diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml new file mode 100644 index 0000000..291c10c --- /dev/null +++ b/.github/workflows/pre-commit.yml @@ -0,0 +1,16 @@ +name: pre-commit + +on: + pull_request: + push: + branches: [main] + +jobs: + pre-commit: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: "3.11" + - uses: pre-commit/action@v3.0.0 diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..ff5359a --- /dev/null +++ b/.gitignore @@ -0,0 +1,15 @@ +.idea/ +.vscode/ + +data/ +.env + +.venv/ +venv/ +node_modules/ + +.DS_Store +.ipynb_checkpoints/ +__pycache__/ +*.egg-info +*.swp diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..ca8dbdf --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,36 @@ +default_language_version: + python: python3.10 +repos: + - repo: https://github.com/astral-sh/ruff-pre-commit + # Ruff version. + rev: v0.4.7 + hooks: + - id: ruff + types_or: [python, pyi, jupyter] + args: [--fix] + - id: ruff-format + types_or: [python, pyi, jupyter] + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v2.3.0 + hooks: + - id: check-yaml + - id: end-of-file-fixer + - id: trailing-whitespace + - repo: https://github.com/roy-ht/pre-commit-jupyter + rev: v1.2.1 + hooks: + - id: jupyter-notebook-cleanup + args: + # - --remove-kernel-metadata + - --pin-patterns + - "[pin];[donotremove]" + - repo: https://github.com/pre-commit/mirrors-prettier + rev: v3.1.0 + hooks: + - id: prettier + types_or: + - javascript + - ts + - tsx + - yaml + - css diff --git a/README.md b/README.md new file mode 100644 index 0000000..489e00b --- /dev/null +++ b/README.md @@ -0,0 +1,86 @@ +# Better Python Code + +MyWord is a small demonstration project that shows how you can write better research code in Python. + +## Setup + +This project has been tested on Python 3.10, but earlier or later versions may work as well. +First, clone this repo: + +```bash +git clone https://github.com/reglab/better-python.git myword +``` + +Next, install uv if you haven't already: + +```bash +curl -LsSf https://astral.sh/uv/install.sh | sh +``` + +Then, create a virtual environment: + +```bash +cd myword +uv venv # optionally add --python 3.11 or another version +``` + +To activate the virtual environment: + +```bash +source .venv/bin/activate # If using fish shell, use `source .venv/bin/activate.fish` instead +``` + +Generally, you will want to activate the virtual environment before running any of the scripts +in this project. However, if you use `uv`, it can handle everything for you! Just run code with +`uv run python `. (You can also run anything else installed to your venv, e.g., +`uv run ruff check --fix`.) + +Using `uv run` will also automatically sync your environment with any new/removed packages +in your `pyproject.toml` file. (See the Development section below, or the `uv` docs, for +information about installing/maintaining dependencies.) You can read the `uv` documentation +[here](https://docs.astral.sh/uv/getting-started/features/#projects). + +Then, install the dependencies and this package: + +```bash +brew install tesseract # If not on Mac, look up how to install Tesseract for your OS + +uv sync +``` + +Finally, install the git hooks: + +```bash +# If you don't already have pre-commit, run: `uv tool install pre-commit` +pre-commit install +``` + +## Usage + +To run the download script: + +```bash +python myword/download_data.py +``` + +To run the "train" script: + +```bash +python myword/train_word2vec.py +``` + +With each of these, you can add the `--help` flag to see the available options. + + +## Development + +To add/remove dependencies later on: +```bash +uv add # or uv remove +uv add --dev # For dev dependencies, like pre-commit +``` + +## Activity + +The `main` branch contains the "final" version of the code, while the `initial` branch +contains the code before the caching optimization. diff --git a/myword/__init__.py b/myword/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/myword/download_data.py b/myword/download_data.py new file mode 100644 index 0000000..f8d0b9f --- /dev/null +++ b/myword/download_data.py @@ -0,0 +1,38 @@ +import zipfile +from pathlib import Path + +import fire +import gdown + +import myword.utils + +_DEFAULT_ZIP_URL = "https://drive.google.com/file/d/1ho19xLFmgKWWi0xCoKEPV_maKwrhl51k/view?usp=drive_link" +_DEFAULT_OUTPUT_DIR = myword.utils.get_data_path() / "pdf" + + +def download_gdrive_folder( + zip_url: str = _DEFAULT_ZIP_URL, + output_dir: str = _DEFAULT_OUTPUT_DIR, +) -> None: + """Download a zip file from Google Drive and extract it to a local directory. + + :param zip_url: URL to the folder to download. + :param output_dir: Local directorty to save the folder to. + """ + output_dir = Path(output_dir) + # Name the zip file after the output directory and place it in the same parent directory. + zip_output_path = output_dir.parent / f"{output_dir.name}.zip" + gdown.download(zip_url, str(zip_output_path), quiet=False, fuzzy=True) + + # Unzip the folder + print(f"Unzipping {zip_output_path} to {output_dir}...") + with zipfile.ZipFile(zip_output_path, "r") as zip_ref: + # We extract to the output's parent directory to avoid creating a redundant nested directory. + zip_ref.extractall(output_dir.parent) + # Delete the zip file + print(f"Extraction completed. Deleting {zip_output_path}...") + zip_output_path.unlink() + + +if __name__ == "__main__": + fire.Fire(download_gdrive_folder) diff --git a/myword/train_word2vec.py b/myword/train_word2vec.py new file mode 100644 index 0000000..ea3a214 --- /dev/null +++ b/myword/train_word2vec.py @@ -0,0 +1,76 @@ +"""Train word2vec model from a directory of PDFs""" + +import time +from pathlib import Path + +import fire +import pdf2image +import pytesseract +import tqdm +from diskcache import Cache + +import myword.utils + +# This translates to the `data/pdf` directory in the repository root. +PDF_DIR = myword.utils.get_data_path() / "pdf" + +pdf_text_cache = Cache(str(myword.utils.get_data_path() / "cache" / "pdf_text")) + + +def get_text_windows_from_pdf(pdf_path: Path, window_size) -> list[list[str]]: + if pdf_path in pdf_text_cache: + text = pdf_text_cache[pdf_path] + else: + images = pdf2image.convert_from_path(pdf_path, dpi=200) + page_texts = [pytesseract.image_to_string(img) for img in images] + text = "\n".join(page_texts) + pdf_text_cache[pdf_path] = text + + words = text.lower().split() + windows = [words[i : i + window_size] for i in range(len(words) - window_size + 1)] + return windows + + +def train_model( + word_windows: list[list[str]], + output_path: str = "word2vec.model", + *, + vector_dim: int = 300, + num_epochs: int = 10, +) -> None: + # A dummy function to simulate training a word2vec model. + for _ in tqdm.trange(num_epochs, desc="Epochs"): + time.sleep(len(word_windows) * vector_dim * 1e-7) + print(f"Training complete. Saved model to {output_path}.") + + +def main( + pdf_dir: str = str(PDF_DIR), + output_path: str = "word2vec.model", + vector_dim: int = 300, + window_size: int = 5, + num_epochs: int = 10, +) -> None: + pdf_dir = Path(pdf_dir) + pdf_files = list(pdf_dir.glob("*.pdf")) + print(f"Found {len(pdf_files)} PDFs in {pdf_dir}.") + word_windows = [] + for pdf_file in tqdm.tqdm(pdf_files, desc="PDFs"): + word_windows.extend( + get_text_windows_from_pdf(pdf_file, window_size=window_size), + ) + print(f"Training word2vec model with {len(word_windows)} word windows...") + train_model( + word_windows, + output_path=output_path, + vector_dim=vector_dim, + num_epochs=num_epochs, + ) + + +def entrypoint(): + fire.Fire(main) + + +if __name__ == "__main__": + entrypoint() diff --git a/myword/utils.py b/myword/utils.py new file mode 100644 index 0000000..e45c503 --- /dev/null +++ b/myword/utils.py @@ -0,0 +1,5 @@ +from pathlib import Path + + +def get_data_path() -> Path: + return 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