Setup Diataxis and fix side bar

.python-version

@@ -1 +1 @@
-3.11
+3.12

_brand.yml

@@ -5,6 +5,10 @@ color:
     brown: "#806040"
     gray: "#868b85"
 
-
-logo: 
-  medium: public/Bedrock.png
+# https://quarto.org/docs/authoring/brand.html#logo
+# When setting a logo here, the logo is added by default to both the navbar and sidebar
+# and there seems to be no option to turn off the logo in just the sidebar.
+# logo:
+#   small:
+#   medium: public/Bedrock.png
+#   large:

_quarto.yml

@@ -16,22 +16,31 @@ website:
     image: "public/Bedrock_TextRight.png"
     locale: en_US
   twitter-card: true
+  google-analytics:
+    tracking-id: "G-JH73EGWYL6"
+    anonymize-ip: true
   site-url: https://bedrock.engineer
   repo-url: https://github.com/bedrock-engineer/bedrock-web
   issue-url: https://github.com/bedrock-engineer/bedrock-ge/issues/new/choose
   repo-actions: [source, edit, issue]
+
+  # page-footer: 
+  #   right:
+  #     - icon: github
+  #       href: https://github.com/bedrock-gi/bedrock-gi
+  #     - icon: linkedin
+  #       href: https://www.linkedin.com/company/bedrock-gi/
+
   page-navigation: true
   bread-crumbs: true
   navbar:
     logo: "public/Bedrock.png"
     logo-alt: "Bedrock"
     left:
-      - text: "Documentation"
+      - text: "Docs"
         href: docs/index.qmd
       - text: "Articles"
         href: articles.qmd
-      - text: "API Reference"
-        href: reference/index.qmd
       # - text: "Community"
       #   href: community.qmd
       - text: "Help"
@@ -57,52 +66,101 @@ website:
       - icon: linkedin
         href: https://www.linkedin.com/company/bedrock-engineer
         text: Bedrock's LinkedIn
-  page-footer: 
-    right:
-      - icon: github
-        href: https://github.com/bedrock-engineer/bedrock-ge
-      - icon: linkedin
-        href: https://www.linkedin.com/company/bedrock-engineer
+
+  sidebar:
+    - id: docs
+      style: "floating"
+      contents:
+        - docs/index.qmd
+        - docs/getting-started.qmd
+        - docs/tutorials/index.qmd
+        - docs/how-to/index.qmd
+        - section: "Explanations"
+          href: docs/explanations/index.qmd
+          contents:
+            - docs/explanations/gi/index.qmd
+            - docs/explanations/gi/soil-classification.qmd
+        - section: "Reference"
+          href: docs/reference/index.qmd
+          contents:
+            - docs/reference/glossary/index.qmd
+            - section: "`bedrock-ge` API"
+              href: docs/reference/bedrock-ge-api/index.qmd
+              contents:
+                - contents:
+                  - docs/reference/bedrock-ge-api/gi.mapper.map_to_brgi_db.qmd
+                  - docs/reference/bedrock-ge-api/gi.db_operations.merge_dbs.qmd
+                  - docs/reference/bedrock-ge-api/gi.geospatial.create_brgi_geodb.qmd
+                  - docs/reference/bedrock-ge-api/gi.geospatial.create_location_geodf.qmd
+                  - docs/reference/bedrock-ge-api/gi.geospatial.create_lon_lat_height_geodf.qmd
+                  - docs/reference/bedrock-ge-api/gi.geospatial.interpolate_gi_geometry.qmd
+                  - docs/reference/bedrock-ge-api/gi.geospatial.interpolate_3d.qmd
+                  - docs/reference/bedrock-ge-api/gi.geospatial.substring_3d.qmd
+                  section: Map to Bedrock GI
+                - contents:
+                  - docs/reference/bedrock-ge-api/gi.write.write_brgi_db_to_file.qmd
+                  - docs/reference/bedrock-ge-api/gi.validate.check_foreign_key.qmd
+                  - docs/reference/bedrock-ge-api/gi.io_utils.geodf_to_df.qmd
+                  - docs/reference/bedrock-ge-api/gi.io_utils.brgi_db_to_dfs.qmd
+                  - docs/reference/bedrock-ge-api/gi.io_utils.open_text_data_source.qmd
+                  - docs/reference/bedrock-ge-api/gi.io_utils.detect_encoding.qmd
+                  - docs/reference/bedrock-ge-api/gi.io_utils.coerce_string.qmd
+                  section: IO
+                - contents:
+                  - docs/reference/bedrock-ge-api/gi.ags.ags_to_brgi_db_mapping.qmd
+                  - docs/reference/bedrock-ge-api/gi.ags4.ags4_to_dfs.qmd
+                  - docs/reference/bedrock-ge-api/gi.ags3.ags3_to_brgi_db_mapping.qmd
+                  - docs/reference/bedrock-ge-api/gi.ags3.ags3_to_dfs.qmd
+                  - docs/reference/bedrock-ge-api/gi.ags_schemas.check_ags_proj_group.qmd
+                  section: AGS
+            - docs/reference/bibliography/index.qmd
+
   search:
     type: textbox
     show-item-context: true
-  google-analytics:
-    tracking-id: "G-JH73EGWYL6"
-    anonymize-ip: true
-
-execute:
-  freeze: auto
 
 language: 
   search-box-placeholder: Search
 
-# options specified here will apply to all pages in this folder
-# https://quarto.org/docs/websites/website-navigation.html#side-navigation
-# Sidebar Navigation goes into _quarto.yml, not here in the _metadata.yml
-# quarto.org uses id's to identify sections
+quartodoc:
+  # the name used to import the package you want to create reference docs for
+  package: bedrock_ge
+  parser: google
+  dir: docs/reference/bedrock-ge-api
+  sidebar: _quartodoc-sidebar.yml
+
+  sections:
+    - title: Map to Bedrock GI
+      desc: Functions for mapping any type of GI data to the Bedrock GI geospatial database schema.
+      contents:
+        - gi.mapper.map_to_brgi_db
+        - gi.db_operations.merge_dbs
+        - gi.geospatial.create_brgi_geodb
+        - gi.geospatial.create_location_geodf
+        - gi.geospatial.create_lon_lat_height_geodf
+        - gi.geospatial.interpolate_gi_geometry
+        - gi.geospatial.interpolate_3d
+        - gi.geospatial.substring_3d
 
-# website:
-#   sidebar:
-#     style: "floating"
-#     contents:
-#       - text: "Documentation"
-#         href: index.qmd
-#       - section: "Getting Started"
-#         href: getting-started.qmd
-#         contents:
-#           - index.qmd
-#           - basics-knitr.qmd
-#           - basics-jupyter.qmd
-#       - section: "Layout"
-#         contents:
-#           - layout.qmd
-#           - layout-knitr.qmd
-#           - layout-jupyter.qmd
-#       - section: advanced.qmd
-#         contents:
-#           - raw-code.qmd
-#           - custom-theme.qmd
-#       - acknowlegment.qmd
+    - title: IO
+      desc: Validate Bedrock GI databases
+      contents: 
+        - gi.write.write_brgi_db_to_file
+        - gi.validate.check_foreign_key
+        - gi.io_utils.geodf_to_df
+        - gi.io_utils.brgi_db_to_dfs
+        - gi.io_utils.open_text_data_source
+        - gi.io_utils.detect_encoding
+        - gi.io_utils.coerce_string
+
+    - title: AGS
+      desc: Functions for creating Bedrock GI mapping objects from AGS files.
+      contents:
+        - gi.ags.ags_to_brgi_db_mapping
+        - gi.ags4.ags4_to_dfs
+        - gi.ags3.ags3_to_brgi_db_mapping
+        - gi.ags3.ags3_to_dfs
+        - gi.ags_schemas.check_ags_proj_group
 
 format:
   html:
@@ -119,48 +177,5 @@ format:
     include-in-header:
       - text: <link rel="icon" href="./public/Bedrock.svg" type="image/svg+xml">
 
-quartodoc:
-  # the name used to import the package you want to create reference docs for
-  package: bedrock_ge
-  parser: google
-
-  # write sidebar data to this file
-  sidebar: _sidebar.yml
-
-  sections:
-    - title: AGS
-      desc: Read, transform & validate AGS Files
-      contents:
-        - gi.ags.read.ags_to_dfs
-        - gi.ags.read.ags3_to_dfs
-        - gi.ags.read.ags4_to_dfs
-        - gi.ags.transform.ags3_db_to_no_gis_brgi_db
-        - gi.ags.transform.ags_proj_to_brgi_project
-        - gi.ags.validate.check_ags_proj_group
-
-    - title: Validate
-      desc: Validate Bedrock GI databases
-      contents: 
-        - gi.validate.check_brgi_database
-        - gi.validate.check_no_gis_brgi_database
-        - gi.validate.check_foreign_key
-
-    - title: Write
-      desc: Write Bedrock GI databases to different file formats
-      contents: 
-        - gi.write.write_gi_db_to_gpkg
-        - gi.write.write_gi_db_to_excel
-        - gi.write.sanitize_table_name
-
-    - title: Concatenate
-      contents: 
-        - gi.concatenate.concatenate_databases
-
-    - title: GIS Geometry
-      desc: Calculate GIS Geometry for Bedrock GI databases and GI locations
-      contents: 
-        - gi.gis_geometry.calculate_gis_geometry
-        - gi.gis_geometry.calculate_location_gis_geometry
-        - gi.gis_geometry.calculate_wgs84_coordinates
-        - gi.gis_geometry.create_lon_lat_height_table
-        - gi.gis_geometry.calculate_in_situ_gis_geometry
+execute:
+  freeze: auto