fix table of content nesting (#269)

segment large API calling module to allow correct nesting move navigation fully to the left (integrated)
biocypher · Feb 11, 2025 · 704ae5a · 704ae5a
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diff --git a/docs/api-docs/api-calling-base.md b/docs/api-docs/api-calling-base.md
@@ -0,0 +1,12 @@
+# API Calling: Base Classes
+
+We provide base classes for the API Agent implementation to align individual
+modules.
+
+## Abstract base classes
+
+::: biochatter.api_agent.base.agent_abc
+
+## The API Agent
+
+::: biochatter.api_agent.base.api_agent
diff --git a/docs/api-docs/api-calling-python.md b/docs/api-docs/api-calling-python.md
@@ -0,0 +1,41 @@
+# API Calling: Python APIs
+
+API calling for large Python APIs is currently experimental. In particular, we
+observe a decrease in stability with increasing number of total parameters
+offered to the LLM. Due to this limitation, we recommend benchmarking the
+stability of the calls using our benchmarking framework. If you're interested in
+the performance of a specific API / LLM combination, don't hesitate to get in
+touch.
+
+## Generic Python API ingestion
+
+Using Pydantic parsing, we autogenerate API descriptions for tool bindings.
+While this allows better scaling (given suitable structure of the ingested code,
+particularly with respect to the docstrings), it offers less control than the
+manual implementation of API descriptions. For instance, it is much harder to
+reduce the set of parameters to the essentials.
+
+::: biochatter.api_agent.python.generic_agent
+
+::: biochatter.api_agent.python.autogenerate_model
+
+## Scanpy modules
+
+We manually define the API descriptions for select Scanpy modules.
+
+::: biochatter.api_agent.python.anndata_agent
+
+::: biochatter.api_agent.python.scanpy_pl_full
+
+::: biochatter.api_agent.python.scanpy_pp_full
+
+::: biochatter.api_agent.python.scanpy_pl_reduced
+
+::: biochatter.api_agent.python.scanpy_pp_reduced
+
+# API Calling: Utility functions
+
+## Formatters to parse the calls
+
+::: biochatter.api_agent.base.formatters
+
diff --git a/docs/api-docs/api-calling-web.md b/docs/api-docs/api-calling-web.md
@@ -0,0 +1,13 @@
+# API Calling: Web APIs
+
+## BLAST
+
+::: biochatter.api_agent.web.blast
+
+## OncoKB
+
+::: biochatter.api_agent.web.oncokb
+
+## bio.tools
+
+::: biochatter.api_agent.web.bio_tools
diff --git a/docs/api-docs/api-calling.md b/docs/api-docs/api-calling.md
diff --git a/docs/images/boxplot-medical-exam-domain.png b/docs/images/boxplot-medical-exam-domain.png
diff --git a/docs/images/boxplot-medical-exam-language-domain.png b/docs/images/boxplot-medical-exam-language-domain.png
diff --git a/docs/images/boxplot-medical-exam-language.png b/docs/images/boxplot-medical-exam-language.png
diff --git a/docs/images/boxplot-medical-exam-task.png b/docs/images/boxplot-medical-exam-task.png
diff --git a/docs/images/boxplot-naive-vs-biochatter.pdf b/docs/images/boxplot-naive-vs-biochatter.pdf
diff --git a/docs/images/boxplot-naive-vs-biochatter.png b/docs/images/boxplot-naive-vs-biochatter.png
diff --git a/docs/images/boxplot-per-quantisation.png b/docs/images/boxplot-per-quantisation.png
diff --git a/docs/images/boxplot-tasks.png b/docs/images/boxplot-tasks.png
diff --git a/docs/images/boxplot-text2cypher.png b/docs/images/boxplot-text2cypher.png
diff --git a/docs/images/dotplot-per-task.pdf b/docs/images/dotplot-per-task.pdf
diff --git a/docs/images/dotplot-per-task.png b/docs/images/dotplot-per-task.png
diff --git a/docs/images/histogram-image-caption-confidence.png b/docs/images/histogram-image-caption-confidence.png
diff --git a/docs/images/scatter-naive-vs-biochatter.pdf b/docs/images/scatter-naive-vs-biochatter.pdf
diff --git a/docs/images/scatter-naive-vs-biochatter.png b/docs/images/scatter-naive-vs-biochatter.png
diff --git a/docs/images/scatter-per-quantisation-name.pdf b/docs/images/scatter-per-quantisation-name.pdf
diff --git a/docs/images/scatter-per-quantisation-name.png b/docs/images/scatter-per-quantisation-name.png
diff --git a/docs/images/scatter-quantisation-accuracy.pdf b/docs/images/scatter-quantisation-accuracy.pdf
diff --git a/docs/images/scatter-quantisation-accuracy.png b/docs/images/scatter-quantisation-accuracy.png
diff --git a/docs/images/scatter-size-accuracy.pdf b/docs/images/scatter-size-accuracy.pdf
diff --git a/docs/images/scatter-size-accuracy.png b/docs/images/scatter-size-accuracy.png
diff --git a/docs/images/stripplot-extraction-tasks.png b/docs/images/stripplot-extraction-tasks.png
diff --git a/docs/images/stripplot-per-model.png b/docs/images/stripplot-per-model.png
diff --git a/docs/images/stripplot-rag-tasks.pdf b/docs/images/stripplot-rag-tasks.pdf
diff --git a/docs/images/stripplot-rag-tasks.png b/docs/images/stripplot-rag-tasks.png
diff --git a/docs/images/stripplot-text2cypher-safety.png b/docs/images/stripplot-text2cypher-safety.png
diff --git a/docs/images/violin-naive-vs-biochatter.pdf b/docs/images/violin-naive-vs-biochatter.pdf
diff --git a/docs/images/violin-naive-vs-biochatter.png b/docs/images/violin-naive-vs-biochatter.png
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -33,7 +33,7 @@ theme:
     - search.highlight
     - navigation.instant
     - navigation.tabs
-    - navigation.sections
+    - toc.integrate
 
   icon:
     repo: fontawesome/brands/github
@@ -42,6 +42,10 @@ plugins:
   - search
   - mkdocstrings:
       default_handler: python
+      handlers:
+        python:
+          options:
+            heading_level: 3
   - table-reader
   - social
   - redirects:
@@ -97,7 +101,9 @@ nav:
       - LLM Connectivity: api-docs/llm_connect.md
       - Vectorstore Agent: api-docs/vectorstore.md
       - Knowledge Graph Agent: api-docs/kg.md
-      - API Agent: api-docs/api-calling.md
+      - "API Calling: Base Classes": api-docs/api-calling-base.md
+      - "API Calling: Web APIs": api-docs/api-calling-web.md
+      - "API Calling: Python APIs": api-docs/api-calling-python.md
       - Reflexion Agent: api-docs/reflexion.md
       - Podcast: api-docs/podcast.md
 
@@ -130,6 +136,8 @@ markdown_extensions:
   - md_in_html
   - admonition
   - pymdownx.details
+  - toc:
+      toc_depth: 3
 
 extra_javascript:
   - https://unpkg.com/[email protected]/dist/tablesort.min.js