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Update cgat-apps to 0.7.4 (#51682)
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* Update cgat-apps to 0.7.4

* clean up recipe

* add cplus_include_path

* Update build.sh

* clean up recipe

* Update meta.yaml

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
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@BiocondaBot @mencian
3 people authored Nov 13, 2024
1 parent c2742ac commit 80a6ddc
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327 changes: 327 additions & 0 deletions recipes/cgat-apps/0001-setup.py.patch
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@@ -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,
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",
)
30 changes: 9 additions & 21 deletions recipes/cgat-apps/build.sh
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Original file line number Diff line number Diff line change
@@ -1,28 +1,16 @@
#!/bin/bash

# export compiler flags
#export CFLAGS=${CFLAGS}" -I${PREFIX}/include -L${PREFIX}/lib"
#export CPPFLAGS=${CPPFLAGS}" -I${PREFIX}/include -L${PREFIX}/lib"
export LDFLAGS=${LDFLAGS}" -I${PREFIX}/include -L${PREFIX}/lib"
export CPATH=${CPATH}" -I${PREFIX}/include -L${PREFIX}/lib"
export C_INCLUDE_PATH=${C_INCLUDE_PATH}:${PREFIX}/include
export CPLUS_INCLUDE_PATH=${CPLUS_INCLUDE_PATH}:${PREFIX}/include
export LIBRARY_PATH=${LIBRARY_PATH}:${PREFIX}/lib
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${PREFIX}/lib:${PREFIX}/lib/R/lib

# linking htslib, see:
# http://pysam.readthedocs.org/en/latest/installation.html#external
# https://github.com/pysam-developers/pysam/blob/v0.9.0/setup.py#L79
#export CFLAGS="-I$PREFIX/include -DHAVE_LIBDEFLATE"
#export CPPFLAGS="-I$PREFIX/include -DHAVE_LIBDEFLATE"
#export LDFLAGS="-L$PREFIX/lib"

#export HTSLIB_LIBRARY_DIR=$PREFIX/lib
#export HTSLIB_INCLUDE_DIR=$PREFIX/include
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'' -e '/REPO_REQUIREMENT/,/pass/d' setup.py
sed -i'' -e '/# dependencies/,/dependency_links=dependency_links,/d' setup.py
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 setup.py install --single-version-externally-managed --record=record.txt
$PYTHON -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
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