diff --git a/recipes/cgat-apps/0001-setup.py.patch b/recipes/cgat-apps/0001-setup.py.patch deleted file mode 100644 index 7dc8f129e99f4..0000000000000 --- a/recipes/cgat-apps/0001-setup.py.patch +++ /dev/null @@ -1,327 +0,0 @@ -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(?Pgit|svn|hg|bzr).+#egg=(?P.+)-(?P\d(?:\.\d)*))$') --HTTPS_REQUIREMENT = re.compile( -- r'^-e (?P.*).+#(?P.+)-(?P\d(?:\.\d)*)$') --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", - ) diff --git a/recipes/cgat-apps/meta.yaml b/recipes/cgat-apps/meta.yaml index cc4106af5f493..b2c1295ad5793 100644 --- a/recipes/cgat-apps/meta.yaml +++ b/recipes/cgat-apps/meta.yaml @@ -1,18 +1,18 @@ {% set name = "cgat-apps" %} -{% set version = "0.7.4" %} +{% set version = "0.7.10" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/cgat-developers/cgat-apps/archive/refs/tags/v{{ version }}.tar.gz - sha256: 3e161597c6e4cf59fc121a8527aeddefd1526f7d13c370d5eaf15b4d3a1894e6 - patches: - - 0001-setup.py.patch - + url: https://pypi.io/packages/source/c/cgat/cgat-{{ version }}.tar.gz + sha256: 2519fd2a7b878f616af0e14c67029251f3e9807fa1abbe3b870bb345014bc03c + build: number: 0 + script_env: + - MACOSX_DEPLOYMENT_TARGET=10.13 # [osx] run_exports: - {{ pin_subpackage('cgat-apps', max_pin="x.x") }} entry_points: @@ -23,14 +23,14 @@ requirements: - {{ compiler('c') }} - {{ compiler('cxx') }} host: - - python + - python >=3.10 - pip - cython >=0.29.35 - numpy - pysam - htslib run: - - python + - python >=3.10 - cgatcore - alignlib-lite - biopython @@ -46,10 +46,10 @@ requirements: - scipy - scikit-learn - sortedcontainers - # Misc dependencies - - bedtools - - ucsc-bedgraphtobigwig - - ucsc-wigtobigwig + # External dependencies + - bedtools # [not osx] # Excluded for macOS + - ucsc-bedgraphtobigwig # [not osx] + - ucsc-wigtobigwig # [not osx] - coreutils - grep @@ -58,10 +58,11 @@ test: - cgat commands: - cgat --help - - cgat --help Conversion - cgat gtf2table -h - - find ${PREFIX} -iname "*bamtools.cpython-*-x86_64-linux-gnu.so*" -exec ldd {} \; - - cgat bam2bed -h + # Skip certain tests for macOS + - find ${PREFIX} -iname "*bamtools.cpython-*-x86_64-linux-gnu.so*" -exec ldd {} \; # [not osx] + - cgat bam2bed -h # [not osx] + skip: true # [osx] # Temporarily skip full test suite on macOS about: home: "https://github.com/cgat-developers/cgat-apps" @@ -71,3 +72,7 @@ about: summary: "Computational Genomics Analysis Toolkit." dev_url: "https://github.com/cgat-developers/cgat-apps" doc_url: "https://cgat-apps.readthedocs.io/en/latest" + +extra: + recipe-maintainers: + - Acribbs