cibrrig.run_sasquatch
=====================

.. py:module:: cibrrig.run_sasquatch

.. autoapi-nested-parse::

   Need:
   1) Local run path
   2) Sasquatch directory
   3) active ALF target
   4) Archive ALF target

   Steps:
   1) Compress local
   2) Backup to Baker
   3) Copy to Sasquatch
   4) Remove local
   5) Submit slurm job
   5) Move to helens



Attributes
----------

.. autoapisummary::

   cibrrig.run_sasquatch.SASQUATCH_WORKING_DIR
   cibrrig.run_sasquatch.BAKER_DEST
   cibrrig.run_sasquatch.BAKER_DEST_RSS
   cibrrig.run_sasquatch.HELENS_DEST
   cibrrig.run_sasquatch.job_params


Functions
---------

.. autoapisummary::

   cibrrig.run_sasquatch.gen_sbatch_script
   cibrrig.run_sasquatch.gen_tarball_script
   cibrrig.run_sasquatch.remove_empty_folders
   cibrrig.run_sasquatch.main
   cibrrig.run_sasquatch.from_NPX
   cibrrig.run_sasquatch.from_baker


Module Contents
---------------

.. py:data:: SASQUATCH_WORKING_DIR

.. py:data:: BAKER_DEST

.. py:data:: BAKER_DEST_RSS

.. py:data:: HELENS_DEST

.. py:data:: job_params

.. py:function:: gen_sbatch_script(job_params: dict, run_folder: pathlib.Path, helens_dest: pathlib.Path | None = None, baker_dest_rss: pathlib.Path | None = None, opto_flag=True, QC_flag=True) -> str

   Generate SLURM batch script as a string.

   :param job_params: Dictionary containing job parameters.
   :type job_params: dict
   :param run_folder: Path to the run folder on the remote server.
   :type run_folder: Path
   :param helens_dest: Path to the destination folder on Helen's server.
   :type helens_dest: Path
   :param baker_dest_rss: Path to the destination folder on Baker's RSS server.
   :type baker_dest_rss: Path

   :returns: SLURM batch script as a string.
   :rtype: str


.. py:function:: gen_tarball_script(run_folder: pathlib.Path) -> str

   Generate SLURM batch script as a string.

   :param run_folder: Path to the run folder on the remote server.
   :type run_folder: Path

   :returns: SLURM batch script as a string.
   :rtype: str


.. py:function:: remove_empty_folders(root_dir)

.. py:function:: main()

.. py:function:: from_NPX(local_run_path, sasquatch_working_dir=SASQUATCH_WORKING_DIR, helens_dest=HELENS_DEST, baker_dest_rss=BAKER_DEST_RSS, opto_flag=True, QC_flag=True)

   Run the pipeline on sasquatch from the acquisition computer using SSH commands

   :param local_run_path: Path to the local run directory.
   :type local_run_path: Path
   :param sasquatch_working_dir: Path to sasquatch working directory. Defaults to SASQUATCH_WORKING_DIR.
   :type sasquatch_working_dir: Path, optional
   :param helens_dest: Path to Helen's destination directory. Defaults to HELENS_DEST.
   :type helens_dest: Path, optional
   :param baker_dest_rss: Path to Baker's RSS destination directory. Defaults to BAKER_DEST_RSS.
   :type baker_dest_rss: Path, optional
   :param opto_flag: Whether to remove opto artifact. Defaults to True.
   :type opto_flag: bool, optional
   :param QC_flag: Whether to run ephys QC. Defaults to True.
   :type QC_flag: bool, optional

   :returns: None

   :raises FileNotFoundError: If the local run path does not exist.


.. py:function:: from_baker(run_src, sasquatch_working_dir=SASQUATCH_WORKING_DIR, helens_dest=HELENS_DEST, opto=True, qc=True)

   Run the pipeline on sasquatch from data already on baker.
   Must be run from the login node.

   This script is accessed by the entry point `pipeline_hpc` after installing cibrrig in a conda environment.
   e.g.:
       pipeline_hpc /data/rss/baker/ramirez_j/ramirezlab/alf_data_repo/ramirez/Subjects/m2025-01

   Best practice is to create a tmux session on login node since you will move large files, activate iblenv, then run this

   :param run_src: Source run path, e.g. '/data/rss/baker/ramirez_j/ramirezlab/alf_data_repo/ramirez/Subjects/m2025-01'
   :type run_src: str
   :param sasquatch_working_dir: Path to sasquatch working directory. Defaults to SASQUATCH_WORKING_DIR.
   :type sasquatch_working_dir: Path, optional
   :param helens_dest: Path to Helen's destination directory. Defaults to HELENS_DEST.
   :type helens_dest: Path, optional
   :param opto_flag: Whether to remove opto artifact. Defaults to True.
   :type opto_flag: bool, optional
   :param QC_flag: Whether to run ephys QC. Defaults to True.
   :type QC_flag: bool, optional

   :raises FileNotFoundError: If the baker path does not exist.