diff --git a/README.md b/README.md
index ad70b68..5843cc5 100644
--- a/README.md
+++ b/README.md
@@ -3,9 +3,7 @@
 Quick and easy AI components to build Kotaemon - applicable in client
 project.
 
-## Documentation
-
-https://docs.promptui.dm.cinnamon.is
+[Documentation](https://docs.bleh-internal.cinnamon.is/)
 
 ## Install
 
diff --git a/docs/contributing.md b/docs/contributing.md
index e6c5ece..7334bef 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -139,8 +139,8 @@ Examples: https://github.com/Cinnamon/kotaemon/pull/2
 - 1st line message is the PR title.
 - The text area is the PR description.
 
-![image](https://github.com/Cinnamon/kotaemon/assets/35283585/e2593010-d7ef-46e3-8719-6fcae0315b5d)
-![image](https://github.com/Cinnamon/kotaemon/assets/35283585/bfe6a117-85cd-4dd4-b432-197c791a9901)
+![image](images/274787925-e2593010-d7ef-46e3-8719-6fcae0315b5d.png)
+![image](images/274787941-bfe6a117-85cd-4dd4-b432-197c791a9901.png)
 
 ## Develop pipelines
 
diff --git a/docs/images/269170170-af94ff6b-b8b4-4602-ab6e-2947deb30dff.png b/docs/images/269170170-af94ff6b-b8b4-4602-ab6e-2947deb30dff.png
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diff --git a/docs/overview.md b/docs/overview.md
index c55c991..093adf8 100644
--- a/docs/overview.md
+++ b/docs/overview.md
@@ -3,8 +3,17 @@
 `kotaemon` library focuses on the AI building blocks to implement the Kotaemon. It can be used in both client project and in product development. It consists of base interfaces, core components and a list of utilities:
 
 - Base interfaces: `kotaemon` defines the base interface of a component in a pipeline. A pipeline is also a component. By clearly define this interface, a pipeline of steps can be easily constructed and orchestrated.
-- Core components: `kotaemon` implements (or wraps 3rd-party libraries like Langchain, llama-index,... when possible) commonly used components in kotaemon use cases. Some of these components are: LLM, vector store, document store, retriever... For a detailed list and description of these components, please refer to the [Pipeline Components](Pipeline-Components) and [Data & Data Structure Components](Data-&-Data-Structure-Components) sections.
-- List of utilities: `lib-knowledge` provides utilities and tools that are usually needed in client project. For example, it provides a prompt engineering UI for AI developers in a project to quickly create a prompt engineering tool for DMs and QALs. It also provides a command to quickly spin up a project code base. For a full list and description of these utilities, please refer to the [Utilities](Utilities) section.
+- Core components: `kotaemon` implements (or wraps 3rd-party libraries
+  like Langchain, llama-index,... when possible) commonly used components in
+  kotaemon use cases. Some of these components are: LLM, vector store,
+  document store, retriever... For a detailed list and description of these
+  components, please refer to the [API Reference](/reference/nav/) section.
+- List of utilities: `lib-knowledge` provides utilities and tools that are
+  usually needed in client project. For example, it provides a prompt
+  engineering UI for AI developers in a project to quickly create a prompt
+  engineering tool for DMs and QALs. It also provides a command to quickly spin
+  up a project code base. For a full list and description of these utilities,
+  please refer to the [Tutorial/Utilities](/ultilities) section.
 
 ```mermaid
 mindmap
diff --git a/docs/scripts/generate_reference_docs.py b/docs/scripts/generate_reference_docs.py
index f533cb3..33bdad4 100644
--- a/docs/scripts/generate_reference_docs.py
+++ b/docs/scripts/generate_reference_docs.py
@@ -13,6 +13,8 @@ while doc_dir.name != doc_dir_name and doc_dir != doc_dir.parent:
 if doc_dir == doc_dir.parent:
     raise ValueError(f"root_name ({doc_dir_name}) not in path ({str(Path(__file__))}).")
 
+nav_title_map = {"cli": "CLI", "llms": "LLMs"}
+
 
 def generate_docs_for_src_code(
     code_dir: Path, target_doc_folder: str, ignored_modules: Iterable[Any] = []
@@ -53,7 +55,9 @@ def generate_docs_for_src_code(
         if ignore:
             continue
 
-        nav_titles = [name.replace("_", " ").title() for name in parts]
+        nav_titles = [
+            nav_title_map.get(name, name.replace("_", " ").title()) for name in parts
+        ]
         nav[nav_titles] = doc_path.as_posix()
 
         with mkdocs_gen_files.open(full_doc_path, "w") as f:
@@ -69,7 +73,7 @@ def generate_docs_for_src_code(
 
 
 generate_docs_for_src_code(
-    code_dir=doc_dir.parent / "libs" / "kotaemon",
+    code_dir=doc_dir.parent / "libs" / "kotaemon" / "kotaemon",
     target_doc_folder="reference",
     ignored_modules={"contribs"},
 )
diff --git a/docs/ultilities.md b/docs/ultilities.md
index 225b443..53a9da3 100644
--- a/docs/ultilities.md
+++ b/docs/ultilities.md
@@ -2,7 +2,7 @@ Utilities detail can be referred in the sub-pages of this section.
 
 ## Prompt engineering UI
 
-![chat-ui](https://github.com/Cinnamon/kotaemon/assets/35283585/ac8f9aac-d853-4571-a48b-d866a99eaf3e)
+![chat-ui](images/271332562-ac8f9aac-d853-4571-a48b-d866a99eaf3e.png)
 
 **_Important:_** despite the name prompt engineering UI, this tool allows DMs to test any kind of parameters that are exposed by AIRs. Prompt is one kind of param. There can be other type of params that DMs can tweak (e.g. top_k, temperature...).
 
@@ -146,7 +146,7 @@ $ kh promptui run <path/to/config/file.yml>
 
 This will generate an UI as follow:
 
-![Screenshot from 2023-09-20 12-20-31](https://github.com/Cinnamon/kotaemon/assets/35283585/9ac1b95a-b667-42e7-b318-98a1b805d6df)
+![Screenshot from 2023-09-20 12-20-31](images/269170198-9ac1b95a-b667-42e7-b318-98a1b805d6df.png)
 
 where:
 
diff --git a/libs/kotaemon/kotaemon/agents/io/base.py b/libs/kotaemon/kotaemon/agents/io/base.py
index da6e3b9..c27eed0 100644
--- a/libs/kotaemon/kotaemon/agents/io/base.py
+++ b/libs/kotaemon/kotaemon/agents/io/base.py
@@ -5,9 +5,10 @@ from dataclasses import dataclass
 from enum import Enum
 from typing import Any, Dict, Literal, NamedTuple, Optional, Union
 
-from kotaemon.base import LLMInterface
 from pydantic import Extra
 
+from kotaemon.base import LLMInterface
+
 
 def check_log():
     """
diff --git a/libs/kotaemon/kotaemon/agents/langchain_based.py b/libs/kotaemon/kotaemon/agents/langchain_based.py
index 7bdb7aa..3083b70 100644
--- a/libs/kotaemon/kotaemon/agents/langchain_based.py
+++ b/libs/kotaemon/kotaemon/agents/langchain_based.py
@@ -1,10 +1,11 @@
 from typing import List, Optional
 
-from kotaemon.llms import LLM, ChatLLM
 from langchain.agents import AgentType as LCAgentType
 from langchain.agents import initialize_agent
 from langchain.agents.agent import AgentExecutor as LCAgentExecutor
 
+from kotaemon.llms import LLM, ChatLLM
+
 from .base import BaseAgent
 from .io import AgentOutput, AgentType
 from .tools import BaseTool
diff --git a/libs/kotaemon/kotaemon/agents/tools/base.py b/libs/kotaemon/kotaemon/agents/tools/base.py
index 42f7533..1caf3d2 100644
--- a/libs/kotaemon/kotaemon/agents/tools/base.py
+++ b/libs/kotaemon/kotaemon/agents/tools/base.py
@@ -1,9 +1,10 @@
 from typing import Any, Callable, Dict, Optional, Tuple, Type, Union
 
-from kotaemon.base import BaseComponent
 from langchain.agents import Tool as LCTool
 from pydantic import BaseModel
 
+from kotaemon.base import BaseComponent
+
 
 class ToolException(Exception):
     """An optional exception that tool throws when execution error occurs.
diff --git a/libs/kotaemon/kotaemon/agents/tools/llm.py b/libs/kotaemon/kotaemon/agents/tools/llm.py
index 2df87cc..750462e 100644
--- a/libs/kotaemon/kotaemon/agents/tools/llm.py
+++ b/libs/kotaemon/kotaemon/agents/tools/llm.py
@@ -1,8 +1,9 @@
 from typing import AnyStr, Optional, Type
 
-from kotaemon.llms import BaseLLM
 from pydantic import BaseModel, Field
 
+from kotaemon.llms import BaseLLM
+
 from .base import BaseTool, ToolException
 
 
diff --git a/libs/kotaemon/kotaemon/agents/tools/wikipedia.py b/libs/kotaemon/kotaemon/agents/tools/wikipedia.py
index 3046522..9e6a362 100644
--- a/libs/kotaemon/kotaemon/agents/tools/wikipedia.py
+++ b/libs/kotaemon/kotaemon/agents/tools/wikipedia.py
@@ -1,8 +1,9 @@
 from typing import Any, AnyStr, Optional, Type, Union
 
-from kotaemon.base import Document
 from pydantic import BaseModel, Field
 
+from kotaemon.base import Document
+
 from .base import BaseTool
 
 
diff --git a/libs/kotaemon/kotaemon/base/component.py b/libs/kotaemon/kotaemon/base/component.py
index 2f8abf5..4e6f7b8 100644
--- a/libs/kotaemon/kotaemon/base/component.py
+++ b/libs/kotaemon/kotaemon/base/component.py
@@ -1,9 +1,10 @@
 from abc import abstractmethod
 from typing import Iterator, Optional
 
-from kotaemon.base.schema import Document
 from theflow import Function, Node, Param, lazy
 
+from kotaemon.base.schema import Document
+
 
 class BaseComponent(Function):
     """A component is a class that can be used to compose a pipeline.
diff --git a/libs/kotaemon/kotaemon/chatbot/base.py b/libs/kotaemon/kotaemon/chatbot/base.py
index f4b8c86..b6a3baf 100644
--- a/libs/kotaemon/kotaemon/chatbot/base.py
+++ b/libs/kotaemon/kotaemon/chatbot/base.py
@@ -1,9 +1,10 @@
 from abc import abstractmethod
 from typing import List, Optional
 
+from theflow import SessionFunction
+
 from kotaemon.base import BaseComponent, LLMInterface
 from kotaemon.base.schema import AIMessage, BaseMessage, HumanMessage, SystemMessage
-from theflow import SessionFunction
 
 
 class BaseChatBot(BaseComponent):
diff --git a/libs/kotaemon/kotaemon/cli.py b/libs/kotaemon/kotaemon/cli.py
index 84a29b1..75101ff 100644
--- a/libs/kotaemon/kotaemon/cli.py
+++ b/libs/kotaemon/kotaemon/cli.py
@@ -36,9 +36,10 @@ def export(export_path, output):
     """Export a pipeline to a config file"""
     import sys
 
-    from kotaemon.contribs.promptui.config import export_pipeline_to_config
     from theflow.utils.modules import import_dotted_string
 
+    from kotaemon.contribs.promptui.config import export_pipeline_to_config
+
     sys.path.append(os.getcwd())
     cls = import_dotted_string(export_path, safe=False)
     export_pipeline_to_config(cls, output)
diff --git a/libs/kotaemon/kotaemon/contribs/promptui/config.py b/libs/kotaemon/kotaemon/contribs/promptui/config.py
index e660168..e9098b1 100644
--- a/libs/kotaemon/kotaemon/contribs/promptui/config.py
+++ b/libs/kotaemon/kotaemon/contribs/promptui/config.py
@@ -4,6 +4,7 @@ from pathlib import Path
 from typing import Any, Dict, Optional, Type, Union
 
 import yaml
+
 from kotaemon.base import BaseComponent
 from kotaemon.chatbot import BaseChatBot
 
diff --git a/libs/kotaemon/kotaemon/contribs/promptui/export.py b/libs/kotaemon/kotaemon/contribs/promptui/export.py
index ce152f1..8b174ea 100644
--- a/libs/kotaemon/kotaemon/contribs/promptui/export.py
+++ b/libs/kotaemon/kotaemon/contribs/promptui/export.py
@@ -6,10 +6,11 @@ from typing import Any, Dict, List, Type, Union
 
 import pandas as pd
 import yaml
-from kotaemon.base import BaseComponent
 from theflow.storage import storage
 from theflow.utils.modules import import_dotted_string
 
+from kotaemon.base import BaseComponent
+
 from .logs import ResultLog
 
 
diff --git a/libs/kotaemon/kotaemon/contribs/promptui/ui/chat.py b/libs/kotaemon/kotaemon/contribs/promptui/ui/chat.py
index 6c4b743..78eecb5 100644
--- a/libs/kotaemon/kotaemon/contribs/promptui/ui/chat.py
+++ b/libs/kotaemon/kotaemon/contribs/promptui/ui/chat.py
@@ -3,11 +3,12 @@ from datetime import datetime
 from pathlib import Path
 
 import gradio as gr
+from theflow.storage import storage
+
 from kotaemon.chatbot import ChatConversation
 from kotaemon.contribs.promptui.base import get_component
 from kotaemon.contribs.promptui.export import export
 from kotaemon.contribs.promptui.ui.blocks import ChatBlock
-from theflow.storage import storage
 
 from ..logs import ResultLog
 
diff --git a/libs/kotaemon/kotaemon/contribs/promptui/ui/pipeline.py b/libs/kotaemon/kotaemon/contribs/promptui/ui/pipeline.py
index 12b1133..725893d 100644
--- a/libs/kotaemon/kotaemon/contribs/promptui/ui/pipeline.py
+++ b/libs/kotaemon/kotaemon/contribs/promptui/ui/pipeline.py
@@ -6,9 +6,10 @@ from typing import Any, Dict
 
 import gradio as gr
 import pandas as pd
+from theflow.storage import storage
+
 from kotaemon.contribs.promptui.base import get_component
 from kotaemon.contribs.promptui.export import export
-from theflow.storage import storage
 
 from ..logs import ResultLog
 
diff --git a/libs/kotaemon/kotaemon/indices/base.py b/libs/kotaemon/kotaemon/indices/base.py
index 0de39c7..938be66 100644
--- a/libs/kotaemon/kotaemon/indices/base.py
+++ b/libs/kotaemon/kotaemon/indices/base.py
@@ -3,9 +3,10 @@ from __future__ import annotations
 from abc import abstractmethod
 from typing import Any, Type
 
-from kotaemon.base import BaseComponent, Document, RetrievedDocument
 from llama_index.node_parser.interface import NodeParser
 
+from kotaemon.base import BaseComponent, Document, RetrievedDocument
+
 
 class DocTransformer(BaseComponent):
     """This is a base class for document transformers
diff --git a/libs/kotaemon/kotaemon/indices/ingests/files.py b/libs/kotaemon/kotaemon/indices/ingests/files.py
index b3b4f48..22e7db9 100644
--- a/libs/kotaemon/kotaemon/indices/ingests/files.py
+++ b/libs/kotaemon/kotaemon/indices/ingests/files.py
@@ -1,5 +1,7 @@
 from pathlib import Path
 
+from llama_index.readers.base import BaseReader
+
 from kotaemon.base import BaseComponent, Document, Param
 from kotaemon.indices.extractors import BaseDocParser
 from kotaemon.indices.splitters import BaseSplitter, TokenSplitter
@@ -11,7 +13,6 @@ from kotaemon.loaders import (
     PandasExcelReader,
     UnstructuredReader,
 )
-from llama_index.readers.base import BaseReader
 
 
 class DocumentIngestor(BaseComponent):
diff --git a/libs/kotaemon/kotaemon/indices/qa/citation.py b/libs/kotaemon/kotaemon/indices/qa/citation.py
index bafa2d4..4c1281a 100644
--- a/libs/kotaemon/kotaemon/indices/qa/citation.py
+++ b/libs/kotaemon/kotaemon/indices/qa/citation.py
@@ -1,9 +1,10 @@
 from typing import Iterator, List
 
+from pydantic import BaseModel, Field
+
 from kotaemon.base import BaseComponent
 from kotaemon.base.schema import HumanMessage, SystemMessage
 from kotaemon.llms import BaseLLM
-from pydantic import BaseModel, Field
 
 
 class FactWithEvidence(BaseModel):
diff --git a/libs/kotaemon/kotaemon/indices/rankings/llm.py b/libs/kotaemon/kotaemon/indices/rankings/llm.py
index 7b280f1..bff81ff 100644
--- a/libs/kotaemon/kotaemon/indices/rankings/llm.py
+++ b/libs/kotaemon/kotaemon/indices/rankings/llm.py
@@ -2,9 +2,10 @@ from __future__ import annotations
 
 from concurrent.futures import ThreadPoolExecutor
 
+from langchain.output_parsers.boolean import BooleanOutputParser
+
 from kotaemon.base import Document
 from kotaemon.llms import BaseLLM, PromptTemplate
-from langchain.output_parsers.boolean import BooleanOutputParser
 
 from .base import BaseReranking
 
diff --git a/libs/kotaemon/kotaemon/llms/base.py b/libs/kotaemon/kotaemon/llms/base.py
index 56bd910..ff315ea 100644
--- a/libs/kotaemon/kotaemon/llms/base.py
+++ b/libs/kotaemon/kotaemon/llms/base.py
@@ -1,6 +1,7 @@
-from kotaemon.base import BaseComponent
 from langchain_core.language_models.base import BaseLanguageModel
 
+from kotaemon.base import BaseComponent
+
 
 class BaseLLM(BaseComponent):
     def to_langchain_format(self) -> BaseLanguageModel:
diff --git a/libs/kotaemon/kotaemon/llms/branching.py b/libs/kotaemon/kotaemon/llms/branching.py
index 09fe3c2..a9cbbe8 100644
--- a/libs/kotaemon/kotaemon/llms/branching.py
+++ b/libs/kotaemon/kotaemon/llms/branching.py
@@ -156,6 +156,7 @@ class GatedBranchingPipeline(SimpleBranchingPipeline):
 
 if __name__ == "__main__":
     import dotenv
+
     from kotaemon.llms import AzureChatOpenAI, BasePromptComponent
     from kotaemon.parsers import RegexExtractor
 
diff --git a/libs/kotaemon/kotaemon/llms/cot.py b/libs/kotaemon/kotaemon/llms/cot.py
index bac2a22..7eaf5d1 100644
--- a/libs/kotaemon/kotaemon/llms/cot.py
+++ b/libs/kotaemon/kotaemon/llms/cot.py
@@ -1,9 +1,10 @@
 from copy import deepcopy
 from typing import Callable, List
 
-from kotaemon.base import BaseComponent, Document
 from theflow import Function, Node, Param
 
+from kotaemon.base import BaseComponent, Document
+
 from .chats import AzureChatOpenAI
 from .completions import LLM
 from .prompts import BasePromptComponent
@@ -84,7 +85,7 @@ class Thought(BaseComponent):
     @Node.auto(depends_on="prompt")
     def prompt_template(self):
         """Automatically wrap around param prompt. Can ignore"""
-        return BasePromptComponent(self.prompt)
+        return BasePromptComponent(template=self.prompt)
 
     def run(self, **kwargs) -> Document:
         """Run the chain of thought"""
diff --git a/libs/kotaemon/kotaemon/llms/prompts/base.py b/libs/kotaemon/kotaemon/llms/prompts/base.py
index 564279d..ca84d57 100644
--- a/libs/kotaemon/kotaemon/llms/prompts/base.py
+++ b/libs/kotaemon/kotaemon/llms/prompts/base.py
@@ -1,4 +1,6 @@
-from typing import Callable, Union
+from typing import Callable
+
+from theflow import Param
 
 from kotaemon.base import BaseComponent, Document
 
@@ -19,14 +21,18 @@ class BasePromptComponent(BaseComponent):
         middleware_switches = {"theflow.middleware.CachingMiddleware": False}
         allow_extra = True
 
-    def __init__(self, template: Union[str, PromptTemplate], **kwargs):
-        super().__init__()
-        self.template = (
-            template
-            if isinstance(template, PromptTemplate)
-            else PromptTemplate(template)
+    template: str | PromptTemplate
+
+    @Param.auto(depends_on="template")
+    def template__(self):
+        return (
+            self.template
+            if isinstance(self.template, PromptTemplate)
+            else PromptTemplate(self.template)
         )
 
+    def __init__(self, **kwargs):
+        super().__init__(**kwargs)
         self.__set(**kwargs)
 
     def __check_redundant_kwargs(self, **kwargs):
@@ -42,7 +48,7 @@ class BasePromptComponent(BaseComponent):
         Returns:
             None
         """
-        self.template.check_redundant_kwargs(**kwargs)
+        self.template__.check_redundant_kwargs(**kwargs)
 
     def __check_unset_placeholders(self):
         """
@@ -58,7 +64,7 @@ class BasePromptComponent(BaseComponent):
         Returns:
             None
         """
-        self.template.check_missing_kwargs(**self.__dict__)
+        self.template__.check_missing_kwargs(**self.__dict__)
 
     def __validate_value_type(self, **kwargs):
         """
@@ -76,6 +82,8 @@ class BasePromptComponent(BaseComponent):
         """
         type_error = []
         for k, v in kwargs.items():
+            if k.startswith("template"):
+                continue
             if not isinstance(v, (str, int, Document, Callable)):  # type: ignore
                 type_error.append((k, type(v)))
 
@@ -122,7 +130,7 @@ class BasePromptComponent(BaseComponent):
             )
 
         kwargs = {}
-        for k in self.template.placeholders:
+        for k in self.template__.placeholders:
             v = getattr(self, k)
 
             # if get a callable, execute to get its output
@@ -141,7 +149,7 @@ class BasePromptComponent(BaseComponent):
 
         return kwargs
 
-    def set(self, **kwargs):
+    def set_value(self, **kwargs):
         """
         Similar to `__set` but for external use.
 
@@ -172,7 +180,7 @@ class BasePromptComponent(BaseComponent):
         self.__check_unset_placeholders()
         prepared_kwargs = self.__prepare_value()
 
-        text = self.template.populate(**prepared_kwargs)
+        text = self.template__.populate(**prepared_kwargs)
         return Document(text=text, metadata={"origin": "PromptComponent"})
 
     def flow(self):
diff --git a/libs/kotaemon/kotaemon/loaders/base.py b/libs/kotaemon/kotaemon/loaders/base.py
index 956002f..cb92d5b 100644
--- a/libs/kotaemon/kotaemon/loaders/base.py
+++ b/libs/kotaemon/kotaemon/loaders/base.py
@@ -1,10 +1,11 @@
 from pathlib import Path
 from typing import Any, List, Type, Union
 
-from kotaemon.base import BaseComponent, Document
 from llama_index import SimpleDirectoryReader, download_loader
 from llama_index.readers.base import BaseReader
 
+from kotaemon.base import BaseComponent, Document
+
 
 class AutoReader(BaseComponent):
     """General auto reader for a variety of files. (based on llama-hub)"""
diff --git a/libs/kotaemon/kotaemon/loaders/excel_loader.py b/libs/kotaemon/kotaemon/loaders/excel_loader.py
index 5fab7c5..d903aea 100644
--- a/libs/kotaemon/kotaemon/loaders/excel_loader.py
+++ b/libs/kotaemon/kotaemon/loaders/excel_loader.py
@@ -6,9 +6,10 @@ Pandas parser for .xlsx files.
 from pathlib import Path
 from typing import Any, List, Optional, Union
 
-from kotaemon.base import Document
 from llama_index.readers.base import BaseReader
 
+from kotaemon.base import Document
+
 
 class PandasExcelReader(BaseReader):
     r"""Pandas-based CSV parser.
diff --git a/libs/kotaemon/kotaemon/loaders/mathpix_loader.py b/libs/kotaemon/kotaemon/loaders/mathpix_loader.py
index 1f5b602..19f1001 100644
--- a/libs/kotaemon/kotaemon/loaders/mathpix_loader.py
+++ b/libs/kotaemon/kotaemon/loaders/mathpix_loader.py
@@ -5,10 +5,11 @@ from pathlib import Path
 from typing import Any, Dict, List, Optional
 
 import requests
-from kotaemon.base import Document
 from langchain.utils import get_from_dict_or_env
 from llama_index.readers.base import BaseReader
 
+from kotaemon.base import Document
+
 from .utils.table import parse_markdown_text_to_tables, strip_special_chars_markdown
 
 
diff --git a/libs/kotaemon/kotaemon/loaders/ocr_loader.py b/libs/kotaemon/kotaemon/loaders/ocr_loader.py
index 608405f..c751338 100644
--- a/libs/kotaemon/kotaemon/loaders/ocr_loader.py
+++ b/libs/kotaemon/kotaemon/loaders/ocr_loader.py
@@ -3,9 +3,10 @@ from typing import List, Optional
 from uuid import uuid4
 
 import requests
-from kotaemon.base import Document
 from llama_index.readers.base import BaseReader
 
+from kotaemon.base import Document
+
 from .utils.pdf_ocr import parse_ocr_output, read_pdf_unstructured
 from .utils.table import strip_special_chars_markdown
 
diff --git a/libs/kotaemon/kotaemon/loaders/unstructured_loader.py b/libs/kotaemon/kotaemon/loaders/unstructured_loader.py
index 8568d95..82f3255 100644
--- a/libs/kotaemon/kotaemon/loaders/unstructured_loader.py
+++ b/libs/kotaemon/kotaemon/loaders/unstructured_loader.py
@@ -12,9 +12,10 @@ pip install xlrd
 from pathlib import Path
 from typing import Any, Dict, List, Optional
 
-from kotaemon.base import Document
 from llama_index.readers.base import BaseReader
 
+from kotaemon.base import Document
+
 
 class UnstructuredReader(BaseReader):
     """General unstructured text reader for a variety of files."""
diff --git a/libs/kotaemon/kotaemon/storages/vectorstores/base.py b/libs/kotaemon/kotaemon/storages/vectorstores/base.py
index d353886..ba4f3ec 100644
--- a/libs/kotaemon/kotaemon/storages/vectorstores/base.py
+++ b/libs/kotaemon/kotaemon/storages/vectorstores/base.py
@@ -3,12 +3,13 @@ from __future__ import annotations
 from abc import ABC, abstractmethod
 from typing import Any, Optional
 
-from kotaemon.base import DocumentWithEmbedding
 from llama_index.schema import NodeRelationship, RelatedNodeInfo
 from llama_index.vector_stores.types import BasePydanticVectorStore
 from llama_index.vector_stores.types import VectorStore as LIVectorStore
 from llama_index.vector_stores.types import VectorStoreQuery
 
+from kotaemon.base import DocumentWithEmbedding
+
 
 class BaseVectorStore(ABC):
     @abstractmethod
diff --git a/libs/kotaemon/kotaemon/storages/vectorstores/simple_file.py b/libs/kotaemon/kotaemon/storages/vectorstores/simple_file.py
index 407d4fc..6f14a34 100644
--- a/libs/kotaemon/kotaemon/storages/vectorstores/simple_file.py
+++ b/libs/kotaemon/kotaemon/storages/vectorstores/simple_file.py
@@ -3,10 +3,11 @@ from pathlib import Path
 from typing import Any, Optional, Type
 
 import fsspec
-from kotaemon.base import DocumentWithEmbedding
 from llama_index.vector_stores import SimpleVectorStore as LISimpleVectorStore
 from llama_index.vector_stores.simple import SimpleVectorStoreData
 
+from kotaemon.base import DocumentWithEmbedding
+
 from .base import LlamaIndexVectorStore
 
 
diff --git a/libs/kotaemon/tests/test_agent.py b/libs/kotaemon/tests/test_agent.py
index 49740cd..dad9a33 100644
--- a/libs/kotaemon/tests/test_agent.py
+++ b/libs/kotaemon/tests/test_agent.py
@@ -1,6 +1,8 @@
 from unittest.mock import patch
 
 import pytest
+from openai.types.chat.chat_completion import ChatCompletion
+
 from kotaemon.agents import (
     AgentType,
     BaseTool,
@@ -12,7 +14,6 @@ from kotaemon.agents import (
     WikipediaTool,
 )
 from kotaemon.llms import AzureChatOpenAI
-from openai.types.chat.chat_completion import ChatCompletion
 
 FINAL_RESPONSE_TEXT = "Final Answer: Hello Cinnamon AI!"
 REWOO_VALID_PLAN = (
diff --git a/libs/kotaemon/tests/test_composite.py b/libs/kotaemon/tests/test_composite.py
index 85cb35a..464a456 100644
--- a/libs/kotaemon/tests/test_composite.py
+++ b/libs/kotaemon/tests/test_composite.py
@@ -1,6 +1,8 @@
 from copy import deepcopy
 
 import pytest
+from openai.types.chat.chat_completion import ChatCompletion
+
 from kotaemon.llms import (
     AzureChatOpenAI,
     BasePromptComponent,
@@ -10,7 +12,6 @@ from kotaemon.llms import (
     SimpleLinearPipeline,
 )
 from kotaemon.parsers import RegexExtractor
-from openai.types.chat.chat_completion import ChatCompletion
 
 _openai_chat_completion_response = ChatCompletion.parse_obj(
     {
diff --git a/libs/kotaemon/tests/test_cot.py b/libs/kotaemon/tests/test_cot.py
index 58833c1..aef8a69 100644
--- a/libs/kotaemon/tests/test_cot.py
+++ b/libs/kotaemon/tests/test_cot.py
@@ -1,8 +1,9 @@
 from unittest.mock import patch
 
+from openai.types.chat.chat_completion import ChatCompletion
+
 from kotaemon.llms import AzureChatOpenAI
 from kotaemon.llms.cot import ManualSequentialChainOfThought, Thought
-from openai.types.chat.chat_completion import ChatCompletion
 
 _openai_chat_completion_response = [
     ChatCompletion.parse_obj(
diff --git a/libs/kotaemon/tests/test_docstores.py b/libs/kotaemon/tests/test_docstores.py
index af4834c..90bae43 100644
--- a/libs/kotaemon/tests/test_docstores.py
+++ b/libs/kotaemon/tests/test_docstores.py
@@ -3,6 +3,7 @@ from unittest.mock import patch
 
 import pytest
 from elastic_transport import ApiResponseMeta
+
 from kotaemon.base import Document
 from kotaemon.storages import (
     ElasticsearchDocumentStore,
diff --git a/libs/kotaemon/tests/test_indexing_retrieval.py b/libs/kotaemon/tests/test_indexing_retrieval.py
index 032cbde..7393248 100644
--- a/libs/kotaemon/tests/test_indexing_retrieval.py
+++ b/libs/kotaemon/tests/test_indexing_retrieval.py
@@ -3,11 +3,12 @@ from pathlib import Path
 from typing import cast
 
 import pytest
+from openai.resources.embeddings import Embeddings
+
 from kotaemon.base import Document
 from kotaemon.embeddings import AzureOpenAIEmbeddings
 from kotaemon.indices import VectorIndexing, VectorRetrieval
 from kotaemon.storages import ChromaVectorStore, InMemoryDocumentStore
-from openai.resources.embeddings import Embeddings
 
 with open(Path(__file__).parent / "resources" / "embedding_openai.json") as f:
     openai_embedding = json.load(f)
diff --git a/libs/kotaemon/tests/test_llms_completion_models.py b/libs/kotaemon/tests/test_llms_completion_models.py
index ac4794f..a88d3c4 100644
--- a/libs/kotaemon/tests/test_llms_completion_models.py
+++ b/libs/kotaemon/tests/test_llms_completion_models.py
@@ -9,6 +9,7 @@ try:
 except ImportError:
     from langchain.llms import AzureOpenAI as AzureOpenAILC
     from langchain.llms import OpenAI as OpenAILC
+
 from openai.types.completion import Completion
 
 _openai_completion_response = Completion.parse_obj(
diff --git a/libs/kotaemon/tests/test_post_processing.py b/libs/kotaemon/tests/test_post_processing.py
index 0b0359a..d32808f 100644
--- a/libs/kotaemon/tests/test_post_processing.py
+++ b/libs/kotaemon/tests/test_post_processing.py
@@ -1,4 +1,5 @@
 import pytest
+
 from kotaemon.base import Document
 from kotaemon.parsers import RegexExtractor
 
diff --git a/libs/kotaemon/tests/test_prompt.py b/libs/kotaemon/tests/test_prompt.py
index 6e9e4f9..e0fb0c8 100644
--- a/libs/kotaemon/tests/test_prompt.py
+++ b/libs/kotaemon/tests/test_prompt.py
@@ -1,4 +1,5 @@
 import pytest
+
 from kotaemon.base import Document
 from kotaemon.llms import BasePromptComponent, PromptTemplate
 from kotaemon.parsers import RegexExtractor
@@ -58,5 +59,5 @@ def test_run():
 def test_set_method():
     template = PromptTemplate("Hello, {name}!")
     prompt = BasePromptComponent(template=template)
-    prompt.set(name="Alice")
+    prompt.set_value(name="Alice")
     assert prompt.name == "Alice"
diff --git a/libs/kotaemon/tests/test_reader.py b/libs/kotaemon/tests/test_reader.py
index f8f6ef3..4231e18 100644
--- a/libs/kotaemon/tests/test_reader.py
+++ b/libs/kotaemon/tests/test_reader.py
@@ -1,9 +1,10 @@
 from pathlib import Path
 
+from langchain.schema import Document as LangchainDocument
+from llama_index.node_parser import SimpleNodeParser
+
 from kotaemon.base import Document
 from kotaemon.loaders import AutoReader, UnstructuredReader
-from langchain.schema import Document as LangchainDocument
-from llama_index.node_parser import SimpleNodeParser
 
 
 def test_pdf_reader():
diff --git a/libs/kotaemon/tests/test_reranking.py b/libs/kotaemon/tests/test_reranking.py
index 953afdb..d4f7be8 100644
--- a/libs/kotaemon/tests/test_reranking.py
+++ b/libs/kotaemon/tests/test_reranking.py
@@ -1,10 +1,11 @@
 from unittest.mock import patch
 
 import pytest
+from openai.types.chat.chat_completion import ChatCompletion
+
 from kotaemon.base import Document
 from kotaemon.indices.rankings import LLMReranking
 from kotaemon.llms import AzureChatOpenAI
-from openai.types.chat.chat_completion import ChatCompletion
 
 _openai_chat_completion_responses = [
     ChatCompletion.parse_obj(
diff --git a/libs/kotaemon/tests/test_splitter.py b/libs/kotaemon/tests/test_splitter.py
index c87e196..71e63ee 100644
--- a/libs/kotaemon/tests/test_splitter.py
+++ b/libs/kotaemon/tests/test_splitter.py
@@ -1,6 +1,7 @@
+from llama_index.schema import NodeRelationship
+
 from kotaemon.base import Document
 from kotaemon.indices.splitters import TokenSplitter
-from llama_index.schema import NodeRelationship
 
 source1 = Document(
     content="The City Hall and Raffles Place MRT stations are paired cross-platform "
diff --git a/libs/kotaemon/tests/test_table_reader.py b/libs/kotaemon/tests/test_table_reader.py
index 88f56fb..b723778 100644
--- a/libs/kotaemon/tests/test_table_reader.py
+++ b/libs/kotaemon/tests/test_table_reader.py
@@ -2,6 +2,7 @@ import json
 from pathlib import Path
 
 import pytest
+
 from kotaemon.loaders import MathpixPDFReader, OCRReader, PandasExcelReader
 
 input_file = Path(__file__).parent / "resources" / "table.pdf"
diff --git a/libs/kotaemon/tests/test_telemetry.py b/libs/kotaemon/tests/test_telemetry.py
index e5528ab..942b0ef 100644
--- a/libs/kotaemon/tests/test_telemetry.py
+++ b/libs/kotaemon/tests/test_telemetry.py
@@ -51,6 +51,7 @@ def test_disable_telemetry_import_haystack_after_kotaemon():
     import os
 
     import haystack.telemetry
+
     import kotaemon  # noqa: F401
 
     assert haystack.telemetry.telemetry is None
diff --git a/libs/kotaemon/tests/test_template.py b/libs/kotaemon/tests/test_template.py
index 917e494..cf7ad46 100644
--- a/libs/kotaemon/tests/test_template.py
+++ b/libs/kotaemon/tests/test_template.py
@@ -1,4 +1,5 @@
 import pytest
+
 from kotaemon.llms import PromptTemplate
 
 
diff --git a/libs/kotaemon/tests/test_tools.py b/libs/kotaemon/tests/test_tools.py
index 58e519a..b3ee6c7 100644
--- a/libs/kotaemon/tests/test_tools.py
+++ b/libs/kotaemon/tests/test_tools.py
@@ -2,12 +2,13 @@ import json
 from pathlib import Path
 
 import pytest
+from openai.resources.embeddings import Embeddings
+
 from kotaemon.agents.tools import ComponentTool, GoogleSearchTool, WikipediaTool
 from kotaemon.base import Document
 from kotaemon.embeddings import AzureOpenAIEmbeddings
 from kotaemon.indices.vectorindex import VectorIndexing, VectorRetrieval
 from kotaemon.storages import ChromaVectorStore, InMemoryDocumentStore
-from openai.resources.embeddings import Embeddings
 
 with open(Path(__file__).parent / "resources" / "embedding_openai.json") as f:
     openai_embedding = json.load(f)
diff --git a/libs/ktem/khapptests/test_qa.py b/libs/ktem/khapptests/test_qa.py
index 645d9e8..a3993ee 100644
--- a/libs/ktem/khapptests/test_qa.py
+++ b/libs/ktem/khapptests/test_qa.py
@@ -4,10 +4,11 @@ from unittest.mock import patch
 
 import pytest
 from index import ReaderIndexingPipeline
-from kotaemon.llms import AzureChatOpenAI
 from openai.resources.embeddings import Embeddings
 from openai.types.chat.chat_completion import ChatCompletion
 
+from kotaemon.llms import AzureChatOpenAI
+
 with open(Path(__file__).parent / "resources" / "embedding_openai.json") as f:
     openai_embedding = json.load(f)
 
diff --git a/libs/ktem/ktem/components.py b/libs/ktem/ktem/components.py
index 647dce5..e225d32 100644
--- a/libs/ktem/ktem/components.py
+++ b/libs/ktem/ktem/components.py
@@ -3,11 +3,12 @@ import logging
 from functools import cache
 from pathlib import Path
 
-from kotaemon.base import BaseComponent
-from kotaemon.storages import BaseDocumentStore, BaseVectorStore
 from theflow.settings import settings
 from theflow.utils.modules import deserialize
 
+from kotaemon.base import BaseComponent
+from kotaemon.storages import BaseDocumentStore, BaseVectorStore
+
 logger = logging.getLogger(__name__)
 
 
diff --git a/libs/ktem/ktem/indexing/file.py b/libs/ktem/ktem/indexing/file.py
index fc5ef1a..2019660 100644
--- a/libs/ktem/ktem/indexing/file.py
+++ b/libs/ktem/ktem/indexing/file.py
@@ -17,10 +17,6 @@ from ktem.components import (
 from ktem.db.models import Index, Source, SourceTargetRelation, engine
 from ktem.indexing.base import BaseIndexing, BaseRetriever
 from ktem.indexing.exceptions import FileExistsError
-from kotaemon.base import RetrievedDocument
-from kotaemon.indices import VectorIndexing, VectorRetrieval
-from kotaemon.indices.ingests import DocumentIngestor
-from kotaemon.indices.rankings import BaseReranking, CohereReranking, LLMReranking
 from llama_index.vector_stores import (
     FilterCondition,
     FilterOperator,
@@ -31,6 +27,11 @@ from llama_index.vector_stores.types import VectorStoreQueryMode
 from sqlmodel import Session, select
 from theflow.settings import settings
 
+from kotaemon.base import RetrievedDocument
+from kotaemon.indices import VectorIndexing, VectorRetrieval
+from kotaemon.indices.ingests import DocumentIngestor
+from kotaemon.indices.rankings import BaseReranking, CohereReranking, LLMReranking
+
 USER_SETTINGS = {
     "index_parser": {
         "name": "Index parser",
diff --git a/libs/ktem/ktem/reasoning/simple.py b/libs/ktem/ktem/reasoning/simple.py
index 4b2422d..67ae455 100644
--- a/libs/ktem/ktem/reasoning/simple.py
+++ b/libs/ktem/ktem/reasoning/simple.py
@@ -6,6 +6,7 @@ from functools import partial
 import tiktoken
 from ktem.components import llms
 from ktem.indexing.base import BaseRetriever
+
 from kotaemon.base import (
     BaseComponent,
     Document,
diff --git a/mkdocs.yml b/mkdocs.yml
index f9997b8..9ad7b40 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -60,7 +60,7 @@ plugins:
               - "!^_"
             members_order: source
             separate_signature: true
-          paths: [libs/kotaemon]
+          paths: [libs/kotaemon/kotaemon]
   - git-revision-date-localized:
       enable_creation_date: true
       type: timeago
diff --git a/pyproject.toml b/pyproject.toml
index 6500548..3b1cb51 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,3 +4,6 @@ skip = "*.js,*.css,*.map"
 ignore-words-list = "llm,fo"
 quiet-level = 3
 check-filenames = ""
+
+[tool.isort]
+known_first_party = ["kotaemon"]