rectanglepy 0.3.0__tar.gz → 0.4.0__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 (53) hide show
  1. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/.bumpversion.cfg +1 -1
  2. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/PKG-INFO +1 -1
  3. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/pyproject.toml +1 -1
  4. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/src/rectanglepy/tl/deconvolution.py +2 -2
  5. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/.cruft.json +0 -0
  6. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/.editorconfig +0 -0
  7. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/.github/ISSUE_TEMPLATE/bug_report.yml +0 -0
  8. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/.github/ISSUE_TEMPLATE/config.yml +0 -0
  9. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/.github/ISSUE_TEMPLATE/feature_request.yml +0 -0
  10. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/.github/PULL_REQUEST_TEMPLATE.md +0 -0
  11. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/.github/workflows/build.yaml +0 -0
  12. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/.github/workflows/release.yaml +0 -0
  13. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/.github/workflows/release_testpypi.yaml +0 -0
  14. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/.github/workflows/test.yaml +0 -0
  15. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/.gitignore +0 -0
  16. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/.pre-commit-config.yaml +0 -0
  17. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/.readthedocs.yaml +0 -0
  18. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/CHANGELOG.md +0 -0
  19. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/LICENSE +0 -0
  20. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/README.md +0 -0
  21. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/docs/Makefile +0 -0
  22. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/docs/_static/.gitkeep +0 -0
  23. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/docs/_templates/.gitkeep +0 -0
  24. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/docs/_templates/autosummary/class.rst +0 -0
  25. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/docs/api.md +0 -0
  26. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/docs/changelog.md +0 -0
  27. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/docs/conf.py +0 -0
  28. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/docs/contributing.md +0 -0
  29. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/docs/extensions/typed_returns.py +0 -0
  30. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/docs/index.md +0 -0
  31. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/docs/make.bat +0 -0
  32. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/docs/notebooks/example.ipynb +0 -0
  33. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/docs/references.bib +0 -0
  34. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/docs/references.md +0 -0
  35. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/src/rectanglepy/__init__.py +0 -0
  36. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/src/rectanglepy/data/hao1_annotations_small.zip +0 -0
  37. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/src/rectanglepy/data/hao1_counts_small.zip +0 -0
  38. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/src/rectanglepy/data/small_fino_bulks.zip +0 -0
  39. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/src/rectanglepy/pp/__init__.py +0 -0
  40. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/src/rectanglepy/pp/create_signature.py +0 -0
  41. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/src/rectanglepy/pp/rectangle_signature.py +0 -0
  42. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/src/rectanglepy/rectangle.py +0 -0
  43. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/src/rectanglepy/tl/__init__.py +0 -0
  44. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/tests/data/TIL10_signature.txt +0 -0
  45. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/tests/data/bulk_small.csv +0 -0
  46. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/tests/data/cell_annotations_small.txt +0 -0
  47. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/tests/data/quanTIseq_SimRNAseq_mixture_smaller.csv +0 -0
  48. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/tests/data/quanTIseq_SimRNAseq_read_fractions_small.txt +0 -0
  49. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/tests/data/sc_object_small.csv +0 -0
  50. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/tests/data/signature_hao1.csv +0 -0
  51. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/tests/test_pp.py +0 -0
  52. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/tests/test_rectangle.py +0 -0
  53. {rectanglepy-0.3.0 → rectanglepy-0.4.0}/tests/test_tl.py +0 -0
{rectanglepy-0.3.0 → rectanglepy-0.4.0}/.bumpversion.cfg RENAMED
@@ -1,5 +1,5 @@
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  [bumpversion]
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- current_version = 0.3.0
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+ current_version = 0.4.0
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  tag = True
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  commit = True
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{rectanglepy-0.3.0 → rectanglepy-0.4.0}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.3
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  Name: rectanglepy
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- Version: 0.3.0
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+ Version: 0.4.0
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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
{rectanglepy-0.3.0 → rectanglepy-0.4.0}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ requires = ["hatchling"]
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  [project]
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  name = "rectanglepy"
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- version = "0.3.0"
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+ version = "0.4.0"
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  description = "Hierarchical deconvolution of bulk transcriptomics"
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  readme = "README.md"
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  requires-python = ">=3.10"
{rectanglepy-0.3.0 → rectanglepy-0.4.0}/src/rectanglepy/tl/deconvolution.py RENAMED
@@ -311,7 +311,7 @@ def correct_for_unknown_cell_content(
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  if estimates.sum() == 0:
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  estimates_fix = estimates
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  # analysis fails if all cell fractions are zero, so we set the unknown cell content to ß
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- estimates_fix.loc["Unknown"] = 0
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+ estimates_fix["Unknown"] = 0
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  return estimates_fix
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  signature_genes = pseudo_signature_cpm.index
@@ -333,6 +333,6 @@ def correct_for_unknown_cell_content(
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  # Correct (i.e. scale) the cell fraction estimates so that their sum
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  # equals 1 - the unknown cellular content estimated above
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  estimates_fix = estimates / estimates.sum() * (1 - ukn_cc)
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- estimates_fix.loc["Unknown"] = abs(ukn_cc)
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+ estimates_fix["Unknown"] = abs(ukn_cc)
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  return estimates_fix
{rectanglepy-0.3.0 → rectanglepy-0.4.0}/.cruft.json RENAMED
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{rectanglepy-0.3.0 → rectanglepy-0.4.0}/.editorconfig RENAMED
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{rectanglepy-0.3.0 → rectanglepy-0.4.0}/.gitignore RENAMED
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{rectanglepy-0.3.0 → rectanglepy-0.4.0}/CHANGELOG.md RENAMED
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{rectanglepy-0.3.0 → rectanglepy-0.4.0}/LICENSE RENAMED
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{rectanglepy-0.3.0 → rectanglepy-0.4.0}/README.md RENAMED
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{rectanglepy-0.3.0 → rectanglepy-0.4.0}/docs/Makefile RENAMED
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{rectanglepy-0.3.0 → rectanglepy-0.4.0}/docs/api.md RENAMED
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{rectanglepy-0.3.0 → rectanglepy-0.4.0}/docs/conf.py RENAMED
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{rectanglepy-0.3.0 → rectanglepy-0.4.0}/docs/index.md RENAMED
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{rectanglepy-0.3.0 → rectanglepy-0.4.0}/docs/make.bat RENAMED
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