NeurodataWithoutBorders · rly · Dec 9, 2024 · Dec 9, 2024 · Dec 9, 2024 · Dec 9, 2024
diff --git a/.github/workflows/testing_pipelines.yml b/.github/workflows/testing_pipelines.yml
@@ -74,24 +74,29 @@ jobs:
       - name: Get ephy_testing_data current head hash
         id: ephys
         run: echo "::set-output name=HASH_EPHY_DATASET::$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)"
+
       - name: Cache ephys dataset - ${{ steps.ephys.outputs.HASH_EPHY_DATASET }}
         uses: actions/cache@v4
         id: cache-ephys-datasets
         with:
           path: ./ephy_testing_data
           key: ephys-datasets-${{ matrix.os }}-${{ steps.ephys.outputs.HASH_EPHY_DATASET }}
+
       - name: Get ophys_testing_data current head hash
         id: ophys
         run: echo "::set-output name=HASH_OPHYS_DATASET::$(git ls-remote https://gin.g-node.org/CatalystNeuro/ophys_testing_data.git HEAD | cut -f1)"
+
       - name: Cache ophys dataset - ${{ steps.ophys.outputs.HASH_OPHYS_DATASET }}
         uses: actions/cache@v4
         id: cache-ophys-datasets
         with:
           path: ./ophys_testing_data
           key: ophys-datasets-${{ matrix.os }}-${{ steps.ophys.outputs.HASH_OPHYS_DATASET }}
+
       - name: Get behavior_testing_data current head hash
         id: behavior
         run: echo "::set-output name=HASH_BEHAVIOR_DATASET::$(git ls-remote https://gin.g-node.org/CatalystNeuro/behavior_testing_data.git HEAD | cut -f1)"
+
       - name: Cache behavior dataset - ${{ steps.behavior.outputs.HASH_BEHAVIOR_DATASET }}
         uses: actions/cache@v4
         id: cache-behavior-datasets

diff --git a/environments/environment-Linux.yml b/environments/environment-Linux.yml
@@ -7,19 +7,22 @@ dependencies:
   - nodejs = 18.16.1
   - numcodecs = 0.11.0
   # install these from conda-forge so that dependent packages get included in the distributable
-  - jsonschema = 4.18.0  # installs jsonschema-specifications
+  - jsonschema = 4.18.0 # installs jsonschema-specifications
   - pip
   - pip:
       - chardet == 5.1.0
       - configparser == 6.0.0
       - flask == 2.3.2
       - flask-cors == 4.0.0
       - flask_restx == 1.1.0
-      - werkzeug < 3.0  # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
+      - werkzeug < 3.0 # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
       # For stability, NeuroConv is pinned at a commit just prior to breaking SpikeInterface compatibility
       - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@fa636458aa5c321f1c2c08f6e682b4a52d5a83f3#neuroconv[dandi,compressors,ecephys,ophys,behavior,text]
       # For stability, pinning SpikeInterface to a version that works with NeuroConv and with tutorial generation
       - spikeinterface == 0.100.5
-      - scikit-learn == 1.4.0  # Tutorial data generation
-      - tqdm_publisher >= 0.0.1  # Progress bars
-      - tzlocal >= 5.2  # Frontend timezone handling
+      - scikit-learn == 1.4.0 # Tutorial data generation
+      - tqdm_publisher >= 0.0.1 # Progress bars
+      - tzlocal >= 5.2 # Frontend timezone handling
+      - ndx-pose == 0.1.1
+      - nwbinspector==0.6.1
+      - tables
diff --git a/environments/environment-MAC-apple-silicon.yml b/environments/environment-MAC-apple-silicon.yml
@@ -7,11 +7,11 @@ dependencies:
   - nodejs = 18.16.1
   # Install these from conda-forge so that dependent packages get included in the distributable
   - numcodecs = 0.11.0
-  - lxml = 4.9.3  # PyPI build fails due to x64/arm64 mismatch so install from conda-forge
-  - pyedflib = 0.1.32  # PyPI build fails due to x64/arm64 mismatch so install from conda-forge
-  - numpy  # May have x64/arm64 mismatch issues so install from conda-forge
+  - lxml = 4.9.3 # PyPI build fails due to x64/arm64 mismatch so install from conda-forge
+  - pyedflib = 0.1.32 # PyPI build fails due to x64/arm64 mismatch so install from conda-forge
+  - numpy # May have x64/arm64 mismatch issues so install from conda-forge
   - pytables = 3.8 # PyPI build fails on arm64 so install from conda-forge (used by neuroconv deps)
-  - jsonschema = 4.18.0  # Also installs jsonschema-specifications
+  - jsonschema = 4.18.0 # Also installs jsonschema-specifications
   - pip
   - pip:
       - setuptools==70.0.0
@@ -21,13 +21,15 @@ dependencies:
       - flask == 2.3.2
       - flask-cors == 4.0.0
       - flask_restx == 1.1.0
-      - werkzeug < 3.0  # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
+      - werkzeug < 3.0 # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
       # NOTE: the NeuroConv wheel on PyPI includes sonpy which is not compatible with arm64, so build and install
       # NeuroConv from GitHub, which will remove the sonpy dependency when building from Mac arm64
       # For stability, NeuroConv is pinned at a commit just prior to breaking SpikeInterface compatibility
       - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@fa636458aa5c321f1c2c08f6e682b4a52d5a83f3#neuroconv[dandi,compressors,ecephys,ophys,behavior,text]
       # For stability, pinning SpikeInterface to a version that works with NeuroConv and with tutorial generation
       - spikeinterface == 0.100.5
-      - scikit-learn == 1.4.0  # Tutorial data generation
-      - tqdm_publisher >= 0.0.1  # Progress bars
-      - tzlocal >= 5.2  # Frontend timezone handling
+      - scikit-learn == 1.4.0 # Tutorial data generation
+      - tqdm_publisher >= 0.0.1 # Progress bars
+      - tzlocal >= 5.2 # Frontend timezone handling
+      - ndx-pose == 0.1.1
+      - nwbinspector==0.6.1
diff --git a/environments/environment-MAC-intel.yml b/environments/environment-MAC-intel.yml
@@ -7,7 +7,7 @@ dependencies:
   - nodejs = 18.16.1
   - numcodecs = 0.11.0
   # install these from conda-forge so that dependent packages get included in the distributable
-  - jsonschema = 4.18.0  # installs jsonschema-specifications
+  - jsonschema = 4.18.0 # installs jsonschema-specifications
   - pip
   - pip:
       - setuptools==70.0.0
@@ -18,11 +18,14 @@ dependencies:
       - flask == 2.3.2
       - flask-cors == 4.0.0
       - flask_restx == 1.1.0
-      - werkzeug < 3.0  # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
+      - werkzeug < 3.0 # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
       # For stability, NeuroConv is pinned at a commit just prior to breaking SpikeInterface compatibility
       - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@fa636458aa5c321f1c2c08f6e682b4a52d5a83f3#neuroconv[dandi,compressors,ecephys,ophys,behavior,text]
       # For stability, pinning SpikeInterface to a version that works with NeuroConv and with tutorial generation
       - spikeinterface == 0.100.5
-      - scikit-learn == 1.4.0  # Tutorial data generation
-      - tqdm_publisher >= 0.0.1  # Progress bars
-      - tzlocal >= 5.2  # Frontend timezone handling
+      - scikit-learn == 1.4.0 # Tutorial data generation
+      - tqdm_publisher >= 0.0.1 # Progress bars
+      - tzlocal >= 5.2 # Frontend timezone handling
+      - ndx-pose == 0.1.1
+      - nwbinspector==0.6.1
+      - tables
diff --git a/environments/environment-Windows.yml b/environments/environment-Windows.yml
@@ -12,17 +12,20 @@ dependencies:
   - pip:
       - setuptools==70.0.0
       - PyInstaller==6.7.0
-      - pyinstaller-hooks-contrib == 2024.6  # Fix needed for pydantic v2; otherwise imports pydantic.compiled
+      - pyinstaller-hooks-contrib == 2024.6 # Fix needed for pydantic v2; otherwise imports pydantic.compiled
       - chardet == 5.1.0
       - configparser == 6.0.0
       - flask == 2.3.2
       - flask-cors === 3.0.10
       - flask_restx == 1.1.0
-      - werkzeug < 3.0  # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
+      - werkzeug < 3.0 # werkzeug 3.0 deprecates features used by flask 2.3.2. Remove this when updating flask.
       # For stability, NeuroConv is pinned at a commit just prior to breaking SpikeInterface compatibility
       - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@fa636458aa5c321f1c2c08f6e682b4a52d5a83f3#neuroconv[dandi,compressors,ecephys,ophys,behavior,text]
       # For stability, pinning SpikeInterface to a version that works with NeuroConv and with tutorial generation
       - spikeinterface == 0.100.5
-      - scikit-learn == 1.4.0  # Tutorial data generation
-      - tqdm_publisher >= 0.0.1  # Progress bars
-      - tzlocal >= 5.2  # Frontend timezone handling
+      - scikit-learn == 1.4.0 # Tutorial data generation
+      - tqdm_publisher >= 0.0.1 # Progress bars
+      - tzlocal >= 5.2 # Frontend timezone handling
+      - ndx-pose == 0.1.1
+      - nwbinspector==0.6.1
+      - tables
diff --git a/src/example_pipelines.yml b/src/example_pipelines.yml
@@ -26,80 +26,66 @@ SpikeGLX-Phy:
     PhySortingInterface:
       folder_path: ephy_testing_data/phy/phy_example_0
 
-
 SpikeGLX_v1_SingleProbe_AP:
   SpikeGLXRecordingInterface:
     file_path: ephy_testing_data/spikeglx/Noise4Sam_g0/Noise4Sam_g0_imec0/Noise4Sam_g0_t0.imec0.ap.bin
 
-
 SpikeGLXConverter-Phy:
   SpikeGLXConverterPipe:
     folder_path: ephy_testing_data/spikeglx/Noise4Sam_g0
   PhySortingInterface:
     folder_path: ephy_testing_data/phy/phy_example_0
 
-
 Suite2P_SinglePlane_SingleChannel:
   metadata:
     NWBFile:
       session_start_time: 2024-05-09T00:00
     Ophys:
       ImagingPlane:
-        -
-          excitation_lambda: NaN
+        - excitation_lambda: NaN
           optical_channel:
-            -
-              emission_lambda: NaN
+            - emission_lambda: NaN
 
   interfaces:
     Suite2pSegmentationInterface:
       folder_path: ophys_testing_data/segmentation_datasets/suite2p
 
-
 Caiman_SinglePlane_SingleChannel:
   metadata:
     NWBFile:
       session_start_time: 2024-05-09T00:00
     Ophys:
       ImagingPlane:
-        -
-          excitation_lambda: NaN
+        - excitation_lambda: NaN
           optical_channel:
-            -
-              emission_lambda: NaN
+            - emission_lambda: NaN
 
   interfaces:
     CaimanSegmentationInterface:
       file_path: ophys_testing_data/segmentation_datasets/caiman/caiman_analysis.hdf5
 
-
 ScanImage_SinglePlane_SingleChannel:
-
   metadata:
     Ophys:
       ImagingPlane:
-        -
-          excitation_lambda: NaN
+        - excitation_lambda: NaN
           optical_channel:
-            -
-              emission_lambda: NaN
+            - emission_lambda: NaN
 
   interfaces:
     ScanImageImagingInterface:
       file_path: ophys_testing_data/imaging_datasets/ScanImage/sample_scanimage_version_3_8.tiff
 
-
 TDT:
   metadata:
-      NWBFile:
-        session_start_time: 2024-05-09T00:00
+    NWBFile:
+      session_start_time: 2024-05-09T00:00
 
   interfaces:
     TdtRecordingInterface:
       folder_path: ephy_testing_data/tdt/aep_05
       gain: 1
 
-
 CellExplorer:
   metadata:
     NWBFile:
@@ -109,7 +95,6 @@ CellExplorer:
     CellExplorerRecordingInterface:
       folder_path: ephy_testing_data/cellexplorer/dataset_4/Peter_MS22_180629_110319_concat_stubbed
 
-
 CellExplorerUnits:
   metadata:
     NWBFile:
@@ -121,7 +106,6 @@ 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:
@@ -131,24 +115,19 @@ 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:
       session_start_time: 2024-05-09T00:00
     Ecephys:
       ElectrodeGroup:
-        -
-          location: Test location
-        -
-          location: Test location
-        -
-          location: Test location
+        - location: Test location
+        - location: Test location
+        - location: Test location
   interfaces:
     IntanRecordingInterface:
       file_path: ephy_testing_data/intan/intan_rhd_test_1.rhd
 
-
 MEArec:
   metadata:
     NWBFile:
@@ -158,32 +137,27 @@ MEArec:
     MEArecRecordingInterface:
       file_path: ephy_testing_data/mearec/mearec_test_10s.h5
 
-
 BrukerTiffMultiChannelSinglePlane:
   metadata:
     Ophys:
       ImagingPlane:
-        -
-          excitation_lambda: NaN
+        - excitation_lambda: NaN
           optical_channel:
-            -
-              emission_lambda: NaN
+            - emission_lambda: NaN
 
   interfaces:
     BrukerTiffSinglePlaneConverter:
       folder_path: ophys_testing_data/imaging_datasets/BrukerTif/NCCR32_2023_02_20_Into_the_void_t_series_baseline-000
 
-
 DeepLabCut:
   metadata:
     NWBFile:
       session_start_time: 2024-05-09T00:00
 
   interfaces:
     DeepLabCutInterface:
-      file_path: behavior_testing_data/DLC/m3v1mp4DLC_resnet50_openfieldAug20shuffle1_30000.h5
-      config_file_path: behavior_testing_data/DLC/config.yaml
-
+      file_path: behavior_testing_data/DLC/open_field_with_video/m3v1mp4DLC_resnet50_openfieldOct30shuffle1_1000.h5
+      config_file_path: behavior_testing_data/DLC/open_field_with_video/config.yaml
 
 SLEAP:
   metadata: