Merge branch 'main' into linux-dev

docs/_static/switcher.json

@@ -4,11 +4,17 @@
         "url": "https://nwb-guide.readthedocs.io/en/latest/",
         "preferred": false
     },
+    {
+        "name": "1.0.1",
+        "version": "v1.0.1",
+        "url": "https://nwb-guide.readthedocs.io/en/v1.0.1/",
+        "preferred": true
+    },
     {
         "name": "1.0.0",
         "version": "v1.0.0",
         "url": "https://nwb-guide.readthedocs.io/en/v1.0.0/",
-        "preferred": true
+        "preferred": false
     },
     {
         "name": "0.0.15",

docs/conf.py

@@ -135,6 +135,15 @@
     "doc_path": "docs",
 }
 
+# Workaround for removing the left sidebar on pages without TOC
+# A better solution would be to follow the merge of:
+# https://github.com/pydata/pydata-sphinx-theme/pull/1682
+html_sidebars = {
+    "installation": [],
+    "format_support": [],
+    "developer_guide": [],
+}
+
 
 def _correct_signatures(app, what, name, obj, options, signature, return_annotation):
     if what == "class":

docs/index.rst

@@ -10,12 +10,19 @@ NWB GUIDE documentation
 
 |
 
-The **NWB Graphical User Interface for Data Entry (GUIDE)** is an Electron-based application designed to help you navigate
-the complex process of converting data from common proprietary formats into the :nwb-overview:`Neurodata Without Borders (NWB) <>` standard.
+The **NWB Graphical User Interface for Data Entry (GUIDE)** is a cross-platform desktop application that walks neuroscientists
+through the requirements of converting their data from common proprietary formats to the :nwb-overview:`Neurodata Without Borders (NWB) <>` standard
+and uploading data to the :dandi-archive:`DANDI Archive <>`.
 
-The resulting files are fully compliant with the best practices expected by the :dandi-archive:`Distributed Archives for Neurophysiology Data Integration (DANDI) <>`.
+.. note::
+  Watch a tutorial video of NWB GUIDE `here <https://www.youtube.com/watch?v=EhhdDVuHAZ0>`_.
+
+Get started with NWB GUIDE by :doc:`installing it </installation>` on your computer and following the :doc:`tutorials </tutorials/index>` in this documentation.
+
+.. The TOC below is hidden from the main page contents but needed to generate the top menu
 
 .. toctree::
+   :hidden:
    :maxdepth: 2
 
    installation

docs/installation.rst

@@ -17,7 +17,7 @@ Download and run `NWB-GUIDE-x64.dmg <https://github.com/NeurodataWithoutBorders/
 MacOS - Apple Silicon
 ---------------------
 
-This installation applies to [current-generation Apple computers (M1-M4+)](https://support.apple.com/en-us/116943).
+This installation applies to `current-generation Apple computers (M1-M4+) <https://support.apple.com/en-us/116943>`_.
 
 Download and run `NWB-GUIDE-arm64.dmg <https://github.com/NeurodataWithoutBorders/nwb-guide/releases/latest/download/NWB-GUIDE-arm64.dmg>`_. This will prompt you to move the app into your 'Applications' folder. Then open the 'NWB GUIDE' app from your 'Applications' folder.
 

docs/tutorials/index.rst

@@ -5,6 +5,9 @@ to the Neurodata Without Borders (NWB) format and uploading to the DANDI Archive
 
 In these tutorials, you'll follow along on a :doc:`local installation of the GUIDE </installation>` as we detail the conversion process from initial setup to final upload.
 
+.. note::
+    Watch a video walkthrough of these tutorials `here <https://www.youtube.com/watch?v=EhhdDVuHAZ0>`_.
+
 .. note::
     This tutorial focuses on uploading to the DANDI Development server.
 
@@ -21,7 +24,10 @@ In these tutorials, you'll follow along on a :doc:`local installation of the GUI
 Before you begin these tutorials, **you'll need to generate the tutorial dataset** using the instructions on the Dataset page.
 
 
+.. toctree::
+   :hidden:
 
+   self
 
 .. toctree::
    :maxdepth: 2

nwb-guide.spec

@@ -19,36 +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('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
 

src/electron/frontend/core/components/JSONSchemaForm.js

@@ -599,7 +599,7 @@ export class JSONSchemaForm extends LitElement {
         if (resolvedErrors.length) {
             const len = resolvedErrors.length;
             if (len === 1) this.throw(resolvedErrors[0].message);
-            else this.throw(`${len} JSON Schema errors detected.`);
+            else this.throw(`${len} errors detected: ${resolvedErrors.map((e) => e.message).join(" ")}`);
         }
 
         const allErrors = flaggedInputs

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:
@@ -168,3 +183,14 @@ DeepLabCut:
     DeepLabCutInterface:
       file_path: behavior_testing_data/DLC/m3v1mp4DLC_resnet50_openfieldAug20shuffle1_30000.h5
       config_file_path: behavior_testing_data/DLC/config.yaml
+
+
+SLEAP:
+  metadata:
+    NWBFile:
+      session_start_time: 2024-05-09T00:00
+
+  interfaces:
+    SLEAPInterface:
+      file_path: behavior_testing_data/sleap/predictions_1.2.7_provenance_and_tracking.slp
+      video_file_path: behavior_testing_data/sleap/melanogaster_courtship.mp4