rectanglepy 0.4.4__tar.gz → 0.4.6__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-0.4.4 → rectanglepy-0.4.6}/.bumpversion.cfg +1 -1
  2. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/PKG-INFO +1 -2
  3. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/pyproject.toml +1 -1
  4. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/src/rectanglepy/rectangle.py +6 -1
  5. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/.cruft.json +0 -0
  6. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/.editorconfig +0 -0
  7. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/.github/ISSUE_TEMPLATE/bug_report.yml +0 -0
  8. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/.github/ISSUE_TEMPLATE/config.yml +0 -0
  9. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/.github/ISSUE_TEMPLATE/feature_request.yml +0 -0
  10. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/.github/PULL_REQUEST_TEMPLATE.md +0 -0
  11. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/.github/workflows/build.yaml +0 -0
  12. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/.github/workflows/release.yaml +0 -0
  13. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/.github/workflows/release_testpypi.yaml +0 -0
  14. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/.github/workflows/test.yaml +0 -0
  15. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/.gitignore +0 -0
  16. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/.pre-commit-config.yaml +0 -0
  17. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/.readthedocs.yaml +0 -0
  18. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/CHANGELOG.md +0 -0
  19. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/LICENSE +0 -0
  20. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/README.md +0 -0
  21. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/docs/Makefile +0 -0
  22. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/docs/_static/.gitkeep +0 -0
  23. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/docs/_templates/.gitkeep +0 -0
  24. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/docs/_templates/autosummary/class.rst +0 -0
  25. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/docs/api.md +0 -0
  26. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/docs/changelog.md +0 -0
  27. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/docs/conf.py +0 -0
  28. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/docs/contributing.md +0 -0
  29. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/docs/extensions/typed_returns.py +0 -0
  30. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/docs/index.md +0 -0
  31. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/docs/make.bat +0 -0
  32. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/docs/notebooks/example.ipynb +0 -0
  33. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/docs/references.bib +0 -0
  34. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/docs/references.md +0 -0
  35. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/src/rectanglepy/__init__.py +0 -0
  36. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/src/rectanglepy/data/hao1_annotations_small.zip +0 -0
  37. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/src/rectanglepy/data/hao1_counts_small.zip +0 -0
  38. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/src/rectanglepy/data/small_fino_bulks.zip +0 -0
  39. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/src/rectanglepy/pp/__init__.py +0 -0
  40. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/src/rectanglepy/pp/create_signature.py +0 -0
  41. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/src/rectanglepy/pp/rectangle_signature.py +0 -0
  42. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/src/rectanglepy/tl/__init__.py +0 -0
  43. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/src/rectanglepy/tl/deconvolution.py +0 -0
  44. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/tests/data/TIL10_signature.txt +0 -0
  45. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/tests/data/bulk_small.csv +0 -0
  46. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/tests/data/cell_annotations_small.txt +0 -0
  47. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/tests/data/quanTIseq_SimRNAseq_mixture_smaller.csv +0 -0
  48. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/tests/data/quanTIseq_SimRNAseq_read_fractions_small.txt +0 -0
  49. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/tests/data/sc_object_small.csv +0 -0
  50. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/tests/data/signature_hao1.csv +0 -0
  51. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/tests/test_pp.py +0 -0
  52. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/tests/test_rectangle.py +0 -0
  53. {rectanglepy-0.4.4 → rectanglepy-0.4.6}/tests/test_tl.py +0 -0
{rectanglepy-0.4.4 → rectanglepy-0.4.6}/.bumpversion.cfg RENAMED
@@ -1,5 +1,5 @@
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  [bumpversion]
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- current_version = 0.4.4
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+ current_version = 0.4.6
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  tag = True
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  commit = True
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{rectanglepy-0.4.4 → rectanglepy-0.4.6}/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: 0.4.4
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+ Version: 0.4.6
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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
@@ -28,7 +28,6 @@ License: MIT License
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  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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  SOFTWARE.
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- License-File: LICENSE
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  Requires-Python: >=3.10
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  Requires-Dist: anndata<0.10.9,>=0.8.0
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  Requires-Dist: loguru
{rectanglepy-0.4.4 → rectanglepy-0.4.6}/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 = "0.4.4"
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+ version = "0.4.6"
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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-0.4.4 → rectanglepy-0.4.6}/src/rectanglepy/rectangle.py RENAMED
@@ -112,7 +112,11 @@ def rectangle_consens(
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  cell_fractions = deconvolution(signatures, bulks, correct_mrna_bias, n_cpus)
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  estimations.append(cell_fractions)
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  if "Unknown" in cell_fractions.columns:
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- unkn_gene_corr = _genes_linked_to_unkn(bulks, cell_fractions["Unknown"])
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+ try:
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+ unkn_gene_corr = _genes_linked_to_unkn(bulks, cell_fractions["Unknown"])
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+ except Exception as e:
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+ logger.warning(f"Could not calculate gene correlation with unknown cell type: {e}")
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+ unkn_gene_corr = None
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  else:
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  unkn_gene_corr = None
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  signatures.unkn_gene_corr = unkn_gene_corr
@@ -121,6 +125,7 @@ def rectangle_consens(
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  # normalize the estimations to 1, needed for the consensus
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  consensus_estimations = consensus_estimations.div(consensus_estimations.sum(axis=1), axis=0)
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+ consensus_estimations[consensus_estimations < 0] = 0
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  consensus_results = ConsensusResult(estimations, rectangle_signature_results)
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  return consensus_estimations, most_recent_signatures, consensus_results
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{rectanglepy-0.4.4 → rectanglepy-0.4.6}/.cruft.json RENAMED
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{rectanglepy-0.4.4 → rectanglepy-0.4.6}/.editorconfig RENAMED
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{rectanglepy-0.4.4 → rectanglepy-0.4.6}/.gitignore RENAMED
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{rectanglepy-0.4.4 → rectanglepy-0.4.6}/CHANGELOG.md RENAMED
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{rectanglepy-0.4.4 → rectanglepy-0.4.6}/LICENSE RENAMED
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{rectanglepy-0.4.4 → rectanglepy-0.4.6}/README.md RENAMED
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{rectanglepy-0.4.4 → rectanglepy-0.4.6}/docs/Makefile RENAMED
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{rectanglepy-0.4.4 → rectanglepy-0.4.6}/docs/api.md RENAMED
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{rectanglepy-0.4.4 → rectanglepy-0.4.6}/docs/conf.py RENAMED
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{rectanglepy-0.4.4 → rectanglepy-0.4.6}/docs/index.md RENAMED
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{rectanglepy-0.4.4 → rectanglepy-0.4.6}/docs/make.bat RENAMED
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