navexa 0.1.6

Navexa document indexing and reasoning workflows

Navexa

Tree-first PDF indexing and reasoning RAG for structured, semi-structured, unstructured, and transcript documents.

Documentation · GitHub Repository · Contributing · Release Notes · Issues · Installation · Quick Start

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Navexa is a Python library for turning PDFs into a hierarchical tree and running reasoning-based retrieval (vectorless RAG) on top of that tree.

Core capabilities:

• PDF indexing into tree_navexa.json
• Structured, semi-structured, unstructured, and transcript indexing flows
• Optional LLM-assisted TOC/outline/summaries
• Reasoning-based node retrieval and grounded answering
• Built-in usage and estimated cost tracking for LLM calls

What's New in 0.1.6

• Preferred grouped runtime config:
  • model_config={...} for provider/model credentials and routing
  • parser_config={...} for parser name, output format, and Docling options
• CLI now matches the Python API:
  • --model-config
  • --parser-config
• semi_structured supports both llm and no-llm
• transcript remains the only indexing flow that is strictly LLM-required
• Recoverable Docling issues are surfaced as:
  • one-line Navexa warnings at runtime
  • structured entries in tree_navexa.pipeline.warnings
• External reasoning integrations use BaseExternalLLM

For the full version history, see RELEASE.md.

Installation

Option 1: Use the current local source (editable)

cd navexa
python3 -m pip install -e .

Option 2: From source (regular)

cd navexa
python3 -m pip install .

Option 3: From PyPI (recommended for users)

python3 -m pip install navexa

Update Navexa

Upgrade to latest:

python3 -m pip install --upgrade navexa

Install a specific version:

python3 -m pip install navexa==0.1.6

For Jupyter Notebook/Lab, install the notebook extra to avoid the common tqdm warning (TqdmWarning: IProgress not found):

python3 -m pip install "navexa[notebook]"

Check the installed version

import navexa
print(navexa.__version__)

Option 4: From GitHub source

python3 -m pip install git+https://github.com/debugger404/navexa.git

Use the local source in notebooks

If you want a notebook to use the current local copy of Navexa:

cd navexa
python3 -m pip install -e .

If a notebook shows ModuleNotFoundError: navexa, check which Python environment the notebook kernel is using:

import navexa, sys
print(navexa.__file__)
print(sys.executable)

Environment and LLM Setup

You do not need a .env file for parser/indexing behavior. Use parser_config={...} in API calls when you want per-run parser behavior.

Use environment variables only when needed for:

• LLM credentials/provider routing, or
• global defaults you want shared across runs.

Navexa reads environment from OS variables and .env files.

Env loading order:

1. NAVEXA_ENV_FILE (explicit file path)
2. .env in current working directory (or parent)
3. repo-local .env (backward compatibility)

Minimal setup for OpenAI:

export NAVEXA_LLM_PROVIDER="openai"
export OPENAI_API_KEY="..."
export OPENAI_MODEL_NAME="gpt-4.1-mini"

Minimal setup for Azure OpenAI:

export NAVEXA_LLM_PROVIDER="azure"
export AZURE_OPENAI_API_KEY="..."
export AZURE_OPENAI_BASE_URL="https://<resource>.openai.azure.com"
export AZURE_DEPLOYMENT_NAME="<deployment-name>"
export AZURE_DEPLOYMENT_RAW_NAME="gpt-4.1-mini"

If AZURE_OPENAI_BASE_URL is set to just the resource URL, Navexa appends /openai/v1 automatically.

Use custom .env path (optional):

export NAVEXA_ENV_FILE="./.env"

You can also copy and fill (optional):

• .env.example

Direct model_config in Code

If you do not want to rely on .env loading, you can pass provider/model settings directly in API calls with model_config={...}.

Recommended shape:

model_config = {
    "provider": "openai",      # openai | azure
    "model": "gpt-4.1-mini",   # Azure: deployment name
    "api_key": "...",
    "base_url": None,          # required for azure
    "pricing_model": None,     # optional; useful for Azure custom deployment names
}

Azure example:

model_config = {
    "provider": "azure",
    "model": "my-gpt41mini-deployment",
    "api_key": "...",
    "base_url": "https://<resource>.openai.azure.com",
    "pricing_model": "gpt-4.1-mini",
}

Azure aliases also work:

• deployment_name instead of model
• deployment_raw_name instead of pricing_model

For Azure, model_config takes the same core values as the env setup:

• provider="azure"
• api_key -> same value as AZURE_OPENAI_API_KEY
• base_url -> same value as AZURE_OPENAI_BASE_URL
• model or deployment_name -> same value as AZURE_DEPLOYMENT_NAME
• pricing_model or deployment_raw_name -> same value as AZURE_DEPLOYMENT_RAW_NAME

Use it in API code:

from navexa import index_structured_document_tree

result = index_structured_document_tree(
    pdf_path="/path/to/file.pdf",
    mode="llm",
    model_config={
        "provider": "azure",
        "deployment_name": "my-gpt41mini-deployment",
        "deployment_raw_name": "gpt-4.1-mini",
        "api_key": "...",
        "base_url": "https://<resource>.openai.azure.com",
    },
)

Support:

• Python API supports model_config={...}
• CLI supports --model-config
• legacy model= / --model still work for compatibility but are deprecated

Model/credential precedence:

Preferred usage:

1. env defaults, or
2. model_config={...} in code

Deprecated compatibility path: 3. explicit model=...

Actual resolution order today:

1. explicit model=... (deprecated but still supported)
2. model_config["model"]
3. env default model (OPENAI_MODEL_NAME or AZURE_DEPLOYMENT_NAME)
4. if still missing: configuration error

Credential/base URL precedence:

1. model_config
2. .env / OS environment

Output safety:

• Navexa stores a redacted summary of resolved model settings in tree_navexa.pipeline.model_config
• API keys are never written to output JSON

Recommended Parser Setup

Use this rule:

1. Put long-lived defaults in .env
2. Pass parser_config={...} in the function when you want per-run overrides
3. Avoid mixing parser_config with old parser fields

Recommended parser shape:

parser_config = {
    "name": "docling",
    "output_format": "markdown",
    "options": {
        "profile": "balanced",
        "do_ocr": True,
        "force_full_page_ocr": True,
        "do_table_structure": True,
        "do_picture_description": False,
        "enable_remote_services": False,
        "backend": "torch",
        "image_mode": "placeholder",
        "quiet": True,
    },
}

Precedence order:

1. built-in defaults
2. .env defaults
3. explicit parser_config

For Docling parser options specifically, the merge order is:

1. selected profile defaults
2. matching .env values
3. explicit parser_config["options"]

Example:

• profile: fast_text sets do_ocr=False
• .env: NAVEXA_DOCLING_OCR=1
• code: parser_config["options"]={"do_ocr": False}

Final value:

• do_ocr=False

Why:

• profile is the starting point
• .env overrides the profile
• explicit function config overrides both

Deprecated Python API parser inputs:

• parser_model
• output_format
• docling_options

These legacy Python API fields still work for compatibility, but they are deprecated. If parser_config is provided, it takes precedence and the legacy parser fields are ignored.

Supported Environment Variables

These env values are defaults. If you pass model_config={...} or parser_config={...} in code, the explicit code values win.

LLM credentials and routing

Variable	Purpose	Example
NAVEXA_LLM_PROVIDER	LLM provider switch	openai or azure
OPENAI_API_KEY	OpenAI API key (openai provider)	sk-...
OPENAI_MODEL_NAME	OpenAI model name (openai provider)	gpt-4.1-mini
AZURE_OPENAI_API_KEY	Azure API key (azure provider)	...
AZURE_OPENAI_BASE_URL	Azure base URL (azure provider)	https://<resource>.openai.azure.com
AZURE_DEPLOYMENT_NAME	Azure deployment name (azure provider)	my-deployment
AZURE_DEPLOYMENT_RAW_NAME	Raw model name for pricing map/metadata	gpt-4.1-mini

Model resolution order

Navexa resolves model from:

1. explicit model= parameter (deprecated but still supported)
2. model_config["model"]
3. if provider is openai: OPENAI_MODEL_NAME
4. if provider is azure: AZURE_DEPLOYMENT_NAME
5. if still missing: raise configuration error (no fallback)

Provider resolution order:

1. model_config["provider"]
2. NAVEXA_LLM_PROVIDER
3. default: openai

Pipeline defaults

Variable	Purpose	Default
NAVEXA_MODE	Runtime mode (llm or no-llm)	no-llm
NAVEXA_DOCUMENT_TYPE	Default doc type	structured
NAVEXA_VERBOSE	Verbosity (low,medium,high or 1,2,3)	medium
NAVEXA_IF_ADD_NODE_SUMMARY	Include summaries (yes/no)	yes
NAVEXA_MAX_TOKEN_NUM_EACH_NODE	Max tokens per node	12000
NAVEXA_MAX_PAGE_NUM_EACH_NODE	Max pages per node	8
NAVEXA_DISABLE_SUMMARY	Force-disable summaries	0

Parser Environment Defaults

Variable	Purpose	Default
NAVEXA_DOCLING_PROFILE	Docling profile preset (balanced, image_manual, fast_text)	balanced
NAVEXA_PARSER_MODEL	Parser backend	docling
NAVEXA_DOCLING_OUTPUT_FORMAT	markdown or text	markdown
NAVEXA_DOCLING_OCR	Enable OCR (0/1)	1
NAVEXA_RAPIDOCR_BACKEND	OCR backend	torch
NAVEXA_DOCLING_FORCE_FULL_PAGE_OCR	Force OCR on full page	1
NAVEXA_DOCLING_TABLE_STRUCTURE	Enable table structure extraction (0/1)	1
NAVEXA_DOCLING_PICTURE_DESCRIPTION	Picture descriptions	0
NAVEXA_DOCLING_REMOTE_SERVICES	Enable remote services	0
NAVEXA_DOCLING_IMAGE_MODE	placeholder, embedded, referenced, none	placeholder
NAVEXA_DOCLING_QUIET	Reduce Docling/RapidOCR logs	1

These env values act as defaults for parser_config when the matching field is not passed explicitly in code.

Quick Start

from navexa import index_structured_document_tree, save_document_tree

result = index_structured_document_tree(
    pdf_path="/path/to/file.pdf",
    mode="llm",
    model_config={
        "provider": "openai",
        "model": "gpt-4.1-mini",
        "api_key": "...",
    },
    verbosity="medium",
    parser_config={
        "name": "docling",
        "output_format": "markdown",
        "options": {
            "profile": "balanced",            # balanced | image_manual | fast_text
            "do_ocr": True,                   # optional override
            "force_full_page_ocr": True,      # optional override
            "do_table_structure": True,       # optional override
            "do_picture_description": False,  # optional override
            "backend": "torch",               # torch | onnxruntime
            "image_mode": "placeholder",      # placeholder | embedded | referenced | none
            "quiet": True,
        },
    },
    max_token_num_each_node=12000,
    max_page_num_each_node=8,
    if_add_node_summary="yes",
)

save = save_document_tree(
    index_result=result,
    out_dir=None,               # defaults to <pdf_dir>/<pdf_stem>_navexa_out
    write_tree=True,
    write_validation=True,
    write_compat=False,
)

print(save.out_dir)
print(save.paths)
print(result.tree_navexa["cost"])

Public APIs

Top-level imports (from navexa):

• index_structured_document_tree
• index_semi_structured_document_tree
• index_unstructured_document_tree
• index_transcript_document_tree
• save_document_tree
• index_and_save_document_tree
• fetch_document_tree
• fetch_validation_report
• fetch_compat_tree
• build_search_tree_view
• build_node_index
• reason_over_tree
• print_reasoning_trace
• extract_selected_context
• answer_from_context
• run_reasoning_rag
• load_navexa_env

Indexing Functions

1) index_structured_document_tree(...)

LLM requirement: optional
Best for: documents with clear headings/TOC

2) index_semi_structured_document_tree(...)

LLM requirement: optional
Best for: inconsistent headings/order where deterministic parsing works, but LLM can improve weak heading normalization

Behavior:

• without LLM, Navexa still builds headings deterministically from the markdown tree and base outline pipeline
• if that outline is weak, it falls back to heuristic heading generation from page text
• with LLM enabled, Navexa uses the same deterministic base and then improves weak headings via heading normalization

Runtime signal:

• logs include heading_source=existing|heuristic|llm for semi-structured flow
• output JSON includes pipeline.semi_structured_source

3) index_unstructured_document_tree(...)

LLM requirement: optional
Best for: weak heading structure; builds chunk-based synthetic sections

4) index_transcript_document_tree(...)

LLM requirement: required
Best for: meeting/interview transcript documents

Note: transcript indexing does not use parser/Docling configuration, so this API does not expose parser_config, parser_model, output_format, or docling_options.

TOC/Section Strategy by Document Type

Document Type	Uses TOC Detection Pipeline	Uses LLM for TOC/Heading	Deterministic Fallback
structured	yes	optional	yes
semi_structured	yes	optional (heading normalization enhancer)	yes
unstructured	no (chunk-first synthetic sections)	optional (title generation only)	yes
transcript	n/a (topic grouping flow)	required	no (requires LLM)

Parser Config Summary

New grouped parameter: parser_config

Available in:

• index_structured_document_tree(...)
• index_semi_structured_document_tree(...)
• index_unstructured_document_tree(...)
• compatibility wrappers (index_document_tree(...), index_and_save_document_tree(...))

Recommended usage:

parser_config={
    "name": "docling",
    "output_format": "markdown",
    "options": {"profile": "balanced"},
}

Effective parser config is:

• logged at runtime, and
• stored in output JSON at tree_navexa.pipeline.parser_config
• recoverable Docling extraction warnings are stored at tree_navexa.pipeline.warnings

Recoverable warning behavior:

• Navexa suppresses raw Docling tracebacks when usable content was still recovered
• Navexa logs a one-line warning instead
• the warning is preserved in output JSON for later inspection

Precedence reminder:

• parser profile defaults are applied first
• matching .env values override the profile defaults
• explicit parser_config["options"] overrides both
• if legacy Python API fields are also passed, parser_config wins

Inside parser_config:

• name
• output_format
• options

Current default behavior:

• profile="balanced"
• do_ocr=True
• force_full_page_ocr=True
• do_table_structure=True
• do_picture_description=False
• enable_remote_services=False
• backend="torch"
• image_mode="placeholder"
• quiet=True

Deprecated Python API parser fields:

• parser_model
• output_format
• docling_options

These remain accepted in the Python API for compatibility but are deprecated. Prefer parser_config.

Shared Indexing Parameters and Values

Parameter	Type	Allowed Values	Default
pdf_path	str	valid PDF path	required
model	Optional[str]	provider model/deployment name	deprecated
model_config	Optional[dict]	see model section above	None
mode	Optional[str]	llm, use-llm, with-llm, no-llm	None
verbosity	Optional[str]	low, medium, high, 1, 2, 3, debug, detailed	None
parser_config	Optional[dict]	see parser section below	None
parser_model	Optional[str]	currently docling only	deprecated
output_format	Optional[str]	markdown, text	deprecated
docling_options	Optional[dict]	legacy Docling options	deprecated
max_token_num_each_node	int	>=1	12000
max_page_num_each_node	int	>=1	8
if_add_node_summary	str	yes, no	yes

The parser-related parameters above apply to:

• index_structured_document_tree(...)
• index_semi_structured_document_tree(...)
• index_unstructured_document_tree(...)

Model-related note:

• prefer model_config for in-code configuration
• model still works for compatibility, but it is deprecated
• all indexing APIs accept model
• all indexing APIs accept model_config
• if both are passed, model wins over model_config["model"]

Transcript-specific note:

• index_transcript_document_tree(...) does not expose mode, parser_config, parser_model, output_format, or docling_options

Structured/semi-structured note:

• if you set parser_config["output_format"]="text" or legacy output_format="text" for structured or semi_structured, Navexa will force it to markdown
• reason: heading/tree extraction for these flows depends on markdown heading structure
• Navexa logs a warning when this coercion happens

Function-specific extra parameters:

• semi_heading_prompt_template in index_semi_structured_document_tree
• transcript_topic_prompt_template in index_transcript_document_tree

Backward compatibility:

• index_document_tree(...) still exists and routes to structured flow.

parser_config Dictionary Reference

Use parser_config when you want parser behavior controlled directly in code.

Step by step:

1. set parser name in parser_config["name"]
2. set parser output in parser_config["output_format"]
3. put parser-specific options in parser_config["options"]
4. pass only the fields you want to override

Example:

parser_config = {
    "name": "docling",
    "output_format": "markdown",
    "options": {
        "profile": "image_manual",
        "backend": "torch",
        "do_picture_description": True,
    },
}

Current parser names:

• docling

Current output formats:

• markdown
• text

Important behavior:

• structured and semi_structured do not truly run in text parser mode
• if output_format="text" is requested for those flows, Navexa coerces it to markdown
• unstructured can still use either markdown or text

parser_config["options"] for name="docling":

Key	Type	Allowed Values	Default	Scenario
profile	str	balanced, image_manual, fast_text	balanced	Start-point preset
do_ocr	bool	True, False	True	Turn OCR on/off
force_full_page_ocr	bool	True, False	True	Scanned/image PDFs
do_table_structure	bool	True, False	True	Table-heavy docs
do_picture_description	bool	True, False	False	Image/manual docs
enable_remote_services	bool	True, False	False	Remote enrichment
backend	str	torch, onnxruntime	torch	OCR runtime choice
image_mode	str	placeholder, embedded, referenced, none	placeholder	Markdown image policy
quiet	bool	True, False	True	Reduce parser logs

Profile behavior:

Profile	OCR	Full-page OCR	Table Structure	Picture Description	Best For
balanced	on	on	on	off	Most documents
image_manual	on	on	on	on	Image-heavy manuals/decks
fast_text	off	off	on	off	Native digital text PDFs

Backend note:

• backend="torch": default, generally most stable.
• backend="onnxruntime": often lighter/faster on CPU-only environments.
• onnxruntime is included in Navexa install dependencies.

Quiet note:

• quiet=True reduces normal Docling/RapidOCR log noise
• major failures still raise clear Navexa errors
• recoverable parser issues are still reported through pipeline.warnings

Legacy compatibility note:

• parser_model, output_format, and docling_options still work
• they are deprecated in the Python API
• if parser_config is also passed, parser_config wins

Save and Fetch APIs

Save

save_document_tree(index_result, out_dir=None, save_mode="explicit", write_tree=True, write_validation=False, write_compat=False)

Notes:

• At least one of write_tree/write_validation/write_compat must be True
• If out_dir=None, default is <pdf_dir>/<pdf_stem>_navexa_out

Fetch

• fetch_document_tree(source, file_name="tree_navexa.json")
• fetch_validation_report(source)
• fetch_compat_tree(source)

source can be:

• in-memory dict
• JSON file path
• output directory path
• IndexResult object

Reasoning and RAG APIs

Tree preparation

build_search_tree_view(tree, strip_fields=("exclusive_text", "full_text"))

build_node_index(tree, include_page_ranges=True, exclude_fields=None)

Tree reasoning

reason_over_tree(query, tree, model=None, model_config=None, prompt_template=None, llm_callable=None, return_prompt=False, verbosity=None, strip_fields=("exclusive_text","full_text"), prompt_extra=None)

Return object fields:

• thinking
• node_list
• raw_response
• used_prompt (if requested)
• parsed_json

Trace print

print_reasoning_trace(reasoning_result, node_index)

Context extraction

extract_selected_context(tree, node_list, text_mode="inclusive", dedupe_ancestor=True)

text_mode values:

• inclusive -> uses full_text
• exclusive -> uses exclusive_text

dedupe_ancestor behavior:

• True: if parent and child are both selected, child is dropped
• False: keeps all selected nodes

Answer generation

answer_from_context(query, context_text, model=None, model_config=None, prompt_template=None, llm_callable=None, return_prompt=False, verbosity=None, prompt_extra=None)

End-to-end

run_reasoning_rag(query, tree_or_source, model=None, model_config=None, tree_prompt_template=None, answer_prompt_template=None, llm_callable=None, return_prompt=False, verbosity=None, strip_fields=("exclusive_text","full_text"), text_mode="inclusive", dedupe_ancestor=True, tree_prompt_extra=None, answer_prompt_extra=None)

Returns:

• tree, tree_view, node_index
• reasoning, context, answer
• cost_before, cost_after, cost_delta

Prompt Template + prompt_extra Examples

Important:

• prompt_extra (and tree_prompt_extra / answer_prompt_extra) is passed as JSON payload.
• If your template includes {extra_json}, Navexa replaces it with payload JSON.
• If your template does not include {extra_json} and payload is provided, Navexa appends an Additional ... (JSON) section automatically.
• If payload is empty, nothing is appended.

Example: reason_over_tree(...) with custom prompt template and prompt_extra

from navexa import reason_over_tree

custom_tree_prompt = """
You are a strict node selector.
Question: {query}

Tree:
{tree_json}

Constraints:
{extra_json}

Return JSON:
{"thinking":"...", "node_list":["0001"]}
"""

reasoning = reason_over_tree(
    query="What are key warnings?",
    tree=tree,
    model_config={"provider": "openai", "model": "gpt-4.1-mini", "api_key": "..."},
    prompt_template=custom_tree_prompt,
    prompt_extra={"must_include_terms": ["warning", "precaution"], "max_nodes": 2},
    return_prompt=True,
)

print(reasoning.node_list)
print(reasoning.used_prompt)

Example: answer_from_context(...) with prompt_extra

from navexa import answer_from_context

answer_template = """
Answer only from context.
Question: {query}
Context: {context}
Policy: {extra_json}
"""

answer = answer_from_context(
    query="What are key warnings?",
    context_text="Warnings: liver toxicity; monitor ALT/AST.",
    model_config={"provider": "openai", "model": "gpt-4.1-mini", "api_key": "..."},
    prompt_template=answer_template,
    prompt_extra={"style": "bullet", "max_points": 3},
    return_prompt=True,
)

print(answer.answer)
print(answer.used_prompt)

Example: run_reasoning_rag(...) with separate extras

from navexa import run_reasoning_rag

rag = run_reasoning_rag(
    query="What are key warnings?",
    tree_or_source=tree,
    model_config={"provider": "openai", "model": "gpt-4.1-mini", "api_key": "..."},
    tree_prompt_template=custom_tree_prompt,
    answer_prompt_template=answer_template,
    tree_prompt_extra={"max_nodes": 2},
    answer_prompt_extra={"style": "short"},
    return_prompt=True,
)

print(rag.reasoning.used_prompt)
print(rag.answer.used_prompt)

End-to-End Example (Index + RAG)

from navexa import (
    index_structured_document_tree,
    save_document_tree,
    fetch_document_tree,
    run_reasoning_rag,
    print_reasoning_trace,
)

pdf_path = "/path/to/file.pdf"
query = "What are the key warnings?"

index_result = index_structured_document_tree(
    pdf_path=pdf_path,
    mode="llm",
    model_config={
        "provider": "openai",
        "model": "gpt-4.1-mini",
        "api_key": "...",
    },
    verbosity="high",
)

save_result = save_document_tree(
    index_result=index_result,
    out_dir="/path/to/output",
    write_tree=True,
    write_validation=True,
    write_compat=False,
)

tree = fetch_document_tree(save_result.out_dir)

rag = run_reasoning_rag(
    query=query,
    tree_or_source=tree,
    model_config={
        "provider": "openai",
        "model": "gpt-4.1-mini",
        "api_key": "...",
    },
    return_prompt=True,
    verbosity="high",
)

print_reasoning_trace(rag.reasoning, rag.node_index)
print("\nAnswer:\n", rag.answer.answer)
print("\nCost delta:\n", rag.cost_delta)

CLI Usage

After install, CLI entry point:

navexa-index --pdf /path/file.pdf --out-dir /path/out

If navexa-index is "command not found":

• If you installed into a virtualenv, activate it first: source <venv>/bin/activate
• If you installed with pip install --user, the script is usually at ~/.local/bin/navexa-index. Add it to PATH once:

echo 'export PATH="$HOME/.local/bin:$PATH"' >> ~/.bashrc
source ~/.bashrc

All CLI flags:

Flag	Allowed Values	Default
--pdf	PDF path	required
--out-dir	output dir	required
--model-config	JSON object or JSON file path	None
--model	model/deployment string	deprecated
--mode	llm, no-llm	NAVEXA_MODE or no-llm
--document-type	structured, semi_structured, unstructured, transcript	structured
--parser-config	JSON object or JSON file path	None
--parser-model	docling	docling
--output-format	markdown, text	markdown
--docling-profile	balanced, image_manual, fast_text	balanced
--docling-ocr	0, 1	profile/env resolved
--docling-force-full-page-ocr	0, 1	profile/env resolved
--docling-table-structure	0, 1	profile/env resolved
--docling-picture-description	0, 1	profile/env resolved
--docling-backend	string (e.g. torch, onnxruntime)	profile/env resolved
--docling-image-mode	placeholder, embedded, referenced, none	profile/env resolved
--docling-remote-services	0, 1	profile/env resolved
--docling-quiet	0, 1	profile/env resolved
--verbose	1,2,3,low,medium,high	medium
--max-token-num-each-node	int	12000
--max-page-num-each-node	int	8
--if-add-node-summary	yes, no	yes
--with-validation	switch	off
--with-compat	switch	off

Preferred CLI parser setup:

• use --model-config for grouped provider/model credentials and routing
• use legacy --model only as a compatibility override
• if both --model-config and --model are passed, legacy --model wins for compatibility
• use --parser-config for the grouped parser model
• use the old flat parser flags only as compatibility shorthands
• if --parser-config is passed together with old parser flags, --parser-config wins and the old parser flags are ignored
• if --document-type transcript is used, parser configuration is ignored

Example with grouped model + parser config:

navexa-index \
  --pdf /path/file.pdf \
  --out-dir /path/out \
  --mode llm \
  --document-type structured \
  --model-config '{"provider":"azure","deployment_name":"my-deploy","deployment_raw_name":"gpt-4.1-mini","api_key":"...","base_url":"https://<resource>.openai.azure.com"}' \
  --parser-config '{"name":"docling","output_format":"markdown","options":{"profile":"balanced","backend":"torch","quiet":true}}' \
  --verbose high \
  --if-add-node-summary yes \
  --with-validation

Example with grouped parser config:

navexa-index \
  --pdf /path/file.pdf \
  --out-dir /path/out \
  --mode llm \
  --document-type structured \
  --parser-config '{"name":"docling","output_format":"markdown","options":{"profile":"balanced","backend":"torch","quiet":true}}' \
  --verbose high \
  --if-add-node-summary yes \
  --with-validation

Equivalent legacy shorthand example:

navexa-index \
  --pdf /path/file.pdf \
  --out-dir /path/out \
  --mode llm \
  --document-type structured \
  --output-format markdown \
  --verbose high \
  --if-add-node-summary yes \
  --with-validation

Output Files

Generated files:

• tree_navexa.json (canonical)
• validation_report.json (optional)
• tree_legacy_compat.json (optional)

tree_navexa.json top-level keys include:

• doc_id, doc_name, pages, pipeline_version
• source (path/hash/page count)
• cost (calls/tokens/estimated cost)
• pipeline (mode, document type, parser settings, node limits, steps)
• structure (hierarchical nodes with children)
• transcript (present for transcript flow)

Useful pipeline fields:

• model_config: resolved safe model/provider metadata
• parser_config: resolved parser configuration
• warnings: recoverable parser/runtime warnings

Logging and Cost

Verbosity:

• low: compact result logs
• medium: stage-by-stage logs
• high: debug-level details and usage deltas

Cost fields are available in:

• tree_navexa["cost"]
• IndexResult.meta["cost"]
• RAGResult.cost_delta for reasoning runs

Prompt Overrides and Custom LLM

Detailed docs:

• docs/README.md
• docs/custom_llm_integration.md
• docs/prompt_templates.md

You can override prompts:

• semi_heading_prompt_template
• transcript_topic_prompt_template
• tree_prompt_template
• answer_prompt_template

Use a provider-backed BaseExternalLLM adapter with llm_callable=....

Behavior:

• if llm_callable is provided, Navexa uses your external BaseExternalLLM adapter
• if llm_callable is not provided, Navexa uses internal provider/env client

Failure Behavior and Troubleshooting

Common cases:

• Missing API key in LLM-required flows (transcript) -> raises RuntimeError
• mode="llm" with missing credentials (any document type) -> raises RuntimeError
• Missing API key in optional LLM flow with mode unset (structured / semi_structured / unstructured) -> runs in effective no-llm
• Invalid parser_config["name"] or legacy parser_model -> ValueError (currently only docling)
• Invalid parser_config["output_format"] or legacy output_format -> ValueError (markdown or text)
• Empty/invalid tree input to reasoning APIs -> ValueError
• Recoverable Docling OCR/parser issues -> Navexa logs a one-line warning and stores it in tree_navexa.pipeline.warnings
• Major Docling failure with no usable extracted content -> Navexa raises RuntimeError with retry guidance instead of showing raw third-party traceback

Notebook note:

• asyncio.run() loop conflicts are handled in reasoning functions with thread fallback.
• If you still run into notebook event-loop issues, restart kernel and re-run imports.

Acknowledgment

Navexa is an independent implementation. Some architecture patterns and selected adapted code paths were informed by PageIndex.

Attribution files:

• THIRD_PARTY_NOTICES.md
• LICENSE

License

This project is licensed under MIT.

Practical compliance checklist:

1. Keep this repository LICENSE.
2. Keep third-party attribution notices.
3. Preserve upstream MIT notice for copied/substantially adapted portions.

This documentation is technical guidance, not legal advice.