Develop Reference

error about libpl (shared) when using pyswip (mac)

I got the error libpl (shared) not found.(see below for details) when using pyswip (mac). I know there is a question about it posted several years ago, but it is not solved. I installed swiprolog(>7.0.0) with homebrew and run 2to3 for pyswip. Help me.
PS: I am learning logic programming, I need it.
libpl (shared) not found. Possible reasons: 1) SWI-Prolog not
installed as a shared library. Install SWI-Prolog (5.6.34 works just
fine) An exception has occurred, use %tb to see the full traceback.
The error is thrown here.
# UNIX-like
try:
_lib = CDLL("libpl.dylib")
except IndexError:
# let's try the cwd
_lib = CDLL("./libpl.so")

I finally found a solution: pyswip does not support SWI-Prolog 8.x.x and the only SWI-Prolog version that has worked for me is Homebrew's swi-prolog 7.6.4 (latest 7.x.x stable release). Because Homebrew does not keep track of different versions of swi-prolog, I had to really dig to find the old 7.6.4 "formula". Now it works with the current version of pyswip (0.2.8).
TL; DR: Remove your current SWI-Prolog install (and remove any associated PATH editing), do brew install https://raw.githubusercontent.com/Homebrew/homebrew-core/09a94009142a6265b0b8e322463100610aeda964/Formula/swi-prolog.rb and call it a day.
EDIT:
Caveat: This approach will not let you use some Prolog packages such as library(process) and library(http/json). To correct this, you can install the macOS app and manually install and relink the libncurses.6.dylib in order for PySwip to be able to find it, like this:
brew install ncurses # Specifically install this library
sudo find / -name "libncurses.6.dylib" # You'll see an entry in /usr/local/Cellar/ncurses/6.1/lib/libncurses.6.dylib or something like that in /.../Cellar/ncurses/ (Homebrew folder)
# Now go relink the libswipl.dylib to depend on the newly installed `ncurses` library
cd /Applications/SWI-Prolog.app/Contents/swipl/lib/x86_64-darwin15.6.0 # The "darwin" version may vary depending on your OS/SWI-Prolog version
# You'll see that it is linked against a fake /opt/local/lib/libncurses.6.dylib which doesn't in fact exist
otool -L libncurses.6.dylib
# Now check the top-level lib, libswipl.dylib, it should show a "#executable_path/../swipl/lib/x86_64-darwin15.6.0/libncurses.6.dylib" or something like that depending on your version.
otool -L libswipl.dylib
# Now replace the fake with the real by actually modifying the top-level lib, libswipl.dylib. Contrary to intuition, the way linking works in macOS is that you can only modify the depending library, so libswipl.dylib instead of libncurses.6.dylib.
install_name_tool -change #executable_path/../swipl/lib/x86_64-darwin15.6.0/libncurses.6.dylib /usr/local/Cellar/ncurses/6.1/lib/libncurses.6.dylib libswipl.dylib
# Now you'll see that libswipl.dylib has been successfully modified:
otool -L libswipl.dylib

Nest simulator: python says “no module named nest”

After installing the Nest Neural Simulator, I keep getting the following error when trying to run any of the example python files that came in the installation. I've tried re-installing Nest, Python, and using Anaconda, but no go.
Python error:
ImportError: No module named nest
Suggestions?

At https://nest-simulator.org/documentation you now find many different install instructions and how to solve the "ImportError: no module named nest" depends on the way you installed NEST.
System Python
The problem with the nest python module not being found is usually, that NEST is installed for a specific Python version and you can not load it from another. So while many OS still use Python 2.7 you may need to explicitly run
$ python3
>>> import nest
Additionally, if you have multiple Python 3.x versions installed, modules may still be installed for a different version and you have to explicitly start python with python3.6 or python3.8, etc.
Conda package
As #nosratullah-mohammadi already mentioned, if you have a Conda flavour installed, using the pre-built package is a very quick solution. The link in his post is unfortunately broken; this one should work, then go to "Installation" in the side bar.
$ conda create --name nest -c conda-forge python3 nest-simulator
$ conda activate nest
$ python # this should load the Python from the conda env
>>> import nest # this loads nest which is installed explicitly for that Python
From Source
For every install from source, be sure to have Python and other prerequisites installed before building NEST. Then you can create your temporary build directory (can be deleted afterwards) and configure with the flags you need.
cd somewhere
mkdir nest-build
cd nest-build
cmake -DCMAKE_INSTALL_PREFIX:PATH=/install/path -Dwith-python=3 .../sources/of/nest-simulator
Replace somewhere, /install/path and .../sources/of/nest-simulator with the paths correct for your setup. (A popular choice when compiling from source in conjunction with Conda environments, for example, is to use -CMAKE_INSTALL_PREFIX=$CONDA_PREFIX, which installs NEST directly into the active environment. Conda is however in no way necessary for NEST.)
Add more -D... flags as you prefer. Possible flags you see with cmake -LA .../sources/of/nest-simulator, as pointed out here. You are probably interested in many of the with-xyz at the end. Check the aforementioned documentation for deatils.
Check that the paths and libraries reported in the Configuration Summary make sense (you may need to scroll up a bit to see). It could for example look something like this:
--------------------------------------------------------------------------------
NEST Configuration Summary
--------------------------------------------------------------------------------
[...]
Python bindings : Yes (Python 3.6.8: /home/yourname/miniconda3/envs/nest/bin/python3)
Includes : /home/yourname/miniconda3/envs/nest/include/python3.6m
Libraries : /home/yourname/miniconda3/envs/nest/lib/libpython3.6m.so
Cython bindings : Yes (Cython 0.27.3: /home/yourname/miniconda3/envs/nest/bin/cython)
[...]
--------------------------------------------------------------------------------
[...]
PyNEST will be installed to:
/home/yourname/miniconda3/envs/nest/lib/python3.6/site-packages
--------------------------------------------------------------------------------
In this example CMake configured everything for Python3.6 from my conda environment.
If you are satisfied with your settings and all the found Python versions match, run the usual
$ make # optionally with -j$(nproc)
$ make install
$ make installcheck
In case that works out fine you are done and can delete the build directory to free the space. Congratulations!
Also if things get too mixed up and it doesn't seem to do what you expect, it is sometimes useful to delete the build directory and start off clean.

there is a new method of installation added to other methods, wich is installing nest with conda package and it's in its beta version. but it works and it's really simple.
you can find the installation from here!
simply after install mini conda package run your terminal and type this :
conda create --name ENVNAME -c conda-forge nest-simulator python
then type :
conda activate ENVNAME
and you're good to go!

NEST now provide the solution to that problem and similar ones, by providing a script which automatically sets the relevant system variables:
If your operating system does not find the nest executable or Python
does not find the nest module, your path variables may not be set
correctly. This may also be the case if Python cannot load the nest
module due to missing or incompatible libraries. In this case, please
run
source </path/to/nest_install_dir>/bin/nest_vars.sh
to set the necessary environment variables. You may want to include
this line in your .bashrc file, so that the environment variables are
set automatically.
https://nest-simulator.readthedocs.io/en/latest/installation/linux_install.html

Turns out I needed to move the directory where I installed nest (Users/name/opt/nest) into a nest folder in the following directory in anaconda. Specifically, I moved the contents of the folder (from the nest installation):
/Users/name/opt/nest/lib/python2.7/site-packages/nest
Into this one:
/anaconda/lib/python2.7/site-packages/nest
Disclaimer: I could very well run into problems for not having copied all the contents of the Nest installation, but this little hack is helping me run example files now.

Installing jedi-vim fails: vim says wrongly that +python is not compiled

I am trying to install jedi-vim. I am doing this at work - so I have to use gVim in Windows. I have already read several other posts in this forum. This has somehow made me smarter but still does not solve my problem.
I did the following things:
installed Pathogen
cloned jedi vim from https://github.com/davidhalter/jedi-vim.git and copied it to the bundle/ folder in the vim-dir.
Now, when I open a *.py-file vim always tells me
jedi-vim requires vim compiled with +python
but ':version' tells me that it's compiled with +python/dyn and +python3/dyn.
So what is the problem?
Additional infos:
vim version: 7.4
When I use ctrl+space to autocomplete a python key word, it tells me:
Error detected while processing function jedi#completions: line 1: E492: Not an editor command: Python jedi_vim.completions()
Error detected while processing function jedi#completions: line 1: E492: Not an editor command: Python jedi_vim.completions()
Press ENTER or type command to continue

I'm not sure if your are still experiencing the same issue, but after looking around I found this blog post that solved the problem for me. Essentially, it's just about re-installing vim (don't delete any config files) and then reinstalling from the source at the vim mercurial repo with the right flags. There might be a shorter/simpler version of doing this, but after trying back and forth many solutions, this one was the only one that worked:
Compiling Vim with Python and Ruby support on Ubuntu
These are the steps:
Check if Vim is compiled with Python:
$ vim --version | ack '(python)'
Remove Vim version installed:
$ sudo apt-get remove vim-common vim-runtime
Install dependencies needed to compile Vim:
$ sudo apt-get build-dep vim
Clone Vim repository, compile it and install the new version:
$ hg clone https://vim.googlecode.com/hg/ vim
$ cd vim
$ ./configure --enable-pythoninterp
$ make
$ sudo make install

+python/dyn means that Python support isn't statically compiled it, it's loaded dynamically when needed at runtime.
This is described in the python-dynamic help section:
On MS-Windows the Python library can be loaded dynamically. The |:version| output then includes |+python/dyn|.
This means that Vim will search for the Python DLL file only when needed.
When you don't use the Python interface you don't need it, thus you can use
Vim without this DLL file.
To use the Python interface the Python DLL must be in your search path. In a console window type "path" to see what directories are used.
The name of the DLL must match the Python version Vim was compiled with.
Currently the name is "python24.dll". That is for Python 2.4. To know for
sure edit "gvim.exe" and search for "python\d*.dll\c".
(Don't worry about the 2.4 there; I just happened to find docs from a few years ago. Read the help in your own copy of vim—or, better, do what the last paragraph says.)
So, either you don't have Python, you have the wrong version of Python, it's not on your %PATH%, vim is searching for it incorrectly, or it's failing to load.

At that time the problem was another one. I mixed up the architectures for vim and python - I used vim64Bit, but pyhton for 32bit.
I repaired that already some time ago but the other day I had to restart my computer and do some microsoft-Updates.
Unfortunately my vim (7.4) was totally broken. I had to re-set my home-dir. Then at least my vimrc was accessible again, but still my jedi in vim does not work.
Python is available in vim but still jedi does not seem to load correctly.
When I type "len(" in the beginning of a .py-file, at the place where arguments should be explained there are some strange characters, similar to this:
==jedi=0, == (_object_*) ==jedi==
When I type "self.", it says "unknown function: pythoncomplete#Complete"
I think it's only a configuration-issue, because it worked before the reboot.
Jedi is installed systemwide (with pip). If I try to install it "again", pip says that jedi is already installed.
I would appreciate your help very much ;-)

How to install PySide v0.3.1 on Mac OS X?

I'm trying to install PySide v0.3.1 in Mac OS X, for Qt development in python.
As a pre-requisite, I have installed CMake and the Qt SDK.
I have gone through the documentation and come up with the following installation script:
export PYSIDE_BASE_DIR="<my_dir>"
export APIEXTRACTOR_DIR="$PYSIDE_BASE_DIR/apiextractor-0.5.1"
export GENERATORRUNNER_DIR="$PYSIDE_BASE_DIR/generatorrunner-0.4.2"
export SHIBOKEN_DIR="$PYSIDE_BASE_DIR/shiboken-0.3.1"
export PYSIDE_DIR="$PYSIDE_BASE_DIR/pyside-qt4.6+0.3.1"
export PYSIDE_TOOLS_DIR="$PYSIDE_BASE_DIR/pyside-tools-0.1.3"
pushd .
cd $APIEXTRACTOR_DIR
cmake .
cd $GENERATORRUNNER_DIR
cmake -DApiExtractor_DIR=$APIEXTRACTOR_DIR .
cd $SHIBOKEN_DIR
cmake -DApiExtractor_DIR=$APIEXTRACTOR_DIR -DGeneratorRunner_DIR=$GENERATORRUNNER_DIR .
cd $PYSIDE_DIR
cmake -DShiboken_DIR=$SHIBOKEN_DIR/libshiboken -DGENERATOR=$GENERATORRUNNER_DIR .
cd $PYSIDE_TOOLS_DIR
cmake .
popd
Now, I don't know if this installation script is ok, but apparently everything works fine. Each component (apiextractor, generatorrunner, shiboken, pyside-qt and pyside-tools) gets compiled into its own directory.
The problem is that I don't quite understand how PySide gets into the system's python environment. In fact, when I start a python shell, I cannot import PySide:
>>> import PySide
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named PySide
Note: I am aware of the Installing PySide - OSX question, but that question is not relevant anymore, because it is about a specific a dependency on the Boost libraries, but with version 0.3.0 PySide moved from a Boost based source code to a CPython one.

I don't have any MacOS experience but assuming it's similar to any *nix, let's go:
About the script: Isn't it missing some "make, make install" commands? The version you posted just run cmake to configure the build. Also for testing, I set -DCMAKE_INSTALL_PREFIX= for all modules. That way everything is installed in the same place and CMake takes care of finding them for me, as long as I used the same install prefix for each one. The directory layout in your script is quite complicated and mixes build and source directories.
About finding PySide: once everything is properly compiled and installed, the directory where the "PySide" directory was installed must be available in the PYTHONPATH variable. In the example below,
Here's a simple version of a build script(works on Ubuntu):
#!/bin/bash
BUILD_ROOT=/tmp/pyside-build
INSTALL_PREFIX=/tmp/sandbox
function build_module {
cd $BUILD_ROOT
echo Cloning project $1 from url $2
git clone --depth 1 $2 $BUILD_ROOT/$1
BUILD_DIR=$BUILD_ROOT/$1/build
mkdir -p $BUILD_DIR
cd $BUILD_DIR
echo Configuring $1 build.
cmake -DCMAKE_INSTALL_PREFIX=$INSTALL_PREFIX ..
echo Configured $1. Starting build.
make LD_LIBRARY_PATH=$INSTALL_PREFIX/lib
echo Built $1. Installing.
make install
echo Successfully built and installed $1
}
rm -rf $BUILD_ROOT
mkdir -p $BUILD_ROOT
build_module apiextractor git://gitorious.org/pyside/apiextractor.git
build_module generatorrunner git://gitorious.org/pyside/generatorrunner.git
build_module shiboken git://gitorious.org/pyside/shiboken.git
build_module pyside-shiboken git://gitorious.org/pyside/pyside-shiboken.git
Run it and wait a while (Qt is quite big). :)
This script will download all packages into /tmp/pyside-build, build each one in its own "build" directory and install everything into /tmp/sandbox. Then, I just had to set PYTHONPATH to /tmp/sandbox/lib/python2.6/site-packages and PySide worked fine.

In answer to the original post...
What your script would have done is generate the necessary build files to build the pyside bindings, but it wouldn't have done the build itself. To do the build itself you'd need to execute a 'make', then a 'make install' in each of the build directories.
I've gotten most of the way through getting pyside 0.3.1 up and running on the Mac (SnowLeopard 10.6.3), but am hung up on the final compile step. My script is a bit less straightforward than yours, but in essence similar.
I have run into and worked around a number of problems to get to the final compile, and am hoping that I can help some folks along with the solutions/workarounds I've devised. Also, maybe collectively we can figure out how to get through the final step.
I'm going to include the build script that I'm using, and the log of the changes I had to make in the distro to get it running. But first, the step that I'm stuck on... mainly, I don't understand the error message, and the requested file doesn't seem to exist...
I hope this will help move support for the mac along...
I can't post this directly on stack overflow since its too long, so here is the link to the post on the mailing list over at pyside.
http://lists.openbossa.org/pipermail/pyside/2010-June/000812.html

While it's a been couple months since this question originally was asked I ran across the official PySide build script repo at:
http://qt.gitorious.org/pyside/buildscripts
The README covers the build process:
http://qt.gitorious.org/pyside/buildscripts/blobs/master/README
It seems to be fairly automatic with my only caveat so far being that it pulls down libxslt via brew - I can't say authoritatively if libxslt shipped with Snow Leopard or not - but it's definitely in Lion by default.
Seemingly the only manual install step is putting cmake on your system.

Unable to install python-setuptools: ./configure: No such file or directory

The question is related to the answer to "Unable to install Python without sudo access".
I need to install python-setuptools to install python modules.
I have extracted the installation package.
I get the following error when configuring
[~/wepapps/pythonModules/setuptools-0.6c9]# ./configure --prefix=/home/masi/.local
-bash: ./configure: No such file or directory
I did not find the solution at the program's homepage.
How can I resolve this error?

As Noah states, setuptools isn't an automake package so doesn't use ‘./configure’. Instead it's a pure-Python-style ‘setup.py’ (distutils) script.
You shouldn't normally need to play with .pydistutils.cfg, as long as you run it with the right version of Python. So if you haven't added the .local/bin folder to PATH, you'd have to say explicitly:
/home/masi/.local/bin/python setup.py install
AIUI this should Just Work.
I did not find the solution at the program's homepage.
Yeah, they want you to install it from a shell script egg which uses the default version of Python. Which you don't want.
(Another approach if you can't get setuptools to work is to skip it and install each module and dependency manually. Personally I have a bit of an aversion to setuptools/egg, as it contains far too much “clever” magic for my tastes and makes a mess of my filesystem. But I'm an old curmudgeon like that. Most Python modules can be obtained as simple Python files or plain old distutils scripts, but unfortunately there are some that demand eggs.)

You might want to check http://peak.telecommunity.com/DevCenter/EasyInstall#custom-installation-locations.
EasyInstall is a python module with some shell scripts (or some shell scripts with a python module?) and does not use the unix make tool that gets configured with the "./configure" command. It looks like your best bet is to try editing ~/.pydistutils.cfg to include:
[install]
install_lib = /home/masi/.local/lib/python/site-packages/
install_scripts = /home/masi/.local/bin
You'll also presumably have made the ~/.local/bin/ folder part of your PATH so you can run the easy_install script. (I'm not sure exactly where the site-packages directory will be under .local, but it shouldn't be hard to find.)
Hope this helps.