upgrade tdt 1.0.7

.github/workflows/publish-docs.yml

@@ -0,0 +1,34 @@
+name: Publish mkdocs documentation
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+    paths:
+      - 'docs/**'
+
+permissions:
+  contents: write
+
+jobs:
+  build-and-publish:
+    name: Publish mkdocs documentation
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout main
+        uses: actions/checkout@v3
+
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+            python-version: 3.x
+
+      - run: pip install mkdocs-material mkdocs-include-dir-to-nav mkdocs-nav-weight==0.2.0
+
+      - run: mkdocs gh-deploy --force

.gitignore

@@ -1,6 +1,4 @@
 build/
 .DS_Store
 purl/mytoken.txt
-*.pid
-# Generated by nanobot
-build/nanobot.db*
+*.pid

mkdocs.yml

@@ -0,0 +1,44 @@
+site_name: Human Brain Cell Atlas v1.0 (Neurons)
+repo_url: https://github.com/brain-bican/human-brain-cell-atlas_v1_neurons
+repo_name: brain-bican/human-brain-cell-atlas_v1_neurons
+docs_dir: docs
+
+nav:
+  - Taxonomy: index.md
+  - Cell Sets: cell_sets
+
+theme:
+  name: material
+  features:
+    - navigation.instant
+    - navigation.tabs
+    - navigation.tabs.sticky
+    - navigation.top
+    - navigation.tracking
+    - search.highlight
+    - search.share
+    - search.suggest
+    - toc.follow
+  palette:
+    # Palette toggle for light mode
+    - scheme: default
+      toggle:
+        icon: material/brightness-7
+        name: Switch to dark mode
+    # Palette toggle for dark mode
+    - scheme: slate
+      toggle:
+        icon: material/brightness-4
+        name: Switch to light mode
+  favicon: assets/logo.webp
+  logo: assets/logo.webp
+
+plugins:
+  - search
+  - include_dir_to_nav
+  - mkdocs-nav-weight:
+      section_renamed: false
+      index_weight: -10
+      warning: true
+      reverse: false
+      headless_included: true

src/schema/column.tsv

@@ -84,4 +84,4 @@ review	reviewer	reviewer	empty	text
 review	review	review	empty	text		
 review	explanation	explanation	empty	text		
 flags	accession_id	accession_id		text	primary	
-flags	flag	flag	empty	text		
+flags	flag	flag	empty	text		

src/schema/datatype.tsv

@@ -1,7 +1,7 @@
 datatype	parent	transform	condition	structure	description	SQL type	HTML type
 CURIE	nonspace		match(/\w+:\w+/)		a Compact URI		
 IRI	nonspace		exclude(/\s/)		an Internationalized Resource Identifier		
-OBI_ID	CURIE		match(/OBI:\S+/)	concat(prefix, ":", suffix)	an OBI ID		
+OBI_ID	CURIE		match(/OBI:\S+/)	"concat(prefix, "":"", suffix)"	an OBI ID		
 boolean	word	lowercase	in('true', 'false')		a boolean: true or false		radio
 class_type	word		in('equivalent', 'subclass')		an OWL class type: equivalent or subclass		search
 column_name	trimmed_line				a column name		
@@ -48,4 +48,4 @@ html_type	word		in('input', 'textarea', 'search', 'radio', 'number', 'select')
 trimmed_line	line		match(/\S([^\n]*\S)*/)				
 cell_type	word		in('gross', 'family', 'leaf_node', 'None')		a cell type		search
 autocomplete_cl	line		exclude(/^\s+|\s+$/)		a cell type		
-autocomplete_uberon	line		exclude(/^\s+|\s+$/)		a cell type		
+autocomplete_uberon	line		exclude(/^\s+|\s+$/)		a cell type		

src/schema/table.tsv

@@ -7,4 +7,4 @@ labelset	curation_tables/labelset.tsv
 metadata	curation_tables/metadata.tsv			
 annotation_transfer	curation_tables/annotation_transfer.tsv			
 review	curation_tables/review.tsv			
-flags	curation_tables/flags.tsv			
+flags	curation_tables/flags.tsv