gsMap 1.63__tar.gz → 1.64__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 (66) hide show
  1. {gsmap-1.63 → gsmap-1.64}/PKG-INFO +6 -1
  2. {gsmap-1.63 → gsmap-1.64}/pyproject.toml +5 -0
  3. {gsmap-1.63 → gsmap-1.64}/src/gsMap/__init__.py +1 -1
  4. {gsmap-1.63 → gsmap-1.64}/src/gsMap/spatial_ldsc_multiple_sumstats.py +2 -2
  5. {gsmap-1.63 → gsmap-1.64}/src/gsMap/utils/generate_r2_matrix.py +1 -1
  6. {gsmap-1.63 → gsmap-1.64}/.github/workflows/publish-to-pypi.yml +0 -0
  7. {gsmap-1.63 → gsmap-1.64}/.gitignore +0 -0
  8. {gsmap-1.63 → gsmap-1.64}/LICENSE +0 -0
  9. {gsmap-1.63 → gsmap-1.64}/README.md +0 -0
  10. {gsmap-1.63 → gsmap-1.64}/docs/Makefile +0 -0
  11. {gsmap-1.63 → gsmap-1.64}/docs/make.bat +0 -0
  12. {gsmap-1.63 → gsmap-1.64}/docs/requirements.txt +0 -0
  13. {gsmap-1.63 → gsmap-1.64}/docs/source/_static/schematic.svg +0 -0
  14. {gsmap-1.63 → gsmap-1.64}/docs/source/api/cauchy_combination.rst +0 -0
  15. {gsmap-1.63 → gsmap-1.64}/docs/source/api/find_latent_representations.rst +0 -0
  16. {gsmap-1.63 → gsmap-1.64}/docs/source/api/format_sumstats.rst +0 -0
  17. {gsmap-1.63 → gsmap-1.64}/docs/source/api/generate_ldscore.rst +0 -0
  18. {gsmap-1.63 → gsmap-1.64}/docs/source/api/latent_to_gene.rst +0 -0
  19. {gsmap-1.63 → gsmap-1.64}/docs/source/api/quick_mode.rst +0 -0
  20. {gsmap-1.63 → gsmap-1.64}/docs/source/api/report.rst +0 -0
  21. {gsmap-1.63 → gsmap-1.64}/docs/source/api/spatial_ldsc.rst +0 -0
  22. {gsmap-1.63 → gsmap-1.64}/docs/source/api.rst +0 -0
  23. {gsmap-1.63 → gsmap-1.64}/docs/source/charts/cortex/Cortex_151507_Height.json +0 -0
  24. {gsmap-1.63 → gsmap-1.64}/docs/source/charts/cortex/Cortex_151507_IQ.json +0 -0
  25. {gsmap-1.63 → gsmap-1.64}/docs/source/charts/cortex/Cortex_151507_MCHC.json +0 -0
  26. {gsmap-1.63 → gsmap-1.64}/docs/source/charts/cortex/Cortex_151507_SCZ.json +0 -0
  27. {gsmap-1.63 → gsmap-1.64}/docs/source/charts/mouse_embryo/E16.5_E1S1_Height.json +0 -0
  28. {gsmap-1.63 → gsmap-1.64}/docs/source/charts/mouse_embryo/E16.5_E1S1_IQ.json +0 -0
  29. {gsmap-1.63 → gsmap-1.64}/docs/source/charts/mouse_embryo/E16.5_E1S1_MCHC.json +0 -0
  30. {gsmap-1.63 → gsmap-1.64}/docs/source/charts/mouse_embryo/E16.5_E1S1_SCZ.json +0 -0
  31. {gsmap-1.63 → gsmap-1.64}/docs/source/charts/test.json +0 -0
  32. {gsmap-1.63 → gsmap-1.64}/docs/source/conf.py +0 -0
  33. {gsmap-1.63 → gsmap-1.64}/docs/source/data.rst +0 -0
  34. {gsmap-1.63 → gsmap-1.64}/docs/source/data_format.md +0 -0
  35. {gsmap-1.63 → gsmap-1.64}/docs/source/index.rst +0 -0
  36. {gsmap-1.63 → gsmap-1.64}/docs/source/install.rst +0 -0
  37. {gsmap-1.63 → gsmap-1.64}/docs/source/mouse.rst +0 -0
  38. {gsmap-1.63 → gsmap-1.64}/docs/source/mouse_example.md +0 -0
  39. {gsmap-1.63 → gsmap-1.64}/docs/source/quick_mode.md +0 -0
  40. {gsmap-1.63 → gsmap-1.64}/docs/source/release.rst +0 -0
  41. {gsmap-1.63 → gsmap-1.64}/docs/source/tutorials.rst +0 -0
  42. {gsmap-1.63 → gsmap-1.64}/schematic.png +0 -0
  43. {gsmap-1.63 → gsmap-1.64}/src/gsMap/GNN_VAE/__init__.py +0 -0
  44. {gsmap-1.63 → gsmap-1.64}/src/gsMap/GNN_VAE/adjacency_matrix.py +0 -0
  45. {gsmap-1.63 → gsmap-1.64}/src/gsMap/GNN_VAE/model.py +0 -0
  46. {gsmap-1.63 → gsmap-1.64}/src/gsMap/GNN_VAE/train.py +0 -0
  47. {gsmap-1.63 → gsmap-1.64}/src/gsMap/__main__.py +0 -0
  48. {gsmap-1.63 → gsmap-1.64}/src/gsMap/cauchy_combination_test.py +0 -0
  49. {gsmap-1.63 → gsmap-1.64}/src/gsMap/config.py +0 -0
  50. {gsmap-1.63 → gsmap-1.64}/src/gsMap/diagnosis.py +0 -0
  51. {gsmap-1.63 → gsmap-1.64}/src/gsMap/find_latent_representation.py +0 -0
  52. {gsmap-1.63 → gsmap-1.64}/src/gsMap/format_sumstats.py +0 -0
  53. {gsmap-1.63 → gsmap-1.64}/src/gsMap/generate_ldscore.py +0 -0
  54. {gsmap-1.63 → gsmap-1.64}/src/gsMap/latent_to_gene.py +0 -0
  55. {gsmap-1.63 → gsmap-1.64}/src/gsMap/main.py +0 -0
  56. {gsmap-1.63 → gsmap-1.64}/src/gsMap/report.py +0 -0
  57. {gsmap-1.63 → gsmap-1.64}/src/gsMap/run_all_mode.py +0 -0
  58. {gsmap-1.63 → gsmap-1.64}/src/gsMap/templates/report_template.html +0 -0
  59. {gsmap-1.63 → gsmap-1.64}/src/gsMap/utils/__init__.py +0 -0
  60. {gsmap-1.63 → gsmap-1.64}/src/gsMap/utils/jackknife.py +0 -0
  61. {gsmap-1.63 → gsmap-1.64}/src/gsMap/utils/make_annotations.py +0 -0
  62. {gsmap-1.63 → gsmap-1.64}/src/gsMap/utils/manhattan_plot.py +0 -0
  63. {gsmap-1.63 → gsmap-1.64}/src/gsMap/utils/regression_read.py +0 -0
  64. {gsmap-1.63 → gsmap-1.64}/src/gsMap/visualize.py +0 -0
  65. {gsmap-1.63 → gsmap-1.64}/test/GPS-snakemake-workflow-macaque.smk +0 -0
  66. {gsmap-1.63 → gsmap-1.64}/test/GPS-snakemake-workflow.smk +0 -0
{gsmap-1.63 → gsmap-1.64}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: gsMap
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- Version: 1.63
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+ Version: 1.64
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  Summary: Genetics-informed pathogenic spatial mapping
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  Author-email: liyang <songliyang@westlake.edu.cn>, wenhao <chenwenhao@westlake.edu.cn>
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  Requires-Python: >=3.8
@@ -27,6 +27,11 @@ Requires-Dist: pyfiglet
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  Requires-Dist: plotly
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  Requires-Dist: kaleido
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  Requires-Dist: jinja2
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+ Requires-Dist: scanpy
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+ Requires-Dist: zarr
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+ Requires-Dist: bitarray
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+ Requires-Dist: pyarrow
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+ Requires-Dist: scikit-misc
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  Requires-Dist: sphinx ; extra == "doc"
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  Requires-Dist: sphinx-argparse ; extra == "doc"
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  Requires-Dist: sphinx-autobuild ; extra == "doc"
{gsmap-1.63 → gsmap-1.64}/pyproject.toml RENAMED
@@ -35,6 +35,11 @@ dependencies = [
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  'plotly',
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  'kaleido',
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  'jinja2',
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+ 'scanpy',
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+ 'zarr',
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+ 'bitarray',
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+ 'pyarrow',
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+ 'scikit-misc'
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  ]
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  [project.optional-dependencies]
{gsmap-1.63 → gsmap-1.64}/src/gsMap/__init__.py RENAMED
@@ -2,4 +2,4 @@
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  Genetics-informed pathogenic spatial mapping
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  '''
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- __version__ = '1.63'
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+ __version__ = '1.64'
{gsmap-1.63 → gsmap-1.64}/src/gsMap/spatial_ldsc_multiple_sumstats.py RENAMED
@@ -15,7 +15,7 @@ import gsMap.utils.jackknife as jk
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  from gsMap.config import SpatialLDSCConfig
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  from gsMap.utils.regression_read import _read_sumstats, _read_w_ld, _read_ref_ld_v2
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- logger = logging.getLogger(__name__)
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+ logger = logging.getLogger('gsMap.spatial_ldsc')
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  # %%
@@ -204,7 +204,7 @@ def _get_sumstats_with_common_snp_from_sumstats_dict(sumstats_config_dict: dict,
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  for trait_name, sumstats in sumstats_cleaned_dict.items():
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  sumstats_cleaned_dict[trait_name] = sumstats.loc[common_snp_among_all_sumstats]
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- logger.info(f'!Common SNPs among all sumstats: {len(common_snp_among_all_sumstats)}')
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+ logger.info(f'Common SNPs among all sumstats: {len(common_snp_among_all_sumstats)}')
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  return sumstats_cleaned_dict, common_snp_among_all_sumstats
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{gsmap-1.63 → gsmap-1.64}/src/gsMap/utils/generate_r2_matrix.py RENAMED
@@ -2,7 +2,7 @@ from pathlib import Path
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  import bitarray as ba
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  import numpy as np
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  import pandas as pd
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- from scipy.sparse import csr_matrix,csc_matrix
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+ from scipy.sparse import csr_matrix
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  from scipy.sparse import save_npz, load_npz
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  from tqdm import trange, tqdm
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{gsmap-1.63 → gsmap-1.64}/.gitignore RENAMED
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{gsmap-1.63 → gsmap-1.64}/LICENSE RENAMED
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{gsmap-1.63 → gsmap-1.64}/README.md RENAMED
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{gsmap-1.63 → gsmap-1.64}/docs/Makefile RENAMED
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{gsmap-1.63 → gsmap-1.64}/docs/make.bat RENAMED
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{gsmap-1.63 → gsmap-1.64}/docs/requirements.txt RENAMED
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{gsmap-1.63 → gsmap-1.64}/docs/source/api/report.rst RENAMED
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{gsmap-1.63 → gsmap-1.64}/docs/source/api.rst RENAMED
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{gsmap-1.63 → gsmap-1.64}/docs/source/charts/test.json RENAMED
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{gsmap-1.63 → gsmap-1.64}/docs/source/conf.py RENAMED
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{gsmap-1.63 → gsmap-1.64}/docs/source/data.rst RENAMED
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{gsmap-1.63 → gsmap-1.64}/docs/source/data_format.md RENAMED
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{gsmap-1.63 → gsmap-1.64}/docs/source/index.rst RENAMED
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{gsmap-1.63 → gsmap-1.64}/docs/source/install.rst RENAMED
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{gsmap-1.63 → gsmap-1.64}/docs/source/mouse.rst RENAMED
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{gsmap-1.63 → gsmap-1.64}/docs/source/mouse_example.md RENAMED
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{gsmap-1.63 → gsmap-1.64}/docs/source/quick_mode.md RENAMED
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{gsmap-1.63 → gsmap-1.64}/docs/source/release.rst RENAMED
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{gsmap-1.63 → gsmap-1.64}/docs/source/tutorials.rst RENAMED
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{gsmap-1.63 → gsmap-1.64}/schematic.png RENAMED
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{gsmap-1.63 → gsmap-1.64}/src/gsMap/GNN_VAE/__init__.py RENAMED
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{gsmap-1.63 → gsmap-1.64}/src/gsMap/GNN_VAE/model.py RENAMED
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{gsmap-1.63 → gsmap-1.64}/src/gsMap/GNN_VAE/train.py RENAMED
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{gsmap-1.63 → gsmap-1.64}/src/gsMap/__main__.py RENAMED
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{gsmap-1.63 → gsmap-1.64}/src/gsMap/config.py RENAMED
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{gsmap-1.63 → gsmap-1.64}/src/gsMap/diagnosis.py RENAMED
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{gsmap-1.63 → gsmap-1.64}/src/gsMap/format_sumstats.py RENAMED
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{gsmap-1.63 → gsmap-1.64}/src/gsMap/generate_ldscore.py RENAMED
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{gsmap-1.63 → gsmap-1.64}/src/gsMap/latent_to_gene.py RENAMED
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{gsmap-1.63 → gsmap-1.64}/src/gsMap/main.py RENAMED
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{gsmap-1.63 → gsmap-1.64}/src/gsMap/report.py RENAMED
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{gsmap-1.63 → gsmap-1.64}/src/gsMap/run_all_mode.py RENAMED
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{gsmap-1.63 → gsmap-1.64}/src/gsMap/utils/__init__.py RENAMED
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{gsmap-1.63 → gsmap-1.64}/src/gsMap/utils/jackknife.py RENAMED
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{gsmap-1.63 → gsmap-1.64}/src/gsMap/visualize.py RENAMED
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