rctd-py 0.1.1__tar.gz

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Files changed (37) hide show
  1. rctd_py-0.1.1/.gitignore +47 -0
  2. rctd_py-0.1.1/CITATION.cff +39 -0
  3. rctd_py-0.1.1/LICENSE +674 -0
  4. rctd_py-0.1.1/PKG-INFO +238 -0
  5. rctd_py-0.1.1/README.md +205 -0
  6. rctd_py-0.1.1/analysis_region3.html +1176 -0
  7. rctd_py-0.1.1/analysis_region3.qmd +614 -0
  8. rctd_py-0.1.1/pyproject.toml +63 -0
  9. rctd_py-0.1.1/src/rctd/__init__.py +28 -0
  10. rctd_py-0.1.1/src/rctd/_doublet.py +387 -0
  11. rctd_py-0.1.1/src/rctd/_full.py +86 -0
  12. rctd_py-0.1.1/src/rctd/_irwls.py +224 -0
  13. rctd_py-0.1.1/src/rctd/_likelihood.py +324 -0
  14. rctd_py-0.1.1/src/rctd/_multi.py +357 -0
  15. rctd_py-0.1.1/src/rctd/_normalize.py +87 -0
  16. rctd_py-0.1.1/src/rctd/_rctd.py +291 -0
  17. rctd_py-0.1.1/src/rctd/_reference.py +242 -0
  18. rctd_py-0.1.1/src/rctd/_sigma.py +165 -0
  19. rctd_py-0.1.1/src/rctd/_simplex.py +30 -0
  20. rctd_py-0.1.1/src/rctd/_types.py +73 -0
  21. rctd_py-0.1.1/src/rctd/_version.py +34 -0
  22. rctd_py-0.1.1/src/rctd/py.typed +0 -0
  23. rctd_py-0.1.1/test_py.py +25 -0
  24. rctd_py-0.1.1/tests/conftest.py +89 -0
  25. rctd_py-0.1.1/tests/test_doublet.py +49 -0
  26. rctd_py-0.1.1/tests/test_full.py +37 -0
  27. rctd_py-0.1.1/tests/test_irwls.py +154 -0
  28. rctd_py-0.1.1/tests/test_likelihood.py +176 -0
  29. rctd_py-0.1.1/tests/test_multi.py +52 -0
  30. rctd_py-0.1.1/tests/test_normalize.py +29 -0
  31. rctd_py-0.1.1/tests/test_q_matrices.py +39 -0
  32. rctd_py-0.1.1/tests/test_rctd.py +69 -0
  33. rctd_py-0.1.1/tests/test_reference.py +144 -0
  34. rctd_py-0.1.1/tests/test_sigma.py +34 -0
  35. rctd_py-0.1.1/tests/test_simplex.py +61 -0
  36. rctd_py-0.1.1/uv.lock +1421 -0
  37. rctd_py-0.1.1/vignette_bench.sh +26 -0
rctd_py-0.1.1/.gitignore ADDED
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+ # Virtual environments
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+ .venv/
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+ .env/
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+
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+ # Python
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+ __pycache__/
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+ *.pyc
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+ *.pyo
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+ *.egg-info/
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+ dist/
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+ build/
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+
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+ # Testing
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+ .pytest_cache/
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+ htmlcov/
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+ .coverage
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+ coverage.xml
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+
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+ # Data (large reference/validation files)
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+ data/
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+
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+ # R reference validation data
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+ scripts/r_reference/
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+
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+ # Package data (keep q_matrices.npz, ignore everything else)
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+ src/rctd/data/*
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+ !src/rctd/data/q_matrices.npz
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+
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+ # IDE
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+ .vscode/
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+ .idea/
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+
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+ # OS
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+ .DS_Store
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+ Thumbs.db
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+
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+ # SLURM / HPC
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+ *.log
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+ *.err
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+ /scratch/
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+
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+ # Build artifacts
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+ *.knit.md
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+
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+ # Generated version file
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+ src/rctd/_version.py
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+ docs/plans/
rctd_py-0.1.1/CITATION.cff ADDED
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+ cff-version: 1.2.0
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+ title: "rctd-py: GPU-accelerated RCTD for spatial transcriptomics"
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+ message: >-
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+ If you use this software, please cite the original
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+ spacexr RCTD paper.
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+ type: software
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+ authors:
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+ - given-names: Paul
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+ family-names: Gueguen
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+ license: GPL-3.0-or-later
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+ repository-code: "https://github.com/p-gueguen/rctd-py"
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+ keywords:
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+ - spatial-transcriptomics
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+ - deconvolution
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+ - single-cell
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+ - JAX
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+ - GPU
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+ references:
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+ - type: article
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+ title: "Robust decomposition of cell type mixtures in spatial transcriptomics"
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+ authors:
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+ - given-names: Dylan M
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+ family-names: Cable
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+ - given-names: Evan
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+ family-names: Murray
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+ - given-names: Luli S
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+ family-names: Zou
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+ - given-names: Aleksandrina
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+ family-names: Goeva
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+ - given-names: Evan Z
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+ family-names: Macosko
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+ - given-names: Fei
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+ family-names: Chen
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+ journal: "Nature Biotechnology"
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+ volume: 40
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+ start: 517
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+ end: 526
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+ year: 2022
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+ doi: "10.1038/s41587-021-00830-w"