Move sgkit-bgen into main repo #256

Author: eric-czech

requirements-dev.txt

@@ -13,5 +13,8 @@ scikit-learn
 partd
 fsspec
 bed-reader
+git+https://github.com/pangeo-data/rechunker.git
+cachetools
+cbgen
 cyvcf2; platform_system != "Windows"
 yarl

setup.cfg

@@ -57,6 +57,10 @@ vcf =
     cyvcf2
     fsspec
     yarl
+bgen =
+    git+https://github.com/pangeo-data/rechunker.git
+    cachetools
+    cbgen
 
 [coverage:report]
 fail_under = 100
@@ -115,10 +119,14 @@ ignore_missing_imports = True
 ignore_missing_imports = True
 [mypy-setuptools]
 ignore_missing_imports = True
-[mypy-sgkit_plink.*]
-ignore_missing_imports = True
 [mypy-sklearn.*]
 ignore_missing_imports = True
+[mypy-cbgen.*]
+ignore_missing_imports = True
+[mypy-rechunker.*]
+ignore_missing_imports = True
+[mypy-cachetools.*]
+ignore_missing_imports = True
 [mypy-bed_reader.*]
 ignore_missing_imports = True
 [mypy-sphinx.*]

sgkit/io/bgen/__init__.py

@@ -0,0 +1,11 @@
+try:
+    from .bgen_reader import bgen_to_zarr, read_bgen, rechunk_bgen  # noqa: F401
+
+    __all__ = ["read_bgen", "bgen_to_zarr", "rechunk_bgen"]
+except ImportError as e:
+    msg = (
+        "sgkit bgen requirements are not installed.\n\n"
+        "Please install them via pip :\n\n"
+        "  pip install 'git+https://github.com/pystatgen/sgkit#egg=sgkit[bgen]'"
+    )
+    raise ImportError(str(e) + "\n\n" + msg) from e