gsMap 1.63__py3-none-any.whl → 1.65__py3-none-any.whl

gsMap/__init__.py

@@ -2,4 +2,4 @@
 Genetics-informed pathogenic spatial mapping
 '''
 
-__version__ = '1.63'
+__version__ = '1.65'

gsMap/setup.py

@@ -0,0 +1,5 @@
+#!/usr/bin/env python
+import setuptools
+
+if __name__ == "__main__":
+    setuptools.setup(name='gsMap')

gsMap/spatial_ldsc_multiple_sumstats.py

@@ -15,7 +15,7 @@ import gsMap.utils.jackknife as jk
 from gsMap.config import SpatialLDSCConfig
 from gsMap.utils.regression_read import _read_sumstats, _read_w_ld, _read_ref_ld_v2
 
-logger = logging.getLogger(__name__)
+logger = logging.getLogger('gsMap.spatial_ldsc')
 
 
 # %%
@@ -204,7 +204,7 @@ def _get_sumstats_with_common_snp_from_sumstats_dict(sumstats_config_dict: dict,
     for trait_name, sumstats in sumstats_cleaned_dict.items():
         sumstats_cleaned_dict[trait_name] = sumstats.loc[common_snp_among_all_sumstats]
 
-    logger.info(f'!Common SNPs among all sumstats: {len(common_snp_among_all_sumstats)}')
+    logger.info(f'Common SNPs among all sumstats: {len(common_snp_among_all_sumstats)}')
     return sumstats_cleaned_dict, common_snp_among_all_sumstats
 
 

gsMap/utils/generate_r2_matrix.py

@@ -2,7 +2,7 @@ from pathlib import Path
 import bitarray as ba
 import numpy as np
 import pandas as pd
-from scipy.sparse import csr_matrix,csc_matrix
+from scipy.sparse import csr_matrix
 from scipy.sparse import save_npz, load_npz
 from tqdm import trange, tqdm
 

{gsmap-1.63.dist-info → gsmap-1.65.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gsMap
-Version: 1.63
+Version: 1.65
 Summary: Genetics-informed pathogenic spatial mapping
 Author-email: liyang <songliyang@westlake.edu.cn>, wenhao <chenwenhao@westlake.edu.cn>
 Requires-Python: >=3.8
@@ -27,6 +27,11 @@ Requires-Dist: pyfiglet
 Requires-Dist: plotly
 Requires-Dist: kaleido
 Requires-Dist: jinja2
+Requires-Dist: scanpy
+Requires-Dist: zarr
+Requires-Dist: bitarray
+Requires-Dist: pyarrow
+Requires-Dist: scikit-misc
 Requires-Dist: sphinx ; extra == "doc"
 Requires-Dist: sphinx-argparse ; extra == "doc"
 Requires-Dist: sphinx-autobuild ; extra == "doc"

{gsmap-1.63.dist-info → gsmap-1.65.dist-info}/RECORD

@@ -1,4 +1,4 @@
-gsMap/__init__.py,sha256=-ypQPCajXkPi0WsnYpUZiY_0tA_qXZ4Ux42ji7z_2UY,78
+gsMap/__init__.py,sha256=NYWCyAKqoOz2vzIYw1ANwlhl7o8CrEyE60d5Oraeyto,78
 gsMap/__main__.py,sha256=jR-HT42Zzfj2f-7kFJy0bkWjNxcV1MyfQHXFpef2nSE,62
 gsMap/cauchy_combination_test.py,sha256=zBPR7DOaNkr7rRoua4tAjRZL7ArjCyMRSQlPSUdHNSE,5694
 gsMap/config.py,sha256=hMUvlwlKZXeRdTJZfMINz_8DadVhEIT6X6fyJf11M9E,41134
@@ -10,7 +10,8 @@ gsMap/latent_to_gene.py,sha256=6TlOWDhzzrj18o9gJk2b-WMOkeXqscK8CJJKxCtilHg,9640
 gsMap/main.py,sha256=skyBtESdjvuXd9HNq5c83OPxQTNgLVErkYhwuJm8tE4,1285
 gsMap/report.py,sha256=H0uYAru2L5-d41_LFHPPdoJbtiTzP4f8kX-mirUNAfc,6963
 gsMap/run_all_mode.py,sha256=sPEct9fRw7aAQuU7BNChxk-I8YQcXuq--mtBn-2wTTY,8388
-gsMap/spatial_ldsc_multiple_sumstats.py,sha256=YHgXvsophnIbihqQyPCzXBPIa6Zd2-cblpQpb2Be0Ug,18459
+gsMap/setup.py,sha256=eOoPalGAHTY06_7a35nvbOaKQhq0SBE5GK4pc4bp3wc,102
+gsMap/spatial_ldsc_multiple_sumstats.py,sha256=09j2zG98JUjQvSHPaRIDQVMZZLYDd1JBFaZTkW7tdvY,18470
 gsMap/visualize.py,sha256=FLIRHHj1KntLMFDjAhg1jZnJUdvrncR74pCW2Kj5pus,7453
 gsMap/GNN_VAE/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 gsMap/GNN_VAE/adjacency_matrix.py,sha256=pmSfK9TTwdrsWTmHvCqVrbRE0PAiq1lvgmxzrdQgpiU,3500
@@ -18,13 +19,13 @@ gsMap/GNN_VAE/model.py,sha256=Fixl8-2zN3T5MmMtpMIvxsBYydM3QVR4uC3Hhsg0DzI,3349
 gsMap/GNN_VAE/train.py,sha256=KnvZYHImRzTwJl1H0dkZZqWASdZ5VgYTCifQVW8TavM,3389
 gsMap/templates/report_template.html,sha256=pdxHFl_W0W351NUzuJTf_Ay_BfKlEbD_fztNabAGmmg,8214
 gsMap/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-gsMap/utils/generate_r2_matrix.py,sha256=CshzmdXYYyIOjTqqVAFkh_S3ucv62OPiG3YG1eB2j4g,29363
+gsMap/utils/generate_r2_matrix.py,sha256=A1BrUnlTrYjRwEKxK0I1FbZ5SCQzcviWVM-JzFHHRkw,29352
 gsMap/utils/jackknife.py,sha256=nEDPVQJOPQ_uqfUCGX_v5cQwokgCqUmJTT_8rVFuIQo,18244
 gsMap/utils/make_annotations.py,sha256=lCbtahT27WFOwLgZrEUE5QcNRuMXmAFYUfsFR-cT-m0,22197
 gsMap/utils/manhattan_plot.py,sha256=k3n-NNgMsov9-8UQrirVqG560FUfJ4d6wNG8C0OeCjY,26235
 gsMap/utils/regression_read.py,sha256=n_hZZzQXHU-CSLvSofXmQM5Jw4Zpufv3U2HoUW344ko,8768
-gsmap-1.63.dist-info/entry_points.txt,sha256=s_P2Za22O077tc1FPLKMinbdRVXaN_HTcDBgWMYpqA4,41
-gsmap-1.63.dist-info/LICENSE,sha256=Ni2F-lLSv_H1xaVT3CoSrkiKzMvlgwh-dq8PE1esGyI,1094
-gsmap-1.63.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
-gsmap-1.63.dist-info/METADATA,sha256=ffylpqXB-e2fI2TRKYUS7GneOttI6uqebiigsPCRFkg,3260
-gsmap-1.63.dist-info/RECORD,,
+gsmap-1.65.dist-info/entry_points.txt,sha256=s_P2Za22O077tc1FPLKMinbdRVXaN_HTcDBgWMYpqA4,41
+gsmap-1.65.dist-info/LICENSE,sha256=Ni2F-lLSv_H1xaVT3CoSrkiKzMvlgwh-dq8PE1esGyI,1094
+gsmap-1.65.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
+gsmap-1.65.dist-info/METADATA,sha256=mhbeULrpbr0ymhFID-_b-dO7q872vu3oyR9KQT9sO4o,3376
+gsmap-1.65.dist-info/RECORD,,