = ...
-
-@dataclass
-class SpikeDeconvolution:
-    """Stores settings used to deconvolve calcium signals to infer spike trains."""
-
-    spikedetect: bool = ...
-    neucoeff: float = ...
-    baseline: str = ...
-    win_baseline: float = ...
-    sig_baseline: float = ...
-    prctile_baseline: float = ...
-
-@dataclass
-class Classification:
-    """Stores settings used to classify detected ROIs as real cells or artifacts."""
-
-    soma_crop: bool = ...
-    use_builtin_classifier: bool = ...
-    classifier_path: str = ...
-
-@dataclass
-class Channel2:
-    """Stores settings for processing the second channel in multichannel datasets."""
-
-    chan2_thres: float = ...
-
-@dataclass
-class Suite2PConfiguration(YamlConfig):
-    """Stores the user-addressable suite2p configuration parameters, organized into subsections.
-
-    This class is used during processing to instruct suite2p on how to process the data. Specifically, it provides a
-    user-friendly way of specifying all user-addressable parameters through a .YAML file. The sl-forgery library then
-    loads the data from .yaml file and uses it to configure the single-day suite2p pipeline and the multiday suite2p
-    pipeline.
-
-    Notes:
-        The .YAML file uses section names that match the suite2p documentation sections. This way, users can always
-        consult the suite2p documentation for information on the purpose of each field inside every subsection.
-    """
-
-    main: Main = field(default_factory=Main)
-    file_io: FileIO = field(default_factory=FileIO)
-    output: Output = field(default_factory=Output)
-    registration: Registration = field(default_factory=Registration)
-    one_p_registration: OnePRegistration = field(default_factory=OnePRegistration)
-    non_rigid: NonRigid = field(default_factory=NonRigid)
-    roi_detection: ROIDetection = field(default_factory=ROIDetection)
-    cellpose_detection: CellposeDetection = field(default_factory=CellposeDetection)
-    signal_extraction: SignalExtraction = field(default_factory=SignalExtraction)
-    spike_deconvolution: SpikeDeconvolution = field(default_factory=SpikeDeconvolution)
-    classification: Classification = field(default_factory=Classification)
-    channel2: Channel2 = field(default_factory=Channel2)
-    def to_ops(self) -> dict[str, Any]:
-        """Converts the class instance to a dictionary and returns it to caller.
-
-        This dictionary can be passed to suite2p functions either as an 'ops' or 'db' argument to control the
-        processing runtime.
-        """

sl_shared_assets/transfer_tools.pyi

@@ -1,53 +0,0 @@
-from pathlib import Path
-
-from .packaging_tools import calculate_directory_checksum as calculate_directory_checksum
-
-def _transfer_file(source_file: Path, source_directory: Path, destination_directory: Path) -> None:
-    """Copies the input file from the source directory to the destination directory while preserving the file metadata.
-
-    This is a worker method used by the transfer_directory() method to move multiple files in parallel.
-
-    Notes:
-        If the file is found under a hierarchy of subdirectories inside the input source_directory, that hierarchy will
-        be preserved in the destination directory.
-
-    Args:
-        source_file: The file to be copied.
-        source_directory: The root directory where the file is located.
-        destination_directory: The destination directory where to move the file.
-    """
-
-def transfer_directory(source: Path, destination: Path, num_threads: int = 1, verify_integrity: bool = True) -> None:
-    """Copies the contents of the input directory tree from source to destination while preserving the folder
-    structure.
-
-    This function is used to assemble the experimental data from all remote machines used in the acquisition process on
-    the VRPC before the data is preprocessed. It is also used to transfer the preprocessed data from the VRPC to the
-    SynologyNAS and the Sun lab BioHPC server.
-
-    Notes:
-        This method recreates the moved directory hierarchy on the destination if the hierarchy does not exist. This is
-        done before copying the files.
-
-        The method executes a multithreading copy operation. It does not clean up the source files. That job is handed
-        to the specific preprocessing function from the sl_experiment or sl-forgery libraries that calls this function.
-
-        If the method is configured to verify transferred file integrity, it reruns the xxHash3-128 checksum calculation
-        and compares the returned checksum to the one stored in the source directory. The method assumes that all input
-        directories contain the 'ax_checksum.txt' file that stores the 'source' directory checksum at the highest level
-        of the input directory tree.
-
-    Args:
-        source: The path to the directory that needs to be moved.
-        destination: The path to the destination directory where to move the contents of the source directory.
-        num_threads: The number of threads to use for parallel file transfer. This number should be set depending on the
-            type of transfer (local or remote) and is not guaranteed to provide improved transfer performance. For local
-            transfers, setting this number above 1 will likely provide a performance boost. For remote transfers using
-            a single TCP / IP socket (such as non-multichannel SMB protocol), the number should be set to 1.
-        verify_integrity: Determines whether to perform integrity verification for the transferred files. Note,
-            integrity verification is a time-consuming process and generally would not be a concern for most runtimes.
-            Therefore, it is often fine to disable this option to optimize method runtime speed.
-
-    Raises:
-        RuntimeError: If the transferred files do not pass the xxHas3-128 checksum integrity verification.
-    """

sl_shared_assets-1.0.0rc8.dist-info/RECORD

@@ -1,20 +0,0 @@
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-sl_shared_assets/suite2p.py,sha256=sQ5Zj0TJFD-gUHqtWnRvapBpr8QgmaiVil123cWxGxc,20511
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