Update 'latest' in docs deploy

.github/workflows/publish-docs.yml

@@ -21,6 +21,12 @@ jobs:
       contents: write
       issues: write
     steps:
+      - name: Get version
+        uses: actions/checkout@v3
+        run: |
+          echo "MAJOR_VERSION=${GITHUB_REF#refs/*/}" | cut -c1-3 >> $GITHUB_ENV
+          echo ${{ env.MAJOR_VERSION }}
+
       - name: Checkout repository
         uses: actions/checkout@v3
         with:

docs/build-docs.sh

@@ -1,8 +1,7 @@
 #!/bin/bash
 # Run this script from repo root to serve site: > bash ./docs/build-docs.sh serve
 # Then, navigate to localhost:8000/ to inspect site, then ctrl+c to exit
-# For auto-reload during dev, use `mkdocs serve -f ./docs/mkdosc.yaml`
-
+# For auto-reload during dev, use `mkdocs serve -f ./docs/mkdocs.yaml`
 
 # Copy top-level repo files for docs display
 cp ./CHANGELOG.md ./docs/src/
@@ -14,26 +13,29 @@ mv ./docs/src/notebooks/README.md ./docs/src/notebooks/index.md
 cp -r ./notebook-images ./docs/src/notebooks/
 cp -r ./notebook-images ./docs/src/
 
-# Get major version
-version_line=$(grep "__version__ =" ./src/spyglass/_version.py)
-version_string=$(echo "$version_line" | awk -F"[\"']" '{print $2}')
-export MAJOR_VERSION="${version_string:0:3}"
-echo "$MAJOR_VERSION"
+if [ -z "$MAJOR_VERSION" ]; then # Get version from file
+  version_line=$(grep "__version__ =" ./src/spyglass/_version.py)
+  version_string=$(echo "$version_line" | awk -F"[\"']" '{print $2}')
+  export MAJOR_VERSION="${version_string:0:3}"
+fi
+echo "$MAJOR_VERSION" # May be available as env var
 
 # Get ahead of errors
 export JUPYTER_PLATFORM_DIRS=1
-# jupyter notebook --generate-config
+jupyter notebook --generate-config -y &> /dev/null
+jupyter trust ./docs/src/notebooks/*.ipynb &> /dev/null
 
 # Generate site docs
-mike deploy "$MAJOR_VERSION" --config ./docs/mkdocs.yml -b documentation
+mike deploy "$MAJOR_VERSION" --config ./docs/mkdocs.yml -b documentation \
+  2>&1 | grep -v 'kernel_spec' # Suppress kernel_spec errors
 
 # Label this version as latest, set as default
-mike alias "$MAJOR_VERSION" latest --config ./docs/mkdocs.yml -b documentation
-mike set-default latest --config ./docs/mkdocs.yml -b documentation
+mike alias "$MAJOR_VERSION" latest -u --config ./docs/mkdocs.yml -b documentation
+# mike set-default latest --config ./docs/mkdocs.yml -b documentation
 
 # # Serve site to localhost
 if [ "$1" == "serve" ]; then # If first arg is serve, serve docs
-  mike serve --config ./docs/mkdocs.yml -b documentation
+  mike serve --config ./docs/mkdocs.yml -b documentation | grep -v 'kernel_spec'
 elif [ "$1" == "push" ]; then # if first arg is push
     if [ -z "$2" ]; then # When no second arg, use local git user
         git_user=$(git config user.name)

docs/mkdocs.yml

@@ -61,7 +61,7 @@ nav:
       - Spikes:
           - Spike Sorting V0: notebooks/10_Spike_SortingV0.ipynb
           - Spike Sorting V1: notebooks/10_Spike_SortingV1.ipynb
-          - Curation: notebooks/11_Curation.ipynb
+          - Curation: notebooks/11_CurationV0.ipynb
       - Position:
           - Position Trodes: notebooks/20_Position_Trodes.ipynb
           - DLC Models: notebooks/21_DLC.ipynb
@@ -75,6 +75,7 @@ nav:
           - Extract Clusterless: notebooks/41_Extracting_Clusterless_Waveform_Features.ipynb
           - Decoding Clusterless: notebooks/42_Decoding_Clusterless.ipynb
           - Decoding Sorted Spikes: notebooks/43_Decoding_SortedSpikes.ipynb
+          - MUA Detection: notebooks/51_MUA_Detection.ipynb
   - API Reference: api/ # defer to gen-files + literate-nav
   - How to Contribute: contribute.md
   - Change Log: CHANGELOG.md

notebooks/04_PopulateConfigFile.ipynb

@@ -2,6 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
+   "id": "68303e8a",
    "metadata": {},
    "source": [
     "# Customizing Data Insertion into Spyglass\n",
@@ -44,6 +45,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "bcc87f67",
    "metadata": {},
    "source": [
     "## Define a Configuration YAML File\n",
@@ -85,6 +87,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "fc6d0986",
    "metadata": {},
    "source": [
     "## Create Entries to Reference in the Configuration YAML\n",
@@ -145,6 +148,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "9d641e00",
    "metadata": {},
    "source": [
     "## Example Ingestion with Real Data\n",
@@ -171,6 +175,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "37aa5182",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -180,6 +185,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "aab5b47a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -195,6 +201,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "d132e797",
    "metadata": {},
    "source": [
     "Then call `insert_sessions` as usual."
@@ -203,6 +210,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "bed5c6e1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -213,6 +221,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "d875b158",
    "metadata": {},
    "source": [
     "Confirm the session was inserted with the correct `DataAcquisitionDevice`"
@@ -221,6 +230,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "8411cb43",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -234,6 +244,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "d85b1416",
    "metadata": {},
    "source": []
   }

src/spyglass/utils/dj_chains.py

@@ -221,7 +221,7 @@ def objects(self) -> List[dj.FreeTable]:
         )
 
     def join(
-        self, restricton: str = None, reverse_order: bool = False
+        self, restriction: str = None, reverse_order: bool = False
     ) -> dj.expression.QueryExpression:
         """Return join of tables in chain with restriction applied to parent.
 
@@ -237,7 +237,7 @@ def join(
             return None
 
         objects = self.objects[::-1] if reverse_order else self.objects
-        restriction = restricton or self.parent.restriction or True
+        restriction = restriction or self.parent.restriction or True
         join = objects[0] & restriction
         for table in objects[1:]:
             try:

src/spyglass/utils/dj_mixin.py

@@ -30,7 +30,7 @@ class SpyglassMixin:
         a NWBFile table (including AnalysisNwbfile) or a _nwb_table attribute to
         determine which table to use.
     delte_downstream_merge(restriction=None, dry_run=True, reload_cache=False)
-        Delete downstream merge table entries associated with restricton.
+        Delete downstream merge table entries associated with restriction.
         Requires caching of merge tables and links, which is slow on first call.
         `restriction` can be set to a string to restrict the delete. `dry_run`
         can be set to False to commit the delete. `reload_cache` can be set to
@@ -178,7 +178,7 @@ def delete_downstream_merge(
         return_parts: bool = True,
         **kwargs,
     ) -> Union[List[QueryExpression], Dict[str, List[QueryExpression]]]:
-        """Delete downstream merge table entries associated with restricton.
+        """Delete downstream merge table entries associated with restriction.
 
         Requires caching of merge tables and links, which is slow on first call.