Add package interface

bnd/__init__.py

@@ -1,33 +1,6 @@
-import logging
-import warnings
+# Package interface
+from .cli import dl, up, to_pyal, batch_ks
+from .data_transfer import upload_session, download_session, download_animal
 
+__all__ = [dl, up, to_pyal, batch_ks, upload_session, download_session, download_animal]
 
-# Create a logger for the package
-def set_logging(
-    file_name: str,
-) -> logging.Logger:
-    """
-    Set project-wide logging
-
-    Parameters
-    ----------
-    file_name: str
-        Name of the module being logged
-
-    Returns
-    -------
-    logger: logging.Logger
-        logger object
-    """
-    logging.basicConfig(level=logging.INFO, format="%(levelname)s - %(message)s")
-    logging.captureWarnings(True)
-
-    logger = logging.getLogger(file_name)
-
-    def custom_warning_handler(message, category, filename, lineno, file=None, line=None):
-        logger.warning(f"{category.__name__}: {message}")
-
-    # Set the custom handler
-    warnings.showwarning = custom_warning_handler
-
-    return logger

bnd/cli.py

@@ -7,7 +7,7 @@
 
 from rich import print
 
-from bnd.config import (
+from .config import (
     _check_is_git_track,
     _check_root,
     _check_session_directory,
@@ -17,9 +17,9 @@
     get_last_session,
     list_session_datetime,
 )
-from bnd.data_transfer import download_session, upload_session
-from bnd.pipeline import _check_processing_dependencies
-from bnd.update_bnd import check_for_updates, update_bnd
+from .data_transfer import download_session, upload_session
+from .pipeline import _check_processing_dependencies
+from .update_bnd import check_for_updates, update_bnd
 
 # Create a Typer app
 app = typer.Typer(

bnd/config.py

@@ -2,7 +2,7 @@
 from datetime import datetime
 from pathlib import Path
 
-from bnd import set_logging
+from .logger import set_logging
 
 logger = set_logging(__name__)
 

bnd/data_transfer.py

@@ -3,8 +3,8 @@
 import shutil
 from pathlib import Path
 
-from bnd import set_logging
-from bnd.config import _load_config, list_session_datetime
+from .logger import set_logging
+from .config import _load_config, list_session_datetime
 
 logger = set_logging(__name__)
 
@@ -132,3 +132,14 @@ def download_session(session_name: str, file_extension: str, max_size_MB: float,
             logger.info(f'"{file.name}" is too large. Skipping.')
 
     logger.info("Download complete.")
+
+def download_animal(animal_name: str, file_extension: str, max_size_MB: float, do_video: bool) -> None:
+    """
+    Download a session from the server.
+    """
+    config = _load_config()
+
+    remote_animal_path = config.get_remote_animal_path(animal_name)
+    _,session_list = list_session_datetime(remote_animal_path)
+    for session_name in session_list:
+        download_session(session_name, file_extension, max_size_MB, do_video)

bnd/logger.py

@@ -0,0 +1,33 @@
+import logging
+import warnings
+
+
+# Create a logger for the package
+def set_logging(
+    file_name: str,
+) -> logging.Logger:
+    """
+    Set project-wide logging
+
+    Parameters
+    ----------
+    file_name: str
+        Name of the module being logged
+
+    Returns
+    -------
+    logger: logging.Logger
+        logger object
+    """
+    logging.basicConfig(level=logging.INFO, format="%(levelname)s - %(message)s")
+    logging.captureWarnings(True)
+
+    logger = logging.getLogger(file_name)
+
+    def custom_warning_handler(message, category, filename, lineno, file=None, line=None):
+        logger.warning(f"{category.__name__}: {message}")
+
+    # Set the custom handler
+    warnings.showwarning = custom_warning_handler
+
+    return logger

bnd/pipeline/__init__.py

@@ -5,9 +5,9 @@
 
 def _check_processing_dependencies():
     try:
-        from bnd.pipeline.kilosort import run_kilosort_on_session
-        from bnd.pipeline.nwb import run_nwb_conversion
-        from bnd.pipeline.pyaldata import run_pyaldata_conversion
+        from .kilosort import run_kilosort_on_session
+        from .nwb import run_nwb_conversion
+        from .pyaldata import run_pyaldata_conversion
     except Exception as e:
         raise ImportError(
             f"Could not import processing dependencies: {e}. Update your environment "

bnd/pipeline/kilosort.py

@@ -6,8 +6,8 @@
 from kilosort import run_kilosort
 from kilosort.utils import PROBE_DIR, download_probes
 
-from bnd import set_logging
-from bnd.config import Config, _load_config
+from ..logger import set_logging
+from ..config import Config, _load_config
 from ..config import find_file
 
 logger = set_logging(__name__)

bnd/pipeline/nwb.py

@@ -4,12 +4,12 @@
 import numpy as np
 from rich import print
 
-from bnd import set_logging
-from bnd.config import _load_config
-from bnd.pipeline.kilosort import run_kilosort_on_session
-from bnd.pipeline.nwbtools.anipose_interface import AniposeInterface
-from bnd.pipeline.nwbtools.beneuro_converter import BeNeuroConverter
-from bnd.pipeline.nwbtools.multiprobe_kilosort_interface import (
+from ..logger import set_logging
+from ..config import _load_config
+from .kilosort import run_kilosort_on_session
+from .nwbtools.anipose_interface import AniposeInterface
+from .nwbtools.beneuro_converter import BeNeuroConverter
+from .nwbtools.multiprobe_kilosort_interface import (
     MultiProbeKiloSortInterface,
 )
 

bnd/pipeline/nwbtools/beneuro_converter.py

@@ -6,13 +6,13 @@
 from neuroconv.datainterfaces import SpikeGLXRecordingInterface  # PhySortingInterface
 from neuroconv.tools.signal_processing import get_rising_frames_from_ttl
 
-from bnd import set_logging
-from bnd.config import _load_config
-from bnd.pipeline.nwbtools.anipose_interface import AniposeInterface
-from bnd.pipeline.nwbtools.multiprobe_kilosort_interface import (
+from ...logger import set_logging
+from ...config import _load_config
+from .anipose_interface import AniposeInterface
+from .multiprobe_kilosort_interface import (
     MultiProbeKiloSortInterface,
 )
-from bnd.pipeline.nwbtools.pycontrol_interface import PyControlInterface
+from .pycontrol_interface import PyControlInterface
 
 logger = set_logging(__name__)
 config = _load_config()

bnd/pipeline/nwbtools/multiprobe_kilosort_interface.py

@@ -15,7 +15,7 @@
 from neuroconv.utils import DeepDict
 from pynwb import NWBFile
 
-from bnd import set_logging
+from ...logger import set_logging
 
 logger = set_logging(__name__)
 

bnd/pipeline/nwbtools/pycontrol_data_import.py

@@ -8,7 +8,7 @@
 
 import numpy as np
 
-from bnd import set_logging
+from ...logger import set_logging
 
 logger = set_logging(__name__)
 

bnd/pipeline/nwbtools/pycontrol_interface.py

@@ -15,7 +15,7 @@
 from pynwb.behavior import BehavioralEvents, Position, SpatialSeries
 from pynwb.epoch import TimeIntervals
 
-from bnd import set_logging
+from ...logger import set_logging
 
 from .pycontrol_data_import import Event, Print, Session, State
 

bnd/pipeline/pyaldata.py

@@ -12,9 +12,9 @@
 from pynwb.behavior import SpatialSeries
 from pynwb.misc import Units
 
-from bnd import set_logging
-from bnd.config import _load_config
-from bnd.pipeline.nwb import run_nwb_conversion
+from ..logger import set_logging
+from ..config import _load_config
+from ..pipeline.nwb import run_nwb_conversion
 
 logger = set_logging(__name__)
 

bnd/update_bnd.py

@@ -3,8 +3,8 @@
 import warnings
 from pathlib import Path
 
-from bnd import set_logging
-from bnd.config import _load_config
+from .logger import set_logging
+from .config import _load_config
 
 logger = set_logging(__name__)