rectanglepy 0.1.2__tar.gz → 0.1.3__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 (52) hide show
  1. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/.bumpversion.cfg +1 -1
  2. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/PKG-INFO +1 -1
  3. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/pyproject.toml +1 -1
  4. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/src/rectanglepy/pp/create_signature.py +2 -0
  5. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/.cruft.json +0 -0
  6. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/.editorconfig +0 -0
  7. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/.github/ISSUE_TEMPLATE/bug_report.yml +0 -0
  8. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/.github/ISSUE_TEMPLATE/config.yml +0 -0
  9. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/.github/ISSUE_TEMPLATE/feature_request.yml +0 -0
  10. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/.github/PULL_REQUEST_TEMPLATE.md +0 -0
  11. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/.github/workflows/build.yaml +0 -0
  12. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/.github/workflows/release.yaml +0 -0
  13. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/.github/workflows/test.yaml +0 -0
  14. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/.gitignore +0 -0
  15. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/.pre-commit-config.yaml +0 -0
  16. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/.readthedocs.yaml +0 -0
  17. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/CHANGELOG.md +0 -0
  18. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/LICENSE +0 -0
  19. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/README.md +0 -0
  20. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/docs/Makefile +0 -0
  21. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/docs/_static/.gitkeep +0 -0
  22. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/docs/_templates/.gitkeep +0 -0
  23. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/docs/_templates/autosummary/class.rst +0 -0
  24. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/docs/api.md +0 -0
  25. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/docs/changelog.md +0 -0
  26. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/docs/conf.py +0 -0
  27. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/docs/contributing.md +0 -0
  28. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/docs/extensions/typed_returns.py +0 -0
  29. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/docs/index.md +0 -0
  30. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/docs/make.bat +0 -0
  31. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/docs/notebooks/example.ipynb +0 -0
  32. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/docs/references.bib +0 -0
  33. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/docs/references.md +0 -0
  34. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/src/rectanglepy/__init__.py +0 -0
  35. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/src/rectanglepy/data/hao1_annotations_small.zip +0 -0
  36. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/src/rectanglepy/data/hao1_counts_small.zip +0 -0
  37. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/src/rectanglepy/data/small_fino_bulks.zip +0 -0
  38. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/src/rectanglepy/pp/__init__.py +0 -0
  39. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/src/rectanglepy/pp/rectangle_signature.py +0 -0
  40. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/src/rectanglepy/rectangle.py +0 -0
  41. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/src/rectanglepy/tl/__init__.py +0 -0
  42. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/src/rectanglepy/tl/deconvolution.py +0 -0
  43. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/tests/data/TIL10_signature.txt +0 -0
  44. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/tests/data/bulk_small.csv +0 -0
  45. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/tests/data/cell_annotations_small.txt +0 -0
  46. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/tests/data/quanTIseq_SimRNAseq_mixture_smaller.csv +0 -0
  47. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/tests/data/quanTIseq_SimRNAseq_read_fractions_small.txt +0 -0
  48. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/tests/data/sc_object_small.csv +0 -0
  49. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/tests/data/signature_hao1.csv +0 -0
  50. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/tests/test_pp.py +0 -0
  51. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/tests/test_rectangle.py +0 -0
  52. {rectanglepy-0.1.2 → rectanglepy-0.1.3}/tests/test_tl.py +0 -0
{rectanglepy-0.1.2 → rectanglepy-0.1.3}/.bumpversion.cfg RENAMED
@@ -1,5 +1,5 @@
1
1
  [bumpversion]
2
- current_version = 0.1.2
2
+ current_version = 0.1.3
3
3
  tag = True
4
4
  commit = True
5
5
 
{rectanglepy-0.1.2 → rectanglepy-0.1.3}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.3
2
2
  Name: rectanglepy
3
- Version: 0.1.2
3
+ Version: 0.1.3
4
4
  Summary: Hierarchical deconvolution of bulk transcriptomics
5
5
  Project-URL: Documentation, https://rectanglepy.readthedocs.io/
6
6
  Project-URL: Source, https://github.com/ComputationalBiomedicineGroup/Rectangle
{rectanglepy-0.1.2 → rectanglepy-0.1.3}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ requires = ["hatchling"]
4
4
 
5
5
  [project]
6
6
  name = "rectanglepy"
7
- version = "0.1.2"
7
+ version = "0.1.3"
8
8
  description = "Hierarchical deconvolution of bulk transcriptomics"
9
9
  readme = "README.md"
10
10
  requires-python = ">=3.10"
{rectanglepy-0.1.2 → rectanglepy-0.1.3}/src/rectanglepy/pp/create_signature.py RENAMED
@@ -142,6 +142,8 @@ def _run_deseq2(countsig: pd.DataFrame, n_cpus: int = None) -> dict[str | int, p
142
142
  clinical_df = pd.DataFrame({"condition": condition}, index=countsig.columns)
143
143
  dds = DeseqDataSet(counts=count_df, metadata=clinical_df, design_factors="condition", quiet=True, n_cpus=n_cpus)
144
144
  dds.deseq2()
145
+ dds.varm["LFC"] = dds.varm["LFC"].round(4)
146
+ dds.varm["dispersions"] = dds.varm["dispersions"].round(3)
145
147
 
146
148
  stat_res = DeseqStats(dds, n_cpus=n_cpus, quiet=True)
147
149
  stat_res.summary(quiet=True)
{rectanglepy-0.1.2 → rectanglepy-0.1.3}/.cruft.json RENAMED
File without changes
{rectanglepy-0.1.2 → rectanglepy-0.1.3}/.editorconfig RENAMED
File without changes
{rectanglepy-0.1.2 → rectanglepy-0.1.3}/.gitignore RENAMED
File without changes
{rectanglepy-0.1.2 → rectanglepy-0.1.3}/CHANGELOG.md RENAMED
File without changes
{rectanglepy-0.1.2 → rectanglepy-0.1.3}/LICENSE RENAMED
File without changes
{rectanglepy-0.1.2 → rectanglepy-0.1.3}/README.md RENAMED
File without changes
{rectanglepy-0.1.2 → rectanglepy-0.1.3}/docs/Makefile RENAMED
File without changes
{rectanglepy-0.1.2 → rectanglepy-0.1.3}/docs/api.md RENAMED
File without changes
{rectanglepy-0.1.2 → rectanglepy-0.1.3}/docs/conf.py RENAMED
File without changes
{rectanglepy-0.1.2 → rectanglepy-0.1.3}/docs/index.md RENAMED
File without changes
{rectanglepy-0.1.2 → rectanglepy-0.1.3}/docs/make.bat RENAMED
File without changes