Initial commit

Author: sebasmos

.github/workflows/docs.yml

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+name: Deploy Docs
+
+on:
+  push:
+    branches: [main]
+
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install PyTorch (CPU)
+        run: pip install torch==2.2.0 torchvision==0.17.0 --index-url https://download.pytorch.org/whl/cpu
+
+      - name: Install package and docs dependencies
+        run: pip install -e ".[all,docs]"
+
+      - name: Deploy to GitHub Pages
+        run: mkdocs gh-deploy --force

.github/workflows/tests.yml

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+name: Tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
+          pip install -e ".[all]"
+
+      - name: Run tests with coverage
+        run: pytest tests/ -v --cov=shortcut_detect --cov-report=xml -m "not e2e"
+
+      - name: Upload coverage
+        uses: codecov/codecov-action@v4
+        continue-on-error: true
+        with:
+          file: ./coverage.xml

.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+*.egg
+*.egg-info/
+dist/
+build/
+.eggs/
+
+# Virtual Environment
+.venv/
+.venv-docs/
+venv/
+ENV/
+env/
+
+# Jupyter
+.ipynb_checkpoints/
+*.ipynb_checkpoints
+.jupyter/
+.local/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+.tox/
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Output files (keep structure, ignore generated reports)
+output/*/
+!output/.gitkeep
+!output/paper_tables/
+!output/paper_benchmark/
+
+# Data files — large embeddings/images hosted on HuggingFace, not in git
+# Keep only small config/manifest files; ignore .npy, .pkl, images
+data/*.npy
+data/*.pkl
+data/celeba/
+data/celeba_real/
+data/chexpert_multibackbone/
+data/mimic_cxr/*.npy
+data/mimic_cxr/*_metadata.csv
+data/mimic_cxr/*_metadata_orig.csv
+data/mimic_cxr/*_metadata_dx.csv
+data/mimic_cxr/mimic-cxr-*.csv
+data/train.csv
+data/valid.csv
+data/*.xlsx
+
+# Keep manifests (small, needed for reproducibility)
+!data/chexpert_manifest.csv
+!data/mimic_cxr/mimic_cxr_manifest.csv
+
+# Paper drafts and roadmap (kept locally, not in repo)
+docs-temp/
+
+# MkDocs build output
+site/
+
+# Temporary files
+*.log
+*.tmp
+temp/
+tmp/

.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+      - id: black
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.4
+    hooks:
+      - id: ruff
+        args: [--fix]
+
+# Note: Full test suite runs in GitHub Actions CI
+# To run tests locally: pytest tests/ -v

Dockerfile

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+# Reproducible environment for ShortKIT-ML paper benchmarks
+# Build:  docker build -t shortcut-detect .
+# Run:    docker run --rm -v $(pwd)/output:/app/output shortcut-detect smoke
+FROM python:3.10-slim
+
+LABEL maintainer="ShortKIT-ML Team"
+LABEL description="Reproducible environment for ShortKIT-ML paper benchmarks"
+
+# System dependencies required by weasyprint / PDF export and general build tools
+RUN apt-get update && apt-get install -y --no-install-recommends \
+        build-essential \
+        libpango1.0-dev \
+        libgdk-pixbuf2.0-dev \
+        libffi-dev \
+        git \
+    && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /app
+
+# Copy dependency manifest first for layer caching
+COPY pyproject.toml ./
+
+# Install the package in editable mode (with all extras for reproducibility)
+COPY . .
+RUN pip install --no-cache-dir -e ".[dev]"
+
+# Make the reproduce script executable
+RUN chmod +x scripts/reproduce_paper.sh
+
+# Default entrypoint runs the reproducibility script.
+# Pass a profile as the CMD argument: smoke | default | full
+ENTRYPOINT ["scripts/reproduce_paper.sh"]
+CMD ["default"]

LICENSE

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+MIT License
+
+Copyright (c) 2024 ShortKIT-ML Team
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.