PageIndex/run_pageindex.py

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import argparse
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import os
import json
from pageindex.index.page_index import *
fix: address xhigh code-review findings on 2d46d68..8f536cb Verified 12 findings from an xhigh-effort review of the prior review-fix batch; all confirmed real. Most trace back to one root cause: the build_index() text-stripping fix (8f536cb) correctly stopped Markdown from leaking full text by default, but broke every path that assumed text could be re-read later. Correctness: - LocalBackend._fill_node_text (get_document(include_text=True)) only handled PDF's start_index/end_index convention; Markdown nodes use line_num and got silently empty text. Now handles both. - get_page_content's Markdown fallback (triggered when a StorageEngine legitimately returns None from get_pages()) read from the now-text-stripped structure. It now re-derives from the source file, mirroring the PDF fallback, so it no longer depends on structure text at all. - add_document's PDF-only text-stripping branch (with the stale "markdown needs text in structure for fallback retrieval" comment) is now dead/wrong since build_index() already applies if_add_node_text uniformly — removed. - _validate_llm_provider's keyless-provider allowlist was missing several local LiteLLM providers (xinference, llamafile, triton, oobabooga, openai_like, docker_model_runner, custom, custom_openai, petals) that need no API key just like ollama/lm_studio; expanded. - The three agent-tool closures (get_document, get_document_structure, get_page_content) had three different not-found patterns; two bypassed the backend's DocumentNotFoundError entirely. Extracted LocalBackend. _require_document as the single existence check every method/tool now uses. - examples/agentic_vectorless_rag_demo.py's hand-rolled Agent() didn't apply the litellm/ prefix normalization the SDK does internally, so its own documented "any LiteLLM provider" claim broke for non-openai models. - cloud delete_collection's cache eviction removed the "folders unavailable" None sentinel too, forcing a wasted re-fetch; now only pops on a real id. Cleanup / altitude: - build_index() skips the remove_structure_text walk entirely when text was never added (content_based + if_add_node_summary=False + if_add_node_text= False) instead of a guaranteed no-op tree walk. - page_index()'s locals()-capture-as-kwargs (fragile by construction) replaced with an explicit dict of the named parameters. - run_pageindex.py's _cli_bool and the page_index_md.py legacy shim's _coerce_bool were duplicate, diverging implementations; both now bind directly to the canonical pageindex.index.page_index_md._coerce_bool. - retrieve.py's _get_md_page_content delegated its own traversal instead of calling the canonical get_md_page_content; now a one-line delegation. - FileTypeError's docstring now calls out the except-ordering gotcha from also subclassing ValueError. 17 new regression tests (tests/test_review_fixes_2.py) plus 2 updated in tests/test_legacy_shims.py for the simplified md_to_tree shim. Full suite: 210 passed, 2 skipped. Claude-Session: https://claude.ai/code/session_01Kx5DgKbhK1N8autqXH8SmS
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# Reuse the canonical yes/no coercion (as _cli_bool) instead of a second copy —
# a bare ``--flag`` (no value) resolves to True via argparse's ``const``; an
# explicit value keeps the legacy yes/no style working, so ``--flag no`` turns
# it off. argparse only ever passes a str here (const/default bypass type=).
from pageindex.index.page_index_md import md_to_tree, _coerce_bool as _cli_bool
from pageindex.config import IndexConfig
if __name__ == "__main__":
# Set up argument parser
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parser = argparse.ArgumentParser(description='Process PDF or Markdown document and generate structure')
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parser.add_argument('--pdf_path', type=str, help='Path to the PDF file')
parser.add_argument('--md_path', type=str, help='Path to the Markdown file')
parser.add_argument('--model', type=str, default=None, help='Model to use')
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Integrate LiteLLM for multi-provider LLM support (#168) * Integrate litellm for multi-provider LLM support * recover the default config yaml * Use litellm.acompletion for native async support * fix tob * Rename llm_complete/allm_complete to llm_completion/llm_acompletion, remove unused llm_complete_stream * Pin litellm to version 1.82.0 * resolve comments * args from cli is used to overrides config.yaml * Fix get_page_tokens hardcoded model default Pass opt.model to get_page_tokens so tokenization respects the configured model instead of always using gpt-4o-2024-11-20. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Remove explicit openai dependency from requirements.txt openai is no longer directly imported; it comes in as a transitive dependency of litellm. Pinning it explicitly risks version conflicts. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Restore openai==1.101.0 pin in requirements.txt litellm==1.82.0 and openai-agents have conflicting openai version requirements, but openai==1.101.0 works at runtime for both. The pin is necessary to prevent litellm from pulling in openai>=2.x which would break openai-agents. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Remove explicit openai dependency from requirements.txt openai is not directly used; it comes in as a transitive dependency of litellm. No openai-agents in this branch so no pin needed. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * fix an litellm error log * resolve comments --------- Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
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parser.add_argument('--toc-check-pages', type=int, default=None,
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help='Number of pages to check for table of contents (PDF only)')
Integrate LiteLLM for multi-provider LLM support (#168) * Integrate litellm for multi-provider LLM support * recover the default config yaml * Use litellm.acompletion for native async support * fix tob * Rename llm_complete/allm_complete to llm_completion/llm_acompletion, remove unused llm_complete_stream * Pin litellm to version 1.82.0 * resolve comments * args from cli is used to overrides config.yaml * Fix get_page_tokens hardcoded model default Pass opt.model to get_page_tokens so tokenization respects the configured model instead of always using gpt-4o-2024-11-20. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Remove explicit openai dependency from requirements.txt openai is no longer directly imported; it comes in as a transitive dependency of litellm. Pinning it explicitly risks version conflicts. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Restore openai==1.101.0 pin in requirements.txt litellm==1.82.0 and openai-agents have conflicting openai version requirements, but openai==1.101.0 works at runtime for both. The pin is necessary to prevent litellm from pulling in openai>=2.x which would break openai-agents. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Remove explicit openai dependency from requirements.txt openai is not directly used; it comes in as a transitive dependency of litellm. No openai-agents in this branch so no pin needed. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * fix an litellm error log * resolve comments --------- Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
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parser.add_argument('--max-pages-per-node', type=int, default=None,
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help='Maximum number of pages per node (PDF only)')
Integrate LiteLLM for multi-provider LLM support (#168) * Integrate litellm for multi-provider LLM support * recover the default config yaml * Use litellm.acompletion for native async support * fix tob * Rename llm_complete/allm_complete to llm_completion/llm_acompletion, remove unused llm_complete_stream * Pin litellm to version 1.82.0 * resolve comments * args from cli is used to overrides config.yaml * Fix get_page_tokens hardcoded model default Pass opt.model to get_page_tokens so tokenization respects the configured model instead of always using gpt-4o-2024-11-20. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Remove explicit openai dependency from requirements.txt openai is no longer directly imported; it comes in as a transitive dependency of litellm. Pinning it explicitly risks version conflicts. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Restore openai==1.101.0 pin in requirements.txt litellm==1.82.0 and openai-agents have conflicting openai version requirements, but openai==1.101.0 works at runtime for both. The pin is necessary to prevent litellm from pulling in openai>=2.x which would break openai-agents. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Remove explicit openai dependency from requirements.txt openai is not directly used; it comes in as a transitive dependency of litellm. No openai-agents in this branch so no pin needed. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * fix an litellm error log * resolve comments --------- Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
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parser.add_argument('--max-tokens-per-node', type=int, default=None,
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help='Maximum number of tokens per node (PDF only)')
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# Bare flag (e.g. --if-add-node-id) turns the option on; an explicit value
# keeps the legacy yes/no style, so --if-add-node-id no turns it off.
parser.add_argument('--if-add-node-id', nargs='?', const=True, type=_cli_bool, default=None,
help='Add node IDs (on by default). Bare flag or yes/no, e.g. --if-add-node-id no')
parser.add_argument('--if-add-node-summary', nargs='?', const=True, type=_cli_bool, default=None,
help='Add node summaries (on by default). Bare flag or yes/no')
parser.add_argument('--if-add-doc-description', nargs='?', const=True, type=_cli_bool, default=None,
help='Add a document description (on by default). Bare flag or yes/no')
parser.add_argument('--if-add-node-text', nargs='?', const=True, type=_cli_bool, default=None,
help='Add raw text to nodes (off by default). Bare flag or yes/no')
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# Markdown specific arguments
fix: CMYK image drop, empty-doc crash, page_index shadowing, sqlite hardening, flaky tests Addresses items 9-13 and a/b/c/f from the max-effort review of PR #272. - pdf.py: image colorspace check was `pix.n > 4`, which treats CMYK-without- alpha (n==4, same as RGBA) as not needing RGB conversion; pix.save() as .png then raises "unsupported colorspace", silently dropped by the surrounding except. Fixed to `pix.n - pix.alpha >= 4` (correctly converts CMYK, leaves RGBA untouched). - pipeline.py: detect_strategy([]) (an empty/whitespace-only source file) returned "content_based", routing into the PDF-oriented TOC-detection pipeline -- wasting a real LLM call before raising IndexingError. Empty node lists now route to level_based, whose build_tree_from_levels([]) returns an empty structure instantly with zero LLM calls. - page_index.py (shim): pageindex/__init__.py binds the canonical `page_index` function as the package attribute, but this file is ALSO a real submodule of the same name -- importing it anywhere (import machinery, unconditional) overwrites that attribute with the module object, breaking `from pageindex import page_index; page_index(x)` for the rest of the process. Made the shim module itself callable (delegates to the real function via a ModuleType subclass), so whichever object ends up in that slot is callable regardless of import order. - storage/sqlite.py: create_collection let a raw sqlite3.IntegrityError escape on a duplicate name (new CollectionAlreadyExistsError); the collections table's CHECK constraint only validated the name's first character (GLOB '*' is a wildcard, not a regex quantifier over the preceding class) -- fixed to validate the whole string, and SQLiteStorage now also validates in Python (it's a public StorageEngine usable directly, bypassing LocalBackend's own check). - tests/test_review_fixes_2.py: two tests used a ContentNode with no `level` set, so build_index took the content_based path and made real (retried, slow, and -- with a valid key -- billable) LLM calls instead of testing the text-stripping logic they claimed to. Mocked out _content_based_pipeline. - retrieve.py: _parse_pages/_get_pdf_page_content were independent copies of the canonical parse_pages/get_pdf_page_content that had already drifted (missing the p>=1 filter and 1000-page DoS cap) -- delegate to canonical now, so the legacy pageindex.get_page_content path can't silently regress again. - parser/markdown.py: a leading UTF-8 BOM broke first-header detection (not whitespace, .strip() doesn't remove it) -- decode utf-8-sig. Only backtick fences were recognized as code blocks, so a '#'-prefixed line inside a ~~~-fenced block (valid CommonMark) was misparsed as a heading -- recognize both fence styles. - run_pageindex.py: --if-thinning wasn't migrated to the bare-flag + legacy-yes/no convention the other four --if-add-* flags got; bare usage raised an argparse error and it never went through the shared coercion. - types.py: DocumentDetail's `structure` field was inside the class's total=False body, so TypedDict rules made it optional even though every backend always populates it. Split into a required base class. Adds regression tests for all of the above. Full suite: 244 passed, 2 skipped (one pre-existing, unrelated flaky cloud-streaming test). Claude-Session: https://claude.ai/code/session_01Kx5DgKbhK1N8autqXH8SmS
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parser.add_argument('--if-thinning', nargs='?', const=True, type=_cli_bool, default=None,
help='Apply tree thinning (off by default, markdown only). Bare flag or yes/no')
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parser.add_argument('--thinning-threshold', type=int, default=5000,
help='Minimum token threshold for thinning (markdown only)')
parser.add_argument('--summary-token-threshold', type=int, default=200,
help='Token threshold for generating summaries (markdown only)')
args = parser.parse_args()
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# Validate that exactly one file type is specified
if not args.pdf_path and not args.md_path:
raise ValueError("Either --pdf_path or --md_path must be specified")
if args.pdf_path and args.md_path:
raise ValueError("Only one of --pdf_path or --md_path can be specified")
# Build IndexConfig from CLI args (None values use defaults)
config_overrides = {
k: v for k, v in {
"model": args.model,
"toc_check_page_num": args.toc_check_pages,
"max_page_num_each_node": args.max_pages_per_node,
"max_token_num_each_node": args.max_tokens_per_node,
"if_add_node_id": args.if_add_node_id,
"if_add_node_summary": args.if_add_node_summary,
"if_add_doc_description": args.if_add_doc_description,
"if_add_node_text": args.if_add_node_text,
}.items() if v is not None
}
opt = IndexConfig(**config_overrides)
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if args.pdf_path:
# Validate PDF file
if not args.pdf_path.lower().endswith('.pdf'):
raise ValueError("PDF file must have .pdf extension")
if not os.path.isfile(args.pdf_path):
raise ValueError(f"PDF file not found: {args.pdf_path}")
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# Process the PDF
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toc_with_page_number = page_index_main(args.pdf_path, opt)
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print('Parsing done, saving to file...')
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# Save results
pdf_name = os.path.splitext(os.path.basename(args.pdf_path))[0]
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output_dir = './results'
output_file = f'{output_dir}/{pdf_name}_structure.json'
os.makedirs(output_dir, exist_ok=True)
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with open(output_file, 'w', encoding='utf-8') as f:
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json.dump(toc_with_page_number, f, indent=2)
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print(f'Tree structure saved to: {output_file}')
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elif args.md_path:
# Validate Markdown file
if not args.md_path.lower().endswith(('.md', '.markdown')):
raise ValueError("Markdown file must have .md or .markdown extension")
if not os.path.isfile(args.md_path):
raise ValueError(f"Markdown file not found: {args.md_path}")
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# Process markdown file
print('Processing markdown file...')
import asyncio
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toc_with_page_number = asyncio.run(md_to_tree(
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md_path=args.md_path,
fix: CMYK image drop, empty-doc crash, page_index shadowing, sqlite hardening, flaky tests Addresses items 9-13 and a/b/c/f from the max-effort review of PR #272. - pdf.py: image colorspace check was `pix.n > 4`, which treats CMYK-without- alpha (n==4, same as RGBA) as not needing RGB conversion; pix.save() as .png then raises "unsupported colorspace", silently dropped by the surrounding except. Fixed to `pix.n - pix.alpha >= 4` (correctly converts CMYK, leaves RGBA untouched). - pipeline.py: detect_strategy([]) (an empty/whitespace-only source file) returned "content_based", routing into the PDF-oriented TOC-detection pipeline -- wasting a real LLM call before raising IndexingError. Empty node lists now route to level_based, whose build_tree_from_levels([]) returns an empty structure instantly with zero LLM calls. - page_index.py (shim): pageindex/__init__.py binds the canonical `page_index` function as the package attribute, but this file is ALSO a real submodule of the same name -- importing it anywhere (import machinery, unconditional) overwrites that attribute with the module object, breaking `from pageindex import page_index; page_index(x)` for the rest of the process. Made the shim module itself callable (delegates to the real function via a ModuleType subclass), so whichever object ends up in that slot is callable regardless of import order. - storage/sqlite.py: create_collection let a raw sqlite3.IntegrityError escape on a duplicate name (new CollectionAlreadyExistsError); the collections table's CHECK constraint only validated the name's first character (GLOB '*' is a wildcard, not a regex quantifier over the preceding class) -- fixed to validate the whole string, and SQLiteStorage now also validates in Python (it's a public StorageEngine usable directly, bypassing LocalBackend's own check). - tests/test_review_fixes_2.py: two tests used a ContentNode with no `level` set, so build_index took the content_based path and made real (retried, slow, and -- with a valid key -- billable) LLM calls instead of testing the text-stripping logic they claimed to. Mocked out _content_based_pipeline. - retrieve.py: _parse_pages/_get_pdf_page_content were independent copies of the canonical parse_pages/get_pdf_page_content that had already drifted (missing the p>=1 filter and 1000-page DoS cap) -- delegate to canonical now, so the legacy pageindex.get_page_content path can't silently regress again. - parser/markdown.py: a leading UTF-8 BOM broke first-header detection (not whitespace, .strip() doesn't remove it) -- decode utf-8-sig. Only backtick fences were recognized as code blocks, so a '#'-prefixed line inside a ~~~-fenced block (valid CommonMark) was misparsed as a heading -- recognize both fence styles. - run_pageindex.py: --if-thinning wasn't migrated to the bare-flag + legacy-yes/no convention the other four --if-add-* flags got; bare usage raised an argparse error and it never went through the shared coercion. - types.py: DocumentDetail's `structure` field was inside the class's total=False body, so TypedDict rules made it optional even though every backend always populates it. Split into a required base class. Adds regression tests for all of the above. Full suite: 244 passed, 2 skipped (one pre-existing, unrelated flaky cloud-streaming test). Claude-Session: https://claude.ai/code/session_01Kx5DgKbhK1N8autqXH8SmS
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if_thinning=bool(args.if_thinning),
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min_token_threshold=args.thinning_threshold,
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if_add_node_summary=opt.if_add_node_summary,
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summary_token_threshold=args.summary_token_threshold,
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model=opt.model,
if_add_doc_description=opt.if_add_doc_description,
if_add_node_text=opt.if_add_node_text,
if_add_node_id=opt.if_add_node_id
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))
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print('Parsing done, saving to file...')
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# Save results
md_name = os.path.splitext(os.path.basename(args.md_path))[0]
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output_dir = './results'
output_file = f'{output_dir}/{md_name}_structure.json'
os.makedirs(output_dir, exist_ok=True)
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with open(output_file, 'w', encoding='utf-8') as f:
json.dump(toc_with_page_number, f, indent=2, ensure_ascii=False)
print(f'Tree structure saved to: {output_file}')