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Pygraphviz on macOS not installing

I've been trying to install pygraphviz and have followed the following command from another post but it didn't seem to work.
pip install pygraphviz --install-option="--include-path=/Users/ahmedhamadto/PycharmProjects/Kaggle Titanic/venv/lib/python3.10/site-packages/pygments/lexers/graphviz.py" \
--install-option="--library-path=/Users/ahmedhamadto/PycharmProjects/Kaggle Titanic/venv/lib/python3.10/site-packages/pygments/lexers/graphviz.py"
I received the following error:
DEPRECATION: pygraphviz is being installed using the legacy 'setup.py install' method, because the '--no-binary' option was enabled for it and this currently disables local wheel building for projects that don't have a 'pyproject.toml' file. pip 23.1 will enforce this behaviour change. A possible replacement is to enable the '--use-pep517' option. Discussion can be found at https://github.com/pypa/pip/issues/11451
Running setup.py install for pygraphviz ... error
error: subprocess-exited-with-error
× Running setup.py install for pygraphviz did not run successfully.
│ exit code: 1
╰─> [6 lines of output]
usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
or: setup.py --help [cmd1 cmd2 ...]
or: setup.py --help-commands
or: setup.py cmd --help
error: option --include-path not recognized
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure
× Encountered error while trying to install package.
╰─> pygraphviz
note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.
I need it for the program I am coding in an attempt to make flowcharts:
# Draw and display the fault tree diagram
pos = nx.drawing.nx_agraph.graphviz_layout(G)
nx.draw(G, pos, with_labels=True, node_shape='rectangle')
# Save the diagram to a file
plt.savefig(file_name, format="pdf")

Cython openMP in OSX... no build

I 'm fighting 3 days now to setup my venv...
I need cython, openmp....
My IDE is PyCharm Prof in macOS... I have tried plenty solutions with no result...
when i try to build with PyCharm... the building result is:
UserWarning: Unknown distribution option: 'cmd_class' warnings.warn(msg)
usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
or: setup.py --help [cmd1 cmd2 ...]
or: setup.py --help-commands
or: setup.py cmd --help
error: no commands supplied
so, when i try with:
python setup.py install build_ext --inplace
No build again.... The error is following:
ld: warning: directory not found for option '-L/install/prefix/lib'
ld: warning: -L path '/usr/local/Cellar/llvm/9.0.1/lib/libomp.dylib' is not a directory
ld: warning: directory not found for option '-L/install/prefix/lib'
ld: warning: directory not found for option '-L/usr/local/Cellar/gcc/9/gcc/x86_64-apple-darwin19/9.3.0/include/omp.h'
ld: library not found for -lomp
clang-9: error: linker command failed with exit code 1 (use -v to see invocation)
error: command '/usr/local/opt/llvm/bin/clang++' failed with exit status 1
i have already install:
brew install llvm
brew install libomp
clang version 9.0.1
Target: x86_64-apple-darwin19.3.0
Thread model: posix
InstalledDir: /usr/local/opt/llvm/bin
The setup.py is according to https://cython.readthedocs.io/en/latest/src/userguide/parallelism.html but i have try a lot of differents mods... i am trying to setup 3-days now...
Finally... i know that the compilation is completed with errors. Although if i try to run it... i have the following resutlts... maybe it helps...
ImportError: dlopen(myfile.pyx, 2): Symbol not found: _omp_get_num_threads
Referenced from: myfile.pyx
Expected in: flat namespace
in myfile.pyx.cpython-36m-darwin.so
I 've read somewhere that there is no way to implement in OSX Cython-App with usage of openMP but i m still believe that there is a way...
My system is macOS Catalina 10.15.3 ...
I need your help!!!

Finally i find the solution...
In your venv:
pip install Cython setuptools
Find where is your gcc compiler... if you have already install do as follows, in other case find and install one...
$ mdfind gcc | grep gcc
Put the whole gcc directory in your project's venv.
(path: /My_Project/venv/gcc)
and setup.py should be the following... (path: /My_Project/package/setup.py)
from distutils.core import setup
from distutils.extension import Extension
from Cython.Build import cythonize
from Cython.Distutils import build_ext
import os
os.environ["CC"]="../venv/gcc/9.3.0/bin/gcc-9"
os.environ["CXX"]="../venv/gcc/9.3.0/bin/gcc-9"
ext_modules = [Extension(
"filename",
["filename.pyx"],
language='c',
extra_compile_args=['-fopenmp',"-Os",],
extra_link_args=['-fopenmp', ],
)
]
setup(
name='filename',
cmd_class = {'build_ext': build_ext},
ext_modules= cythonize(ext_modules),
)
Your cython file: filename.pyx ... could starts with a compiler directive comment at the top of filename.pyx as following:
# distutils: extra_compile_args = -fopenmp
# distutils: extra_link_args = -fopenmp
Run in your venv the compilation command:
$ python setup.py build_ext -i
Finally you can import your cython file in your code... at the top of your python file etc. mycode.py :
import filename
filename.myCythonFunc()
The above gives the solution for OSX-10.15.3 macOS Catalina.

Cannot run bdist_wheel build command on my setup.py

I have created a pypi package for educational purposes, and I wanted to do an upgrade. I did through the usual steps(do the changes, run setup.py etc)
but when I do:
python3 setup.py bdist_wheel
I am getting the error
python3 setup.py build bdist_wheel
usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
or: setup.py --help [cmd1 cmd2 ...]
or: setup.py --help-commands
or: setup.py cmd --help
error: invalid command 'bdist_wheel'
Wheel and pip are installed and up to date:
pip3 install wheel
Requirement already satisfied: wheel in /usr/local/lib/python3.4/dist-
packages (0.31.0)
The help of the command, does not seem to support bdist_wheel.
Am I missing something?
python3 setup.py --help-commands
Standard commands:
build build everything needed to install
build_py "build" pure Python modules (copy to build directory)
build_ext build C/C++ extensions (compile/link to build directory)
build_clib build C/C++ libraries used by Python extensions
build_scripts "build" scripts (copy and fixup #! line)
clean clean up temporary files from 'build' command
install install everything from build directory
install_lib install all Python modules (extensions and pure Python)
install_headers install C/C++ header files
install_scripts install scripts (Python or otherwise)
install_data install data files
sdist create a source distribution (tarball, zip file, etc.)
register register the distribution with the Python package index
bdist create a built (binary) distribution
bdist_dumb create a "dumb" built distribution
bdist_rpm create an RPM distribution
bdist_wininst create an executable installer for MS Windows
check perform some checks on the package
upload upload binary package to PyPI
Extra commands:
alias define a shortcut to invoke one or more commands
bdist_egg create an "egg" distribution
develop install package in 'development mode'
easy_install Find/get/install Python packages
egg_info create a distribution's .egg-info directory
install_egg_info Install an .egg-info directory for the package
rotate delete older distributions, keeping N newest files
saveopts save supplied options to setup.cfg or other config file
setopt set an option in setup.cfg or another config file
test run unit tests after in-place build
upload_docs Upload documentation to PyPI
usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
or: setup.py --help [cmd1 cmd2 ...]
or: setup.py --help-commands
or: setup.py cmd --help
EDIT:
python3 --version
Python 3.6.3
pip3 --version
pip 10.0.1 from /usr/local/lib/python3.4/dist-packages/pip (python 3.4)

Looks like pip version and python version didnt match...fixing this removed the problem.

Wheel issue with BigARTM

I am trying to install BigARTM on Ubuntu following the instruction.
Everything goes fine until I run sudo make.
It generates the following error:
[ 99%] Building python package bigartm
running build
running build_py
[ 99%] Built target python_bigartm_build
[100%] Building wheel bigartm
usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
or: setup.py --help [cmd1 cmd2 ...]
or: setup.py --help-commands
or: setup.py cmd --help
error: invalid command 'bdist_wheel'
python/CMakeFiles/python_bigartm_wheel.dir/build.make:57: recipe for target 'python/CMakeFiles/python_bigartm_wheel' failed
make[2]: *** [python/CMakeFiles/python_bigartm_wheel] Error 1
CMakeFiles/Makefile2:781: recipe for target 'python/CMakeFiles/python_bigartm_wheel.dir/all' failed
make[1]: *** [python/CMakeFiles/python_bigartm_wheel.dir/all] Error 2
Makefile:140: recipe for target 'all' failed
I suspected that the problem is connected with wheel. So I updated wheel:
user#user:~/bigartm/build$ pip install wheel
Collecting wheel
Using cached wheel-0.31.0-py2.py3-none-any.whl
Installing collected packages: wheel
Successfully installed wheel-0.31.0
Also I updated wheel in conda, and it shows now:
$ conda list | grep wheel
wheel 0.31.0 py36_0
wheel 0.31.0 <pip>
That did not help.

Unable to install MySQL-python " invalid command 'egg_info' "

I'm getting a weird error after running
$ pip install mysql-python
Has anyone seen an error like this with "egg_info" being invalid?
I'm running OSX mountain lion
Downloading/unpacking MySQL-python
Using download cache from /Users/Marcus/.pip/cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2Fsource%2FM%2FMySQL-python%2FMySQL-python-1.2.4.zip
Running setup.py egg_info for package MySQL-python
Downloading http://pypi.python.org/packages/source/d/distribute/distribute-0.6.28.tar.gz
Extracting in /var/folders/ss/nxvs3w690xqbpvr_l0v31mrw0000gn/T/tmpg_MvY6
Now working in /var/folders/ss/nxvs3w690xqbpvr_l0v31mrw0000gn/T/tmpg_MvY6/distribute-0.6.28
Building a Distribute egg in /Users/Marcus/sites/venv/build/MySQL-python
/Users/Marcus/sites/venv/build/MySQL-python/distribute-0.6.28-py2.7.egg
usage: -c [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
or: -c --help [cmd1 cmd2 ...]
or: -c --help-commands
or: -c cmd --help
error: invalid command 'egg_info'
Complete output from command python setup.py egg_info:
Downloading http://pypi.python.org/packages/source/d/distribute/distribute-0.6.28.tar.gz
Extracting in /var/folders/ss/nxvs3w690xqbpvr_l0v31mrw0000gn/T/tmpg_MvY6
Now working in /var/folders/ss/nxvs3w690xqbpvr_l0v31mrw0000gn/T/tmpg_MvY6/distribute-0.6.28
Building a Distribute egg in /Users/Marcus/sites/venv/build/MySQL-python
/Users/Marcus/sites/venv/build/MySQL-python/distribute-0.6.28-py2.7.egg
usage: -c [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
or: -c --help [cmd1 cmd2 ...]
or: -c --help-commands
or: -c cmd --help
error: invalid command 'egg_info'
----------------------------------------
Cleaning up...
Command python setup.py egg_info failed with error code 1 in /Users/Marcus/sites/venv/build/MySQL-python
Storing complete log in /Users/Marcus/.pip/pip.log
Thanks
--- I'm getting this same error when I run
$ pip install django

You need distribute package which is now inside setuptools:
pip install --upgrade setuptools