We Keep Coding

Install via pacman to specific version of Python

The default Python version for MSYS2 seems to be 3.8. I need to use 3.7 at the moment because I have to use PyInstaller and it is not currently compatible with 3.8 in MSYS2. I can download the earlier version of Python from http://repo.msys2.org/ and install it using pacman. With a fresh install of MSYS2 I run the following commands:
pacman -S glib2-devel
pacman -U python-3.7.4-1-x86_64.pkg.tar.xz
pacman -S python-pip
pacman -S python-setuptools
If I try to run a python script I am met with an error:
File "setup.py", line 15, in <module>
from setuptools import setup
ModuleNotFoundError: No module named 'setuptools'
This is due to the fact that everything installed after Python is actually installing in the default Python 3.8 location rather than 3.7:
C:\msys64\usr\lib\python3.8\site-packages
If I copy and paste the contents of site-packages into Python 3.7 and then try running a script I get the error:
File "setup.py", line 15, in <module>
from setuptools import setup
File "/usr/lib/python3.7/site-packages/setuptools/__init__.py", line 19, in <module>
from setuptools.dist import Distribution
File "/usr/lib/python3.7/site-packages/setuptools/dist.py", line 34, in <module>
from setuptools import windows_support
File "/usr/lib/python3.7/site-packages/setuptools/windows_support.py", line 2, in <module>
import ctypes
File "/usr/lib/python3.7/ctypes/__init__.py", line 7, in <module>
from _ctypes import Union, Structure, Array
ImportError: No such file or directory
Which is supposed to be resolved via libffi, which was installed prior to Python, but likely does not go to a location that 3.7 can recognize?
Is there a way to set a specific version of Python as the default in MSYS2? Perhaps a path that can be set in the .bashrc file? I tried to set PYTHONPATH in there to Python 3.7 but it didn't make a difference as to where the packages ended up being installed to.

Go to the following URL...
https://repo.msys2.org/msys/x86_64/
Look for the version of the package you need and download it. Use
pacman -U pkgname
To install it...
The reason I know this is because gcc11 on MSYS is non-functional... it produces programs which crash and say
"During startup your program exited with code..." mentioned here:
During startup program exited with code 0xc0000139
The only workaround is to downgrade to the previous compiler which does work or use clang, which was not an option for me.

Trying to use an old version of Python is probably possible, but I think it will be very difficult. You would need to make sure all the other installed packages are compatible.
I am using PyInstaller with Python 3.8 in MSYS2 without issues. I would recommend trying to work through any issues with that, instead of trying to use older versions of packages.

How to install ruamel.yaml python library offline?

I am trying to install ruamel.yaml python library in a Centos 7 machine where I don't have internet connection. I tried this:
installed libyaml-devel, python-devel, python-pip using a local repository
downloaded ruamel.yaml-0.13.14.tar & ruamel.ordereddict-0.4.6.tar(dependency) from pypi.
now I am able to install ruamel.ordereddict using pip install .,
but when I tried to install ruamel.yaml in the same way, I got the following exception:
[root#limulus ruamel.yaml-0.13.14]# pip install .
Processing /tmp/python/ruamel.yaml-0.13.14
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/usr/lib/python2.7/site-packages/setuptools/__init__.py", line 2, in <module>
from setuptools.extension import Extension, Library
File "/usr/lib/python2.7/site-packages/setuptools/extension.py", line 5, in <module>
from setuptools.dist import _get_unpatched
File "/usr/lib/python2.7/site-packages/setuptools/dist.py", line 7, in <module>
from setuptools.command.install import install
File "/usr/lib/python2.7/site-packages/setuptools/command/__init__.py", line 8, in <module>
from setuptools.command import install_scripts
File "/usr/lib/python2.7/site-packages/setuptools/command/install_scripts.py", line 3, in <module>
from pkg_resources import Distribution, PathMetadata, ensure_directory
File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 74, in <module>
import parser
File "parser.py", line 77, in <module>
from ruamel.yaml.error import MarkedYAMLError # type: ignore
File "/usr/lib64/python2.7/site-packages/ruamel/__init__.py", line 5, in <module>
__import__('pkg_resources').declare_namespace(__name__)
AttributeError: 'module' object has no attribute 'declare_namespace'
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-oOWX1x-build/
What is the correct way of installing a python library in offline mode?

It looks like you have been expanding the tar files, which is not necessary, but I am not sure if that is the reason why you get this error, you probably are also missing the typing dependency.
What you shouldn't do is use the system installed pip, it is almost out of date and on some systems actually causes problems because of unfixed bugs in those old versions.
What you also should not do is install packages using pip outside of a Python virtualenv, as this might break your system when it updates/overwrites things in the systems site-packages/dist-packages directory. The solution provided below only installs pip/wheels/virtualenv in the system directory, that is AFAIK safe, but there are ways around that as well if it would necessary.
You should also consider using the provided wheels to install packages. That way C extension don't need compilation.
On a machine that is online do:
mkdir /tmp/offline
cd /tmp/offline
# your python-pip installed pip might not support wheels
wget https://pypi.python.org/packages/11/b6/abcb525026a4be042b486df43905d6893fb04f05aac21c32c638e939e447/pip-9.0.1.tar.gz
wget https://pypi.python.org/packages/a7/37/947b4329c4a3c72093b6c8e9b4be8c7f10c32dbb78848d3a234ce01c059d/wheel-0.30.0a0.tar.gz
wget https://pypi.python.org/packages/6f/86/3dc328ee7b1a6419ebfac7896d882fba83c48e3561d22ddddf38294d3e83/virtualenv-15.1.0-py2.py3-none-any.whl
Now download the required wheels (.tar.gz if not available):
wget https://pypi.python.org/packages/96/4b/5251bf469f37e49e0c92f841b5b3ef01a1c9d652cc018df470e5ae235eb8/ruamel.ordereddict-0.4.9-cp27-cp27mu-manylinux1_x86_64.whl
wget https://pypi.python.org/packages/63/40/c38b857ec6a083e534ee9a9f655741120d4bfd9139232681f976cf44272b/ruamel.yaml-0.13.14-cp27-cp27mu-manylinux1_x86_64.whl
wget https://pypi.python.org/packages/b6/0c/53c42edca789378b8c05a5496e689f44e5dd82bc6861d1ae5a926ee51b84/typing-3.5.3.0.tar.gz
Copy the six files to a new directory your offline system, and there do
sudo pip install pip*.tar.gz wheel*.tar.gz
sudo pip install virtualenv*
virtualenv ~/ruamel
source ~/ruamel/bin/activate
pip install typing* ruamel*
That gives you a virtualenv with ruamel.yaml installed, just add your application in there as well.
The downloads used here are current as of 2017-01-07, you can get more up-to-date ones using your browser (on the on-line system) if necessary.

Error using pelican-quickstart "No module named html_parser"

I decided to give pelican a try, but when I run pelican-quickstart, I get the following dialog:
$ pelican-quickstart
Traceback (most recent call last):
File "/usr/local/bin/pelican-quickstart", line 9, in <module>
load_entry_point('pelican==3.4.0', 'console_scripts', 'pelican-quickstart')()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 357, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 2394, in load_entry_point
return ep.load()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 2108, in load
entry = __import__(self.module_name, globals(),globals(), ['__name__'])
File "/Library/Python/2.7/site-packages/pelican-3.4.0-py2.7.egg/pelican/__init__.py", line 20, in <module>
from pelican.generators import (ArticlesGenerator, PagesGenerator,
File "/Library/Python/2.7/site-packages/pelican-3.4.0-py2.7.egg/pelican/generators.py", line 23, in <module>
from pelican.readers import Readers
File "/Library/Python/2.7/site-packages/pelican-3.4.0-py2.7.egg/pelican/readers.py", line 24, in <module>
from six.moves.html_parser import HTMLParser
ImportError: No module named html_parser `
There was a similar error message in this post, and since I'm running Python 2.7.6 on OS X 10.10 (Yosemite), there may be a similar issue.
What's the best way to address this?

Reinstall Pelican doesn't help me, so I made a little fix in pelican
Modifications were made in following file
/Library/Python/2.7/site-packages/pelican/readers.py
at line 24 place
from six.moves import html_parser
instead of
from six.moves.html_parser import HTMLParser
and at line 299
class _HTMLParser(html_parser.HTMLParser):
instead of
class _HTMLParser(HTMLParser):
Modification actual for pelican 3.6.0, but seems to applicable for other version if search for this lines in readers.py file. This is just quick workaround, hope this problem will be solved at pelican's side.

This error seems to come from Python 2.7.6 on OSX. When I install python via Homebrew and reinstall this module I got rid of this error.
$ pip uninstall pelican
$ brew install python
$ which python # should show /usr/local/bin/python
$ python -V # should show Python 2.7.8
$ pip install pelican

I think that you've probably encountered with version conflict problem in module six.
Try sudo pip install virtualenv to create an isolate python environment.
start
create your pelican path mkdir /path/to/pelican
go to /path/to/pelican and create an isolate python environment with virtualenv venv
activate virtualenv source venv/bin/activate
install pelican under the venv(without sudo!) pip install pelican markdown
done
and now you are free to any problem mentioned above. all the dependencies in the venv are isolated from the global environment.
To quit the venv, type deactivate

I was running into the same error message.
six was also already installed, but an old version (1.4.1)
pip install six --upgrade
Installed six 1.10.0, which made pelican-quickstart finally work :)

You may need to install six.
if you're using pip, try
pip install six
and then restart pelican-quickstart

How to rebuild virtualenvs after deleting associated python interpreter

I have a number of django projects organized with the following directory structure using win7 (I'm using GIT_BASH/mingw for my command line) :
envs--r1--project1
--project2
--Include
--Library
--Scripts--python.exe
python275--
The idea being here that the different projects have a common environment and I can activate that environment from each projects root directory using:
$ source ../Scripts/activate
I don't understand exactly how it happened but it turned out that the interpreter ( listed above as python.exe ) was linked somehow to a second python folder above.
I deleted the python275 folder ( AAHH!!) , not realizing its importance, resulting in:
Traceback (most recent call last): File "C:\envs\r1\lib\site.py", line 703, in main() File "C:\envs\r1\lib\site.py", line 692, in main aliasmbcs() File "C:\envs\r1\lib\site.py", line 515, in aliasmbcs import locale, codecs File "C:\envs\r1\lib\locale.py", line 19, in import functools ImportError: No module named functools
I have reinstalled the correct python folder but the error persists. Can anyone advise me on how to rebuild the virtualenvs so I can go back to the way it was?
edit:
(r1)
/C/envs/r1/Scripts
$ import reload(functools)
sh: syntax error near unexpected token `('
(r1)
/C/envs/r1/Scripts
$ python.exe import reload(functools)
sh: syntax error near unexpected token `('
(r1)
/C/envs/r1/Scripts
$ python.exe reload functools
Traceback (most recent call last):
File "C:\envs\r1\lib\site.py", line 703, in <module>
main()
File "C:\envs\r1\lib\site.py", line 692, in main
aliasmbcs()
File "C:\envs\r1\lib\site.py", line 515, in aliasmbcs
import locale, codecs
File "C:\envs\r1\lib\locale.py", line 19, in <module>
import functools
ImportError: No module named functools
(r1)
/C/envs/r1/Scripts
$ reload(functools)
sh: syntax error near unexpected token `('
(r1)
/C/envs/r1/Scripts
$ python.exe reload(functools)
sh: syntax error near unexpected token `('
(r1)
/C/envs/r1/Scripts
$ python.exe test.py
Traceback (most recent call last):
File "f:\envs\r1\lib\site.py", line 703, in <module>
main()
File "f:\envs\r1\lib\site.py", line 692, in main
aliasmbcs()
File "f:\envs\r1\lib\site.py", line 515, in aliasmbcs
import locale, codecs
File "f:\envs\r1\lib\locale.py", line 19, in <module>
import functools
ImportError: No module named functools

I suggest reinstalling Python and virtualenv from scratch in your case, and then re-creating the environment(s).
Make sure you have a working Python 2.7.5 installation on your system.
Make sure you have pip installed (see docs).
Make sure pip is linked to the Python installation above (check the output of pip -V, it should contain the correct system-wide Python path).
Do a clean install of virtualenv using pip install virtualenv.
Create and activate the environment for your projects.
Reinstall within your new environment all the modules you had installed in your old environment.
This may be a tricky one.
If you have an up-to-date file such as requirements.txt
with all the packages required, then
you're all set (pip install -r requirements.txt should do it).
If you don't have requirements listed, or they aren't up-to-date, then
check manually which packages you had installed in your old environment.
For that you should locate site-packages directory within your old virtualenv
(should be under Library probably) and look what's in there.
Every non-system package you recognize in site-packages directory
you install into your new environment (normally using pip install but
some packages may have custom instructions).
That's what I did when it happened to me. I wasn't able to simply rebuild the environment, so I did the reinstall for cleanness.

Taken from other post. You can associate the virtualenv to a python version.
You indicate the Python interpreter to use with the flag -p or --python (e.g --python=python2.5)
virtualenv -p /usr/bin/python2.6 <path/to/new/virtualenv/>
But this is just works for creating new environments. You would need to access your old virtualenv and execute:
pip freeze > requirements.txt
The file requirements.txt would contain all the apps you installed in the old virtual environment and their respective versions. Now, from the new environment you have created, run:
pip install -r requirements.txt
You should active the virtual environment.
$ source /yourvirtualenvpath/bin/activate
$ pip freeze > /home/user/requirements.txt
$ deactivate
$ source /yourNEWvirtualenvpath/bin/activate
$ pip install -r /home/user/requirements.txt

Possible conflicting python installations

I'm not sure if the default python installation is the one that I've been installing modules to, and if that may be the cause of a conflicting Unicode byte size compatibility error. In short, I've installed Numpy 1.7 using Python 2.7.3 and when I try to install this other program that uses Python and Numpy as dependencies, I get this error:
Traceback (most recent call last):
File "setup.py", line 20, in <module>
from weblogolib import __version__
File "/home/chris/Documents/IS/Bioinformatics-Software/weblogo-3.3/weblogolib/__init__.py", line 108, in <module>
from numpy import array, asarray, float64, ones, zeros, int32,all,any, shape
File "/usr/lib/python2.7/dist-packages/numpy/__init__.py", line 137, in <module>
import add_newdocs
File "/usr/lib/python2.7/dist-packages/numpy/add_newdocs.py", line 9, in <module>
from numpy.lib import add_newdoc
File "/usr/lib/python2.7/dist-packages/numpy/lib/__init__.py", line 4, in <module>
from type_check import *
File "/usr/lib/python2.7/dist-packages/numpy/lib/type_check.py", line 8, in <module>
import numpy.core.numeric as _nx
File "/usr/lib/python2.7/dist-packages/numpy/core/__init__.py", line 5, in <module>
import multiarray
ImportError: /usr/lib/python2.7/dist-packages/numpy/core/multiarray.so: undefined symbol: PyUnicodeUCS4_AsUnicodeEscapeString
So I guess I have a conflicting unicode byte size (2-byte vs. 4-byte). I went to check to see if I had conflicting versions of Python that could be messing this up.
python --version
Python 2.7.3
But this seems at odds with
which python
/usr/local/bin/python
When I go to /usr/local/bin I find these files (relevant to python):
python
python2
python2.7
python-config
python2-config
python2.7-config
Now I've installed numpy into the dist-packages directory of /usr/lib/python2.7/dist-packages which corresponds to what I get for python --version. But the fact that when I try which python and get a directory for python and not python2.7 concerns me that this might be conflicting when I try to install the program that uses python and numpy as dependencies.
So I guess to clarify my question(s): Are these normal files to find for a python installation or have I somehow installed three different versions? Could they be causing my error with the unrecognized symbol? Is there a way to uninstall if they are indeed extraneous versions?
Thanks for any help you can provide!
Oh and here is a link to a previous question I had, where I edited the PYTHONPATH while trying to fix an ImportError I was getting, if that might be affecting things....ImportError: No module named numpy
Here are the results of trying virtualenv:
chris#ubuntu:~/Documents/IS/Bioinformatics-Software$ virtualenv weblogo-3.3
New python executable in weblogo-3.3/bin/python
Installing setuptools.............done.
Installing pip...............done.
chris#ubuntu:~/Documents/IS/Bioinformatics-Software$ cd weblogo-3.3
chris#ubuntu:~/Documents/IS/Bioinformatics-Software/weblogo-3.3$ source bin/activate
(weblogo-3.3)chris#ubuntu:~/Documents/IS/Bioinformatics-Software/weblogo-3.3$ pip install numpy
Requirement already satisfied (use --upgrade to upgrade): numpy in /usr/lib/python2.7/dist-packages
Cleaning up...

The problem indeed seems to be a mismatch of Python and Numpy compile settings.
/usr/local/bin is where custom Python is installed, you should try to run using /usr/bin/python instead.
Another solution is to use a virtualenv. Try this:
virtualenv myproject
cd myproject
source bin/activate
pip install numpy
Basically virtualenv sets up a different Python installation with its own packages in the "myproject" directory. Running the "activate" command tells the system that you want to use this installation instead of the default system. This lets you have a different Python environment for different projects. Using virtualenv, each project can have its own versions of Python packages even if they're incompatible with other projects or system packages.
Note you will have to repeat the "source" command each time you open a new shell and want to use that virtual environment. Also you might have to install the virtualenv command by using your OS package manager. If this isn't possible (e.g. you don't have root access) or your OS version is too old for some reason, you can also download it manually from https://pypi.python.org/packages/source/v/virtualenv/
If you do ls -l /usr/local/bin/python* you should see that python and python2 are actually symlinks to python2.7, and likewise python-config and python2-config are symlinks to python2.7-config.

What OS are you on? This is more a question for superuser, but try something like this. Ditch easy_install and use pip if you haven't already.
On Ubuntu:
sudo apt-get install python-setuptools
sudo easy_install pip
pip install --user numpy