From 44f91db6fff9004098994bf7b845b0c68d5efbbb Mon Sep 17 00:00:00 2001 From: Cody Baker Date: Mon, 24 Jun 2024 13:39:57 -0400 Subject: [PATCH 1/3] fix mearec build --- nwb-guide.spec | 2 ++ src/example_pipelines.yml | 20 ++++++++++++++++++-- 2 files changed, 20 insertions(+), 2 deletions(-) diff --git a/nwb-guide.spec b/nwb-guide.spec index 5e0fd67c5..53955e6af 100644 --- a/nwb-guide.spec +++ b/nwb-guide.spec @@ -51,6 +51,8 @@ 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] +tmp_ret = collect_all('elephant') +datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2] block_cipher = None diff --git a/src/example_pipelines.yml b/src/example_pipelines.yml index 857d8e1e8..cd5803376 100644 --- 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: From bd9c5d55cd132995001e85e8183c4facd3504cd9 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Mon, 24 Jun 2024 14:55:01 -0400 Subject: [PATCH 2/3] enhance readability --- nwb-guide.spec | 61 ++++++++++++++++++++++---------------------------- 1 file changed, 27 insertions(+), 34 deletions(-) diff --git a/nwb-guide.spec b/nwb-guide.spec index 53955e6af..691880ac1 100644 --- a/nwb-guide.spec +++ b/nwb-guide.spec @@ -19,40 +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] -tmp_ret = collect_all('elephant') -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 From 42cfb8f8f4755bc2f6c4763098282ffaffd8fa52 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 24 Jun 2024 18:55:21 +0000 Subject: [PATCH 3/3] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- nwb-guide.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nwb-guide.spec b/nwb-guide.spec index 691880ac1..0fb2d28f2 100644 --- a/nwb-guide.spec +++ b/nwb-guide.spec @@ -42,7 +42,7 @@ modules_to_collect = [ ] for module_name in modules_to_collect: collection = collect_all(module_name) - + datas += collection[0] binaries += collection[1] hiddenimports += collection[2]