gsMap3D 0.1.0a1__tar.gz → 0.1.0a2__tar.gz

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Files changed (74) hide show
  1. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/PKG-INFO +5 -3
  2. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/pyproject.toml +7 -3
  3. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/.gitignore +0 -0
  4. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/LICENSE +0 -0
  5. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/README.md +0 -0
  6. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/__init__.py +0 -0
  7. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/__main__.py +0 -0
  8. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/cauchy_combination_test.py +0 -0
  9. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/cli.py +0 -0
  10. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/config/__init__.py +0 -0
  11. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/config/base.py +0 -0
  12. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/config/cauchy_config.py +0 -0
  13. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/config/dataclasses.py +0 -0
  14. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/config/decorators.py +0 -0
  15. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/config/find_latent_config.py +0 -0
  16. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/config/format_sumstats_config.py +0 -0
  17. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/config/latent2gene_config.py +0 -0
  18. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/config/ldscore_config.py +0 -0
  19. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/config/quick_mode_config.py +0 -0
  20. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/config/report_config.py +0 -0
  21. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/config/spatial_ldsc_config.py +0 -0
  22. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/config/utils.py +0 -0
  23. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/find_latent/__init__.py +0 -0
  24. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/find_latent/find_latent_representation.py +0 -0
  25. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/find_latent/gnn/distribution.py +0 -0
  26. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/find_latent/gnn/encoder_decoder.py +0 -0
  27. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/find_latent/gnn/gcn.py +0 -0
  28. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/find_latent/gnn/gene_former.py +0 -0
  29. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/find_latent/gnn/loss.py +0 -0
  30. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/find_latent/gnn/st_model.py +0 -0
  31. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/find_latent/gnn/train_step.py +0 -0
  32. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/find_latent/st_process.py +0 -0
  33. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/format_sumstats.py +0 -0
  34. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/generate_ldscore.py +0 -0
  35. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/latent2gene/__init__.py +0 -0
  36. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/latent2gene/connectivity.py +0 -0
  37. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/latent2gene/entry_point.py +0 -0
  38. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/latent2gene/marker_scores.py +0 -0
  39. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/latent2gene/memmap_io.py +0 -0
  40. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/latent2gene/rank_calculator.py +0 -0
  41. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/latent2gene/row_ordering.py +0 -0
  42. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/latent2gene/row_ordering_jax.py +0 -0
  43. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/ldscore/__init__.py +0 -0
  44. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/ldscore/batch_construction.py +0 -0
  45. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/ldscore/compute.py +0 -0
  46. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/ldscore/constants.py +0 -0
  47. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/ldscore/io.py +0 -0
  48. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/ldscore/mapping.py +0 -0
  49. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/ldscore/pipeline.py +0 -0
  50. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/pipeline/quick_mode.py +0 -0
  51. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/report/__init__.py +0 -0
  52. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/report/diagnosis.py +0 -0
  53. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/report/report.py +0 -0
  54. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/report/report_data.py +0 -0
  55. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/report/static/js_lib/alpine.min.js +0 -0
  56. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/report/static/js_lib/tailwindcss.js +0 -0
  57. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/report/static/template.html +0 -0
  58. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/report/three_d_combine.py +0 -0
  59. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/report/three_d_plot/three_d_plot_decorate.py +0 -0
  60. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/report/three_d_plot/three_d_plot_prepare.py +0 -0
  61. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/report/three_d_plot/three_d_plots.py +0 -0
  62. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/report/visualize.py +0 -0
  63. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/setup.py +0 -0
  64. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/spatial_ldsc/__init__.py +0 -0
  65. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/spatial_ldsc/io.py +0 -0
  66. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/spatial_ldsc/ldscore_quick_mode.py +0 -0
  67. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/spatial_ldsc/spatial_ldsc_jax.py +0 -0
  68. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/spatial_ldsc/spatial_ldsc_multiple_sumstats.py +0 -0
  69. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/utils/__init__.py +0 -0
  70. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/utils/generate_r2_matrix.py +0 -0
  71. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/utils/jackknife.py +0 -0
  72. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/utils/manhattan_plot.py +0 -0
  73. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/utils/regression_read.py +0 -0
  74. {gsmap3d-0.1.0a1 → gsmap3d-0.1.0a2}/src/gsMap/utils/torch_utils.py +0 -0
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: gsMap3D
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- Version: 0.1.0a1
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+ Version: 0.1.0a2
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  Summary: Genetically informed spatial mapping of cells for complex traits
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  Project-URL: Home, https://github.com/Ganten-Hornby/gsMap3D
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  Project-URL: Documentation, https://yanglab.westlake.edu.cn/gsmap3d/docs
@@ -40,7 +40,7 @@ Requires-Dist: bitarray<3.0.0,>=2.9.2
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  Requires-Dist: distinctipy>=1.3.4
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  Requires-Dist: einops
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  Requires-Dist: h5py>=3.0.0
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- Requires-Dist: jax~=0.9.0
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+ Requires-Dist: jax<1.0.0,>=0.7.2
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  Requires-Dist: jinja2
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  Requires-Dist: kaleido
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  Requires-Dist: matplotlib
@@ -66,7 +66,7 @@ Requires-Dist: tqdm
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  Requires-Dist: typer~=0.20.0
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  Requires-Dist: zarr>=2.18.0
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  Provides-Extra: cuda
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- Requires-Dist: jax[cuda12]>=0.8.1; extra == 'cuda'
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+ Requires-Dist: jax[cuda13]<1.0.0,>=0.7.2; extra == 'cuda'
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  Provides-Extra: doc
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  Requires-Dist: furo; extra == 'doc'
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  Requires-Dist: myst-parser; extra == 'doc'
@@ -93,6 +93,8 @@ Provides-Extra: tests
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  Requires-Dist: coverage; extra == 'tests'
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  Requires-Dist: pytest-cov>=4.0.0; extra == 'tests'
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  Requires-Dist: pytest>=7.0.0; extra == 'tests'
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+ Provides-Extra: tpu
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+ Requires-Dist: jax[tpu]<1.0.0,>=0.7.2; extra == 'tpu'
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  Description-Content-Type: text/markdown
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  # gsMap3D
@@ -17,7 +17,7 @@ classifiers = [
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  "Programming Language :: Python :: 3.13",
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  "Operating System :: POSIX :: Linux",
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  ]
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- version = "0.1.0.a1"
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+ version = "0.1.0.a2"
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  description = "Genetically informed spatial mapping of cells for complex traits"
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  dependencies = [
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  "numpy ~= 2.2",
@@ -39,7 +39,7 @@ dependencies = [
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  "bitarray >=2.9.2, <3.0.0",
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  "pyarrow",
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  "numba",
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- "jax ~= 0.9.0",
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+ "jax >=0.7.2, <1.0.0",
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  "pandas_plink",
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  "rich >= 14.1.0",
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  "anndata >= 0.8.0",
@@ -84,7 +84,11 @@ tests = [
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  ]
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  cuda = [
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- "jax[cuda12] >= 0.8.1",
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+ "jax[cuda13] >=0.7.2, <1.0.0",
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+ ]
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+
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+ tpu = [
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+ "jax[tpu] >=0.7.2, <1.0.0",
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  ]
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  [project.urls]
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