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Merge pull request #113 from rseng/update/analysis-2024-03-20
Update from update/analysis-2024-03-20
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| { | ||
| "Python": 5938, | ||
| "R": 2230, | ||
| "Python": 5964, | ||
| "R": 2235, | ||
| "Cpp": 441, | ||
| "Js": 1691, | ||
| "Go": 246 | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,9 +1,9 @@ | ||
| { | ||
| "python_deps": 4906, | ||
| "python_deps": 4928, | ||
| "cpp_deps": 441, | ||
| "r_deps": 2230, | ||
| "r_deps": 2235, | ||
| "js_deps": 1691, | ||
| "go_deps": 246, | ||
| "total_repos": 5375, | ||
| "total_parsed": 2748 | ||
| "total_repos": 5390, | ||
| "total_parsed": 2758 | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,19 @@ | ||
| --- | ||
| title: github/BonsonW/slow5curl | ||
| layout: repo | ||
| tipue_search_active: true | ||
| exclude_from_search: true | ||
| --- | ||
| # Software Credit | ||
|
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| |Manager|Name|Credit| | ||
| |-------|----|------| | ||
| |setup.py|github/BonsonW/slow5curl|0.01| | ||
| |pypi|[numpy](https://www.numpy.org)|0.007| | ||
| |pypi|[Cython](https://cython.org/)|0.003| | ||
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| > Note that credit values are rounded and expanded (so shared dependencies are represented as one record) and may not add to 1.0. Rounded values that hit zero are removed. | ||
|
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| - Generated by [CiteLang](https://github.com/vsoch/citelang) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,18 @@ | ||
| { | ||
| "setup.py": { | ||
| "github/BonsonW/slow5curl": { | ||
| "credit": 0.01, | ||
| "url": null | ||
| } | ||
| }, | ||
| "pypi": { | ||
| "numpy": { | ||
| "credit": 0.006600000000000001, | ||
| "url": "https://www.numpy.org" | ||
| }, | ||
| "Cython": { | ||
| "credit": 0.0033000000000000004, | ||
| "url": "https://cython.org/" | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,114 @@ | ||
| try: | ||
| from setuptools import setup, Extension | ||
| from setuptools.command.install import install | ||
|
|
||
| except ImportError: | ||
| from distutils.core import setup | ||
| from distutils.extension import Extension | ||
|
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| import sys | ||
| import platform | ||
| import os | ||
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| include_dirs = [] | ||
| # import numpy as np | ||
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| # creat dummy closures for metadata reading on first parse of setup.py | ||
| # that way it picks up the requirements and installs them, then can use them | ||
| # for the install. | ||
| try: | ||
| import numpy as np | ||
| include_dirs = ['include/', np.get_include(), 'thirdparty/streamvbyte/include'] | ||
| except ImportError: | ||
| include_dirs = ['include/', 'thirdparty/streamvbyte/include'] | ||
| def np(*args, ** kwargs ): | ||
| import numpy as np | ||
| return np(*args, ** kwargs) | ||
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| try: | ||
| from Cython.Build import build_ext | ||
| except ImportError: | ||
| def build_ext(*args, ** kwargs ): | ||
| from Cython.Build import build_ext | ||
| return build_ext(*args, ** kwargs) | ||
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| # from Cython.Build import build_ext | ||
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| #adapted from https://github.com/lh3/minimap2/blob/master/setup.py | ||
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| sources=['python/pys5curl.pyx', | ||
| 'src/s5curl.c', 'src/curlget.c', 'src/fetch.c', 'src/index.c',] | ||
| depends=['python/pys5curl.pxd', 'python/pys5curl.h', | ||
| 'src/fetch.h', 'include/slow5curl/s5curl.h', 'src/fetch.h', | ||
| 'slow5lib/src/slow5_idx.h', 'slow5lib/src/slow5_extra.h', | ||
| 'slow5lib/include/slow5/slow5.h'] | ||
| extra_compile_args = ['-g', '-Wall', '-O2', '-std=c99', '-DSLOW5_ENABLE_MT=1' ] | ||
| # extra_compile_args = [] | ||
| # os.environ["CFLAGS"] = '-g -Wall -O2 -std=c99' | ||
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| if platform.system() != 'Darwin': | ||
| arch=platform.machine() | ||
| if arch in ["aarch64"]: | ||
| extra_compile_args.append('-D__ARM_NEON__') | ||
| elif arch in ["armv7l"]: | ||
| extra_compile_args.append('-mfpu=neon') | ||
| elif arch in ["x86_64"]: | ||
| extra_compile_args.extend(['-DSTREAMVBYTE_SSSE3=1', '-mssse3']) # WARNING: ancient x86_64 CPUs don't have SSSE3 | ||
| # note that on macos, for now we just let it compile without simd | ||
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| # include_dirs = ['include/', np.get_include(), 'thirdparty/streamvbyte/include'] | ||
| libraries = ['m', 'z'] | ||
| library_dirs = ['.'] | ||
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| # a nasty hack to provide option to build with zstd | ||
| zstd=0 | ||
| try: | ||
| zstd=os.environ["PYSLOW5_ZSTD"] | ||
| except: | ||
| zstd=0 | ||
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| if zstd=="1": | ||
| extra_compile_args.append('-DSLOW5_USE_ZSTD=1') | ||
| libraries.append('zstd') | ||
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| extensions = [Extension('pys5curl', | ||
| sources = sources, | ||
| depends = depends, | ||
| extra_compile_args = extra_compile_args, | ||
| libraries = libraries, | ||
| include_dirs = include_dirs, | ||
| library_dirs = library_dirs, | ||
| language = 'c' )] | ||
|
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| def readme(): | ||
| with open('docs/pys5curl_api/pys5curl.md') as f: | ||
| return f.read() | ||
|
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|
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| setup( | ||
| name = 'pys5curl', | ||
| version='1.1.0', | ||
| url = 'https://github.com/BonsonW/slow5curl', | ||
| description='slow5lib python bindings', | ||
| long_description=readme(), | ||
| long_description_content_type='text/markdown', | ||
| author='Hasindu Gamaarachchi, Sasha Jenner, James Ferguson, Bonson Wong', | ||
| author_email='bonson.ym@gmail.com', | ||
| maintainer='Bonson Wong', | ||
| maintainer_email='bonson.ym@gmail.com', | ||
| license = 'MIT', | ||
| keywords = ['nanopore','slow5','signal','slow5curl','s5curl'], | ||
| ext_modules=extensions, | ||
| cmdclass= {'build_ext': build_ext}, | ||
| classifiers = [ | ||
| 'Development Status :: 5 - Production/Stable', | ||
| 'License :: OSI Approved :: MIT License', | ||
| 'Programming Language :: C', | ||
| 'Programming Language :: Cython', | ||
| 'Programming Language :: Python :: 3', | ||
| 'Intended Audience :: Science/Research', | ||
| 'Topic :: Scientific/Engineering :: Bio-Informatics'], | ||
| python_requires='>=3.4.3', | ||
| install_requires=["numpy"], | ||
| setup_requires=["Cython", "numpy"] | ||
| ) |
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