rectanglepy 1.0.0__tar.gz → 1.2.1__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (57) hide show
  1. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/.bumpversion.cfg +1 -1
  2. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/CHANGELOG.md +6 -0
  3. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/PKG-INFO +4 -3
  4. rectanglepy-1.2.1/docs/notebooks/example.ipynb +1131 -0
  5. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/docs/references.bib +22 -0
  6. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/pyproject.toml +4 -3
  7. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/src/rectanglepy/pp/rectangle_signature.py +28 -0
  8. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/src/rectanglepy/tl/deconvolution.py +92 -33
  9. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/tests/test_rectangle.py +11 -0
  10. rectanglepy-1.0.0/docs/notebooks/example.ipynb +0 -1145
  11. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/.cruft.json +0 -0
  12. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/.editorconfig +0 -0
  13. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/.github/ISSUE_TEMPLATE/bug_report.yml +0 -0
  14. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/.github/ISSUE_TEMPLATE/config.yml +0 -0
  15. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/.github/ISSUE_TEMPLATE/feature_request.yml +0 -0
  16. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/.github/PULL_REQUEST_TEMPLATE.md +0 -0
  17. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/.github/workflows/build.yaml +0 -0
  18. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/.github/workflows/release.yaml +0 -0
  19. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/.github/workflows/release_testpypi.yaml +0 -0
  20. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/.github/workflows/test.yaml +0 -0
  21. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/.gitignore +0 -0
  22. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/.pre-commit-config.yaml +0 -0
  23. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/.readthedocs.yaml +0 -0
  24. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/LICENSE +0 -0
  25. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/README.md +0 -0
  26. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/docs/Makefile +0 -0
  27. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/docs/_static/.gitkeep +0 -0
  28. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/docs/_static/rec_logo.001.png +0 -0
  29. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/docs/_templates/.gitkeep +0 -0
  30. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/docs/_templates/autosummary/class.rst +0 -0
  31. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/docs/api.md +0 -0
  32. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/docs/changelog.md +0 -0
  33. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/docs/conf.py +0 -0
  34. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/docs/contributing.md +0 -0
  35. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/docs/extensions/typed_returns.py +0 -0
  36. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/docs/index.md +0 -0
  37. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/docs/installation.md +0 -0
  38. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/docs/make.bat +0 -0
  39. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/docs/references.md +0 -0
  40. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/docs/tutorials.md +0 -0
  41. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/src/rectanglepy/__init__.py +0 -0
  42. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/src/rectanglepy/data/hao1_annotations_small.zip +0 -0
  43. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/src/rectanglepy/data/hao1_counts_small.zip +0 -0
  44. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/src/rectanglepy/data/small_fino_bulks.zip +0 -0
  45. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/src/rectanglepy/pp/__init__.py +0 -0
  46. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/src/rectanglepy/pp/create_signature.py +0 -0
  47. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/src/rectanglepy/rectangle.py +0 -0
  48. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/src/rectanglepy/tl/__init__.py +0 -0
  49. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/tests/data/TIL10_signature.txt +0 -0
  50. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/tests/data/bulk_small.csv +0 -0
  51. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/tests/data/cell_annotations_small.txt +0 -0
  52. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/tests/data/quanTIseq_SimRNAseq_mixture_smaller.csv +0 -0
  53. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/tests/data/quanTIseq_SimRNAseq_read_fractions_small.txt +0 -0
  54. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/tests/data/sc_object_small.csv +0 -0
  55. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/tests/data/signature_hao1.csv +0 -0
  56. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/tests/test_pp.py +0 -0
  57. {rectanglepy-1.0.0 → rectanglepy-1.2.1}/tests/test_tl.py +0 -0
{rectanglepy-1.0.0 → rectanglepy-1.2.1}/.bumpversion.cfg RENAMED
@@ -1,5 +1,5 @@
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  [bumpversion]
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- current_version = 1.0.0
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+ current_version = 1.2.1
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  tag = True
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  commit = True
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{rectanglepy-1.0.0 → rectanglepy-1.2.1}/CHANGELOG.md RENAMED
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  ## [Unreleased]
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+ ## [1.2.0] - 2026-01-31
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+
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+ ### Changed
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+
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+ - Switched the quadratic programming solver from quadprog to OSQP.
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+
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  ## [1.0.0] - 2025-08-14
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  ### Added
{rectanglepy-1.0.0 → rectanglepy-1.2.1}/PKG-INFO RENAMED
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  Metadata-Version: 2.4
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  Name: rectanglepy
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- Version: 1.0.0
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+ Version: 1.2.1
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  Summary: Hierarchical deconvolution of bulk transcriptomics
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  Project-URL: Documentation, https://rectanglepy.readthedocs.io/
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  Project-URL: Source, https://github.com/ComputationalBiomedicineGroup/Rectangle
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  Requires-Dist: anndata<0.10.9,>=0.8.0
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  Requires-Dist: loguru
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  Requires-Dist: numpy<2.0.0,>=1.0.0
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+ Requires-Dist: osqp>=1.0.5
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+ Requires-Dist: pandas<3.0.0,>=2.0.0
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  Requires-Dist: pydeseq2==0.4.11
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- Requires-Dist: quadprog==0.1.12
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  Requires-Dist: scipy==1.13.0
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- Requires-Dist: setuptools<70.0.0,>=69.0.0
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+ Requires-Dist: setuptools>=80.0.0
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  Requires-Dist: statsmodels>=0.14.1
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  Provides-Extra: dev
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  Requires-Dist: bump2version; extra == 'dev'