Better packaging; Fix #69; Fix #81

MANIFEST.in

@@ -0,0 +1,19 @@
+include *.rst
+include aldy/resources/*.rst
+include aldy/resources/genes/*.yml
+include aldy/resources/genes/pharmacoscan/*.yml
+include aldy/resources/profiles/*.yml
+include aldy/tests/resources/*.json
+include aldy/tests/resources/*.bam
+include aldy/tests/resources/*.bai
+include aldy/tests/resources/*.expected
+include aldy/tests/resources/*.yml
+include aldy/tests/resources/*.profile
+include aldy/tests/resources/*.hg38
+include aldy/tests/resources/*.vcf
+include aldy/tests/resources/*.gz
+include aldy/tests/resources/*.tbi
+include aldy/indelpost/*.pyx
+include aldy/indelpost/*.pxd
+include aldy/indelpost/ssw.h
+include aldy/indelpost/sse2neon.h

setup.py

@@ -96,47 +96,7 @@
     ],
     entry_points={"console_scripts": ["aldy = aldy.__main__:console"]},
     packages=find_packages(),
-    package_data={
-        "aldy.resources": ["*.rst", "aldy/resources/*.rst"],
-        "aldy.resources.genes": [
-            "*.yml",
-            "aldy/resources/genes/*.yml",
-            "aldy/resources/genes/pharmacoscan/*.yml",
-        ],
-        "aldy.resources.profiles": ["*.yml", "aldy/resources/profiles/*.yml"],
-        "aldy.tests.resources": [
-            "*.json",
-            "aldy/tests/resources/*.json",
-            "*.bai",
-            "aldy/tests/resources/*.bai",
-            "*.bam",
-            "aldy/tests/resources/*.bam",
-            "*.expected",
-            "aldy/tests/resources/*.expected",
-            "*.yml",
-            "aldy/tests/resources/*.yml",
-            "aldy/tests/resources/pharmacoscan/*.yml",
-            "*.profile",
-            "aldy/tests/resources/*.profile",
-            "*.hg38",
-            "aldy/tests/resources/*.hg38",
-            "*.vcf",
-            "aldy/tests/resources/*.vcf",
-            "*.gz",
-            "aldy/tests/resources/*.gz",
-            "*.tbi",
-            "aldy/tests/resources/*.tbi",
-        ],
-        "aldy.indelpost": [
-            "*.pyx",
-            "aldy/indelpost/*.pyx",
-            "*.pxd",
-            "aldy/indelpost/*.pxd",
-            "*.h",
-            "aldy/indelpost/ssw.h",
-            "aldy/indelpost/sse2neon.h",
-        ],
-    },
+    include_package_data=True,
     cmdclass={"build_ext": build_ext},
     ext_modules=cythonize(extensions, compiler_directives={"language_level": "3"}),
     test_suite="pytest-runner",