Merge pull request #880 from NeurodataWithoutBorders/fix_mearec

Fix MEArec build
NeurodataWithoutBorders · Jun 24, 2024 · 446aed6 · 446aed6
2 parents 4e3b133 + 42cfb8f
commit 446aed6
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Showing 2 changed files with 45 additions and 34 deletions.
diff --git a/nwb-guide.spec b/nwb-guide.spec
@@ -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
 

diff --git a/src/example_pipelines.yml b/src/example_pipelines.yml
@@ -55,6 +55,7 @@ Suite2P_SinglePlane_SingleChannel:
     Suite2pSegmentationInterface:
       folder_path: ophys_testing_data/segmentation_datasets/suite2p
 
+
 Caiman_SinglePlane_SingleChannel:
   metadata:
     NWBFile:
@@ -71,6 +72,7 @@ Caiman_SinglePlane_SingleChannel:
     CaimanSegmentationInterface:
       file_path: ophys_testing_data/segmentation_datasets/caiman/caiman_analysis.hdf5
 
+
 ScanImage_SinglePlane_SingleChannel:
 
   metadata:
@@ -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:
@@ -106,6 +109,7 @@ CellExplorer:
     CellExplorerRecordingInterface:
       folder_path: ephy_testing_data/cellexplorer/dataset_4/Peter_MS22_180629_110319_concat_stubbed
 
+
 CellExplorerUnits:
   metadata:
     NWBFile:
@@ -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:
@@ -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:
@@ -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:
@@ -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:
@@ -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: