diff --git a/.cursor/rules/python-developer.mdc b/.cursor/rules/python-developer.mdc new file mode 100644 index 0000000..6a0d566 --- /dev/null +++ b/.cursor/rules/python-developer.mdc @@ -0,0 +1,29 @@ +--- +description: +globs: +alwaysApply: true +--- +You are an AI assistant specialized in Python development. Your approach emphasizes: + +1. Clear project structure with separate directories for source code, tests, docs, and config. +2. Modular design with distinct files for models, services, controllers, and utilities. +3. Configuration management using environment variables. +4. Robust error handling and logging, including context capture. +5. Comprehensive testing with pytest. All tests should be fully annotated and should contain docstrings. +6. Detailed documentation using docstrings and README files. +7. Dependency management via uv. +8. Code style consistency using pylint and black. +9. CI/CD implementation with GitHub Actions. +10. AI-friendly coding practices: + - Descriptive variable and function names + - Type hints using the built-in types if possible + - Detailed comments for complex logic + - Rich error context for debugging + +Follow the following rules: + - For any python file, be sure to ALWAYS add typing annotations to each function or class. + - Be sure to include return types when necessary. + - Add descriptive google docstrings to all python functions and classes as well. Please use pep257 convention. Update existing docstrings if need be. + - Make sure you keep any comments that exist in a file. + +You provide code snippets and explanations tailored to these principles, optimizing for clarity and AI-assisted development. \ No newline at end of file diff --git a/.cursor/rules/python-type-hints.mdc b/.cursor/rules/python-type-hints.mdc new file mode 100644 index 0000000..54d0cd9 --- /dev/null +++ b/.cursor/rules/python-type-hints.mdc @@ -0,0 +1,81 @@ +--- +description: +globs: +alwaysApply: true +--- +# Python Type Hints Rule + +This rule enforces the use of built-in types for type hints in Python code when applicable. This follows modern Python practices (Python 3.9+) and makes the code more intuitive and maintainable. + +## Rules + +1. Use built-in types for type hints instead of their typing module counterparts when possible: + - Use `list[T]` instead of `List[T]` + - Use `dict[K, V]` instead of `Dict[K, V]` + - Use `set[T]` instead of `Set[T]` + - Use `tuple[T, ...]` instead of `Tuple[T, ...]` + - Use `frozenset[T]` instead of `FrozenSet[T]` + +2. Only use typing module types when: + - You need to support Python versions older than 3.9 + - You're using special types like `Union`, `Optional`, `Any`, etc. + - You're using generic types that don't have built-in equivalents + +## Examples + +✅ Good: +```python +def process_data(data: list[str]) -> dict[str, int]: + return {"count": len(data)} + +def get_items() -> set[int]: + return {1, 2, 3} + +def create_pairs() -> tuple[str, int]: + return ("key", 42) +``` + +❌ Bad: +```python +from typing import List, Dict, Set, Tuple + +def process_data(data: List[str]) -> Dict[str, int]: + return {"count": len(data)} + +def get_items() -> Set[int]: + return {1, 2, 3} + +def create_pairs() -> Tuple[str, int]: + return ("key", 42) +``` + +## Exceptions + +1. Keep using typing module types for: + - `Any` + - `Union` + - `Optional` + - `Literal` + - `TypeVar` + - `Generic` + - `Protocol` + - Other special typing constructs + +2. When backward compatibility is required (Python < 3.9), use the typing module types. + +## Benefits + +1. More intuitive code that uses actual types rather than special typing module versions +2. Reduced imports from typing module +3. Better IDE support and type checking +4. Follows modern Python best practices +5. Makes the code more maintainable and easier to understand + +## Implementation + +When reviewing or modifying code: +1. Check for typing module imports +2. Replace typing module types with built-in types where applicable +3. Keep special typing module types when needed +4. Update docstrings to reflect the use of built-in types +5. Ensure type hints are consistent throughout the codebase \ No newline at end of file diff --git a/.cursor/rules/uv-dependency-manager.mdc b/.cursor/rules/uv-dependency-manager.mdc new file mode 100644 index 0000000..2920ba3 --- /dev/null +++ b/.cursor/rules/uv-dependency-manager.mdc @@ -0,0 +1,71 @@ +--- +description: +globs: +alwaysApply: true +--- +# UV Dependency Manager Rule + +This rule enforces the use of `uv` as the primary dependency management tool for Python projects. + +## Requirements + +1. All Python dependencies must be managed using `uv`: + - Use `uv.lock` for lockfile + - Use `pyproject.toml` for project metadata and dependencies + - Use `requirements.txt` only for development dependencies or when explicitly required + +2. Project Structure: + - Must have a `pyproject.toml` file + - Must have a `uv.lock` file + - Should not use `poetry.lock` or `Pipfile.lock` + +3. Commands: + - Use `uv pip install` instead of `pip install` + - Use `uv pip freeze` instead of `pip freeze` + - Use `uv pip compile` for generating requirements files + +4. Virtual Environment: + - Use `uv venv` for creating virtual environments + - Use `uv pip install -r requirements.txt` for installing dependencies + +## Examples + +✅ Correct: +```bash +# Creating a virtual environment +uv venv + +# Installing dependencies +uv pip install -r requirements.txt + +# Updating dependencies +uv pip install --upgrade -r requirements.txt +``` + +❌ Incorrect: +```bash +# Using pip directly +pip install -r requirements.txt + +# Using poetry +poetry install + +# Using pipenv +pipenv install +``` + +## Benefits + +1. Faster dependency resolution and installation +2. Better reproducibility with lockfile +3. Modern Python packaging standards +4. Improved security with dependency scanning +5. Better integration with modern Python tooling + +## Implementation + +When implementing this rule: +1. Ensure all dependency management commands use `uv` +2. Keep `uv.lock` and `pyproject.toml` in version control +3. Document the use of `uv` in project README +4. Set up CI/CD to use `uv` for dependency installation \ No newline at end of file diff --git a/.cursorignore b/.cursorignore new file mode 100644 index 0000000..d4837ee --- /dev/null +++ b/.cursorignore @@ -0,0 +1,15 @@ +# Ignore all .env files +.env* + +# Ignore all config files +config* + +# Ignore all settings files +settings* + +# Ignore all input files +input* + +# Ignore all output files +output* + diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml new file mode 100644 index 0000000..bb1ebea --- /dev/null +++ b/.github/workflows/lint.yml @@ -0,0 +1,46 @@ +name: Lint and Test + +on: + push: + branches: [main] + pull_request: + branches: [main] + +jobs: + lint: + runs-on: ubuntu-latest + permissions: + contents: read + + steps: + - uses: actions/checkout@v4 + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: "3.13" + + - name: Install uv + run: | + curl -LsSf https://astral.sh/uv/install.sh | sh + echo "$HOME/.cargo/bin" >> $GITHUB_PATH + + - name: Install dependencies + run: | + make install + + - name: Run pylint + run: | + make check-lint + + - name: Run black + run: | + make check-format + + - name: Run mypy + run: | + make check-types + + - name: Run tests with coverage + run: | + make test diff --git a/.gitignore b/.gitignore index 5ccb9ee..e0e107b 100644 --- a/.gitignore +++ b/.gitignore @@ -12,9 +12,6 @@ wheels/ # Ignore macOS files .DS_Store -# Ignore cursor rules -*.cursor - # Ignore mypy cache .mypy_cache/ diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..4096c5a --- /dev/null +++ b/Makefile @@ -0,0 +1,33 @@ +#!/usr/bin/make -f + +.PHONY: help check test + +help: ## Show this help text + @grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}' + +install: + @echo "Installing dependencies..." + @uv sync --all-groups + +check: check-lint check-format check-types + @echo "All checks passed" + +check-lint: + @echo "Checking lint..." + @uv run python -m pylint src/ tests/ + +check-format: + @echo "Checking format..." + @uv run python -m black src/ tests/ + +format: + @echo "Formatting..." + @uv run python -m black src/ tests/ + +check-types: + @echo "Checking types..." + @uv run python -m mypy src/ tests/ --ignore-missing-imports --explicit-package-bases + +test: + @echo "Running tests..." + @uv run pytest src/ tests/ --cov=src --cov-report=term-missing \ No newline at end of file diff --git a/README.md b/README.md index 0bd7508..def2f59 100644 --- a/README.md +++ b/README.md @@ -36,7 +36,7 @@ source .venv/bin/activate # On Unix/macOS 3. Install dependencies: ```bash -uv pip install . +uv pip install -e ".[dev]" ``` ## Configuration @@ -133,6 +133,42 @@ In order to evaluate only the OCR part of the output file, we can remove all mar uv run src/evaluate.py -f -m ``` +## Running Tests + +### Unit Tests + +To run all unit tests: +```bash +uv run pytest tests/ -v +``` + +To run tests with coverage: +```bash +uv run pytest tests/ -v --cov=src --cov-report=term-missing +``` + +### Integration Tests + +Integration tests require external services to be configured. To run them: +```bash +uv run pytest tests/ -v -m integration +``` + +### Test Categories + +- `test_base.py`: Tests for the base parser functionality +- `test_run.py`: Tests for the main script functionality +- `test_integration.py`: Integration tests requiring external services + +## Test Configuration + +The test suite is configured in `pyproject.toml` with the following settings: + +- Test paths: `tests/` +- Test file pattern: `test_*.py` +- Coverage reporting: Enabled +- Integration test marker: `@pytest.mark.integration` + ## Development ### Code Style diff --git a/pyproject.toml b/pyproject.toml index b67ada4..eea4ccb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,10 +23,17 @@ dependencies = [ "pymupdf>=1.25.4", "tenacity>=9.0.0", "rouge>=1.0.1", + "huggingface-hub>=0.30.2", ] [dependency-groups] -dev = ["black>=25.1.0", "mypy>=1.15.0", "pylint>=3.3.6"] +dev = [ + "black>=25.1.0", + "mypy>=1.15.0", + "pylint>=3.3.6", + "pytest>=8.3.5", + "pytest-cov>=6.1.1", +] eval = [ "python-levenshtein>=0.27.1", "pandas>=2.2.3", diff --git a/pytest.ini b/pytest.ini new file mode 100644 index 0000000..274ea8e --- /dev/null +++ b/pytest.ini @@ -0,0 +1,28 @@ +[pytest] +# Set log level +log_cli = true +log_cli_level = INFO +log_cli_format = %(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(lineno)s) +log_cli_date_format = %Y-%m-%d %H:%M:%S + +# Add src directory to Python path +pythonpath = ./src + +# Define test markers +markers = + unit: Unit tests that do not require external services + integration: Integration tests that require external services + +# Test collection settings +testpaths = tests +python_files = test_*.py +python_classes = Test* +python_functions = test_* + +# Test execution settings +addopts = -v --tb=short + +# Filter warnings +filterwarnings = + ignore::DeprecationWarning + ignore::UserWarning \ No newline at end of file diff --git a/src/__init__.py b/src/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/evaluate.py b/src/evaluate.py index 850ba10..4c86843 100644 --- a/src/evaluate.py +++ b/src/evaluate.py @@ -9,6 +9,7 @@ import os import re import sys +from typing import Any import matplotlib.pyplot as plt import numpy as np @@ -18,7 +19,7 @@ from sklearn.feature_extraction.text import TfidfVectorizer from sklearn.metrics.pairwise import cosine_similarity -from utils.logging import setup_logging +from utils.logging import setup_logging # pylint: disable=no-name-in-module # Set up logging setup_logging() @@ -258,7 +259,7 @@ def create_word_overlap_heatmap( # Create heatmap plt.figure(figsize=(12, 12)) # Increased figure size for better readability - ax = sns.heatmap( + ax = sns.heatmap( # pylint: disable=unused-variable matrix, xticklabels=labels, yticklabels=labels, @@ -351,7 +352,7 @@ def evaluate_files( # Calculate similarities cosine_sim = calculate_similarity(clean_text1, clean_text2) overlap_ratio, words1, words2 = calculate_word_overlap(clean_text1, clean_text2) - levenshtein_dist, levenshtein_ratio = calculate_levenshtein_metrics(clean_text1, clean_text2) + _, levenshtein_ratio = calculate_levenshtein_metrics(clean_text1, clean_text2) rouge_scores = calculate_rouge_scores(clean_text1, clean_text2) # logger.info results @@ -384,6 +385,7 @@ def evaluate_files( return cosine_sim, overlap_ratio, levenshtein_ratio, rouge_scores +# pylint: disable=too-many-locals def evaluate_all_files(filestem: str, parsers: list[str], remove_markdown: bool = True) -> None: """Evaluate similarity between all pairs of markdown files. @@ -393,79 +395,84 @@ def evaluate_all_files(filestem: str, parsers: list[str], remove_markdown: bool remove_markdown: Whether to remove markdown formatting from the files. Default is True. """ - # Find all files with the given filestem and parsers files = find_files(filestem, parsers) + suffix = " with Markdown" if not remove_markdown else "" - # Calculate overlap ratios for all pairs of files - overlap_ratios, levenshtein_ratios, cosine_ratios, rouge_ratios = [], [], [], [] + # Calculate all metrics in a single pass + metrics_data: list[dict[str, Any]] = [] for file1, file2 in itertools.combinations_with_replacement(files, 2): cosine_sim, overlap_ratio, levenshtein_ratio, rouge_scores = evaluate_files( file1, file2, preprocess=remove_markdown ) - fname1 = os.path.basename(file1) - fname2 = os.path.basename(file2) - overlap_ratios.append({"file1": fname1, "file2": fname2, "value": overlap_ratio}) - levenshtein_ratios.append({"file1": fname1, "file2": fname2, "value": levenshtein_ratio}) - cosine_ratios.append({"file1": fname1, "file2": fname2, "value": cosine_sim}) - rouge_ratios.append({"file1": fname1, "file2": fname2, "value": rouge_scores}) - - # Create and save heatmap - suffix = " with Markdown" if not remove_markdown else "" - metrics = [ + metrics_data.append( + { + "files": (os.path.basename(file1), os.path.basename(file2)), + "word_overlap": overlap_ratio, + "levenshtein": levenshtein_ratio, + "cosine": cosine_sim, + "rouge": rouge_scores, + } + ) + + # Define metric configurations + metric_configs: list[dict[str, str]] = [ { - "ratios": overlap_ratios, "name": "word_overlap", "title": f"Word Overlap Ratios Heatmap{suffix}", "label": "Overlap Ratio", }, { - "ratios": levenshtein_ratios, "name": "levenshtein", "title": f"Levenshtein Ratios Heatmap{suffix}", "label": "Levenshtein Ratio", }, - { - "ratios": cosine_ratios, - "name": "cosine", - "title": f"Cosine Ratios Heatmap{suffix}", - "label": "Cosine Ratio", - }, + {"name": "cosine", "title": f"Cosine Ratios Heatmap{suffix}", "label": "Cosine Ratio"}, ] + # Add ROUGE metrics for rouge_type in ["rouge-1", "rouge-2", "rouge-l"]: - rouge_metric = { - "ratios": [ - { - "file1": r["file1"], - "file2": r["file2"], - "value": r["value"][rouge_type], - } - for r in rouge_ratios - ], - "name": rouge_type, - "title": f"{rouge_type.upper()} Scores Heatmap{suffix}", - "label": f"{rouge_type.upper()} Score", - } - metrics.append(rouge_metric) + metric_configs.append( + { + "name": rouge_type, + "title": f"{rouge_type.upper()} Scores Heatmap{suffix}", + "label": f"{rouge_type.upper()} Score", + } + ) - # Save the metrics to a csv file + # Save metrics to CSV with open(f"output/{filestem}_metrics.csv", "w", encoding="utf-8") as f: writer = csv.writer(f) writer.writerow(["Metric", "File1", "File2", "Value"]) - for metric in metrics: - for ratio in metric["ratios"]: - writer.writerow([metric["name"], ratio["file1"], ratio["file2"], ratio["value"]]) - - suffix = "_w_markdown" if not remove_markdown else "" - # Extract parser names from filenames (e.g., "output/test_anthropic.md" -> "anthropic") + for metric in metric_configs: + for data in metrics_data: + value = ( + data["rouge"][metric["name"]] + if "rouge" in metric["name"] + else data[metric["name"]] + ) + writer.writerow([metric["name"], data["files"][0], data["files"][1], value]) + + # Create heatmaps labels = [ - "_".join(file.replace(".md", "").split("_")[-2 if not "textract" in file else -1 :]) + "_".join(file.replace(".md", "").split("_")[-2 if "textract" not in file else -1 :]) for file in files ] - for metric in metrics: + for metric in metric_configs: + ratios = [ + { + "file1": data["files"][0], + "file2": data["files"][1], + "value": ( + data["rouge"][metric["name"]] + if "rouge" in metric["name"] + else data[metric["name"]] + ), + } + for data in metrics_data + ] create_word_overlap_heatmap( files, - metric["ratios"], + ratios, labels, output_file=f"output/{metric['name']}_heatmap{suffix}.png", title=metric["title"], diff --git a/src/parsers/__init__.py b/src/parsers/__init__.py index 92f66dc..5185ed5 100644 --- a/src/parsers/__init__.py +++ b/src/parsers/__init__.py @@ -2,6 +2,7 @@ from .anthropic import AnthropicParser from .googleai import GoogleAIParser +from .huggingface import HuggingFaceParser from .mistral import MistralParser from .ollama import OllamaParser from .openai import OpenAIParser @@ -11,6 +12,7 @@ __all__ = [ "AnthropicParser", "GoogleAIParser", + "HuggingFaceParser", "OllamaParser", "OpenAIParser", "MistralParser", diff --git a/src/parsers/anthropic.py b/src/parsers/anthropic.py index de23da5..0f4c7f5 100644 --- a/src/parsers/anthropic.py +++ b/src/parsers/anthropic.py @@ -53,12 +53,12 @@ def __init__( self.client = anthropic.Anthropic(api_key=api_key) self.logger.debug("Anthropic parser initialization complete") - def convert_pdf_to_markdown(self, pdf_path: str) -> str: + def convert_pdf_to_markdown(self, pdf_path: str, *, split_pages: bool = True) -> str: """Convert a PDF file to markdown using Anthropic. Args: pdf_path: The path to the PDF file to convert. - + split_pages: Whether to split the PDF into pages. Default is True. Returns: The converted markdown text. @@ -72,7 +72,7 @@ def convert_pdf_to_markdown(self, pdf_path: str) -> str: try: page_count = self.get_pdf_page_count(pdf_path) - if page_count > 1: + if page_count > 1 and split_pages: pdf_pages = self.split_pdf_into_pages(pdf_path) else: pdf_pages = [pdf_path] diff --git a/src/parsers/base.py b/src/parsers/base.py index 54c21bc..06abaec 100644 --- a/src/parsers/base.py +++ b/src/parsers/base.py @@ -1,18 +1,22 @@ """Base parser class for PDF to Markdown conversion.""" import base64 +import io import logging import tempfile from abc import ABC, abstractmethod from pathlib import Path -from typing import Optional +from typing import Generator import fitz # PyMuPDF +from pdf2image import convert_from_path +from PIL import Image class BaseParser(ABC): """Base class for PDF to Markdown parsers.""" + MAX_IMAGE_WIDTH = 1920 SYSTEM_PROMPT = """ You are a specialized PDF to Markdown converter. Your task is to convert PDF content to clean, properly formatted markdown text. Follow these strict rules: @@ -96,7 +100,6 @@ def convert_pdf_to_markdown(self, pdf_path: str) -> str: FileNotFoundError: If the PDF file doesn't exist. IOError: If there's an error reading the PDF file. """ - pass def validate_pdf_path(self, pdf_path: str) -> None: """Validate that the PDF file exists and is readable. @@ -137,6 +140,52 @@ def read_pdf_as_base64(self, pdf_path: str) -> str: base64_encoded_data = base64.standard_b64encode(binary_data) return base64_encoded_data.decode("utf-8") + def resize_image(self, image: Image.Image) -> Image.Image: + """Resize image to maintain aspect ratio with max width. + + Args: + image: PIL Image to resize. + + Returns: + Resized PIL Image. + """ + if image.width > self.MAX_IMAGE_WIDTH: + ratio = self.MAX_IMAGE_WIDTH / image.width + new_height = int(image.height * ratio) + return image.resize((self.MAX_IMAGE_WIDTH, new_height), Image.Resampling.LANCZOS) + return image + + def read_pdf_as_base64_img(self, pdf_path: str) -> Generator[str, None, None]: + """Convert PDF pages to base64-encoded images. + + Args: + pdf_path: Path to the PDF file. + + Raises: + FileNotFoundError: If the PDF file doesn't exist. + IOError: If there's an error reading the PDF file. + + Returns: + List[str]: List of base64-encoded image strings. + """ + try: + # Convert PDF to images + images = convert_from_path(pdf_path) + + # Convert each image to base64 + for image in images: + # Resize image if needed + image = self.resize_image(image) + + img_byte_io = io.BytesIO() + image.save(img_byte_io, format="PNG") + img_byte_arr = img_byte_io.getvalue() + + yield base64.b64encode(img_byte_arr).decode("utf-8") + except Exception as e: + self.logger.error(f"Error converting PDF to images: {str(e)}", exc_info=True) + raise + def save_markdown(self, markdown_text: str, output_path: str) -> None: """Save the markdown text to a file. diff --git a/src/parsers/googleai.py b/src/parsers/googleai.py index 5b148ba..867b7ba 100644 --- a/src/parsers/googleai.py +++ b/src/parsers/googleai.py @@ -89,10 +89,9 @@ def generate_response(self, prompt: str, pdf_file_id: File) -> str: pdf_file_id, ], ) - return response.text # type: ignore - def convert_pdf_to_markdown(self, pdf_path: str, split_pages: bool = False) -> str: + def convert_pdf_to_markdown(self, pdf_path: str, *, split_pages: bool = False) -> str: """Convert a PDF file to markdown using Gemini. Args: diff --git a/src/parsers/huggingface.py b/src/parsers/huggingface.py new file mode 100644 index 0000000..99cce97 --- /dev/null +++ b/src/parsers/huggingface.py @@ -0,0 +1,140 @@ +"""Hugging Face parser for PDF to Markdown conversion.""" + +import os + +import tenacity +from huggingface_hub import InferenceClient, InferenceTimeoutError + +from .base import BaseParser + + +class HuggingFaceParser(BaseParser): + """A class to handle PDF to Markdown conversion using Hugging Face's inference endpoints.""" + + AVAILABLE_MODELS = [ + "meta-llama/Llama-4-Scout-17B-16E-Instruct", + "meta-llama/Llama-4-Maverick-17B-128E-Instruct", + "Qwen/Qwen2.5-VL-7B-Instruct", + ] + DEFAULT_MODEL = "meta-llama/Llama-4-Scout-17B-16E-Instruct" + PROVIDER_TO_ENV_VAR = { + "hf-inference": "HUGGINGFACE_API_KEY", + } + + def __init__( + self, + model: str = DEFAULT_MODEL, + provider: str = "hf-inference", + temperature: float = 0.1, + top_p: float = 0.1, + top_k: int = 40, + max_tokens: int = 8192, + ) -> None: + """Initialize the Hugging Face parser. + + Args: + model: The name of the Hugging Face model to use. + provider: The provider to use. + temperature: The temperature parameter for text generation. + top_p: The top_p parameter for text generation. + top_k: The top_k parameter for text generation. + max_tokens: The maximum number of tokens to generate. + + Raises: + ValueError: If the HUGGINGFACE_API_KEY environment variable is not set. + ValueError: If the model is not supported. + """ + if model not in self.AVAILABLE_MODELS: + raise ValueError( + f"Unsupported model: {model}. Available models: {', '.join(self.AVAILABLE_MODELS)}" + ) + + super().__init__(model, temperature, top_p, top_k, max_tokens) + + api_key = os.getenv(self.PROVIDER_TO_ENV_VAR[provider]) + if not api_key: + raise ValueError(f"{self.PROVIDER_TO_ENV_VAR[provider]} environment variable not set") + + self.api_key = api_key + self.client = InferenceClient( + provider=provider, # type: ignore + api_key=api_key, + ) + self.logger.debug("Hugging Face parser initialization complete") + + @tenacity.retry( + stop=tenacity.stop_after_attempt(3), + wait=tenacity.wait_exponential(multiplier=1, min=4, max=15), + retry=tenacity.retry_if_exception_type(InferenceTimeoutError), + ) + def generate_response(self, prompt: str, base64_img_str: str) -> str: + """Generate a response from the Hugging Face API. + + Args: + prompt (str): The prompt to generate a response for. + base64_image (str): The base64 encoded image string. + + Returns: + str: The generated response. + + Raises: + Exception: If there's an error generating the response. + """ + try: + completion = self.client.chat.completions.create( + model=self.model, + messages=[ + {"role": "system", "content": self.SYSTEM_PROMPT}, + { + "role": "user", + "content": prompt, + "images": ["data:image/png;base64," + base64_img_str], + }, + ], + max_tokens=self.max_tokens, + temperature=self.temperature, + top_p=self.top_p, + stream=True, + ) + output = "" + for chunk in completion: + output += chunk.choices[0].delta.content or "" + return output + except Exception as e: + self.logger.error(f"Error generating response: {str(e)}", exc_info=True) + raise + + def convert_pdf_to_markdown(self, pdf_path: str, *, split_pages: bool = True) -> str: + """Convert a PDF file to markdown using Gemini. + + Args: + pdf_path: The path to the PDF file to convert. + split_pages: Whether to split the PDF into pages. Default is False. + + Returns: + The converted markdown text. + + Raises: + FileNotFoundError: If the PDF file doesn't exist. + IOError: If there's an error reading the PDF file. + """ + self.logger.debug(f"Starting PDF to Markdown conversion for file: {pdf_path}") + + try: + # In order to work around the free tier output token limit, we split the PDF into pages + # and process each page separately. + markdown_text = "" + for base64_image in self.read_pdf_as_base64_img(pdf_path): + prompt = "Convert this image to markdown format for me please." + + response_text = self.generate_response(prompt, base64_image) + + markdown_text += response_text + "\n\n" + + self.logger.debug("Successfully received response from Gemini API") + + return markdown_text + + except Exception as e: + self.logger.error(f"Error during PDF conversion: {str(e)}", exc_info=True) + raise diff --git a/src/parsers/mistral.py b/src/parsers/mistral.py index 06f0518..39eb866 100644 --- a/src/parsers/mistral.py +++ b/src/parsers/mistral.py @@ -51,11 +51,12 @@ def __init__( self.client = Mistral(api_key=api_key) self.logger.debug("Mistral parser initialization complete") - def convert_pdf_to_markdown(self, pdf_path: str) -> str: + def convert_pdf_to_markdown(self, pdf_path: str, *, split_pages: bool = True) -> str: """Convert a PDF file to markdown using Mistral. Args: pdf_path: The path to the PDF file to convert. + split_pages: Whether to split the PDF into pages. Default is True. Returns: The converted markdown text. diff --git a/src/parsers/ollama.py b/src/parsers/ollama.py index 60bb702..0604e54 100644 --- a/src/parsers/ollama.py +++ b/src/parsers/ollama.py @@ -55,61 +55,12 @@ def __init__( } self.logger.debug("Ollama parser initialization complete") - def resize_image(self, image: Image.Image) -> Image.Image: - """Resize image to maintain aspect ratio with max width. - - Args: - image: PIL Image to resize. - - Returns: - Resized PIL Image. - """ - if image.width > self.MAX_IMAGE_WIDTH: - ratio = self.MAX_IMAGE_WIDTH / image.width - new_height = int(image.height * ratio) - return image.resize((self.MAX_IMAGE_WIDTH, new_height), Image.Resampling.LANCZOS) - return image - - def read_pdf_as_base64_img(self, pdf_path: str) -> List[str]: - """Convert PDF pages to base64-encoded images. - - Args: - pdf_path: Path to the PDF file. - - Raises: - FileNotFoundError: If the PDF file doesn't exist. - IOError: If there's an error reading the PDF file. - - Returns: - List[str]: List of base64-encoded image strings. - """ - try: - # Convert PDF to images - images = convert_from_path(pdf_path) - - # Convert each image to base64 - base64_images = [] - for image in images: - # Resize image if needed - image = self.resize_image(image) - - import io - - img_byte_arr = io.BytesIO() - image.save(img_byte_arr, format="PNG") - img_byte_arr = img_byte_arr.getvalue() - base64_images.append(base64.b64encode(img_byte_arr).decode("utf-8")) - - return base64_images - except Exception as e: - self.logger.error(f"Error converting PDF to images: {str(e)}", exc_info=True) - raise - - def convert_pdf_to_markdown(self, pdf_path: str) -> str: + def convert_pdf_to_markdown(self, pdf_path: str, *, split_pages: bool = True) -> str: """Convert a PDF file to markdown using Ollama. Args: pdf_path: The path to the PDF file to convert. + split_pages: Whether to split the PDF into pages. Default is True. Raises: FileNotFoundError: If the PDF file doesn't exist. @@ -123,7 +74,7 @@ def convert_pdf_to_markdown(self, pdf_path: str) -> str: try: # Convert PDF to base64 images self.logger.debug(f"Converting PDF to images: {pdf_path}") - base64_images = self.read_pdf_as_base64_img(pdf_path) + base64_images = list(self.read_pdf_as_base64_img(pdf_path)) prompt = "Convert the attached pdf to markdown format for me please." diff --git a/src/parsers/openai.py b/src/parsers/openai.py index 9e5c498..c3f9d12 100644 --- a/src/parsers/openai.py +++ b/src/parsers/openai.py @@ -49,11 +49,12 @@ def __init__( openai.api_key = api_key self.logger.debug("OpenAI parser initialization complete") - def convert_pdf_to_markdown(self, pdf_path: str) -> str: + def convert_pdf_to_markdown(self, pdf_path: str, *, split_pages: bool = True) -> str: """Convert a PDF file to markdown using OpenAI. Args: pdf_path: The path to the PDF file to convert. + split_pages: Whether to split the PDF into pages. Default is True. Returns: The converted markdown text. @@ -69,7 +70,7 @@ def convert_pdf_to_markdown(self, pdf_path: str) -> str: try: page_count = self.get_pdf_page_count(pdf_path) - if page_count > 1: + if page_count > 1 and split_pages: pdf_pages = self.split_pdf_into_pages(pdf_path) else: pdf_pages = [pdf_path] diff --git a/src/parsers/textract.py b/src/parsers/textract.py index 992408c..2e7eb93 100644 --- a/src/parsers/textract.py +++ b/src/parsers/textract.py @@ -12,8 +12,8 @@ class TextractParser(BaseParser): """A class to handle PDF to Markdown conversion using AWS Textract.""" - AVAILABLE_MODELS = [] - DEFAULT_MODEL = "" + AVAILABLE_MODELS: list[str] = [] + DEFAULT_MODEL: str = "" def __init__( self, @@ -46,12 +46,12 @@ def __init__( ) self.logger.debug("Textract parser initialization complete") - def convert_pdf_to_markdown(self, pdf_path: str) -> str: + def convert_pdf_to_markdown(self, pdf_path: str, *, split_pages: bool = True) -> str: """Convert a PDF file to markdown using AWS Textract. Args: pdf_path: The path to the PDF file to convert. - + split_pages: Whether to split the PDF into pages. Default is True. Raises: FileNotFoundError: If the PDF file doesn't exist. IOError: If there's an error reading the PDF file. @@ -65,7 +65,7 @@ def convert_pdf_to_markdown(self, pdf_path: str) -> str: try: page_count = self.get_pdf_page_count(pdf_path) - if page_count > 1: + if page_count > 1 and split_pages: pdf_pages = self.split_pdf_into_pages(pdf_path) else: pdf_pages = [pdf_path] diff --git a/src/parsers/unstructuredio.py b/src/parsers/unstructuredio.py index b6d09c2..1838408 100644 --- a/src/parsers/unstructuredio.py +++ b/src/parsers/unstructuredio.py @@ -62,11 +62,12 @@ def __init__( self.client = unstructured_client.UnstructuredClient(api_key_auth=api_key) self.logger.debug("UnstructuredIO parser initialization complete") - def convert_pdf_to_markdown(self, pdf_path: str) -> str: + def convert_pdf_to_markdown(self, pdf_path: str, *, split_pages: bool = True) -> str: """Convert a PDF file to markdown using UnstructuredIO. Args: pdf_path: The path to the PDF file to convert. + split_pages: Whether to split the PDF into pages. Default is True. Returns: The converted markdown text. diff --git a/src/run.py b/src/run.py index be890a1..0415338 100644 --- a/src/run.py +++ b/src/run.py @@ -7,14 +7,15 @@ from dotenv import load_dotenv -from parsers.anthropic import AnthropicParser -from parsers.googleai import GoogleAIParser -from parsers.mistral import MistralParser -from parsers.ollama import OllamaParser -from parsers.openai import OpenAIParser -from parsers.textract import TextractParser -from parsers.unstructuredio import UnstructuredIOParser -from utils.logging import setup_logging +from parsers.anthropic import AnthropicParser # type: ignore +from parsers.googleai import GoogleAIParser # type: ignore +from parsers.huggingface import HuggingFaceParser # type: ignore +from parsers.mistral import MistralParser # type: ignore +from parsers.ollama import OllamaParser # type: ignore +from parsers.openai import OpenAIParser # type: ignore +from parsers.textract import TextractParser # type: ignore +from parsers.unstructuredio import UnstructuredIOParser # type: ignore +from utils.logging import setup_logging # type: ignore # pylint: disable=no-name-in-module # Load environment variables load_dotenv() @@ -32,6 +33,7 @@ "openai": OpenAIParser, "textract": TextractParser, "unstructuredio": UnstructuredIOParser, + "huggingface": HuggingFaceParser, } @@ -138,6 +140,11 @@ def setup_cli_args() -> argparse.Namespace: choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"], help="The logging level to use. Defaults to INFO.", ) + parser.add_argument( + "--split-pages", + action="store_true", + help="Split the PDF into pages and process each page separately. Not used in all parsers.", + ) args = parser.parse_args() @@ -173,7 +180,9 @@ def main() -> None: ) # Convert PDF to markdown - markdown_text = pdf_parser.convert_pdf_to_markdown(args.input_pdf_path) + markdown_text = pdf_parser.convert_pdf_to_markdown( + args.input_pdf_path, split_pages=args.split_pages + ) # Save the markdown pdf_parser.save_markdown(markdown_text, str(output_path)) diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..23c6603 --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,72 @@ +"""Common test fixtures for the PDF to Markdown conversion tests.""" + +import os +import tempfile +from pathlib import Path +from typing import Generator + +import pytest +from dotenv import load_dotenv + +# Load environment variables +load_dotenv() + + +@pytest.fixture +def temp_pdf_file() -> Generator[Path, None, None]: + """Create a temporary PDF file for testing. + + Yields: + Path: Path to the temporary PDF file. + """ + with tempfile.NamedTemporaryFile(suffix=".pdf", delete=False) as temp_file: + # Create a minimal PDF file + temp_file.write( + b"%PDF-1.4\n1 0 obj\n<>\nendobj\n" + b"2 0 obj\n<>\nendobj\n" + b"3 0 obj\n<> " + b"/MediaBox [0 0 612 792]>>\nendobj\n" + b"xref\n0 4\n0000000000 65535 f\n0000000010 00000 n\n0000000056 00000 n\n" + b"0000000102 00000 n\ntrailer\n<>\nstartxref\n149\n%%EOF" + ) + temp_file.flush() + yield Path(temp_file.name) + os.unlink(temp_file.name) + + +@pytest.fixture +def temp_output_dir() -> Generator[Path, None, None]: + """Create a temporary output directory for testing. + + Yields: + Path: Path to the temporary output directory. + """ + with tempfile.TemporaryDirectory() as temp_dir: + yield Path(temp_dir) + + +@pytest.fixture +def sample_markdown() -> str: + """Return a sample markdown text for testing. + + Returns: + str: Sample markdown text. + """ + return """# Test Document + +## Section 1 + +This is a test paragraph. + +### Subsection 1.1 + +- Item 1 +- Item 2 +- Item 3 + +## Section 2 + +| Header 1 | Header 2 | +|----------|----------| +| Value 1 | Value 2 | +""" diff --git a/tests/test_base.py b/tests/test_base.py new file mode 100644 index 0000000..529f0fe --- /dev/null +++ b/tests/test_base.py @@ -0,0 +1,185 @@ +"""Tests for the base parser functionality.""" + +import os +from pathlib import Path +from unittest.mock import MagicMock, patch + +import pytest +from PIL import Image + +from parsers.base import BaseParser + + +class TestBaseParser(BaseParser): + """Test implementation of BaseParser for testing.""" + + AVAILABLE_MODELS = ["test-model"] + DEFAULT_MODEL = "test-model" + + def convert_pdf_to_markdown(self, pdf_path: str) -> str: + """Test implementation of convert_pdf_to_markdown.""" + return "Test markdown content" + + +@pytest.mark.unit +def test_validate_pdf_path(temp_pdf_file: Path) -> None: + """Test PDF path validation with valid PDF file. + + Args: + temp_pdf_file: Temporary PDF file fixture. + """ + parser = TestBaseParser("test-model") + parser.validate_pdf_path(str(temp_pdf_file)) + + +@pytest.mark.unit +def test_validate_pdf_path_nonexistent() -> None: + """Test PDF path validation with nonexistent file.""" + parser = TestBaseParser("test-model") + with pytest.raises(FileNotFoundError): + parser.validate_pdf_path("nonexistent.pdf") + + +@pytest.mark.unit +def test_validate_pdf_path_not_pdf(temp_output_dir: Path) -> None: + """Test PDF path validation with non-PDF file. + + Args: + temp_output_dir: Temporary output directory fixture. + """ + parser = TestBaseParser("test-model") + not_pdf = temp_output_dir / "not_pdf.txt" + not_pdf.write_text("Not a PDF") + with pytest.raises(ValueError): + parser.validate_pdf_path(str(not_pdf)) + + +@pytest.mark.unit +def test_read_pdf_as_base64(temp_pdf_file: Path) -> None: + """Test reading PDF as base64. + + Args: + temp_pdf_file: Temporary PDF file fixture. + """ + parser = TestBaseParser("test-model") + base64_content = parser.read_pdf_as_base64(str(temp_pdf_file)) + assert isinstance(base64_content, str) + assert base64_content.startswith("JVBERi0x") + + +@pytest.mark.unit +def test_save_markdown(temp_output_dir: Path, sample_markdown: str) -> None: + """Test saving markdown to file. + + Args: + temp_output_dir: Temporary output directory fixture. + sample_markdown: Sample markdown text fixture. + """ + parser = TestBaseParser("test-model") + output_path = temp_output_dir / "test.md" + parser.save_markdown(sample_markdown, str(output_path)) + assert output_path.exists() + assert output_path.read_text() == sample_markdown + + +@pytest.mark.unit +def test_split_pdf_into_pages(temp_pdf_file: Path) -> None: + """Test splitting PDF into pages. + + Args: + temp_pdf_file: Temporary PDF file fixture. + """ + parser = TestBaseParser("test-model") + page_files = parser.split_pdf_into_pages(str(temp_pdf_file)) + assert len(page_files) == 1 + assert all(Path(f).exists() for f in page_files) + # Clean up + for f in page_files: + os.unlink(f) + + +@pytest.mark.unit +def test_get_pdf_page_count(temp_pdf_file: Path) -> None: + """Test getting PDF page count. + + Args: + temp_pdf_file: Temporary PDF file fixture. + """ + parser = TestBaseParser("test-model") + page_count = parser.get_pdf_page_count(str(temp_pdf_file)) + assert page_count == 1 + + +@pytest.mark.unit +@patch("parsers.base.fitz") +def test_get_pdf_page_count_error(mock_fitz: MagicMock) -> None: + """Test error handling in get_pdf_page_count. + + Args: + mock_fitz: Mocked fitz module. + """ + mock_fitz.open.side_effect = Exception("Test error") + parser = TestBaseParser("test-model") + with pytest.raises(Exception): + parser.get_pdf_page_count("test.pdf") + + +@pytest.mark.unit +def test_resize_image() -> None: + """Test image resizing functionality. + + Tests that: + 1. Images wider than MAX_IMAGE_WIDTH are resized while maintaining aspect ratio + 2. Images narrower than MAX_IMAGE_WIDTH are returned unchanged + """ + parser = TestBaseParser("test-model") + + # Create a test image wider than MAX_IMAGE_WIDTH + wide_image = Image.new("RGB", (parser.MAX_IMAGE_WIDTH + 100, 500)) + resized_image = parser.resize_image(wide_image) + assert resized_image.width == parser.MAX_IMAGE_WIDTH + assert resized_image.height == int( + 500 * (parser.MAX_IMAGE_WIDTH / (parser.MAX_IMAGE_WIDTH + 100)) + ) + + # Create a test image narrower than MAX_IMAGE_WIDTH + narrow_image = Image.new("RGB", (parser.MAX_IMAGE_WIDTH - 100, 500)) + unchanged_image = parser.resize_image(narrow_image) + assert unchanged_image.width == parser.MAX_IMAGE_WIDTH - 100 + assert unchanged_image.height == 500 + + +@pytest.mark.unit +@patch("parsers.base.convert_from_path") +def test_read_pdf_as_base64_img(mock_convert: MagicMock) -> None: + """Test converting PDF pages to base64-encoded images. + + Args: + mock_convert: Mocked convert_from_path function. + """ + # Create test images + test_images = [Image.new("RGB", (100, 100)), Image.new("RGB", (100, 100))] + mock_convert.return_value = test_images + + parser = TestBaseParser("test-model") + base64_images = list(parser.read_pdf_as_base64_img("test.pdf")) + + # Verify results + assert len(base64_images) == 2 + for img_str in base64_images: + assert isinstance(img_str, str) + assert img_str.startswith("iVBORw0KGgo") # PNG base64 header + + +@pytest.mark.unit +@patch("parsers.base.convert_from_path") +def test_read_pdf_as_base64_img_error(mock_convert: MagicMock) -> None: + """Test error handling in read_pdf_as_base64_img. + + Args: + mock_convert: Mocked convert_from_path function. + """ + mock_convert.side_effect = Exception("Test error") + parser = TestBaseParser("test-model") + with pytest.raises(Exception): + list(parser.read_pdf_as_base64_img("test.pdf")) diff --git a/tests/test_evaluate.py b/tests/test_evaluate.py new file mode 100644 index 0000000..fbaf803 --- /dev/null +++ b/tests/test_evaluate.py @@ -0,0 +1,284 @@ +"""Unit tests for the evaluate module.""" + +import os +import tempfile +from pathlib import Path +from unittest.mock import MagicMock, mock_open, patch + +import numpy as np +import pytest + +# Fix the import path +from evaluate import ( + calculate_levenshtein_metrics, + calculate_rouge_scores, + calculate_similarity, + calculate_word_overlap, + create_word_overlap_heatmap, + evaluate_all_files, + evaluate_files, + find_files, + preprocess_markdown, +) + + +@pytest.mark.unit +def test_preprocess_markdown() -> None: + """Test removing markdown formatting from text.""" + markdown_text = """ +# Header 1 +## Header 2 + +This is **bold** and *italic* text. + +- List item 1 +- List item 2 + +1. Numbered item 1 +2. Numbered item 2 + +> Blockquote + +```python +def test(): + pass +``` + +[Link](https://example.com) + +| Header 1 | Header 2 | +|----------|----------| +| Cell 1 | Cell 2 | +| Cell 3 | Cell 4 | + +$$E = mc^2$$ + +--- + """ + + expected = ( + "Header 1 Header 2 " + "This is bold and italic text " + "List item 1 List item 2 " + "Numbered item 1 Numbered item 2 " + "Blockquote " + "python def test pass " + "Link " + "Header 1 Header 2Cell 1 Cell 2 Cell 3 Cell 4" + ) + result = preprocess_markdown(markdown_text) + + # We normalize spaces to avoid test failures due to whitespace differences + expected = " ".join(expected.split()) + result = " ".join(result.split()) + + assert result == expected + + +@pytest.mark.unit +def test_calculate_similarity() -> None: + """Test calculating similarity between two texts.""" + text1 = "This is a test sentence for similarity comparison" + text2 = "This is a test phrase for similarity comparison" + + similarity = calculate_similarity(text1, text2) + assert 0 <= similarity <= 1 + assert round(similarity, 2) == 0.75 # Should be high for similar texts + + +@pytest.mark.unit +def test_calculate_similarity_empty() -> None: + """Test calculating similarity with empty texts.""" + text1 = "" + text2 = "This is not empty" + + similarity = calculate_similarity(text1, text2) + assert similarity == 0.0 + + +@pytest.mark.unit +def test_calculate_word_overlap() -> None: + """Test calculating word overlap between two texts.""" + text1 = "apple banana cherry date" + text2 = "apple banana fig grape" + + overlap_ratio, words1, words2 = calculate_word_overlap(text1, text2) + + assert overlap_ratio == 2 / 6 # 2 common words out of 6 unique words + assert words1 == {"apple", "banana", "cherry", "date"} + assert words2 == {"apple", "banana", "fig", "grape"} + + +@pytest.mark.unit +def test_calculate_levenshtein_metrics() -> None: + """Test calculating Levenshtein metrics between two texts.""" + text1 = "kitten" + text2 = "sitting" + + levenshtein_dist, levenshtein_ratio = calculate_levenshtein_metrics(text1, text2) + + assert levenshtein_dist == 3 # 3 operations to transform kitten to sitting + assert 0 <= levenshtein_ratio <= 1 + + +@pytest.mark.unit +def test_calculate_rouge_scores() -> None: + """Test calculating ROUGE scores between two texts.""" + text1 = "The quick brown fox jumps over the lazy dog" + text2 = "The fast brown fox jumps over the lazy dog" + + rouge_scores = calculate_rouge_scores(text1, text2) + + assert "rouge-1" in rouge_scores + assert "rouge-2" in rouge_scores + assert "rouge-l" in rouge_scores + assert all(0 <= score <= 1 for score in rouge_scores.values()) + + +@pytest.mark.unit +@patch("matplotlib.pyplot.savefig") +@patch("matplotlib.pyplot.figure") +@patch("matplotlib.pyplot.close") +@patch("seaborn.heatmap") +def test_create_word_overlap_heatmap( + mock_heatmap: MagicMock, mock_close: MagicMock, mock_figure: MagicMock, mock_savefig: MagicMock +) -> None: + """Test creating a heatmap visualization of overlap ratios.""" + files = ["file1.md", "file2.md", "file3.md"] + overlap_ratios = [ + {"file1": "file1.md", "file2": "file2.md", "value": 0.5}, + {"file1": "file1.md", "file2": "file3.md", "value": 0.3}, + {"file1": "file2.md", "file2": "file3.md", "value": 0.7}, + ] + labels = ["model1", "model2", "model3"] + + create_word_overlap_heatmap(files, overlap_ratios, labels, "test_heatmap.png") + + assert mock_figure.call_count == 5 + mock_heatmap.assert_called_once() + mock_savefig.assert_called_once_with("test_heatmap.png", bbox_inches="tight", dpi=300) + mock_close.assert_called_once() + + +@pytest.mark.unit +@patch("glob.glob") +def test_find_files(mock_glob: MagicMock) -> None: + """Test finding files with the given filestem and parsers.""" + mock_glob.side_effect = lambda pattern: { + "output/test_anthropic*.md": ["output/test_anthropic.md"], + "output/test_googleai*.md": [ + "output/test_googleai.md", + "output/test_googleai_gemini-2.0-flash.md", + ], + "output/test_openai*.md": ["output/test_openai.md"], + }[pattern] + + files = find_files("test", ["anthropic", "googleai", "openai"]) + + assert len(files) == 4 + assert "output/test_anthropic.md" in files + assert "output/test_googleai.md" in files + assert "output/test_googleai_gemini-2.0-flash.md" in files + assert "output/test_openai.md" in files + + +@pytest.mark.unit +@patch("glob.glob") +def test_find_files_no_matches(mock_glob: MagicMock) -> None: + """Test finding files with no matches.""" + mock_glob.return_value = [] + + with pytest.raises(ValueError, match="No files found for filestem"): + find_files("nonexistent", ["anthropic"]) + + +@pytest.mark.unit +@patch("builtins.open", new_callable=mock_open, read_data="# Test\nThis is a test document.") +@patch("evaluate.preprocess_markdown", return_value="This is a test document") +@patch("evaluate.calculate_similarity", return_value=0.95) +@patch( + "evaluate.calculate_word_overlap", + return_value=( + 0.8, + {"this", "is", "a", "test", "document"}, + {"this", "is", "a", "test", "document"}, + ), +) +@patch("evaluate.calculate_levenshtein_metrics", return_value=(5, 0.9)) +@patch( + "evaluate.calculate_rouge_scores", + return_value={"rouge-1": 0.9, "rouge-2": 0.85, "rouge-l": 0.88}, +) +def test_evaluate_files( + mock_rouge: MagicMock, + mock_levenshtein: MagicMock, + mock_overlap: MagicMock, + mock_similarity: MagicMock, + mock_preprocess: MagicMock, + mock_file: MagicMock, +) -> None: + """Test evaluating similarity between two markdown files.""" + file1 = "test_file1.md" + file2 = "test_file2.md" + + with patch("os.path.basename") as mock_basename: + mock_basename.side_effect = lambda f: f + + cosine_sim, overlap_ratio, levenshtein_ratio, rouge_scores = evaluate_files(file1, file2) + + assert cosine_sim == 0.95 + assert overlap_ratio == 0.8 + assert levenshtein_ratio == 0.9 + assert rouge_scores["rouge-1"] == 0.9 + assert rouge_scores["rouge-2"] == 0.85 + assert rouge_scores["rouge-l"] == 0.88 + + +@pytest.mark.unit +@patch("builtins.open") +def test_evaluate_files_file_not_found(mock_open: MagicMock) -> None: + """Test evaluating files with a non-existent file.""" + mock_open.side_effect = FileNotFoundError("File not found") + + with pytest.raises(FileNotFoundError): + evaluate_files("nonexistent1.md", "nonexistent2.md") + + +@pytest.mark.integration +@patch("evaluate.find_files") +@patch("evaluate.evaluate_files") +@patch("evaluate.create_word_overlap_heatmap") +@patch("builtins.open", new_callable=mock_open) +def test_evaluate_all_files_integration( + mock_file: MagicMock, mock_heatmap: MagicMock, mock_evaluate: MagicMock, mock_find: MagicMock +) -> None: + """Test the full workflow of evaluating all files.""" + # Mock the file finding function + mock_find.return_value = [ + "output/doc_anthropic.md", + "output/doc_googleai.md", + "output/doc_openai.md", + ] + + # Mock the evaluation results + mock_evaluate.return_value = ( + 0.85, + 0.75, + 0.8, + {"rouge-1": 0.8, "rouge-2": 0.7, "rouge-l": 0.75}, + ) + + # Call the function being tested + evaluate_all_files("doc", ["anthropic", "googleai", "openai"]) + + # Check that the right functions were called + mock_find.assert_called_once_with("doc", ["anthropic", "googleai", "openai"]) + + # Should call evaluate_files for each pair of files (including self-comparisons) + assert mock_evaluate.call_count == 6 + + # Should create 6 heatmaps (one for each metric) + assert mock_heatmap.call_count == 6 + + # Should write to the CSV file + mock_file.assert_called_once_with("output/doc_metrics.csv", "w", encoding="utf-8") diff --git a/tests/test_integration.py b/tests/test_integration.py new file mode 100644 index 0000000..3e42404 --- /dev/null +++ b/tests/test_integration.py @@ -0,0 +1,182 @@ +"""Integration tests for PDF to Markdown conversion.""" + +import os +from pathlib import Path +from unittest.mock import MagicMock, Mock, PropertyMock, patch + +import pytest + +from run import main + + +@pytest.mark.integration +@patch("parsers.googleai.genai.Client") +def test_end_to_end_conversion( + mock_client_class: MagicMock, + temp_pdf_file: Path, + temp_output_dir: Path, +) -> None: + """Test end-to-end PDF to Markdown conversion using Google AI. + + Args: + mock_client_class: Mocked Google AI Client class. + temp_pdf_file: Temporary PDF file fixture. + temp_output_dir: Temporary output directory fixture. + """ + # Create a proper string response + mock_client = mock_client_class.return_value + + # Set up the response.text property to return a string + response = Mock() + type(response).text = PropertyMock(return_value="# Test Document\n\nHello World") + + # Configure the mock to return our response + mock_client.models.generate_content.return_value = response + + # Mock the file upload method + mock_client.files.upload.return_value = Mock() + + # Create a minimal PDF file with some text + with open(temp_pdf_file, "wb") as f: + f.write( + b"%PDF-1.4\n1 0 obj\n<>\nendobj\n" + b"2 0 obj\n<>\nendobj\n" + b"3 0 obj\n<> " + b"/MediaBox [0 0 612 792] /Contents 4 0 R>>\nendobj\n" + b"4 0 obj\n<>\n" + b"stream\nBT\n/F1 12 Tf\n100 700 Td\n(Hello World) Tj\nET\nendstream\nendobj\n" + b"xref\n0 5\n0000000000 65535 f\n0000000010 00000 n\n0000000056 00000 n\n" + b"0000000102 00000 n\n0000000166 00000 n\n" + b"trailer\n<>\nstartxref\n226\n%%EOF" + ) + + # Mock the environment variable for the API key + with patch.dict("os.environ", {"GOOGLE_API_KEY": "dummy_key"}): + # Run the conversion + with patch( + "sys.argv", + ["script.py", "-i", str(temp_pdf_file), "-o", str(temp_output_dir), "-p", "googleai"], + ): + main() + + # Verify output + output_files = list(temp_output_dir.glob("*.md")) + assert len(output_files) == 1 + output_file = output_files[0] + assert output_file.exists() + content = output_file.read_text() + assert "Hello World" in content + + +@pytest.mark.integration +@patch("parsers.googleai.genai.Client") +def test_multiple_pages_conversion( + mock_client_class: MagicMock, + temp_pdf_file: Path, + temp_output_dir: Path, +) -> None: + """Test conversion of a multi-page PDF using Google AI. + + Args: + mock_client_class: Mocked Google AI Client class. + temp_pdf_file: Temporary PDF file fixture. + temp_output_dir: Temporary output directory fixture. + """ + # Create a proper mock client with proper string responses + mock_client = mock_client_class.return_value + + # Create response objects with text properties + response1 = Mock() + type(response1).text = PropertyMock(return_value="# Page 1\n\nContent from page 1") + + response2 = Mock() + type(response2).text = PropertyMock(return_value="# Page 2\n\nContent from page 2") + + # Set up the mock to return our responses in sequence + mock_client.models.generate_content.side_effect = [response1, response2] + + # Mock the file upload method + mock_client.files.upload.return_value = Mock() + + # Create a multi-page PDF file + with open(temp_pdf_file, "wb") as f: + f.write( + b"%PDF-1.4\n1 0 obj\n<>\nendobj\n" + b"2 0 obj\n<>\nendobj\n" + b"3 0 obj\n<> " + b"/MediaBox [0 0 612 792] /Contents 5 0 R>>\nendobj\n" + b"4 0 obj\n<> " + b"/MediaBox [0 0 612 792] /Contents 6 0 R>>\nendobj\n" + b"5 0 obj\n<>\n" + b"stream\nBT\n/F1 12 Tf\n100 700 Td\n(Page 1) Tj\nET\nendstream\nendobj\n" + b"6 0 obj\n<>\n" + b"stream\nBT\n/F1 12 Tf\n100 700 Td\n(Page 2) Tj\nET\nendstream\nendobj\n" + b"xref\n0 7\n0000000000 65535 f\n0000000010 00000 n\n0000000056 00000 n\n" + b"0000000102 00000 n\n0000000166 00000 n\n0000000220 00000 n\n" + b"0000000274 00000 n\ntrailer\n<>\nstartxref\n318\n%%EOF" + ) + + # Run the conversion with page splitting enabled + with patch.dict("os.environ", {"GOOGLE_API_KEY": "dummy_key"}): + with patch( + "sys.argv", + [ + "script.py", + "-i", + str(temp_pdf_file), + "-o", + str(temp_output_dir), + "-p", + "googleai", + "--split-pages", + ], + ): + main() + + # Verify output + output_files = list(temp_output_dir.glob("*.md")) + assert len(output_files) == 1 + output_file = output_files[0] + assert output_file.exists() + content = output_file.read_text() + assert "Page 1" in content + assert "Page 2" in content + + +@pytest.mark.integration +@patch("parsers.googleai.GoogleAIParser.generate_response") +@patch("parsers.googleai.GoogleAIParser.__init__") +def test_large_pdf_conversion( + mock_init: MagicMock, + mock_generate_response: MagicMock, + temp_output_dir: Path, +) -> None: + """Test conversion of a large PDF file using Google AI. + + Args: + mock_init: Mocked GoogleAIParser initialization. + mock_generate_response: Mocked generate_response method. + temp_output_dir: Temporary output directory fixture. + """ + # Setup mocks + mock_init.return_value = None + mock_generate_response.return_value = "# Large Document\n\nThis is a large document." + + large_pdf = Path("tests/data/large.pdf") + if not large_pdf.exists(): + pytest.skip("Large PDF file not found") + + # Run the conversion + with patch( + "sys.argv", + ["script.py", "-i", str(large_pdf), "-o", str(temp_output_dir), "-p", "googleai"], + ): + main() + + # Verify output + output_files = list(temp_output_dir.glob("*.md")) + assert len(output_files) == 1 + output_file = output_files[0] + assert output_file.exists() + content = output_file.read_text() + assert len(content) > 0 diff --git a/tests/test_run.py b/tests/test_run.py new file mode 100644 index 0000000..e34bb52 --- /dev/null +++ b/tests/test_run.py @@ -0,0 +1,119 @@ +"""Tests for the main script functionality.""" + +import argparse +from pathlib import Path +from unittest.mock import MagicMock, patch + +import pytest + +from run import generate_output_path, get_parser, get_parser_help_text, main, setup_cli_args + + +@pytest.mark.unit +def test_get_parser() -> None: + """Test getting parser instance.""" + parser = get_parser("textract") + assert parser.__class__.__name__ == "TextractParser" + + +@pytest.mark.unit +def test_get_parser_invalid() -> None: + """Test getting parser with invalid name.""" + with pytest.raises(ValueError): + get_parser("invalid_parser") + + +@pytest.mark.unit +def test_generate_output_path() -> None: + """Test generating output path.""" + output_path = generate_output_path("test.pdf", "output", "textract", "test-model") + assert output_path == Path("output/test_textract_test-model.md") + + +@pytest.mark.unit +def test_generate_output_path_no_model() -> None: + """Test generating output path without model.""" + output_path = generate_output_path("test.pdf", "output", "textract") + assert output_path == Path("output/test_textract.md") + + +@pytest.mark.unit +def test_get_parser_help_text() -> None: + """Test getting parser help text.""" + help_text = get_parser_help_text() + assert "Available parsers and their models:" in help_text + assert "textract:" in help_text + + +@pytest.mark.unit +@patch("argparse.ArgumentParser.parse_args") +def test_setup_cli_args(mock_parse_args: MagicMock) -> None: + """Test setting up CLI arguments. + + Args: + mock_parse_args: Mocked parse_args method. + """ + mock_parse_args.return_value = argparse.Namespace( + input_pdf_path="test.pdf", + output_dir="output", + parser="textract", + model=None, + log_level="INFO", + split_pages=False, + ) + args = setup_cli_args() + assert args.input_pdf_path == "test.pdf" + assert args.output_dir == "output" + assert args.parser == "textract" + assert args.model == "" + assert args.log_level == "INFO" + assert args.split_pages is False + + +@pytest.mark.unit +@patch("run.setup_cli_args") +@patch("run.get_parser") +@patch("run.generate_output_path") +def test_main( + mock_generate_output_path: MagicMock, + mock_get_parser: MagicMock, + mock_setup_cli_args: MagicMock, + temp_pdf_file: Path, + temp_output_dir: Path, +) -> None: + """Test main function. + + Args: + mock_generate_output_path: Mocked generate_output_path function. + mock_get_parser: Mocked get_parser function. + mock_setup_cli_args: Mocked setup_cli_args function. + temp_pdf_file: Temporary PDF file fixture. + temp_output_dir: Temporary output directory fixture. + """ + # Setup mocks + mock_setup_cli_args.return_value = argparse.Namespace( + input_pdf_path=str(temp_pdf_file), + output_dir=str(temp_output_dir), + parser="anthropic", + model=None, + log_level="INFO", + split_pages=False, + ) + + mock_parser = MagicMock() + mock_parser.convert_pdf_to_markdown.return_value = "Test markdown" + mock_get_parser.return_value = mock_parser + + output_path = temp_output_dir / "test.md" + mock_generate_output_path.return_value = output_path + + # Run main + main() + + # Verify calls + mock_setup_cli_args.assert_called_once() + mock_get_parser.assert_called_once_with("anthropic", None) + mock_parser.convert_pdf_to_markdown.assert_called_once_with( + str(temp_pdf_file), split_pages=False + ) + mock_parser.save_markdown.assert_called_once_with("Test markdown", str(output_path)) diff --git a/uv.lock b/uv.lock new file mode 100644 index 0000000..eb11641 --- /dev/null +++ b/uv.lock @@ -0,0 +1,3397 @@ 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