Add Python 3.12 support

.github/workflows/deploy.yml

@@ -11,37 +11,36 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, windows-2019, macos-11]
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v4
-        name: Install Python
-        with:
-          python-version: '3.8'
+      - uses: actions/setup-python@v5
+
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==2.17.0
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.12.3
+        run: python -m cibuildwheel --output-dir wheelhouse
         env:
           # Only build on Python 3 and skip 32-bit builds
           CIBW_BUILD: "cp3*-*"
-          CIBW_SKIP: "cp36-* cp37-* *-win32 *linux_i686"
+          CIBW_SKIP: "cp36-* cp37-* *-win32 *i686 *musl*"
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
 
   build_sdist:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         name: Install Python
-        with:
-          python-version: '3.8'
 
       - name: Build sdist
         run: |
@@ -63,7 +62,7 @@ jobs:
           name: artifact
           path: dist
 
-      - uses: pypa/gh-action-pypi-publish@master
+      - uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/test.yml

@@ -14,16 +14,17 @@ jobs:
         - windows-latest
         - macos-latest
         python-version:
-        - "3.8"
         - "3.9"
         - "3.10"
+        - "3.11"
+        - "3.12"
 
     steps:
 
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -50,12 +51,12 @@ jobs:
         pytest -v allel
 
     - name: Test with doctest
-      if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.10'
+      if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.12'
       run: |
         pytest -v --cov=allel --doctest-modules allel
         coverage report -m
 
     - name: Build docs
-      if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.10'
+      if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.12'
       run: |
         cd docs && make html

allel/stats/roh.py

@@ -201,11 +201,11 @@ def roh_poissonhmm(gv, pos, phet_roh=0.001, phet_nonroh=(0.0025, 0.01), transiti
 
     Notes
     -----
-    This function requires `pomegranate` (>= 0.9.0) to be installed.
+    This function requires `protopunica` to be installed.
 
     """
 
-    from pomegranate import HiddenMarkovModel, PoissonDistribution
+    from protopunica import HiddenMarkovModel, PoissonDistribution
 
     is_accessible = asarray_ndim(is_accessible, 1, dtype=bool, allow_none=True)
 

pyproject.toml

@@ -1,7 +1,10 @@
 [project]
 name = "scikit-allel"
-requires-python = ">=3.6"
-dynamic = ["version", "description"]
+requires-python = ">=3.9"
+description = "A Python package for exploring and analysing genetic variation data."
+readme = "README.rst"
+dynamic = ["version", "classifiers", "license", "maintainers", "dependencies", "optional-dependencies"]
+
 
 [build-system]
 # Minimum requirements for the build system to execute.

requirements_dev_base.txt

@@ -1,4 +1,4 @@
 # required
-cython==0.29.34
-numpy==1.24.3
-dask[array]==2023.4.1
+cython
+numpy
+dask[array]

requirements_dev_optional.txt

@@ -1,13 +1,13 @@
 # optional
-scipy==1.10.1
-matplotlib==3.7.1
-seaborn==0.12.2
-pandas==2.0.1
-scikit-learn==1.2.2
-h5py==3.8.0
-numexpr==2.8.4
-zarr==2.14.2
-hmmlearn==0.3.0
-pomegranate<1.0.0
-pyfasta==0.5.2
-ipython==8.13.0
+scipy
+matplotlib
+seaborn
+pandas
+scikit-learn
+h5py
+numexpr
+zarr
+hmmlearn
+protopunica
+pyfasta
+ipython

setup.py

@@ -3,90 +3,104 @@
 import setuptools_scm
 
 
-DISTNAME = 'scikit-allel'
+DISTNAME = "scikit-allel"
 
-PACKAGE_NAME = 'allel'
+PACKAGE_NAME = "allel"
 
-DESCRIPTION = 'A Python package for exploring and analysing genetic ' \
-              'variation data.'
+DESCRIPTION = "A Python package for exploring and analysing genetic variation data."
 
-with open('README.rst') as f:
-    LONG_DESCRIPTION = f.read()
+MAINTAINER = "Alistair Miles"
 
-MAINTAINER = 'Alistair Miles'
+MAINTAINER_EMAIL = "[email protected]"
 
-MAINTAINER_EMAIL = 'alimanfoo@googlemail.com'
+URL = "https://github.com/cggh/scikit-allel"
 
-URL = 'https://github.com/cggh/scikit-allel'
+DOWNLOAD_URL = "http://pypi.python.org/pypi/scikit-allel"
 
-DOWNLOAD_URL = 'http://pypi.python.org/pypi/scikit-allel'
+LICENSE = "MIT"
 
-LICENSE = 'MIT'
-
-INSTALL_REQUIRES = ['numpy', 'dask[array]']
+INSTALL_REQUIRES = ["numpy", "dask[array]"]
 
 # full installation with all optional dependencies
-EXTRAS_REQUIRE = {'full': ['scipy', 'matplotlib', 'seaborn', 'pandas', 'scikit-learn',
-                           'h5py', 'numexpr', 'zarr', 'hmmlearn', 'pomegranate', 'nose']}
+EXTRAS_REQUIRE = {
+    "full": [
+        "scipy",
+        "matplotlib",
+        "seaborn",
+        "pandas",
+        "scikit-learn",
+        "h5py",
+        "numexpr",
+        "zarr",
+        "hmmlearn",
+        "protopunica",
+        "nose",
+    ]
+}
 
 CLASSIFIERS = [
-    'Development Status :: 4 - Beta',
-    'License :: OSI Approved :: MIT License',
-    'Intended Audience :: Developers',
-    'Intended Audience :: Science/Research',
-    'Programming Language :: Python',
-    'Topic :: Software Development :: Libraries :: Python Modules',
-    'Topic :: Scientific/Engineering',
-    'Operating System :: Microsoft :: Windows',
-    'Operating System :: POSIX',
-    'Operating System :: Unix',
-    'Operating System :: MacOS',
-    'Programming Language :: Python :: 3',
-    'Programming Language :: Python :: 3.8',
-    'Programming Language :: Python :: 3.9',
-    'Programming Language :: Python :: 3.10',
+    "Development Status :: 4 - Beta",
+    "License :: OSI Approved :: MIT License",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "Topic :: Scientific/Engineering",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Operating System :: MacOS",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
 
 
 # noinspection PyUnresolvedReferences
 def setup_extensions(metadata):
     try:
-        print('[scikit-allel] setup extensions with cython')
+        print("[scikit-allel] setup extensions with cython")
         from Cython.Build import cythonize
         import numpy
-        ext_modules = cythonize([
-            Extension('allel.opt.model',
-                      sources=['allel/opt/model.pyx'],
-                      include_dirs=[numpy.get_include()],
-                      ),
-            Extension('allel.opt.stats',
-                      sources=['allel/opt/stats.pyx'],
-                      include_dirs=[numpy.get_include()],
-                      ),
-            Extension('allel.opt.io_vcf_read',
-                      sources=['allel/opt/io_vcf_read.pyx'],
-                      include_dirs=[numpy.get_include()],
-                      ),
-        ])
-        metadata['ext_modules'] = ext_modules
+
+        ext_modules = cythonize(
+            [
+                Extension(
+                    "allel.opt.model",
+                    sources=["allel/opt/model.pyx"],
+                    include_dirs=[numpy.get_include()],
+                ),
+                Extension(
+                    "allel.opt.stats",
+                    sources=["allel/opt/stats.pyx"],
+                    include_dirs=[numpy.get_include()],
+                ),
+                Extension(
+                    "allel.opt.io_vcf_read",
+                    sources=["allel/opt/io_vcf_read.pyx"],
+                    include_dirs=[numpy.get_include()],
+                ),
+            ]
+        )
+        metadata["ext_modules"] = ext_modules
     except ImportError:
-        print('[scikit-allel] cython not available, not including extensions')
+        print("[scikit-allel] cython not available, not including extensions")
 
 
 def setup_package():
-
     metadata = dict(
         name=DISTNAME,
         maintainer=MAINTAINER,
         maintainer_email=MAINTAINER_EMAIL,
         description=DESCRIPTION,
-        long_description=LONG_DESCRIPTION,
         license=LICENSE,
         url=URL,
         download_url=DOWNLOAD_URL,
-        package_dir={'': '.'},
+        package_dir={"": "."},
         packages=find_packages(),
-        package_data={'allel.test': ['data/*']},
+        package_data={"allel.test": ["data/*"]},
         classifiers=CLASSIFIERS,
         install_requires=INSTALL_REQUIRES,
         extras_require=EXTRAS_REQUIRE,
@@ -96,5 +110,5 @@ def setup_package():
     setup(**metadata)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     setup_package()