sciv 0.0.63__tar.gz → 0.0.105__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 (45) hide show
  1. {sciv-0.0.63 → sciv-0.0.105}/PKG-INFO +14 -8
  2. {sciv-0.0.63 → sciv-0.0.105}/pyproject.toml +15 -9
  3. {sciv-0.0.63 → sciv-0.0.105}/requirements.txt +14 -7
  4. sciv-0.0.105/src/sciv/model/_core_.py +801 -0
  5. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/plot/__init__.py +12 -1
  6. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/plot/_bar_.py +47 -13
  7. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/plot/_barcode_.py +9 -8
  8. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/plot/_box_.py +22 -7
  9. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/plot/_bubble_.py +3 -2
  10. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/plot/_core_.py +13 -5
  11. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/plot/_graph_.py +14 -9
  12. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/plot/_heat_map_.py +10 -7
  13. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/plot/_kde_.py +8 -7
  14. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/plot/_line_.py +6 -5
  15. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/plot/_pie_.py +10 -5
  16. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/plot/_radar_.py +5 -2
  17. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/plot/_scatter_.py +162 -8
  18. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/plot/_venn_.py +6 -4
  19. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/plot/_violin_.py +34 -22
  20. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/preprocessing/__init__.py +2 -1
  21. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/preprocessing/_anndata_.py +2 -2
  22. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/preprocessing/_scanpy_.py +106 -2
  23. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/preprocessing/_scvi_.py +25 -12
  24. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/tool/__init__.py +4 -4
  25. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/tool/_algorithm_.py +1438 -1291
  26. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/tool/_matrix_.py +30 -43
  27. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/tool/_random_walk_.py +178 -109
  28. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/util/__init__.py +2 -0
  29. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/util/_constant_.py +5 -3
  30. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/util/_core_.py +91 -17
  31. sciv-0.0.63/src/sciv/model/_core_.py +0 -1140
  32. {sciv-0.0.63 → sciv-0.0.105}/.gitignore +0 -0
  33. {sciv-0.0.63 → sciv-0.0.105}/LICENSE +0 -0
  34. {sciv-0.0.63 → sciv-0.0.105}/MANIFEST.in +0 -0
  35. {sciv-0.0.63 → sciv-0.0.105}/README.en.md +0 -0
  36. {sciv-0.0.63 → sciv-0.0.105}/README.md +0 -0
  37. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/__init__.py +0 -0
  38. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/file/__init__.py +0 -0
  39. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/file/_read_.py +0 -0
  40. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/file/_write_.py +0 -0
  41. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/model/__init__.py +0 -0
  42. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/preprocessing/_gencode_.py +0 -0
  43. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/preprocessing/_gsea_.py +0 -0
  44. {sciv-0.0.63 → sciv-0.0.105}/src/sciv/preprocessing/_snapatac_.py +0 -0
  45. {sciv-0.0.63 → sciv-0.0.105}/tests/scivTest/__init__.py +0 -0
{sciv-0.0.63 → sciv-0.0.105}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: sciv
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- Version: 0.0.63
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+ Version: 0.0.105
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  Summary: Unveiling the pivotal cell types involved in variant function regulation at a single-cell resolution
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  Project-URL: github, https://github.com/YuZhengM/sciv
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  Author-email: Zheng-Min Yu <yuzmbio@163.com>
@@ -29,28 +29,34 @@ Classifier: License :: OSI Approved :: MIT License
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  Classifier: Operating System :: OS Independent
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  Classifier: Programming Language :: Python :: 3
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  Requires-Python: >=3.10
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- Requires-Dist: anndata==0.11.4
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+ Requires-Dist: anndata==0.11.0
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  Requires-Dist: colormap==1.0.4
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  Requires-Dist: easydev==0.13.2
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+ Requires-Dist: fa2-modified==0.4
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+ Requires-Dist: forceatlas2-python==1.1
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  Requires-Dist: gseapy==1.1.9
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- Requires-Dist: h5py==3.12.1
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+ Requires-Dist: h5py==3.7.0
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  Requires-Dist: harmonypy==0.0.10
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  Requires-Dist: leidenalg==0.10.2
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+ Requires-Dist: louvain==0.8.2
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  Requires-Dist: magic-impute==3.0.0
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  Requires-Dist: matplotlib-venn==1.1.2
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- Requires-Dist: matplotlib==3.7.1
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+ Requires-Dist: matplotlib==3.7.5
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  Requires-Dist: mudata==0.3.2
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  Requires-Dist: networkx==3.3
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+ Requires-Dist: numba==0.60.0
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  Requires-Dist: numpy==1.26.4
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  Requires-Dist: palettable==3.3.3
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  Requires-Dist: pandas==1.5.3
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+ Requires-Dist: psutil==7.2.1
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  Requires-Dist: pycomplexheatmap==1.6.1
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- Requires-Dist: scanpy==1.9.6
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+ Requires-Dist: pynndescent==0.5.13
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+ Requires-Dist: scanpy==1.11.5
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  Requires-Dist: scikit-learn==1.5.2
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- Requires-Dist: scipy==1.14.1
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+ Requires-Dist: scipy==1.11.4
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  Requires-Dist: scvi-tools==1.3.3
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- Requires-Dist: seaborn==0.11.2
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- Requires-Dist: statannotations==0.6.0
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+ Requires-Dist: seaborn==0.13.2
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+ Requires-Dist: statannotations==0.7.2
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  Requires-Dist: yzm-file==0.0.2
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  Requires-Dist: yzm-log==0.0.2
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  Description-Content-Type: text/markdown
{sciv-0.0.63 → sciv-0.0.105}/pyproject.toml RENAMED
@@ -3,7 +3,7 @@ requires = ["hatchling"]
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  build-backend = "hatchling.build"
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  [project]
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  name = "sciv"
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- version = "0.0.63"
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+ version = "0.0.105"
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  authors = [
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  { name = "Zheng-Min Yu", email = "yuzmbio@163.com" },
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  ]
@@ -22,28 +22,34 @@ requires-python = ">=3.10"
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  dependencies = [
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  "numpy==1.26.4",
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  "pandas==1.5.3",
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- "matplotlib==3.7.1",
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+ "matplotlib==3.7.5",
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  "matplotlib-venn==1.1.2",
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- "seaborn==0.11.2",
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- "scipy==1.14.1",
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- "scanpy==1.9.6",
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- "anndata==0.11.4",
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+ "seaborn==0.13.2",
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+ "scipy==1.11.4",
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+ "scanpy==1.11.5",
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  "scikit-learn==1.5.2",
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  "networkx==3.3",
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  "palettable==3.3.3",
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  "colormap==1.0.4",
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  "easydev==0.13.2",
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- "h5py==3.12.1",
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+ "h5py==3.7.0",
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  "mudata==0.3.2",
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  "PyComplexHeatmap==1.6.1",
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- "statannotations==0.6.0",
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+ "statannotations==0.7.2",
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  "magic-impute==3.0.0",
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  "leidenalg==0.10.2",
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  "scvi-tools==1.3.3",
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  "yzm_file==0.0.2",
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  "yzm_log==0.0.2",
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  "harmonypy==0.0.10",
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- "gseapy==1.1.9"
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+ "gseapy==1.1.9",
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+ "anndata==0.11.0",
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+ "forceatlas2-python==1.1",
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+ "louvain==0.8.2",
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+ "numba==0.60.0",
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+ "pynndescent==0.5.13",
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+ "fa2-modified==0.4",
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+ "psutil==7.2.1"
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  ]
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  classifiers = [
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  "Programming Language :: Python :: 3",
{sciv-0.0.63 → sciv-0.0.105}/requirements.txt RENAMED
@@ -1,19 +1,19 @@
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  numpy==1.26.4
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  pandas==1.5.3
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- matplotlib==3.7.1
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+ matplotlib==3.7.5
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  matplotlib-venn==1.1.2
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- seaborn==0.11.2
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- scipy==1.14.1
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- scanpy==1.9.6
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+ seaborn==0.13.2
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+ scipy==1.11.4
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+ scanpy==1.11.5
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  scikit-learn==1.5.2
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  networkx==3.3
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  palettable==3.3.3
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  colormap==1.0.4
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  easydev==0.13.2
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- h5py==3.12.1
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+ h5py==3.7.0
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  mudata==0.3.2
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  PyComplexHeatmap==1.6.1
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- statannotations==0.6.0
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+ statannotations==0.7.2
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  magic-impute==3.0.0
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  leidenalg==0.10.2
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  scvi-tools==1.3.3
@@ -22,4 +22,11 @@ yzm_log==0.0.2
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  harmonypy==0.0.10
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  gseapy==1.1.9
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  pysam==0.22.1
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- anndata==0.11.0
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+ anndata==0.11.0
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+ forceatlas2-python==1.1
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+ louvain==0.8.2
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+ snapatac2==2.7.1
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+ numba==0.60.0
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+ pynndescent==0.5.13
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+ fa2-modified==0.4
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+ psutil==7.2.1