[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

README.md

@@ -60,6 +60,7 @@ gsmap --help
 gsMap supports AI-assisted workflows that allow users to run spatial GWAS
 analysis using modern AI coding agents and Vibe coding environments.
 To add the gsMap MCP server and SKILLs in Claude Code:
+
 ```bash
 cd gsMap/gsmap_vibe
 uv pip install -e .
@@ -71,7 +72,6 @@ cp -r gsmap_skill ~/.claude/skills/
 
 Please check out the documentation and tutorials at [gsMap Documentation](https://yanglab.westlake.edu.cn/gsmap/document/software).
 
-
 ## 🌐 Online Visualization
 
 To visualize the traits-cell association spatial maps,

gsmap_vibe/gsmap_mcp/__main__.py

@@ -1,3 +1,3 @@
 from .server import main
 
-main()
+main()

gsmap_vibe/gsmap_mcp/docs.py

@@ -13,8 +13,7 @@ def search_docs(query: str):
     results = []
 
     for line in text.splitlines():
-
         if query.lower() in line.lower():
             results.append(line.strip())
 
-    return "\n".join(results[:20])
+    return "\n".join(results[:20])

gsmap_vibe/gsmap_mcp/server.py

@@ -1,6 +1,7 @@
 from mcp.server.fastmcp import FastMCP
-from .tools import *
+
 from .docs import search_docs
+from .tools import *
 
 mcp = FastMCP("gsmap")
 
@@ -58,11 +59,7 @@ def download_example_dataset(output_dir: str):
 
 
 @mcp.tool()
-def gsmap_format_sumstats(
-    sumstats: str,
-    out: str,
-    args: list[str] = []
-):
+def gsmap_format_sumstats(sumstats: str, out: str, args: list[str] = []):
     """
     Convert GWAS summary statistics into gsMap-compatible format.
 
@@ -107,11 +104,7 @@ def gsmap_format_sumstats(
 
 @mcp.tool()
 def gsmap_quick_mode(
-    workdir: str,
-    hdf5_path: str,
-    sumstats_file: str,
-    trait_name: str,
-    args: list[str] = []
+    workdir: str, hdf5_path: str, sumstats_file: str, trait_name: str, args: list[str] = []
 ):
     """
     Run the gsMap quick_mode pipeline.
@@ -151,21 +144,12 @@ def gsmap_quick_mode(
 
     Use this tool for most spatial GWAS analyses.
     """
-    return run_quick_mode(
-        workdir,
-        hdf5_path,
-        sumstats_file,
-        trait_name,
-        args
-    )
+    return run_quick_mode(workdir, hdf5_path, sumstats_file, trait_name, args)
 
 
 @mcp.tool()
 def gsmap_find_latent_representation(
-    workdir: str,
-    sample_name: str,
-    hdf5_path: str,
-    args: list[str] = []
+    workdir: str, sample_name: str, hdf5_path: str, args: list[str] = []
 ):
     """
     Step 1 of the gsMap step-by-step pipeline.
@@ -188,21 +172,11 @@ def gsmap_find_latent_representation(
         Optional additional CLI parameters for the latent
         representation learning step.
     """
-    return find_latent_representation(
-        workdir,
-        sample_name,
-        hdf5_path,
-        args
-    )
+    return find_latent_representation(workdir, sample_name, hdf5_path, args)
 
 
 @mcp.tool()
-def gsmap_latent_to_gene(
-    workdir: str,
-    sample_name: str,
-    hdf5_path: str,
-    args: list[str] = []
-):
+def gsmap_latent_to_gene(workdir: str, sample_name: str, hdf5_path: str, args: list[str] = []):
     """
     Step 2 of the gsMap step-by-step pipeline.
 
@@ -223,21 +197,11 @@ def gsmap_latent_to_gene(
     args : list[str]
         Optional additional CLI flags.
     """
-    return latent_to_gene(
-        workdir,
-        sample_name,
-        hdf5_path,
-        args
-    )
+    return latent_to_gene(workdir, sample_name, hdf5_path, args)
 
 
 @mcp.tool()
-def gsmap_generate_ldscore(
-    workdir: str,
-    sample_name: str,
-    chromosome: int,
-    args: list[str] = []
-):
+def gsmap_generate_ldscore(workdir: str, sample_name: str, chromosome: int, args: list[str] = []):
     """
     Step 3 of the gsMap step-by-step pipeline.
 
@@ -257,21 +221,12 @@ def gsmap_generate_ldscore(
     args : list[str]
         Optional additional CLI flags.
     """
-    return generate_ldscore(
-        workdir,
-        sample_name,
-        chromosome,
-        args
-    )
+    return generate_ldscore(workdir, sample_name, chromosome, args)
 
 
 @mcp.tool()
 def gsmap_spatial_ldsc(
-    workdir: str,
-    sample_name: str,
-    sumstats_file: str,
-    trait_name: str,
-    args: list[str] = []
+    workdir: str, sample_name: str, sumstats_file: str, trait_name: str, args: list[str] = []
 ):
     """
     Step 4 of the gsMap step-by-step pipeline.
@@ -296,13 +251,7 @@ def gsmap_spatial_ldsc(
     args : list[str]
         Optional additional CLI parameters.
     """
-    return spatial_ldsc(
-        workdir,
-        sample_name,
-        sumstats_file,
-        trait_name,
-        args
-    )
+    return spatial_ldsc(workdir, sample_name, sumstats_file, trait_name, args)
 
 
 @mcp.tool()
@@ -324,4 +273,4 @@ def search_gsmap_docs(query: str):
 
 
 def main():
-    mcp.run()
+    mcp.run()

gsmap_vibe/gsmap_mcp/tools.py

@@ -1,20 +1,15 @@
 import subprocess
-import urllib.request
 import tarfile
+import urllib.request
 from pathlib import Path
 
-
 GSMAP_RESOURCE_URL = "https://yanglab.westlake.edu.cn/data/gsMap/gsMap_resource.tar.gz"
 GSMAP_EXAMPLE_URL = "https://yanglab.westlake.edu.cn/data/gsMap/Visium_example_data.tar.gz"
 
 
 def run_command(cmd):
 
-    result = subprocess.run(
-        cmd,
-        capture_output=True,
-        text=True
-    )
+    result = subprocess.run(cmd, capture_output=True, text=True)
 
     if result.returncode != 0:
         raise RuntimeError(result.stderr)
@@ -66,8 +61,10 @@ def format_sumstats(sumstats, out, args):
     cmd = [
         "gsmap",
         "format_sumstats",
-        "--sumstats", sumstats,
-        "--out", out,
+        "--sumstats",
+        sumstats,
+        "--out",
+        out,
     ]
 
     cmd.extend(args)
@@ -82,10 +79,14 @@ def run_quick_mode(workdir, hdf5_path, sumstats_file, trait_name, args):
     cmd = [
         "gsmap",
         "quick_mode",
-        "--workdir", workdir,
-        "--hdf5_path", hdf5_path,
-        "--sumstats_file", sumstats_file,
-        "--trait_name", trait_name,
+        "--workdir",
+        workdir,
+        "--hdf5_path",
+        hdf5_path,
+        "--sumstats_file",
+        sumstats_file,
+        "--trait_name",
+        trait_name,
     ]
 
     cmd.extend(args)
@@ -100,9 +101,12 @@ def find_latent_representation(workdir, sample_name, hdf5_path, args):
     cmd = [
         "gsmap",
         "run_find_latent_representations",
-        "--workdir", workdir,
-        "--sample_name", sample_name,
-        "--input_hdf5_path", hdf5_path,
+        "--workdir",
+        workdir,
+        "--sample_name",
+        sample_name,
+        "--input_hdf5_path",
+        hdf5_path,
     ]
 
     cmd.extend(args)
@@ -117,9 +121,12 @@ def latent_to_gene(workdir, sample_name, hdf5_path, args):
     cmd = [
         "gsmap",
         "run_latent_to_gene",
-        "--workdir", workdir,
-        "--sample_name", sample_name,
-        "--input_hdf5_path", hdf5_path,
+        "--workdir",
+        workdir,
+        "--sample_name",
+        sample_name,
+        "--input_hdf5_path",
+        hdf5_path,
     ]
 
     cmd.extend(args)
@@ -134,9 +141,12 @@ def generate_ldscore(workdir, sample_name, chromosome, args):
     cmd = [
         "gsmap",
         "run_generate_ldscore",
-        "--workdir", workdir,
-        "--sample_name", sample_name,
-        "--chrom", str(chromosome),
+        "--workdir",
+        workdir,
+        "--sample_name",
+        sample_name,
+        "--chrom",
+        str(chromosome),
     ]
 
     cmd.extend(args)
@@ -151,14 +161,18 @@ def spatial_ldsc(workdir, sample_name, sumstats_file, trait_name, args):
     cmd = [
         "gsmap",
         "run_spatial_ldsc",
-        "--workdir", workdir,
-        "--sample_name", sample_name,
-        "--sumstats_file", sumstats_file,
-        "--trait_name", trait_name,
+        "--workdir",
+        workdir,
+        "--sample_name",
+        sample_name,
+        "--sumstats_file",
+        sumstats_file,
+        "--trait_name",
+        trait_name,
     ]
 
     cmd.extend(args)
 
     run_command(cmd)
 
-    return "Spatial LDSC finished"
+    return "Spatial LDSC finished"