-
Notifications
You must be signed in to change notification settings - Fork 51
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* attempt upgrades * thrash * fix install * upgrade deploy action [ci skip]
- Loading branch information
Showing
8 changed files
with
107 additions
and
119 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| # required | ||
| cython==0.29.34 | ||
| numpy==1.24.3 | ||
| dask[array]==2023.4.1 | ||
| cython | ||
| numpy | ||
| dask[array] |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -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() | ||