overhaul API Reference

biocypher · Jul 29, 2024 · 0b2b3d1 · 0b2b3d1
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diff --git a/biochatter/api_agent/__init__.py b/biochatter/api_agent/__init__.py
@@ -0,0 +1,9 @@
+from .abc import BaseQueryBuilder, BaseFetcher, BaseInterpreter
+from .api_agent import APIAgent
+from .blast import (
+    BlastQueryParameters,
+    BlastQueryBuilder,
+    BlastFetcher,
+    BlastInterpreter,
+)
+from .oncokb import OncoKBQueryBuilder, OncoKBFetcher, OncoKBInterpreter
diff --git a/docs/api-reference.md b/docs/api-reference.md
@@ -0,0 +1,20 @@
+# API Agent Reference
+
+Here we handle the connection to external software tools via the
+parameterisation of API calls by the LLM.
+
+## The abstract base classes
+
+::: biochatter.api_agent.abc
+
+## The API Agent
+
+::: biochatter.api_agent.api_agent
+
+## The API Agent for the BLAST tool
+
+::: biochatter.api_agent.blast
+
+## The API Agent for the OncoKB tool
+
+::: biochatter.api_agent.oncokb
diff --git a/docs/images/boxplot-naive-vs-biochatter.pdf b/docs/images/boxplot-naive-vs-biochatter.pdf
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/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-size-accuracy.pdf b/docs/images/scatter-size-accuracy.pdf
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/kg-reference.md b/docs/kg-reference.md
@@ -0,0 +1,12 @@
+# Knowledge Graph Agent Reference
+
+Here we handle generation of use case-specific database prompts and their
+execution against a database using the database agent.
+
+## Dynamic prompt generation for BioCypher knowledge graphs
+
+::: biochatter.prompts
+
+## Execution of prompts against the database
+
+::: biochatter.database_agent
diff --git a/docs/llm_connect-reference.md b/docs/llm_connect-reference.md
@@ -1,4 +1,4 @@
-# LLM connectivity module
+# LLM Connectivity Reference
 
 Here we handle connections to various LLM services, proprietary and open source.
 

diff --git a/docs/podcast-reference.md b/docs/podcast-reference.md
@@ -1,4 +1,4 @@
-# Podcast module
+# Podcast Reference
 
 Here we handle generation of podcasts from texts.
 

diff --git a/docs/prompts-reference.md b/docs/prompts-reference.md
diff --git a/docs/reflexion-reference.md b/docs/reflexion-reference.md
@@ -0,0 +1,12 @@
+# Reflexion Agent Reference
+
+Here we handle the implementation of a LangGraph-based multi-agent system for
+reflexion on a user-defined task.
+
+## The base module
+
+::: biochatter.langgraph_agent_base
+
+## The KG-based reflexion agent
+
+::: biochatter.kg_langgraph_agent
diff --git a/docs/vectorstore-reference.md b/docs/vectorstore-reference.md
@@ -1,6 +1,13 @@
-# Vectorstore module
+# Vectorstore Agent Reference
 
 Here we handle the application of vectorstore services to retrieval-augmented
-generation tasks by embedding documents.
+generation tasks by embedding documents and connections/management of
+vectorstore services and semantic search.
+
+## Vectorstore Implementation
 
 ::: biochatter.vectorstore
+
+## Vectorstore Agent
+
+::: biochatter.vectorstore_agent
diff --git a/docs/vectorstore_agent-reference.md b/docs/vectorstore_agent-reference.md
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -69,9 +69,10 @@ nav:
       - Customising BioChatter Light - Advanced: vignette-custom-bclight-advanced.md
   - API Reference:
       - LLM Connectivity: llm_connect-reference.md
-      - Vectorstore: vectorstore-reference.md
-      - Vectorstore Agent: vectorstore_agent-reference.md
-      - Prompt Engine: prompts-reference.md
+      - Vectorstore Agent: vectorstore-reference.md
+      - Knowledge Graph Agent: kg-reference.md
+      - API Agent: api-reference.md
+      - Reflexion Agent: reflexion-reference.md
       - Podcast: podcast-reference.md
 
 repo_url: https://github.com/biocypher/biochatter