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Fix MEArec build #880

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merged 3 commits into from
Jun 24, 2024
Merged

Fix MEArec build #880

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44f91db
fix mearec build
CodyCBakerPhD Jun 24, 2024
bd9c5d5
enhance readability
CodyCBakerPhD Jun 24, 2024
42cfb8f
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 24, 2024
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59 changes: 27 additions & 32 deletions nwb-guide.spec
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Original file line number Diff line number Diff line change
Expand Up @@ -19,38 +19,33 @@ hiddenimports = [
]

datas += collect_data_files('jsonschema_specifications')
tmp_ret = collect_all('dandi')
datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
tmp_ret = collect_all('keyrings')
datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
tmp_ret = collect_all('unittest')
datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
tmp_ret = collect_all('nwbinspector')
datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
tmp_ret = collect_all('neuroconv')
datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
tmp_ret = collect_all('pynwb')
datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
tmp_ret = collect_all('hdmf')
datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
tmp_ret = collect_all('hdmf_zarr')
datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
tmp_ret = collect_all('ndx_dandi_icephys')
datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
tmp_ret = collect_all('sklearn')
datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
tmp_ret = collect_all('ci_info')
datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
tmp_ret = collect_all('tifffile')
datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
tmp_ret = collect_all('dlc2nwb')
datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
tmp_ret = collect_all('sleap_io')
datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
tmp_ret = collect_all('ndx_pose')
datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
tmp_ret = collect_all('tzdata')
datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]

# Various consequences of lazy imports
modules_to_collect = [
'dandi',
'keyrings',
'unittest',
'nwbinspector',
'neuroconv',
'pynwb',
'hdmf',
'hdmf_zarr',
'ndx_dandi_icephys',
'sklearn',
'ci_info',
'tifffile',
'dlc2nwb',
'sleap_io',
'ndx_pose',
'tzdata',
'elephant',
]
for module_name in modules_to_collect:
collection = collect_all(module_name)

datas += collection[0]
binaries += collection[1]
hiddenimports += collection[2]

block_cipher = None

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20 changes: 18 additions & 2 deletions src/example_pipelines.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,7 @@ Suite2P_SinglePlane_SingleChannel:
Suite2pSegmentationInterface:
folder_path: ophys_testing_data/segmentation_datasets/suite2p


Caiman_SinglePlane_SingleChannel:
metadata:
NWBFile:
Expand All @@ -71,6 +72,7 @@ Caiman_SinglePlane_SingleChannel:
CaimanSegmentationInterface:
file_path: ophys_testing_data/segmentation_datasets/caiman/caiman_analysis.hdf5


ScanImage_SinglePlane_SingleChannel:

metadata:
Expand All @@ -86,6 +88,7 @@ ScanImage_SinglePlane_SingleChannel:
ScanImageImagingInterface:
file_path: ophys_testing_data/imaging_datasets/ScanImage/sample_scanimage_version_3_8.tiff


TDT:
metadata:
NWBFile:
Expand All @@ -106,6 +109,7 @@ CellExplorer:
CellExplorerRecordingInterface:
folder_path: ephy_testing_data/cellexplorer/dataset_4/Peter_MS22_180629_110319_concat_stubbed


CellExplorerUnits:
metadata:
NWBFile:
Expand All @@ -117,6 +121,7 @@ CellExplorerUnits:
CellExplorerSortingInterface:
file_path: ephy_testing_data/cellexplorer/dataset_4/Peter_MS22_180629_110319_concat_stubbed/Peter_MS22_180629_110319_concat_stubbed.spikes.cellinfo.mat


CellExplorerSortingOnly:
metadata:
NWBFile:
Expand All @@ -126,6 +131,7 @@ CellExplorerSortingOnly:
CellExplorerSortingInterface:
file_path: ephy_testing_data/cellexplorer/dataset_4/Peter_MS22_180629_110319_concat_stubbed/Peter_MS22_180629_110319_concat_stubbed.spikes.cellinfo.mat


IntanSingleFileRecording:
metadata:
NWBFile:
Expand All @@ -138,12 +144,20 @@ IntanSingleFileRecording:
location: Test location
-
location: Test location
interfaces:
IntanRecordingInterface:
file_path: ephy_testing_data/intan/intan_rhd_test_1.rhd


MEArec:
metadata:
NWBFile:
session_start_time: 2024-05-09T00:00

interfaces:
IntanRecordingInterface:
file_path: ephy_testing_data/intan/intan_rhd_test_1.rhd
MEArecRecordingInterface:
file_path: ephy_testing_data/mearec/mearec_test_10s.h5


BrukerTiffMultiChannelSinglePlane:
metadata:
Expand All @@ -159,6 +173,7 @@ BrukerTiffMultiChannelSinglePlane:
BrukerTiffSinglePlaneConverter:
folder_path: ophys_testing_data/imaging_datasets/BrukerTif/NCCR32_2023_02_20_Into_the_void_t_series_baseline-000


DeepLabCut:
metadata:
NWBFile:
Expand All @@ -169,6 +184,7 @@ DeepLabCut:
file_path: behavior_testing_data/DLC/m3v1mp4DLC_resnet50_openfieldAug20shuffle1_30000.h5
config_file_path: behavior_testing_data/DLC/config.yaml


SLEAP:
metadata:
NWBFile:
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