Update cgat-apps to 0.7.4 #51682
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,327 @@ | ||
| diff --git a/requires.txt b/requires.txt | ||
| deleted file mode 100644 | ||
| index e69de29b..00000000 | ||
| diff --git a/setup.py b/setup.py | ||
| index 1cc415ea..56d2ccd8 100644 | ||
| --- a/setup.py | ||
| +++ b/setup.py | ||
| @@ -4,239 +4,73 @@ import os | ||
| import subprocess | ||
| import re | ||
|
|
||
| -######################################################################## | ||
| -####################################################################### | ||
| -# Check for dependencies | ||
| -# | ||
| -# Is there a way to do this more elegantly? | ||
| -# 1. Run "pip install numpy" | ||
| -# 2. Wrap inside functions (works for numpy/pysam, but not cython) | ||
| -try: | ||
| - import numpy | ||
| -except ImportError: | ||
| - raise ImportError( | ||
| - "the CGAT code collection requires numpy to be installed " | ||
| - "before running setup.py (pip install numpy)") | ||
| +# Import setuptools at the beginning | ||
| +import setuptools | ||
| +from setuptools import setup, find_packages, Extension | ||
| +from distutils.version import LooseVersion | ||
| +from Cython.Distutils import build_ext | ||
|
|
||
| +# Ensure dependencies are installed before setup | ||
| try: | ||
| + import numpy | ||
| import Cython | ||
| -except ImportError: | ||
| - raise ImportError( | ||
| - "the CGAT code collection requires cython to " | ||
| - "be installed before running setup.py (pip install cython)") | ||
| - | ||
| -try: | ||
| import pysam | ||
| -except ImportError: | ||
| - raise ImportError( | ||
| - "the CGAT code collection requires pysam to " | ||
| - "be installed before running setup.py (pip install pysam)") | ||
| +except ImportError as e: | ||
| + missing_package = str(e).split("'")[1] | ||
| + raise ImportError(f"{missing_package} must be installed before running setup.py") | ||
|
|
||
| -######################################################################## | ||
| -######################################################################## | ||
| -# Import setuptools | ||
| -# Use existing setuptools, otherwise try ez_setup. | ||
| -try: | ||
| - import setuptools | ||
| -except ImportError: | ||
| - # try to get via ez_setup | ||
| - # ez_setup did not work on all machines tested as | ||
| - # it uses curl with https protocol, which is not | ||
| - # enabled in ScientificLinux | ||
| - import ez_setup | ||
| - ez_setup.use_setuptools() | ||
| +# Enforce Python 3 requirement | ||
| +if sys.version_info < (3, 6): | ||
| + raise SystemExit("Python 3.6 or later is required to install this package.") | ||
|
|
||
| -from setuptools import setup, find_packages, Extension | ||
| - | ||
| -from distutils.version import LooseVersion | ||
| +# Minimum setuptools version requirement | ||
| if LooseVersion(setuptools.__version__) < LooseVersion('1.1'): | ||
| - print("Version detected:", LooseVersion(setuptools.__version__)) | ||
| - raise ImportError( | ||
| - "the CGAT code collection requires setuptools 1.1 higher") | ||
| + raise ImportError("Setuptools version >=1.1 is required") | ||
|
|
||
| -from Cython.Distutils import build_ext | ||
| - | ||
| -######################################################################## | ||
| -######################################################################## | ||
| -IS_OSX = sys.platform == 'darwin' | ||
| - | ||
| -######################################################################## | ||
| -######################################################################## | ||
| -# collect CGAT version | ||
| +# Define version and other package information | ||
| sys.path.insert(0, "cgat") | ||
| import version | ||
| - | ||
| version = version.__version__ | ||
|
|
||
| -############################################################### | ||
| -############################################################### | ||
| -# Check for external dependencies | ||
| -# | ||
| -# Not exhaustive, simply execute a representative tool from a toolkit. | ||
| -external_dependencies = ( | ||
| - ("wigToBigWig", "UCSC tools", 255), | ||
| - ("bedtools", "bedtools", 0), | ||
| - ) | ||
| +IS_OSX = sys.platform == 'darwin' | ||
|
|
||
| +# External dependency check | ||
| +external_dependencies = [("wigToBigWig", "UCSC tools", 255), ("bedtools", "bedtools", 0)] | ||
| for tool, toolkit, expected in external_dependencies: | ||
| - try: | ||
| - # py3k | ||
| - from subprocess import DEVNULL | ||
| - except ImportError: | ||
| - DEVNULL = open(os.devnull, 'wb') | ||
| - | ||
| - try: | ||
| - retcode = subprocess.call(tool, shell=True, | ||
| - stdout=DEVNULL, stderr=DEVNULL) | ||
| - except OSError as msg: | ||
| - print(("WARNING: depency check for %s failed: %s" % (toolkit, msg))) | ||
| - | ||
| - # UCSC tools return 255 when called without arguments | ||
| + retcode = subprocess.call(tool, shell=True, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL) | ||
| if retcode != expected: | ||
| - print(("WARNING: depency check for %s(%s) failed, error %i" % | ||
| - (toolkit, tool, retcode))) | ||
| - | ||
| -############################################################### | ||
| -############################################################### | ||
| -# Define dependencies | ||
| -# | ||
| -major, minor1, minor2, s, tmp = sys.version_info | ||
| - | ||
| -if (major == 2 and minor1 < 7) or major < 2: | ||
| - raise SystemExit("""CGAT requires Python 2.7 or later.""") | ||
| - | ||
| - | ||
| -##################################################################### | ||
| -##################################################################### | ||
| -# Code to install dependencies from a repository | ||
| -##################################################################### | ||
| -# Modified from http://stackoverflow.com/a/9125399 | ||
| -##################################################################### | ||
| -def which(program): | ||
| - """ | ||
| - Detect whether or not a program is installed. | ||
| - Thanks to http://stackoverflow.com/a/377028/70191 | ||
| - """ | ||
| - def is_exe(fpath): | ||
| - return os.path.exists(fpath) and os.access(fpath, os.X_OK) | ||
| - | ||
| - fpath, _ = os.path.split(program) | ||
| - if fpath: | ||
| - if is_exe(program): | ||
| - return program | ||
| - else: | ||
| - for path in os.environ['PATH'].split(os.pathsep): | ||
| - exe_file = os.path.join(path, program) | ||
| - if is_exe(exe_file): | ||
| - return exe_file | ||
| - | ||
| - return None | ||
| - | ||
| -REPO_REQUIREMENT = re.compile( | ||
| - r'^-e (?P<link>(?P<vcs>git|svn|hg|bzr).+#egg=(?P<package>.+)-(?P<version>\d(?:\.\d)*))$') | ||
| -HTTPS_REQUIREMENT = re.compile( | ||
| - r'^-e (?P<link>.*).+#(?P<package>.+)-(?P<version>\d(?:\.\d)*)$') | ||
| -install_requires = [] | ||
| -dependency_links = [] | ||
| - | ||
| -for requirement in ( | ||
| - l.strip() for l in open('requires.txt') if not l.startswith("#")): | ||
| - match = REPO_REQUIREMENT.match(requirement) | ||
| - if match: | ||
| - assert which(match.group('vcs')) is not None, \ | ||
| - ("VCS '%(vcs)s' must be installed in order to " | ||
| - "install %(link)s" % match.groupdict()) | ||
| - install_requires.append("%(package)s==%(version)s" % match.groupdict()) | ||
| - dependency_links.append(match.group('link')) | ||
| - continue | ||
| + print(f"WARNING: Dependency check for {toolkit} ({tool}) failed with error code {retcode}") | ||
|
|
||
| - if requirement.startswith("https"): | ||
| - install_requires.append(requirement) | ||
| - continue | ||
|
|
||
| - match = HTTPS_REQUIREMENT.match(requirement) | ||
| - if match: | ||
| - install_requires.append("%(package)s>=%(version)s" % match.groupdict()) | ||
| - dependency_links.append(match.group('link')) | ||
| - continue | ||
| - | ||
| - install_requires.append(requirement) | ||
| - | ||
| -if major == 2: | ||
| - install_requires.extend(['web.py>=0.37', | ||
| - 'xlwt>=0.7.4', | ||
| - 'matplotlib-venn>=0.5']) | ||
| -elif major == 3: | ||
| - pass | ||
| - | ||
| -cgat_packages = find_packages(exclude=['tests']) | ||
| +# Adjust packages and directories | ||
| +cgat_packages = find_packages(include=["cgat", "cgat.*"], exclude=['tests']) | ||
| cgat_package_dirs = {'cgat': 'cgat'} | ||
|
|
||
| -########################################################## | ||
| -########################################################## | ||
| -# classifiers | ||
| -classifiers = """ | ||
| -Development Status :: 3 - Alpha | ||
| -Intended Audience :: Science/Research | ||
| -Intended Audience :: Developers | ||
| -License :: OSI Approved | ||
| -Programming Language :: Python | ||
| -Topic :: Software Development | ||
| -Topic :: Scientific/Engineering | ||
| -Operating System :: POSIX | ||
| -Operating System :: Unix | ||
| -Operating System :: MacOS | ||
| -""" | ||
| - | ||
| -########################################################## | ||
| -# Cython Extensions | ||
| +# Cython extensions and paths | ||
| conda_includes = [os.path.dirname(sysconfig.get_paths()["include"])] | ||
| conda_libdirs = [os.path.dirname(sysconfig.get_paths()["stdlib"])] | ||
| - | ||
| -# Connected components cython extension | ||
| pysam_libraries = pysam.get_libraries() | ||
| -pysam_libdirs = list(set(os.path.dirname(x) for x in | ||
| - pysam_libraries)) + conda_libdirs | ||
| - | ||
| -# remove lib and .so and add htslib | ||
| -pysam_libs = ["hts"] + list([os.path.basename(x)[3:-3] for x in | ||
| - pysam_libraries]) | ||
| - | ||
| +pysam_libdirs = list(set(os.path.dirname(x) for x in pysam_libraries)) + conda_libdirs | ||
| +pysam_libs = ["hts"] + [os.path.basename(x)[3:-3] for x in pysam_libraries] | ||
| pysam_dirname = os.path.dirname(pysam.__file__) | ||
| -if IS_OSX: | ||
| - # linking against bundles does no work (and apparently is not needed) | ||
| - # within OS X | ||
| - extra_link_args = [] | ||
| -else: | ||
| - extra_link_args = [os.path.join(pysam_dirname, x) for x in | ||
| - pysam.get_libraries()] | ||
| - | ||
| -extra_link_args_pysam = ['-Wl,-rpath,{}'.format(x) for x in pysam_libdirs] +\ | ||
| - ['-Wl,-rpath,{}'.format(x) for x in conda_libdirs] | ||
| +extra_link_args_pysam = [f'-Wl,-rpath,{x}' for x in pysam_libdirs + conda_libdirs] | ||
|
|
||
| extensions = [ | ||
| Extension( | ||
| 'cgat.Components', | ||
| - ['cgat/Components/Components.pyx', | ||
| - 'cgat/Components/connected_components.cpp', ], | ||
| - library_dirs=[], | ||
| - libraries=[], | ||
| + ['cgat/Components/Components.pyx', 'cgat/Components/connected_components.cpp'], | ||
| + include_dirs=[os.path.join('cgat', 'Components')] + conda_includes, | ||
| language="c++", | ||
| ), | ||
| Extension( | ||
| "cgat.NCL.cnestedlist", | ||
| - ["cgat/NCL/cnestedlist.pyx", | ||
| - "cgat/NCL/intervaldb.c"], | ||
| - library_dirs=[], | ||
| - libraries=[], | ||
| + ["cgat/NCL/cnestedlist.pyx", "cgat/NCL/intervaldb.c"], | ||
| language="c", | ||
| ), | ||
| Extension( | ||
| "cgat.GeneModelAnalysis", | ||
| ["cgat/GeneModelAnalysis.pyx"], | ||
| include_dirs=conda_includes + pysam.get_include() + [numpy.get_include()], | ||
| - library_dirs=[], | ||
| - libraries=[], | ||
| define_macros=pysam.get_defines(), | ||
| language="c", | ||
| ), | ||
| @@ -292,11 +126,8 @@ extensions = [ | ||
| ), | ||
| ] | ||
|
|
||
| -for e in extensions: | ||
| - e.cython_directives = {'language_level': "3str"} #all are Python-3 | ||
| - | ||
| +# Build setup configuration | ||
| setup( | ||
| - # package information | ||
| name='cgat', | ||
| version=version, | ||
| description='cgat : the Computational Genomics Analysis Toolkit', | ||
| @@ -306,22 +137,26 @@ setup( | ||
| platforms=["any"], | ||
| keywords="computational genomics", | ||
| long_description='cgat : the Computational Genomics Analysis Toolkit', | ||
| - classifiers=[_f for _f in classifiers.split("\n") if _f], | ||
| + classifiers=[_f for _f in """ | ||
| + Development Status :: 3 - Alpha | ||
| + Intended Audience :: Science/Research | ||
| + Intended Audience :: Developers | ||
| + License :: OSI Approved | ||
| + Programming Language :: Python | ||
| + Topic :: Software Development | ||
| + Topic :: Scientific/Engineering | ||
| + Operating System :: POSIX | ||
| + Operating System :: Unix | ||
| + Operating System :: MacOS | ||
| + """.splitlines() if _f], | ||
| url="http://www.cgat.org/cgat/Tools/", | ||
| - # package contents | ||
| + python_requires=">=3.6", | ||
| packages=cgat_packages, | ||
|
Comment on lines
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There was a problem hiding this comment. Specify 'install_requires' to ensure dependencies are installed The Add the setup(
name='cgat',
version=version,
description='cgat : the Computational Genomics Analysis Toolkit',
...
python_requires=">=3.6",
+ install_requires=[
+ 'numpy',
+ 'Cython>=0.29.35',
+ 'pysam',
+ # Add other dependencies as needed
+ ],
packages=cgat_packages,
package_dir=cgat_package_dirs,
include_package_data=True,
)
|
||
| package_dir=cgat_package_dirs, | ||
| include_package_data=True, | ||
| - entry_points={ | ||
| - 'console_scripts': ['cgat = cgat.cgat:main'] | ||
| - }, | ||
| - # dependencies | ||
| - install_requires=install_requires, | ||
| - dependency_links=dependency_links, | ||
| - # extension modules | ||
| + entry_points={'console_scripts': ['cgat = cgat.cgat:main']}, | ||
| ext_modules=extensions, | ||
| cmdclass={'build_ext': build_ext}, | ||
| - # other options | ||
| zip_safe=False, | ||
| test_suite="tests", | ||
| ) | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,28 +1,16 @@ | ||
| #!/bin/bash | ||
|
|
||
| # export compiler flags | ||
| export INCLUDE_PATH="${PREFIX}/include" | ||
| export LIBRARY_PATH="${PREFIX}/lib" | ||
| export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" | ||
| export CFLAGS="${CFLAGS} -O3 -L${PREFIX}/lib" | ||
| export CPPFLAGS="${CPPFLAGS} -O3 -I${PREFIX}/include" | ||
|
|
||
| # remove install_requires (no longer required with conda package) | ||
| sed -i.bak'' -e '/REPO_REQUIREMENT/,/pass/d' setup.py | ||
| sed -i.bak'' -e '/# dependencies/,/dependency_links=dependency_links,/d' setup.py | ||
| rm -rf *.bak | ||
|
|
||
| # https://bioconda.github.io/linting.html#setup-py-install-args | ||
| $PYTHON -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv |
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Add missing import statement for 'pysam'
The
pysammodule is used in the code (e.g.,pysam.get_libraries()at line 226), but it is not imported. This will result in aNameErrorwhen runningsetup.py.Apply this diff to add the missing import at the beginning of the file:
+import pysam