updating doc nav

Author: carsen-stringer

.readthedocs.yaml

@@ -10,6 +10,6 @@ build:
       - pip install mkdocs-material
       - pip install mkdocstrings
       - pip install mkdocstrings-python
-
+      
 mkdocs:
   configuration: mkdocs.yml

docs/index.md

@@ -24,102 +24,3 @@ paper](http://www.jneurosci.org/content/early/2018/08/06/JNEUROSCI.3339-17.2018)
 
 We make pip installable releases of suite2p, here is the [pypi](https://pypi.org/project/suite2p/). You
 can install it as `pip install suite2p`
-
-# Basics:
-
-* [Installation](installation.md)
-  * [Dependencies](installation.md#dependencies)
-* [Inputs](inputs.md)
-  * [Input format](inputs.md#input-format)
-    * [Directory structure](inputs.md#directory-structure)
-    * [Frame ordering](inputs.md#frame-ordering)
-    * [Recordings with photostim / other artifacts](inputs.md#recordings-with-photostim-other-artifacts)
-  * [Different file types](inputs.md#different-file-types)
-    * [Tiffs](inputs.md#tiffs)
-    * [Bruker](inputs.md#bruker)
-    * [Mesoscope tiffs](inputs.md#mesoscope-tiffs)
-    * [HDF5 files (and \*.sbx)](inputs.md#hdf5-files-and-sbx)
-    * [sbx binary files](inputs.md#sbx-binary-files)
-    * [Nikon nd2 files](inputs.md#nikon-nd2-files)
-  * [BinaryFile](inputs.md#binaryfile)
-* [Parameters](parameters.md)
-  * [db.npy](parameters.md#dbnpy)
-  * [general settings](parameters.md#general-settings)
-  * [run](parameters.md#run)
-  * [io](parameters.md#io)
-  * [registration](parameters.md#registration)
-  * [detection](parameters.md#detection)
-  * [classification](parameters.md#classification)
-  * [extraction](parameters.md#extraction)
-  * [dcnv preprocess](parameters.md#dcnv-preprocess)
-* [Using the GUI](gui.md)
-  * [Different views and colors for ROI panels](gui.md#different-views-and-colors-for-roi-panels)
-    * [Views](gui.md#views)
-    * [Colors](gui.md#colors)
-    * [Correlations](gui.md#correlations)
-    * [Correlations with 1D var](gui.md#correlations-with-1d-var)
-    * [Rastermap / custom](gui.md#rastermap-custom)
-  * [Buttons / shortcuts for cell selection](gui.md#buttons-shortcuts-for-cell-selection)
-    * [Mouse control](gui.md#mouse-control)
-    * [Keyboard shortcuts](gui.md#keyboard-shortcuts)
-    * [Multi-cell selection](gui.md#multi-cell-selection)
-  * [Trace view (bottom row)](gui.md#trace-view-bottom-row)
-  * [Classifying cells](gui.md#classifying-cells)
-    * [Adding data to a classifier](gui.md#adding-data-to-a-classifier)
-    * [Building your own classifier](gui.md#building-your-own-classifier)
-    * [Applying a custom classifier](gui.md#applying-a-custom-classifier)
-  * [Visualizing activity](gui.md#visualizing-activity)
-  * [Manual adding of ROIs](gui.md#manual-adding-of-rois)
-  * [Merging ROIs](gui.md#merging-rois)
-  * [View registered binary](gui.md#view-registered-binary)
-    * [Z-stack Alignment](gui.md#z-stack-alignment)
-  * [View registration metrics](gui.md#view-registration-metrics)
-* [Outputs](outputs.md)
-  * [Main output files](outputs.md#main-output-files)
-  * [MATLAB output](outputs.md#matlab-output)
-  * [NWB Output](outputs.md#nwb-output)
-  * [Multichannel recordings](outputs.md#multichannel-recordings)
-  * [stat.npy fields](outputs.md#statnpy-fields)
-  * [reg_outputs.npy fields](outputs.md#reg_outputsnpy-fields)
-  * [detect_outputs.npy fields](outputs.md#detect_outputsnpy-fields)
-* [Multiday recordings](multiday.md)
-* [Developer Documentation](developer_doc.md)
-  * [Testing](developer_doc.md#testing)
-* [Frequently Asked Questions](FAQ.md)
-  * [Cropped field-of-view](FAQ.md#cropped-field-of-view)
-  * [Deconvolution means what?](FAQ.md#deconvolution-means-what)
-  * [Multiple functional channels](FAQ.md#multiple-functional-channels)
-  * [Z-drift](FAQ.md#z-drift)
-  * [No signals in manually selected ROIs](FAQ.md#no-signals-in-manually-selected-rois)
-
-# How it works:
-
-* [Registration](registration.md)
-  * [Bidirectional phase offset](registration.md#bidirectional-phase-offset-optional)
-  * [Reference image computation](registration.md#reference-image-computation)
-  * [Rigid registration](registration.md#rigid-registration)
-  * [Non-rigid registration](registration.md#non-rigid-registration)
-  * [Valid region estimation](registration.md#valid-region-estimation)
-  * [Two-step registration](registration.md#two-step-registration-optional)
-  * [Registration metrics](registration.md#registration-metrics)
-  * [Key parameters](registration.md#key-parameters-registration)
-* [ROI Detection](roidetection.md)
-  * [Preprocessing](roidetection.md#preprocessing)
-  * [Sparsery (default)](roidetection.md#sparsery-default)
-  * [Sourcery](roidetection.md#sourcery)
-  * [Cellpose](roidetection.md#cellpose)
-  * [Post-detection filtering](roidetection.md#post-detection-filtering)
-* [Signal Extraction](roiextraction.md)
-  * [Cell masks](roiextraction.md#cell-masks)
-  * [Neuropil masks](roiextraction.md#neuropil-masks)
-  * [Trace extraction](roiextraction.md#trace-extraction)
-  * [Neuropil correction and deconvolution](roiextraction.md#neuropil-correction-and-deconvolution)
-  * [SNR-based ROI filtering](roiextraction.md#snr-based-roi-filtering)
-  * [Key parameters](roiextraction.md#key-parameters-extraction)
-* [Spike deconvolution](deconvolution.md)
-* [ROI Classification](classification.md)
-  * [Features](classification.md#features)
-  * [How the classifier works](classification.md#how-the-classifier-works)
-  * [Classifier files](classification.md#classifier-files)
-  * [Pre-classification](classification.md#pre-classification-preclassify)
-  * [Key parameters](classification.md#key-parameters-classification)

mkdocs.yml

@@ -5,6 +5,8 @@ theme:
   favicon: _static/favicon.ico
   palette:
     primary: green
+  features:
+    - navigation.expand
 
 nav:
   - Home: index.md
@@ -30,7 +32,7 @@ nav:
       - Extraction: api/extraction.md
       - Classification: api/classification.md
       - GUI: api/gui.md
-
+  
 #hooks:
 #  - generate_settings_docs.py # Necessary for parameters.md generation
 
@@ -52,7 +54,6 @@ extra_css:
 
 markdown_extensions:
   - admonition
-  - toc
   - pymdownx.superfences
   - pymdownx.highlight
   - pymdownx.emoji
@@ -61,3 +62,8 @@ markdown_extensions:
   - pymdownx.snippets
   - pymdownx.inlinehilite
   - pymdownx.extra
+  - toc:
+      permalink: "#"
+      permalink_title: Anchor link to this section for reference
+
+