pip installation fails in Mac

[mckib2]

pip installation fails in Mac

[mckib2]

This is due to aftermath of #61. setup_helpers.py is missing from MANIFEST.in and so is not uploaded to pypi. Should be a quick fix

[mckib2]

Fix has been uploaded to pypi, try installing again via pip (may have to ignore cache to get latest version, i.e. pip install pygrappa --no-cache-dir).

There are CI tests on the git repo, but some files are not automatically included in PyPI distribution, so please let me know if you find anything else that is missing or breaks. I work primarily on Linux and don't have easy access to Mac

[kingaza]

such a quick reply! thx very much~

and installation from source also fails. is it the same problem?

(base) abu:pygrappa abu$ python setup.py install
Running cython...
Warning: 'keywords' should be a list, got type 'tuple'
running install
running bdist_egg
running egg_info
running build_src
build_src
building extension "pygrappa.cgrappa" sources
building extension "pygrappa.grog_powers" sources
building extension "pygrappa.grog_gridding" sources
build_src: building npy-pkg config files
writing pygrappa.egg-info/PKG-INFO
writing dependency_links to pygrappa.egg-info/dependency_links.txt
writing requirements to pygrappa.egg-info/requires.txt
writing top-level names to pygrappa.egg-info/top_level.txt
reading manifest file 'pygrappa.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'pygrappa.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.7-x86_64/egg
running install_lib
running build_py
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
building 'pygrappa.cgrappa' extension
compiling C++ sources
C compiler: g++ -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Users/abu/anaconda3/include -arch x86_64 -I/Users/abu/anaconda3/include -arch x86_64

compile options: '-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -I./src/ -I/Users/abu/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/Users/abu/anaconda3/include/python3.7m -c'
g++: ./src/cgrappa.cpp
g++ -bundle -undefined dynamic_lookup -L/Users/abu/anaconda3/lib -arch x86_64 -L/Users/abu/anaconda3/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.7-x86_64-3.7/src/cgrappa.o build/temp.macosx-10.7-x86_64-3.7/src/get_sampling_patterns.o -o build/lib.macosx-10.7-x86_64-3.7/pygrappa/cgrappa.cpython-37m-darwin.so
Traceback (most recent call last):
File "setup.py", line 90, in
**configuration(top_path='').todict(),
File "/Users/abu/anaconda3/lib/python3.7/site-packages/numpy/distutils/core.py", line 171, in setup
return old_setup(**new_attr)
File "/Users/abu/anaconda3/lib/python3.7/site-packages/setuptools/init.py", line 145, in setup
return distutils.core.setup(**attrs)
File "/Users/abu/anaconda3/lib/python3.7/distutils/core.py", line 148, in setup
dist.run_commands()
File "/Users/abu/anaconda3/lib/python3.7/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/Users/abu/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/Users/abu/anaconda3/lib/python3.7/site-packages/numpy/distutils/command/install.py", line 62, in run
r = self.setuptools_run()
File "/Users/abu/anaconda3/lib/python3.7/site-packages/numpy/distutils/command/install.py", line 56, in setuptools_run
self.do_egg_install()
File "/Users/abu/anaconda3/lib/python3.7/site-packages/setuptools/command/install.py", line 109, in do_egg_install
self.run_command('bdist_egg')
File "/Users/abu/anaconda3/lib/python3.7/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/Users/abu/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/Users/abu/anaconda3/lib/python3.7/site-packages/setuptools/command/bdist_egg.py", line 172, in run
cmd = self.call_command('install_lib', warn_dir=0)
File "/Users/abu/anaconda3/lib/python3.7/site-packages/setuptools/command/bdist_egg.py", line 158, in call_command
self.run_command(cmdname)
File "/Users/abu/anaconda3/lib/python3.7/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/Users/abu/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/Users/abu/anaconda3/lib/python3.7/site-packages/setuptools/command/install_lib.py", line 11, in run
self.build()
File "/Users/abu/anaconda3/lib/python3.7/distutils/command/install_lib.py", line 107, in build
self.run_command('build_ext')
File "/Users/abu/anaconda3/lib/python3.7/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/Users/abu/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/Users/abu/anaconda3/lib/python3.7/site-packages/numpy/distutils/command/build_ext.py", line 261, in run
self.build_extensions()
File "/Users/abu/anaconda3/lib/python3.7/distutils/command/build_ext.py", line 449, in build_extensions
self._build_extensions_serial()
File "/Users/abu/anaconda3/lib/python3.7/distutils/command/build_ext.py", line 474, in _build_extensions_serial
self.build_extension(ext)
File "/Users/abu/02_Dev/pygrappa/setup_helpers.py", line 47, in build_extension
_run_pre_build_hooks(hooks, (self, ext))
File "/Users/abu/02_Dev/pygrappa/setup_helpers.py", line 83, in _run_pre_build_hooks
hook(*args)
File "setup.py", line 14, in pre_build_hook
from scipy._build_utils.compiler_helper import get_cxx_std_flag
ModuleNotFoundError: No module named 'scipy._build_utils.compiler_helper'

[mckib2]

Yep, this looks like it might be a chicken/egg dependency problem. Do you have scipy installed currently in your environment? If not, try installing scipy first (i.e., pip install scipy), then install pygrappa

[kingaza]

yes, I have installed scipy-1.3.0 already.

pip installation failed again. is the latest version 0.21.3?

Collecting pygrappa
Downloading https://files.pythonhosted.org/packages/ca/ef/0a0e2ff4084e3fd42715201d2e00fcd92c6f4c1f7e7f91c47d920b338a81/pygrappa-0.21.3.tar.gz (432kB)
|████████████████████████████████| 440kB 22kB/s
ERROR: Complete output from command python setup.py egg_info:
ERROR: Traceback (most recent call last):
File "", line 1, in
File "/private/var/folders/my/s_lbvtcn6nb3mylc5cvtp0240000gn/T/pip-install-uljz74s4/pygrappa/setup.py", line 86, in
install_requires=open('requirements.txt').read().split(),
FileNotFoundError: [Errno 2] No such file or directory: 'requirements.txt'
----------------------------------------
ERROR: Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/my/s_lbvtcn6nb3mylc5cvtp0240000gn/T/pip-install-uljz74s4/pygrappa/

[mckib2]

FileNotFoundError: [Errno 2] No such file or directory: 'requirements.txt'

Another missing entry from MANIFEST.in... I'll add that file in and we can give it another go.

yes, I have installed scipy-1.3.0 already.

Most recent should be scipy-1.4.1 -- can you try upgrading? (i.e., pip install --upgrade scipy). There have been some recent changes to their build system that I am trying take advantage of and I don't know if those are present in scipy 1.3.*.

[mckib2]

Latest pygrappa-0.21.5 should now be available including the missing file

[kingaza]

great, 0.21.5 works!
thx a lot~