Docs types fixes (LorenFrankLab#1402)

* Docstring type fixes

* Update jupytext scripts

* Update changelog

Author: CBroz1

CHANGELOG.md

@@ -15,6 +15,7 @@ import all foreign key references.
 
 - Delete extra pyscripts that were renamed # 1363
 - Add note on fetching changes to setup notebook #1371
+- Revise table field docstring heading and `mermaid` diagram generation #1402
 
 ### Infrastructure
 

docs/mkdocs.yml

@@ -55,7 +55,7 @@ nav:
           - Spike Sorting V0: notebooks/10_Spike_SortingV0.ipynb
           - Spike Sorting V1: notebooks/10_Spike_SortingV1.ipynb
           - Spike Sorting Analysis: notebooks/11_Spike_Sorting_Analysis.ipynb
-          - Spike Burst Merge: notebooks/12_Spike_Burst.ipynb
+          - Spike Burst Merge: notebooks/12_Burst_Merge_Curation.ipynb
       - Position:
           - Position Trodes: notebooks/20_Position_Trodes.ipynb
           - DLC Models: notebooks/21_DLC.ipynb
@@ -70,6 +70,7 @@ nav:
           - Decoding Clusterless: notebooks/41_Decoding_Clusterless.ipynb
           - Decoding Sorted Spikes: notebooks/42_Decoding_SortedSpikes.ipynb
       - MUA Detection: notebooks/50_MUA_Detection.ipynb
+      - Behavior Syllables: notebooks/60_MoSeq.ipynb
   - Features:
     - Overview: Features/index.md
     - FigURL: Features/FigURL.md
@@ -95,7 +96,8 @@ extra_css:
 
 plugins:
   - search
-  - mermaid2 # for graphs
+  - mermaid2: # for graphs
+      version: 10.0.2
   - exclude:
       glob:
         - "temp*"
@@ -140,7 +142,11 @@ markdown_extensions:
       pygments_lang_class: true
   - pymdownx.inlinehilite
   - pymdownx.snippets
-  - pymdownx.superfences
+  - pymdownx.superfences:
+      custom_fences:
+        - name: mermaid
+          class: mermaid
+          format: !!python/name:mermaid2.fence_mermaid_custom
   - pymdownx.tabbed:
       alternate_style: true
 

notebooks/README.md

@@ -80,7 +80,7 @@ Spyglass directory
 
 ```bash
 pip install jupytext
-jupytext --to py notebooks/*ipynb
+jupytext --to py:light notebooks/*ipynb
 mv notebooks/*py notebooks/py_scripts
 black .
 ```

notebooks/py_scripts/00_Setup.py

@@ -5,7 +5,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.14.5
+#       jupytext_version: 1.17.0
 #   kernelspec:
 #     display_name: spyglass
 #     language: python

notebooks/py_scripts/01_Concepts.py

@@ -5,7 +5,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.16.7
+#       jupytext_version: 1.17.0
 #   kernelspec:
 #     display_name: spy
 #     language: python

notebooks/py_scripts/02_Insert_Data.py

@@ -5,7 +5,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.16.7
+#       jupytext_version: 1.17.0
 #   kernelspec:
 #     display_name: spy
 #     language: python

notebooks/py_scripts/03_Data_Sync.py

@@ -5,7 +5,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.16.7
+#       jupytext_version: 1.17.0
 #   kernelspec:
 #     display_name: spyglass
 #     language: python

notebooks/py_scripts/04_Merge_Tables.py

@@ -5,7 +5,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.16.7
+#       jupytext_version: 1.17.0
 #   kernelspec:
 #     display_name: spy
 #     language: python

notebooks/py_scripts/05_Export.py

@@ -5,7 +5,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.16.7
+#       jupytext_version: 1.17.0
 #   kernelspec:
 #     display_name: spy
 #     language: python

notebooks/py_scripts/10_Spike_SortingV0.py

@@ -5,7 +5,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.16.7
+#       jupytext_version: 1.17.0
 #   kernelspec:
 #     display_name: Python 3.10.5 64-bit
 #     language: python