-
Notifications
You must be signed in to change notification settings - Fork 132
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
25 changed files
with
4,640 additions
and
4,636 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
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,2 +1,6 @@ | ||
| [*.py] | ||
| indent_style = tab | ||
| [*.{py,pyx,rst}] | ||
| charset=utf-8 | ||
| end_of_line=lf | ||
| insert_final_newline=true | ||
| indent_style=space | ||
| indent_size=4 |
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 |
|---|---|---|
|
|
@@ -13,49 +13,49 @@ | |
| MIN_CYTHON_VERSION = '0.28' | ||
|
|
||
| if sys.version_info[:2] < (3, 4): | ||
| sys.stdout.write('You need at least Python 3.4\n') | ||
| sys.exit(1) | ||
| sys.stdout.write('You need at least Python 3.4\n') | ||
| sys.exit(1) | ||
|
|
||
|
|
||
| def no_cythonize(extensions, **_ignore): | ||
| """ | ||
| Change file extensions from .pyx to .c or .cpp. | ||
| Copied from Cython documentation | ||
| """ | ||
| for extension in extensions: | ||
| sources = [] | ||
| for sfile in extension.sources: | ||
| path, ext = os.path.splitext(sfile) | ||
| if ext in ('.pyx', '.py'): | ||
| if extension.language == 'c++': | ||
| ext = '.cpp' | ||
| else: | ||
| ext = '.c' | ||
| sfile = path + ext | ||
| sources.append(sfile) | ||
| extension.sources[:] = sources | ||
| """ | ||
| Change file extensions from .pyx to .c or .cpp. | ||
| Copied from Cython documentation | ||
| """ | ||
| for extension in extensions: | ||
| sources = [] | ||
| for sfile in extension.sources: | ||
| path, ext = os.path.splitext(sfile) | ||
| if ext in ('.pyx', '.py'): | ||
| if extension.language == 'c++': | ||
| ext = '.cpp' | ||
| else: | ||
| ext = '.c' | ||
| sfile = path + ext | ||
| sources.append(sfile) | ||
| extension.sources[:] = sources | ||
|
|
||
|
|
||
| def check_cython_version(): | ||
| """Exit if Cython was not found or is too old""" | ||
| try: | ||
| from Cython import __version__ as cyversion | ||
| except ImportError: | ||
| sys.stdout.write( | ||
| "ERROR: Cython is not installed. Install at least Cython version " + | ||
| str(MIN_CYTHON_VERSION) + " to continue.\n") | ||
| sys.exit(1) | ||
| if LooseVersion(cyversion) < LooseVersion(MIN_CYTHON_VERSION): | ||
| sys.stdout.write( | ||
| "ERROR: Your Cython is at version '" + str(cyversion) + | ||
| "', but at least version " + str(MIN_CYTHON_VERSION) + " is required.\n") | ||
| sys.exit(1) | ||
| """Exit if Cython was not found or is too old""" | ||
| try: | ||
| from Cython import __version__ as cyversion | ||
| except ImportError: | ||
| sys.stdout.write( | ||
| "ERROR: Cython is not installed. Install at least Cython version " + | ||
| str(MIN_CYTHON_VERSION) + " to continue.\n") | ||
| sys.exit(1) | ||
| if LooseVersion(cyversion) < LooseVersion(MIN_CYTHON_VERSION): | ||
| sys.stdout.write( | ||
| "ERROR: Your Cython is at version '" + str(cyversion) + | ||
| "', but at least version " + str(MIN_CYTHON_VERSION) + " is required.\n") | ||
| sys.exit(1) | ||
|
|
||
|
|
||
| extensions = [ | ||
| Extension('cutadapt._align', sources=['src/cutadapt/_align.pyx']), | ||
| Extension('cutadapt.qualtrim', sources=['src/cutadapt/qualtrim.pyx']), | ||
| Extension('cutadapt._align', sources=['src/cutadapt/_align.pyx']), | ||
| Extension('cutadapt.qualtrim', sources=['src/cutadapt/qualtrim.pyx']), | ||
| ] | ||
|
|
||
| cmdclass = versioneer.get_cmdclass() | ||
|
|
@@ -64,28 +64,28 @@ def check_cython_version(): | |
|
|
||
|
|
||
| class build_ext(versioneer_build_ext): | ||
| def run(self): | ||
| # If we encounter a PKG-INFO file, then this is likely a .tar.gz/.zip | ||
| # file retrieved from PyPI that already includes the pre-cythonized | ||
| # extension modules, and then we do not need to run cythonize(). | ||
| if os.path.exists('PKG-INFO'): | ||
| no_cythonize(extensions) | ||
| else: | ||
| # Otherwise, this is a 'developer copy' of the code, and then the | ||
| # only sensible thing is to require Cython to be installed. | ||
| check_cython_version() | ||
| from Cython.Build import cythonize | ||
| self.extensions = cythonize(self.extensions) | ||
| versioneer_build_ext.run(self) | ||
| def run(self): | ||
| # If we encounter a PKG-INFO file, then this is likely a .tar.gz/.zip | ||
| # file retrieved from PyPI that already includes the pre-cythonized | ||
| # extension modules, and then we do not need to run cythonize(). | ||
| if os.path.exists('PKG-INFO'): | ||
| no_cythonize(extensions) | ||
| else: | ||
| # Otherwise, this is a 'developer copy' of the code, and then the | ||
| # only sensible thing is to require Cython to be installed. | ||
| check_cython_version() | ||
| from Cython.Build import cythonize | ||
| self.extensions = cythonize(self.extensions) | ||
| versioneer_build_ext.run(self) | ||
|
|
||
|
|
||
| class sdist(versioneer_sdist): | ||
| def run(self): | ||
| # Make sure the compiled Cython files in the distribution are up-to-date | ||
| from Cython.Build import cythonize | ||
| check_cython_version() | ||
| cythonize(extensions) | ||
| versioneer_sdist.run(self) | ||
| def run(self): | ||
| # Make sure the compiled Cython files in the distribution are up-to-date | ||
| from Cython.Build import cythonize | ||
| check_cython_version() | ||
| cythonize(extensions) | ||
| versioneer_sdist.run(self) | ||
|
|
||
|
|
||
| cmdclass['build_ext'] = build_ext | ||
|
|
@@ -94,35 +94,35 @@ def run(self): | |
|
|
||
| encoding_arg = {'encoding': 'utf-8'} if sys.version > '3' else dict() | ||
| with open('README.rst', **encoding_arg) as f: | ||
| long_description = f.read() | ||
| long_description = f.read() | ||
|
|
||
| setup( | ||
| name='cutadapt', | ||
| version=versioneer.get_version(), | ||
| author='Marcel Martin', | ||
| author_email='[email protected]', | ||
| url='https://cutadapt.readthedocs.io/', | ||
| description='trim adapters from high-throughput sequencing reads', | ||
| long_description=long_description, | ||
| license='MIT', | ||
| cmdclass=cmdclass, | ||
| ext_modules=extensions, | ||
| package_dir={'': 'src'}, | ||
| packages=find_packages('src'), | ||
| entry_points={'console_scripts': ['cutadapt = cutadapt.__main__:main']}, | ||
| install_requires=['dnaio>=0.3', 'xopen>=0.3.2'], | ||
| extras_require={ | ||
| 'dev': ['Cython', 'pytest', 'pytest-timeout', 'sphinx', 'sphinx_issues'], | ||
| }, | ||
| python_requires='>=3', | ||
| classifiers=[ | ||
| "Development Status :: 5 - Production/Stable", | ||
| "Environment :: Console", | ||
| "Intended Audience :: Science/Research", | ||
| "License :: OSI Approved :: MIT License", | ||
| "Natural Language :: English", | ||
| "Programming Language :: Cython", | ||
| "Programming Language :: Python :: 3", | ||
| "Topic :: Scientific/Engineering :: Bio-Informatics" | ||
| ], | ||
| name='cutadapt', | ||
| version=versioneer.get_version(), | ||
| author='Marcel Martin', | ||
| author_email='[email protected]', | ||
| url='https://cutadapt.readthedocs.io/', | ||
| description='trim adapters from high-throughput sequencing reads', | ||
| long_description=long_description, | ||
| license='MIT', | ||
| cmdclass=cmdclass, | ||
| ext_modules=extensions, | ||
| package_dir={'': 'src'}, | ||
| packages=find_packages('src'), | ||
| entry_points={'console_scripts': ['cutadapt = cutadapt.__main__:main']}, | ||
| install_requires=['dnaio>=0.3', 'xopen>=0.3.2'], | ||
| extras_require={ | ||
| 'dev': ['Cython', 'pytest', 'pytest-timeout', 'sphinx', 'sphinx_issues'], | ||
| }, | ||
| python_requires='>=3', | ||
| classifiers=[ | ||
| "Development Status :: 5 - Production/Stable", | ||
| "Environment :: Console", | ||
| "Intended Audience :: Science/Research", | ||
| "License :: OSI Approved :: MIT License", | ||
| "Natural Language :: English", | ||
| "Programming Language :: Cython", | ||
| "Programming Language :: Python :: 3", | ||
| "Topic :: Scientific/Engineering :: Bio-Informatics" | ||
| ], | ||
| ) | ||
Oops, something went wrong.