fix: vendor ldsc into the package

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "maxgcp"
-version = "0.1.3"
+version = "0.1.4"
 description = "Optimized phenotype definitions boost GWAS power"
 authors = [
     {name = "zietzm", email = "[email protected]"}
@@ -12,9 +12,10 @@ dependencies = [
     "typer>=0.12.4",
     "rich>=13.7.1",
     "polars>=1.5.0",
-    "igwas",
-    "ldsc",
-    "pymbend",
+    "igwas>=0.1.0",
+    "pymbend>=0.1.0",
+    "bitarray>=2.9.2",
+    "pyzstd>=0.16.1",
 ]
 readme = "README.md"
 requires-python = ">= 3.10"
@@ -49,8 +50,3 @@ dev-dependencies = [
     "ruff>=0.6.2",
     "pytest>=8.3.2",
 ]
-
-[tool.uv.sources]
-igwas = { git = "https://github.com/tatonetti-lab/indirect-gwas" }
-ldsc = { git = "https://github.com/zietzm/ldsc", branch = "py3" }
-pymbend = { git = "https://github.com/zietzm/pymbend" }

src/maxgcp/cli/ldsc.py

@@ -2,10 +2,10 @@
 from pathlib import Path
 from typing import Annotated
 
-import ldsc.scripts.ldsc
-import ldsc.scripts.munge_sumstats
 import typer
 
+from maxgcp.ldsc.scripts import ldsc, munge_sumstats
+
 logger = logging.getLogger("rich")
 
 app = typer.Typer(
@@ -50,7 +50,7 @@ def ldsc_munge(
     ] = 0.0,
 ) -> None:
     """Process a GWAS summary statistics file using LDSC."""
-    args = ldsc.scripts.munge_sumstats.parser.parse_args(
+    args = munge_sumstats.parser.parse_args(
         [
             "--sumstats",
             gwas_path.as_posix(),
@@ -70,7 +70,7 @@ def ldsc_munge(
             f"{signed_sumstat_col},{signed_sumstat_null}",
         ]
     )
-    ldsc.scripts.munge_sumstats.munge_sumstats(args)
+    munge_sumstats.munge_sumstats(args)
 
 
 @app.command(name="rg")
@@ -92,7 +92,7 @@ def ldsc_rg(
     ],
 ) -> None:
     """Compute genetic covariances using LDSC."""
-    args = ldsc.scripts.ldsc.parser.parse_args(
+    args = ldsc.parser.parse_args(
         [
             "--rg",
             ",".join(p.as_posix() for p in gwas_paths),
@@ -104,4 +104,4 @@ def ldsc_rg(
             output_stem.as_posix(),
         ]
     )
-    ldsc.scripts.ldsc.main(args)
+    ldsc.main(args)