How can I install Pyomo's "extras" using pip? - pyomo

I am writing because I am having trouble installing Pyomo using pip on Python 3.6 on Mac OSX 10.14
I'm following the installation instructions here.
I can successfully execute the first command:
pip install pyomo
But when I run into trouble when I'm supposed to run the following command to install additional dependencies:
pyomo install-extras
Running this command produces the following error:
Traceback (most recent call last):
File "/usr/local/bin/pyomo", line 11, in <module>
sys.exit(main())
File "/usr/local/lib/python3.6/site-packages/pyomo/scripting/pyomo_main.py", line 82, in main
retval = _options.func(_options)
File "/usr/local/lib/python3.6/site-packages/pyomo/scripting/driver_help.py", line 46, in install_extras_exec
pyutilib.subprocess.run(command, tee=True)
File "/usr/local/lib/python3.6/site-packages/pyutilib/subprocess/processmngr.py", line 690, in run_command
th.join()
UnboundLocalError: local variable 'th' referenced before assignment
There is a post about this here on Google Groups but no solution yet.

This is a documented issue on the github for Pyomo: https://github.com/Pyomo/pyomo/issues/243
They don't appear to have solved the pip installation of pyomo extras.
However, if you have conda installed - https://docs.conda.io/en/latest/
You should be able to use the terminal commands from:
https://pyomo.readthedocs.io/en/latest/installation.html
run this in terminal after conda has been successfully installed:
conda install -c conda-forge pyomo.extras
I know this isn't pip, but it's at least a workaround until pyomo fixes their documentation.
confirmed working on python 3.x and ubuntu 18.04

I got the problem too (in Ubuntu 18.04).
Try installing it from the git project (https://github.com/Pyomo/pyomo):
In Ubuntu 18.04:
git clone https://github.com/Pyomo/pyomo.git
python3 pyomo/scripts/get_pyomo_extras.py
Use the corresponding commands for Mac OSX (I had never used it).
I hope that it works for you.

Related

ERROR: command "pkg-config --modversion libgphoto2" failed

I am getting an error when I try to install Gphoto2 on my windows pc.
I have tried installing following the instructions from https://pypi.org/project/gphoto2/ and downloading the zip from git clone https://github.com/jim-easterbrook/python-gphoto2.git but have had no success.
This module is supposed to install successfully.
Using the PYPI https://pypi.org/project/gphoto2/
I have tried to follow and install this module also downloading and installing the zip from:
git clone https://github.com/jim-easterbrook/python-gphoto2.git
I have had great difficulty, any advice or suggestion would be greatly appreciated.
C:\Users\Sam\Downloads\python-gphoto2-master\python-gphoto2-master> python setup.py install
ERROR: command "pkg-config --modversion libgphoto2" failed
This module Gphoto2 is supposed to install successfully.
This is what the complete error says:
C:\Users\Sam\Downloads\python-gphoto2-master\python-gphoto2-master>
python setup.py install ERROR: command "pkg-config --modversion
libgphoto2" failed Traceback (most recent call last): File "setup.py",
line 36, in <module> cmd, stderr=FNULL,
universal_newlines=True).split('.') File
"C:\python27\lib\subprocess.py", line 212, in check_output process =
Popen(stdout=PIPE, *popenargs, **kwargs) Windows: [Error 2] The system cannot find the file specified
I'm the author of python-gphoto2.
Python-gphoto2 is not expected to work on Windows. The PyPI page (https://pypi.org/project/gphoto2/) shows the supported operating systems - MacOS and POSIX compatible (e.g. Linux).
I have been able to install it in MSYS2 (http://www.msys2.org/) but it isn't useful unless you get Windows to use libusb instead of its normal driver for your camera.

pip2 causes ImportError: Entry point ('console_scripts', 'pip2') not found

I installed python 2 by
brew install python
I can localise pip2 but not use it. In the terminal i get an error as:
elenama#s2078:~$ pip2
Traceback (most recent call last):
File "/usr/local/bin/pip2", line 11, in <module>
load_entry_point('pip==9.0.1', 'console_scripts', 'pip2')()
File "/usr/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 570, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/usr/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2750, in load_entry_point
raise ImportError("Entry point %r not found" % ((group, name),))
ImportError: Entry point ('console_scripts', 'pip2') not found
elenama#s2078:~$ which pip2
/usr/local/bin/pip2
I uninstalled the local python by sudo pip uninstall pip. I also uninstalled python and reinstalled it.
(pip3 works, btw.)
Does anyone have a solution to this problem?
I had the same issue, fixed it by running this
python2 -m pip install --upgrade --force-reinstall pip
Seems to be an issue with current Homebrew Python 2 install. I just installed yesterday and have exactly the same issue (python3 is fine).
I don't have a solution as such, but am able to create a virtualenv with PyCharm, activate that environment, and use pip to install stuff as normal. PyCharm doesn't need virtualenv package to do this.
Since one should use virtualenv (or equivalent) all of the time anyway for real work, it is not so bad a problem that you cannot add packages outside of one. But I think I will file an issue on https://github.com/Homebrew/homebrew-core to see if someone can fix or explain why it is not working.
Also we should all be using Python 3 for everything! This is just one more reminder, as if we needed one.
Need To Install Python2.7 From Here . then restart terminal :
https://www.python.org/downloads/release/python-2714/

PyMC installation error with pip

I am attempting to install PyMC using pip install pymc. I believe this command should install PyMC 2.3.6.
PyMC has a few dependencies, which I have in my PATH. I am running OSX 10.11.2 and my PATH includes Python 2.7.13, NumPy 1.12.0, Matplotlib 2.0.0, gcc, and gfortran.
Python (including pip) was installed using Homebrew. NumPy and Matplotlib were installed using pip. The gfortran compiler was downloaded and installed from the GCC Wiki for the purpose of this installation.
Executing pip install pymc yielded lots of output including the following lines.
Collecting pymc
Using cached pymc-2.3.6.tar.gz
Complete output from command python setup.py egg_info:
running egg_info
running build_src
build_src
building extension "pymc.flib" sources
f2py options: ['skip:ppnd7']
f2py:> build/src.macosx-10.11-x86_64-2.7/pymc/flibmodule.c
creating build
creating build/src.macosx-10.11-x86_64-2.7
creating build/src.macosx-10.11-x86_64-2.7/pymc
IOError: [Errno 2] No such file or directory: 'skip:ppnd7'. Skipping file "skip:ppnd7".
updatevars:gradlike: attempt to change 'dimension(nx)' to 'dimension(na)'. Ignoring.
updatevars:gradlike: attempt to change 'dimension(nx)' to 'dimension(nb)'. Ignoring.
updatevars:gradlike: attempt to change 'dimension (nmu)' to 'dimension(nmu)'. Ignoring.
updatevars:gradlike: attempt to change 'dimension (na)' to 'dimension(na)'. Ignoring.
rmbadname1: Replacing "index" with "index_bn".
Reading fortran codes...
Reading file 'pymc/flib.f' (format:fix,strict)
Line #34 in pymc/flib.f:" PARAMETER (infinity = 1.7976931348623157d308)"
get_parameters: got "unexpected EOF while parsing (<string>, line 0)" on ''
...
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/private/var/folders/2f/cr97n5v93mn04c3qbqd7r3q40000gn/T/pip-build-6Zmgcz/pymc/setup.py", line 124, in <module>
**(config_dict))
File "/usr/local/lib/python2.7/site-packages/numpy/distutils/core.py", line 169, in setup
return old_setup(**new_attr)
...
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/2f/cr97n5v93mn04c3qbqd7r3q40000gn/T/pip-build-6Zmgcz/pymc/
As suggested in these two pip installation threads about egg_info errors [1, 2], I ran pip install —upgrade setuptools and pip install ez_setup. Once these items were installed I ran into the same types of errors pasted above.
As noted in other package installation threads, I am willing to use conda to install PyMC if I cannot resolve these issues. However, I'd like to investigate this installation issue first.
Would anyone happen to know what my issue is here? Might there be some steps I can take to successfully install PyMC using pip?
I had the same problem. I don't understand the root cause, but I fixed it by downgrading numpy to version 1.10.1: pip install numpy==1.10.1
I also met this problem while trying to install pymc from pip or source code, but I found a solution that might be useful.
The reason that causes the problem might be the file setup.py, in which the script check the compile env. I didn't read the code very carefully, but in the function build_ext() I think the codes first check whether some compile environments have already been installed into OS. If installed, the script will use them as defaults; if not, use ones in somewhere else (the comment says 'from netlib sources').
I infer the problem is caused by the compile environments that have already been installed in the OS, so I modify the file setup.py to skip this part of codes, and let the script use the netlib source. Then I run sudo python setup.py install. There are some error and warning messages, but the folder 'pymc' emerges in python library, and some simple test codes run successfully.

How to install and run the reindent.py

I have downloaded the Reindent-0.1.0 and trying to use this for automated indention purpose.
I don't know how to install and run these commands and while I am trying to use this command
I am getting following error
command:
C:\Python26\Scripts\Reindent-0.1.0>Python setup.py
C:\Python26\Scripts\Reindent-0.1.0>Pyth
Traceback (most recent call last):
File "setup.py", line 5, in <module>
from setuptools import setup
ImportError: No module named setuptools
I don't understand the setuptools, where it is and how to put inside
please note my folder files in Reindent-0.1.0
Reindent.egg-info
PKG-INFO
README
reindent
setup.cfg
setup.py
Also how can I run the commands for reindent, for an example, once after I installed the reindent, if I want to
run dryrun command how I should write?
If I write like this, will it be correct ???
C:\ProjFolder\ApplicationDevelopment\GUI>reindent -d Test.py
some realtime example of "-d (--dryrun) Dry run and -r (--recurse) Recurse" will be helpful!!
and where I should target the command file path, in dos
to my application running directory or C:\Python26\Scripts\Reindent-0.1.0 ?? OR Application development folder??
If you get the error "no module X" when you try to run some code, that code has a dependency on module X. When you run setup.py and it says there is no module named "setuptools", it is telling you that setup.py requires the module "setuptools". Since you don't have "setuptools" installed on your machine, you get the error.
The fix is simple: install the setuptools module. Here's one of several places on the internet that shows you how to install setuptools: https://pythonhosted.org/an_example_pypi_project/setuptools.html

Need help installing Biopython

Have mac OS 10.6 and have python verion 2.7 32 bit intalled as
well as numpy and scipy.
also have xcode version 3.2, Im really confused as to what to do at this point. I download
biopython version 1.59 and tried to run the setup code in python but it wont work. what am i missing?
when i try and run the setup file in idle i get this error message:
Traceback (most recent call last):
File "/Users/Cliff/Downloads/biopython-1.58/setup.py", line 379, in <module>
'Bio.PopGen': ['SimCoal/data/*.par'],
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 140, in setup
raise SystemExit, gen_usage(dist.script_name) + "\nerror: %s" % msg
SystemExit: 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
You need to run python setup.py install from Terminal.app. You should be in a bash, tcsh, etc. shell, not in a Python shell.
Just as an probably easier alternative:
Biopython is also available via pip:
pip install biopython
Or (even better) via bioconda (try it out, it's great):
conda install biopython
For this just install miniconda (very easy and does NOT require admin rights) from here. and then add the bioconda channel as per these simple instructions.
Strangly these two simple options are missing in the biopython tutorial
The error shows that you did not supply a command to the install script. The usual command is 'install', so try:
python setup.py install
In any event, as the error suggests, you can use:
python setup.py --help