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Getting Started with PySAL

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Installing PySAL

Prerequisites

Before installing PySAL, make sure the following libraries are properly installed on your machine:

Optional, bundled installation:

With the Enthought Python Distribution (EPD Free), you will install all of PySAL’s required dependencies, as well as iPython and a lot more, rather than installing dependencies one by one. The full-blown EPD package is free for academics, and downloadable here. Note that on OS X, PySAL binary installers will not install to the EPD site-packages directory. We advise EPD users to install PySAL via PyPi or source.

Required to compile the documentation (optional):

Optional, recommended additions:

Getting PySAL

You can install PySAL in a number of ways. We provide system-specific package installers for Windows and Mac OS X that have an intuitive look-and-feel that most users are familiar with. We also build source distributions that self-install by invoking a single command line argument.

PySAL is also available on the Python Package Index, which means it can be downloaded and installed manually or from the command line using easy_install or pip, as follows:

$ pip install pysal
#or
$ easy_install pysal

Downloads

Click-to-download PySAL distributions are available at Google Code. Choose the right one for your system, or grab a source tarball or zipfile.

Windows installer

Grab the Windows installer (ends with .exe) and download to your computer. Double-click to launch the installer and follow the simple wizard. You will have to select the version of Python you want the package to install with, if you have more than one version of Python on your system. You may repeat this procedure for as many versions of Python as you have on your machine.

Source install instructions for all platforms

Grab either of the source distributions (.tar.gz or .zip) and decompress to your selected destination. Open a command shell and navigate to the decompressed PySAL folder. Type:

$ python setup.py install

Development version from Subversion (SVN)

Finally, advanced users and developers can use the popular version control tool svn to check out and use our latest code. Instructions for each of these methods follows.

Users and developers can grab the source code from our Subversion repository using an svn client and the following instructions:

GNU/Linux and Mac OS X

Open a command shell, navigate to a convenient location on your hard drive, and type:

$ svn checkout http://pysal.googlecode.com/svn/trunk/ pysal

This will create a folder called ‘pysal’ containing the source code in trunk. This will allow you to easily update any change to the developer code base by running:

$ svn update

Since PySAL is in active development, changes are made frequently. For that reason, we recommend you ‘tell’ Python to look for PySAL in that folder rather than properly install it as a package. You can do this by adding the PySAL folder to the PYTHONPATH, a UNIX environment variable. To do that, create or edit your command shell profile (.bash_profile if using BASH) and add the following line, substituting where appropriate:

$ export PYTHONPATH=${PYTHONPATH}:"/path_to_desired/folder/pysal/"

Save and quit the file, then source it as follows:

$ source ~/.bash_profile

You are all set. To test your setup, start a Python session and type:

>>> import pysal; pysal.open.check()

Your terminal should reply with the following:

PySAL File I/O understands the following file extensions:
Ext: '.shp', Modes: ['r', 'wb', 'w', 'rb']
Ext: '.mtx', Modes: ['r', 'w']
Ext: '.swm', Modes: ['r', 'w']
Ext: '.mat', Modes: ['r', 'w']
Ext: '.shx', Modes: ['r', 'wb', 'w', 'rb']
Ext: '.stata_text', Modes: ['r', 'w']
Ext: '.geoda_txt', Modes: ['r']
Ext: '.dbf', Modes: ['r', 'w']
Ext: '.dat', Modes: ['r', 'w']
Ext: '.gwt', Modes: ['r']
Ext: '.gal', Modes: ['r', 'w']
Ext: '.arcgis_text', Modes: ['r', 'w']
Ext: '.wk1', Modes: ['r', 'w']
Ext: '.arcgis_dbf', Modes: ['r', 'w']
Ext: '.geobugs_text', Modes: ['r', 'w']
Ext: '.csv', Modes: ['r']
Ext: '.wkt', Modes: ['r']
>>>

Windows

To keep up to date with PySAL development, you will need an SVN client that allows you to access and update the code from our repository. We recommend TortoiseSVN, which is free and easy to install. The following instructions assume you are using it. There are two basic steps. One, checkout a copy of the source code to your local drive. Two, adjust your PYTHONPATH environment variable so that Python looks for PySAL where you have downloaded it.

First, create a folder where you want to store PySAL’s code. For the sake of this example, we will name it PySALsvn and put it in the root folder, so the path is:

C:\PySALsvn

If for some reason you do not have access to the root directory, you can place the PySAL source code anywhere. Adjust your paths as appropriate for the rest of these instructions.

Right-click your PySAL folder and select ‘SVN checkout’ under the Tortoise menu. A dialog will appear. The ‘Checkout Directory’ refers to the path to your PySAL folder (C:\PySALsvn in this case). Copy and paste the following link into the ‘URL of repository’ textbox:

http://pysal.googlecode.com/svn/trunk/

Once you click ‘OK’, a folder called ‘pysal-read-only’ will be created under C:\PySALsvn and all the code will be downloaded to your computer.

Now tell Python where to find PySAL. There are several ways to do this. Here we will use a simple one that requires you to create a text file called sitecustomize.py in the site-packages folder of your Python distribution. That path looks more or less like this:

C:\PythonXX\Lib\site-packages\sitecustomize.py

,where XX corresponds to the version of the Python distribution you are using (25 for 2.5, for example). Edit sitecustomize.py with the following two lines of text:

import sys
sys.path.append("C:/PySALsvn/pysal-read-only")

Save and close the file. You are all set. To test your setup, start a Python session and type:

>>> import pysal; pysal.open.check()

Your terminal should reply with the following:

PySAL File I/O understands the following file extensions:
Ext: '.shp', Modes: ['r', 'wb', 'w', 'rb']
Ext: '.mtx', Modes: ['r', 'w']
Ext: '.swm', Modes: ['r', 'w']
Ext: '.mat', Modes: ['r', 'w']
Ext: '.shx', Modes: ['r', 'wb', 'w', 'rb']
Ext: '.stata_text', Modes: ['r', 'w']
Ext: '.geoda_txt', Modes: ['r']
Ext: '.dbf', Modes: ['r', 'w']
Ext: '.dat', Modes: ['r', 'w']
Ext: '.gwt', Modes: ['r']
Ext: '.gal', Modes: ['r', 'w']
Ext: '.arcgis_text', Modes: ['r', 'w']
Ext: '.wk1', Modes: ['r', 'w']
Ext: '.arcgis_dbf', Modes: ['r', 'w']
Ext: '.geobugs_text', Modes: ['r', 'w']
Ext: '.csv', Modes: ['r']
Ext: '.wkt', Modes: ['r']
>>>

Known Issues

1.5 install fails with scipy 11.0 on Mac OS X

Running python setup.py install results in:

from _cephes import *
ImportError:
dlopen(/Users/serge/Documents/p/pysal/virtualenvs/python1.5/lib/python2.7/site-packages/scipy/special/_cephes.so,
2): Symbol not found: _aswfa_
  Referenced from:
  /Users/serge/Documents/p/pysal/virtualenvs/python1.5/lib/python2.7/site-packages/scipy/special/_cephes.so
    Expected in: dynamic lookup

This occurs when your scipy on Mac OS X was complied with gnu95 and not gfortran. See this thread for possible solutions.

weights.DistanceBand failing

This occurs due to a bug in scipy.sparse prior to version 0.8. If you are running such a version see Issue 73 for a fix.

doc tests and unit tests under Linux

Some Linux machines return different results for the unit and doc tests. We suspect this has to do with the way random seeds are set. See Issue 52

LISA Markov missing a transpose

In versions of PySAL < 1.1 there is a bug in the LISA Markov, resulting in incorrect values. For a fix and more details see Issue 115.

PIP Install Fails

Having numpy and scipy specified in pip requiretments.txt causes PIP install of pysal to fail. For discussion and suggested fixes see Issue 207.

Troubleshooting

If you experience problems when building, installing, or testing PySAL, ask for help on the OpenSpace list or browse the archives of the pysal-dev google group.

Please include the output of the following commands in your message:

  1. Platform information:

    python -c 'import os,sys;print os.name, sys.platform'
    uname -a
  2. Python version:

    python -c 'import sys; print sys.version'
  3. SciPy version:

    python -c 'import scipy; print scipy.__version__'
  1. NumPy version:

    python -c 'import numpy; print numpy.__version__'
  2. Feel free to add any other relevant information. For example, the full output (both stdout and stderr) of the PySAL installation command can be very helpful. Since this output can be rather large, ask before sending it into the mailing list (or better yet, to one of the developers, if asked).