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https://github.com/TREX-CoE/trexio.git
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FIX: bug related to import numpy in setup.py script
use the custom NUMPY_INCLUDEDIR environment variable derived from a call to numpy.get_include
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parent
58b611e21b
commit
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@ -1 +1 @@
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include src/*.c src/trexio*.h
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include src/*.c src/trexio*.h examples/*.ipynb requirements.txt set_NUMPY_INCLUDEDIR.sh
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4
python/set_NUMPY_INCLUDEDIR.sh
Executable file
4
python/set_NUMPY_INCLUDEDIR.sh
Executable file
@ -0,0 +1,4 @@
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INCLUDEDIR=`python -c 'import numpy; print(numpy.get_include())'`
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export NUMPY_INCLUDEDIR=${INCLUDEDIR}
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@ -1,15 +1,36 @@
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#!/usr/bin/env python3
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"""
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setup.py file for TREXIO Python package
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"""
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from distutils.sysconfig import get_python_inc
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from setuptools import setup, Extension
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import os
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from setuptools import setup, Extension
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# this was recommended to solve the problem of the missing numpy header files
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# bit it causes `pip install .` to fail with numpy module not found error
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#try:
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# import numpy
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#except ImportError:
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# raise Exception("numpy Python package cannot be imported.")
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#numpy_includedir = numpy.get_include()
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# this does not cause aforementioned issue but the includedir points to system-wide numpy and not to venv-wide
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#from distutils.sysconfig import get_python_inc
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#numpy_includedir = os.path.join(get_python_inc(plat_specific=1), 'numpy')
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# dirty workaround: get numpy includedir from the environment variable that can be pre-set using set_NUMPY_INCLUDEDIR.sh
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numpy_includedir = os.environ.get("NUMPY_INCLUDEDIR", None)
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numpy_isUndefined = numpy_includedir is None or numpy_includedir==""
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if numpy_isUndefined:
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raise Exception("NUMPY_INCLUDEDIR environment variable is not specified. Please do it manually or execute set_NUMPY_INCLUDEDIR.sh script.")
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rootpath = os.path.dirname(os.path.abspath(__file__))
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srcpath = os.path.join(rootpath, 'src')
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c_files = ['trexio.c', 'trexio_hdf5.c', 'trexio_text.c', 'pytrexio_wrap.c']
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numpy_includedir = os.path.join(get_python_inc(plat_specific=1), 'numpy')
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with open("README.md", "r") as fh:
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long_description = fh.read()
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@ -40,7 +61,7 @@ if h5_ldflags_isUndefined or h5_cflags_isUndefined:
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try:
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import pkgconfig as pk
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except ImportError:
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raise Exception("pkgconfig Python package has not been found")
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raise Exception("pkgconfig Python package cannot be imported.")
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try:
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assert pk.exists('hdf5')
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@ -91,6 +112,8 @@ setup(name = 'trexio',
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"Operating System :: Unix",
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"Operating System :: MacOS"
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],
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python_requires = ">=3.6",
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setup_requires = ['numpy', 'pkgconfig'],
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install_requires = ['numpy']
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)
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