From dcff1b4a8d6c13069c140427350efb9e60893a6a Mon Sep 17 00:00:00 2001 From: Mostafa Safaie Date: Thu, 5 Jun 2025 14:42:07 +0100 Subject: [PATCH 1/4] remove ref to bnd --- bnd/pipeline/nwbtools/anipose_interface.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bnd/pipeline/nwbtools/anipose_interface.py b/bnd/pipeline/nwbtools/anipose_interface.py index fc9472f..74e06b4 100644 --- a/bnd/pipeline/nwbtools/anipose_interface.py +++ b/bnd/pipeline/nwbtools/anipose_interface.py @@ -12,7 +12,7 @@ from neuroconv.utils import DeepDict from pynwb import NWBFile -from bnd import set_logging +from ..logger import set_logging logger = set_logging(__name__) From 048709f295259c570fab6183137d1a7708f18ec4 Mon Sep 17 00:00:00 2001 From: Mostafa Safaie Date: Thu, 5 Jun 2025 14:43:14 +0100 Subject: [PATCH 2/4] Update anipose_interface.py --- bnd/pipeline/nwbtools/anipose_interface.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bnd/pipeline/nwbtools/anipose_interface.py b/bnd/pipeline/nwbtools/anipose_interface.py index 74e06b4..2302ddb 100644 --- a/bnd/pipeline/nwbtools/anipose_interface.py +++ b/bnd/pipeline/nwbtools/anipose_interface.py @@ -12,7 +12,7 @@ from neuroconv.utils import DeepDict from pynwb import NWBFile -from ..logger import set_logging +from ...logger import set_logging logger = set_logging(__name__) From 5400fa7c4dc5702f33f3ba15edc1bb04fe2e3b05 Mon Sep 17 00:00:00 2001 From: Mostafa Safaie Date: Thu, 5 Jun 2025 14:44:23 +0100 Subject: [PATCH 3/4] remove ref to bnd from cli.py --- bnd/cli.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bnd/cli.py b/bnd/cli.py index c5c2e37..2c60e03 100644 --- a/bnd/cli.py +++ b/bnd/cli.py @@ -61,7 +61,7 @@ def to_pyal( `bnd to-pyal M037_2024_01_01_10_00 -c # Uses custom mapping """ _check_processing_dependencies() - from bnd.pipeline.pyaldata import run_pyaldata_conversion + from .pipeline.pyaldata import run_pyaldata_conversion # Load config and get session path config = _load_config() From bbecc6da33772f70ed5292b787dbadf06e45f809 Mon Sep 17 00:00:00 2001 From: Mostafa Safaie Date: Thu, 5 Jun 2025 14:47:24 +0100 Subject: [PATCH 4/4] remove ref to bnd --- bnd/cli.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bnd/cli.py b/bnd/cli.py index 2c60e03..7f591d6 100644 --- a/bnd/cli.py +++ b/bnd/cli.py @@ -105,7 +105,7 @@ def to_nwb( """ # TODO: Add channel map argument: no-map, default-map, custom-map # _check_processing_dependencies() - from bnd.pipeline.nwb import run_nwb_conversion + from .pipeline.nwb import run_nwb_conversion config = _load_config() session_path = config.get_local_session_path(session_name) @@ -129,7 +129,7 @@ def ksort(session_name: str = typer.Argument(help="Session name to kilosort")) - """ # this will throw an error if the dependencies are not available _check_processing_dependencies() - from bnd.pipeline.kilosort import run_kilosort_on_session + from .pipeline.kilosort import run_kilosort_on_session config = _load_config() session_path = config.get_local_session_path(session_name)