update api calling modules in autodoc

docs/api-docs/api-calling.md

@@ -3,18 +3,53 @@
 Here we handle the connection to external software tools via the
 parameterisation of API calls by the LLM.
 
-## The abstract base classes
+## Base classes
 
-::: biochatter.api_agent.abc
+### The abstract base classes
 
-## The API Agent
+::: biochatter.api_agent.base.agent_abc
 
-::: biochatter.api_agent.api_agent
+### The API Agent
 
-## The API Agent for the BLAST tool
+::: biochatter.api_agent.base.api_agent
 
-::: biochatter.api_agent.blast
+## Web APIs
 
-## The API Agent for the OncoKB tool
+### The BLAST tool
+
+::: biochatter.api_agent.web.blast
+
+### The OncoKB tool
+
+::: biochatter.api_agent.web.oncokb
+
+### The bio.tools API
+
+::: biochatter.api_agent.web.bio_tools
+
+## Python APIs
+
+### Generic Python API ingestion
+
+::: biochatter.api_agent.python.generic_agent
+
+::: biochatter.api_agent.python.autogenerate_model
+
+### 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
+
+## Utility functions
+
+### Formatters to parse the calls
+
+::: biochatter.api_agent.base.formatters
 
-::: biochatter.api_agent.oncokb