gsMap3D 0.1.0a2__tar.gz → 0.1.0a3__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 (75) hide show
  1. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/PKG-INFO +1 -1
  2. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/pyproject.toml +1 -1
  3. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/config/utils.py +4 -0
  4. gsmap3d-0.1.0a3/src/gsMap/pipeline/__init__.py +9 -0
  5. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/.gitignore +0 -0
  6. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/LICENSE +0 -0
  7. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/README.md +0 -0
  8. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/__init__.py +0 -0
  9. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/__main__.py +0 -0
  10. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/cauchy_combination_test.py +0 -0
  11. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/cli.py +0 -0
  12. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/config/__init__.py +0 -0
  13. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/config/base.py +0 -0
  14. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/config/cauchy_config.py +0 -0
  15. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/config/dataclasses.py +0 -0
  16. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/config/decorators.py +0 -0
  17. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/config/find_latent_config.py +0 -0
  18. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/config/format_sumstats_config.py +0 -0
  19. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/config/latent2gene_config.py +0 -0
  20. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/config/ldscore_config.py +0 -0
  21. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/config/quick_mode_config.py +0 -0
  22. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/config/report_config.py +0 -0
  23. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/config/spatial_ldsc_config.py +0 -0
  24. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/find_latent/__init__.py +0 -0
  25. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/find_latent/find_latent_representation.py +0 -0
  26. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/find_latent/gnn/distribution.py +0 -0
  27. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/find_latent/gnn/encoder_decoder.py +0 -0
  28. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/find_latent/gnn/gcn.py +0 -0
  29. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/find_latent/gnn/gene_former.py +0 -0
  30. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/find_latent/gnn/loss.py +0 -0
  31. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/find_latent/gnn/st_model.py +0 -0
  32. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/find_latent/gnn/train_step.py +0 -0
  33. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/find_latent/st_process.py +0 -0
  34. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/format_sumstats.py +0 -0
  35. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/generate_ldscore.py +0 -0
  36. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/latent2gene/__init__.py +0 -0
  37. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/latent2gene/connectivity.py +0 -0
  38. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/latent2gene/entry_point.py +0 -0
  39. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/latent2gene/marker_scores.py +0 -0
  40. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/latent2gene/memmap_io.py +0 -0
  41. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/latent2gene/rank_calculator.py +0 -0
  42. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/latent2gene/row_ordering.py +0 -0
  43. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/latent2gene/row_ordering_jax.py +0 -0
  44. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/ldscore/__init__.py +0 -0
  45. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/ldscore/batch_construction.py +0 -0
  46. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/ldscore/compute.py +0 -0
  47. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/ldscore/constants.py +0 -0
  48. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/ldscore/io.py +0 -0
  49. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/ldscore/mapping.py +0 -0
  50. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/ldscore/pipeline.py +0 -0
  51. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/pipeline/quick_mode.py +0 -0
  52. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/report/__init__.py +0 -0
  53. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/report/diagnosis.py +0 -0
  54. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/report/report.py +0 -0
  55. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/report/report_data.py +0 -0
  56. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/report/static/js_lib/alpine.min.js +0 -0
  57. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/report/static/js_lib/tailwindcss.js +0 -0
  58. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/report/static/template.html +0 -0
  59. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/report/three_d_combine.py +0 -0
  60. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/report/three_d_plot/three_d_plot_decorate.py +0 -0
  61. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/report/three_d_plot/three_d_plot_prepare.py +0 -0
  62. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/report/three_d_plot/three_d_plots.py +0 -0
  63. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/report/visualize.py +0 -0
  64. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/setup.py +0 -0
  65. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/spatial_ldsc/__init__.py +0 -0
  66. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/spatial_ldsc/io.py +0 -0
  67. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/spatial_ldsc/ldscore_quick_mode.py +0 -0
  68. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/spatial_ldsc/spatial_ldsc_jax.py +0 -0
  69. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/spatial_ldsc/spatial_ldsc_multiple_sumstats.py +0 -0
  70. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/utils/__init__.py +0 -0
  71. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/utils/generate_r2_matrix.py +0 -0
  72. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/utils/jackknife.py +0 -0
  73. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/utils/manhattan_plot.py +0 -0
  74. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/utils/regression_read.py +0 -0
  75. {gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/utils/torch_utils.py +0 -0
{gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: gsMap3D
3
- Version: 0.1.0a2
3
+ Version: 0.1.0a3
4
4
  Summary: Genetically informed spatial mapping of cells for complex traits
5
5
  Project-URL: Home, https://github.com/Ganten-Hornby/gsMap3D
6
6
  Project-URL: Documentation, https://yanglab.westlake.edu.cn/gsmap3d/docs
{gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/pyproject.toml RENAMED
@@ -17,7 +17,7 @@ classifiers = [
17
17
  "Programming Language :: Python :: 3.13",
18
18
  "Operating System :: POSIX :: Linux",
19
19
  ]
20
- version = "0.1.0.a2"
20
+ version = "0.1.0.a3"
21
21
  description = "Genetically informed spatial mapping of cells for complex traits"
22
22
  dependencies = [
23
23
  "numpy ~= 2.2",
{gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/config/utils.py RENAMED
@@ -234,6 +234,10 @@ def process_h5ad_inputs(config, input_options):
234
234
  sample_h5ad_dict[sample_name] = h5ad_path
235
235
 
236
236
  elif processing_type == 'list':
237
+ # Handle single string or Path input by wrapping in a list
238
+ if isinstance(field_value, (str, Path)):
239
+ field_value = [field_value]
240
+
237
241
  logger.info(f"Using {option_name} with {len(field_value)} files")
238
242
  for h5ad_path in field_value:
239
243
  h5ad_path = Path(h5ad_path)
gsmap3d-0.1.0a3/src/gsMap/pipeline/__init__.py ADDED
@@ -0,0 +1,9 @@
1
+ """
2
+ gsMap pipeline module.
3
+
4
+ This module provides high-level pipeline functions for running gsMap analyses.
5
+ """
6
+
7
+ from gsMap.pipeline.quick_mode import run_quick_mode
8
+
9
+ __all__ = ["run_quick_mode"]
{gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/.gitignore RENAMED
File without changes
{gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/LICENSE RENAMED
File without changes
{gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/README.md RENAMED
File without changes
{gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/cli.py RENAMED
File without changes
{gsmap3d-0.1.0a2 → gsmap3d-0.1.0a3}/src/gsMap/setup.py RENAMED
File without changes