ditch python 3.9

Author: andrewkern

.github/workflows/python-build.yml

@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}

README.md

@@ -25,7 +25,7 @@ I'm going to focus on the steps involved to install on a linux machine using Ana
 package manager. Assuming you have conda installed, create a new conda env
 
 ```
-$ conda create -n diploshic python=3.9 --yes
+$ conda create -n diploshic python=3.10 --yes
 ```
 
 Note that because I'm using the Anaconda version of python, pip will only install this in the anaconda directory

setup.py

@@ -4,38 +4,44 @@
 with open("README.md", "r") as fh:
     long_description = fh.read()
 
-shic_stats = Extension("diploshic.shicstats",
-                       sources=["diploshic/shicstats.pyf",
-                                "diploshic/utils.c"],
-                      )
-setup(name='diploSHIC',
-      version='1.0.6',
-      description='diploSHIC',
-      long_description=long_description,
-      long_description_content_type="text/markdown",
-      url='https://github.com/kr-colab/diploSHIC',
-      author='Andrew Kern',
-      author_email='[email protected]',
-      license='MIT',
-      packages=['diploshic'],
-      install_requires=['numpy',
-                        'scipy',
-                        'matplotlib',
-                        'pandas',
-                        'scikit-allel',
-                        'scikit-learn',
-                        'tensorflow==2.15.0',
-                        'keras'],
-      scripts=['diploshic/diploSHIC',
-              'diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py',
-              'diploshic/makeFeatureVecsForChrArmFromVcf_ogSHIC.py',
-              'diploshic/makeFeatureVecsForSingleMsDiploid.py',
-              'diploshic/makeFeatureVecsForSingleMs_ogSHIC.py',
-              'diploshic/makeTrainingSets.py'],
-      zip_safe=False,
-      extras_require={
-          'dev': [],
-      },
-      setup_requires=[],
-      ext_modules=[shic_stats]
+shic_stats = Extension(
+    "diploshic.shicstats",
+    sources=["diploshic/shicstats.pyf", "diploshic/utils.c"],
+)
+setup(
+    name="diploSHIC",
+    version="1.0.6",
+    description="diploSHIC",
+    python_requires="<3.12,>=3.10",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    url="https://github.com/kr-colab/diploSHIC",
+    author="Andrew Kern",
+    author_email="[email protected]",
+    license="MIT",
+    packages=["diploshic"],
+    install_requires=[
+        "numpy",
+        "scipy",
+        "matplotlib",
+        "pandas",
+        "scikit-allel",
+        "scikit-learn",
+        "tensorflow==2.15.0",
+        "keras",
+    ],
+    scripts=[
+        "diploshic/diploSHIC",
+        "diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py",
+        "diploshic/makeFeatureVecsForChrArmFromVcf_ogSHIC.py",
+        "diploshic/makeFeatureVecsForSingleMsDiploid.py",
+        "diploshic/makeFeatureVecsForSingleMs_ogSHIC.py",
+        "diploshic/makeTrainingSets.py",
+    ],
+    zip_safe=False,
+    extras_require={
+        "dev": [],
+    },
+    setup_requires=[],
+    ext_modules=[shic_stats],
 )