Initial release: GPU-accelerated RCTD for spatial transcriptomics

JAX reimplementation of spacexr RCTD with 63x GPU speedup and 99.7%
agreement with R on 58k Xenium pixels. Supports full, doublet, and
multi deconvolution modes.

Author: p-gueguen

.github/workflows/lint.yml

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+name: Lint
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install ruff
+        run: pip install ruff
+
+      - name: Check linting
+        run: ruff check src/ tests/
+
+      - name: Check formatting
+        run: ruff format --check src/ tests/

.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build tools
+        run: pip install build twine
+
+      - name: Build package
+        run: python -m build
+
+      - name: Validate distribution
+        run: twine check dist/*
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/test.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: pip install ".[dev]"
+
+      - name: Run tests
+        run: pytest tests/ -v --cov=rctd --cov-report=xml
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          files: ./coverage.xml

.gitignore

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+# Virtual environments
+.venv/
+.env/
+
+# Python
+__pycache__/
+*.pyc
+*.pyo
+*.egg-info/
+dist/
+build/
+
+# Testing
+.pytest_cache/
+htmlcov/
+.coverage
+coverage.xml
+
+# Data (large reference/validation files)
+data/
+
+# R reference validation data
+scripts/r_reference/
+
+# Package data (generated at build time)
+src/rctd/data/
+
+# IDE
+.vscode/
+.idea/
+
+# OS
+.DS_Store
+Thumbs.db
+
+# SLURM / HPC
+*.log
+*.err
+/scratch/
+
+# Build artifacts
+*.knit.md
+*.html
+
+# Lock files
+uv.lock
+
+# Generated version file
+src/rctd/_version.py

CITATION.cff

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+cff-version: 1.2.0
+title: "rctd-py: GPU-accelerated RCTD for spatial transcriptomics"
+message: >-
+  If you use this software, please cite the original
+  spacexr RCTD paper.
+type: software
+authors:
+  - given-names: Paul
+    family-names: Gueguen
+license: GPL-3.0-or-later
+repository-code: "https://github.com/p-gueguen/rctd-py"
+keywords:
+  - spatial-transcriptomics
+  - deconvolution
+  - single-cell
+  - JAX
+  - GPU
+references:
+  - type: article
+    title: "Robust decomposition of cell type mixtures in spatial transcriptomics"
+    authors:
+      - given-names: Dylan M
+        family-names: Cable
+      - given-names: Evan
+        family-names: Murray
+      - given-names: Luli S
+        family-names: Zou
+      - given-names: Aleksandrina
+        family-names: Goeva
+      - given-names: Evan Z
+        family-names: Macosko
+      - given-names: Fei
+        family-names: Chen
+    journal: "Nature Biotechnology"
+    volume: 40
+    start: 517
+    end: 526
+    year: 2022
+    doi: "10.1038/s41587-021-00830-w"