In this session we will install a new experimental branch of PySAL that implements methods for point pattern analysis. We will do so using a sandbox that isolates this code from your working installation of Anaconda and PySAL. Learning how to do this is important as it gives you a safe way to explore new developments in Python libraries without risking a production installation.
We will carry out three main tasks in this session Note that this is all being done under Linux, but the commands should be similar to what you would do under OS X and Windows.
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Create a new conda environment
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Install additional packages outside of conda into that environment
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Introduce the first point pattern models in PySAL
Creating a new Conda Environment
In what follows we first check to see that conda is installed:
~ ❯❯❯ which conda
/home/serge/anaconda2/bin/conda
Good. Now we will create a new conda environment called points471 and install several packages into it:
~ ❯❯❯ conda create -n points471 scipy pandas shapely matplotlib jupyter
Fetching package metadata: ....
Solving package specifications: ..........................................................................
Package plan for installation in environment /home/serge/anaconda2/envs/points471:
The following packages will be downloaded:
package | build
---------------------------|-----------------
geos-3.4.2 | 0 15.4 MB defaults
libgfortran-3.0 | 0 261 KB defaults
mkl-11.3.1 | 0 121.2 MB defaults
openssl-1.0.2g | 0 3.2 MB defaults
decorator-4.0.9 | py27_0 12 KB defaults
mistune-0.7.2 | py27_0 570 KB defaults
numpy-1.10.4 | py27_1 6.0 MB defaults
pygments-2.1.1 | py27_0 1.2 MB defaults
pytz-2016.2 | py27_0 176 KB defaults
pyzmq-15.2.0 | py27_0 704 KB defaults
setuptools-20.3 | py27_0 452 KB defaults
shapely-1.5.13 | py27_0 255 KB defaults
wheel-0.29.0 | py27_0 81 KB defaults
cycler-0.10.0 | py27_0 11 KB defaults
pexpect-4.0.1 | py27_0 63 KB defaults
pip-8.1.1 | py27_0 1.5 MB defaults
python-dateutil-2.5.1 | py27_0 235 KB defaults
scipy-0.17.0 | np110py27_2 30.1 MB defaults
traitlets-4.2.1 | py27_0 108 KB defaults
ipython-4.1.2 | py27_1 930 KB defaults
jupyter_core-4.1.0 | py27_0 51 KB defaults
pandas-0.18.0 | np110py27_0 12.0 MB defaults
jupyter_client-4.2.2 | py27_0 96 KB defaults
matplotlib-1.5.1 | np110py27_0 8.2 MB defaults
ipykernel-4.3.1 | py27_0 117 KB defaults
nbconvert-4.1.0 | py27_0 273 KB defaults
jupyter_console-4.1.1 | py27_0 24 KB defaults
notebook-4.1.0 | py27_1 4.4 MB defaults
qtconsole-4.2.0 | py27_0 159 KB defaults
ipywidgets-4.1.1 | py27_0 98 KB defaults
jupyter-1.0.0 | py27_2 2 KB defaults
------------------------------------------------------------
Total: 207.6 MB
The following NEW packages will be INSTALLED:
backports_abc: 0.4-py27_0 defaults
cairo: 1.12.18-6 defaults
cycler: 0.10.0-py27_0 defaults
decorator: 4.0.9-py27_0 defaults
fontconfig: 2.11.1-5 defaults
freetype: 2.5.5-0 defaults
geos: 3.4.2-0 defaults
ipykernel: 4.3.1-py27_0 defaults
ipython: 4.1.2-py27_1 defaults
ipython_genutils: 0.1.0-py27_0 defaults
ipywidgets: 4.1.1-py27_0 defaults
jinja2: 2.8-py27_0 defaults
jsonschema: 2.4.0-py27_0 defaults
jupyter: 1.0.0-py27_2 defaults
jupyter_client: 4.2.2-py27_0 defaults
jupyter_console: 4.1.1-py27_0 defaults
jupyter_core: 4.1.0-py27_0 defaults
libgfortran: 3.0-0 defaults
libpng: 1.6.17-0 defaults
libsodium: 1.0.3-0 defaults
libxml2: 2.9.2-0 defaults
markupsafe: 0.23-py27_0 defaults
matplotlib: 1.5.1-np110py27_0 defaults
mistune: 0.7.2-py27_0 defaults
mkl: 11.3.1-0 defaults
nbconvert: 4.1.0-py27_0 defaults
nbformat: 4.0.1-py27_0 defaults
notebook: 4.1.0-py27_1 defaults
numpy: 1.10.4-py27_1 defaults
openssl: 1.0.2g-0 defaults
pandas: 0.18.0-np110py27_0 defaults
path.py: 8.1.2-py27_1 defaults
pexpect: 4.0.1-py27_0 defaults
pickleshare: 0.5-py27_0 defaults
pip: 8.1.1-py27_0 defaults
pixman: 0.32.6-0 defaults
ptyprocess: 0.5-py27_0 defaults
pycairo: 1.10.0-py27_0 defaults
pygments: 2.1.1-py27_0 defaults
pyparsing: 2.0.3-py27_0 defaults
pyqt: 4.11.4-py27_1 defaults
python: 2.7.11-0 defaults
python-dateutil: 2.5.1-py27_0 defaults
pytz: 2016.2-py27_0 defaults
pyzmq: 15.2.0-py27_0 defaults
qt: 4.8.7-1 defaults
qtconsole: 4.2.0-py27_0 defaults
readline: 6.2-2 defaults
scipy: 0.17.0-np110py27_2 defaults
setuptools: 20.3-py27_0 defaults
shapely: 1.5.13-py27_0 defaults
simplegeneric: 0.8.1-py27_0 defaults
singledispatch: 3.4.0.3-py27_0 defaults
sip: 4.16.9-py27_0 defaults
six: 1.10.0-py27_0 defaults
sqlite: 3.9.2-0 defaults
ssl_match_hostname: 3.4.0.2-py27_0 defaults
terminado: 0.5-py27_1 defaults
tk: 8.5.18-0 defaults
tornado: 4.3-py27_0 defaults
traitlets: 4.2.1-py27_0 defaults
wheel: 0.29.0-py27_0 defaults
zeromq: 4.1.3-0 defaults
zlib: 1.2.8-0 defaults
Proceed ([y]/n)? y
Fetching packages ...
geos-3.4.2-0.t 100% |###############################################################################################################| Time: 0:00:03 5.24 MB/s
libgfortran-3. 100% |###############################################################################################################| Time: 0:00:00 509.61 kB/s
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decorator-4.0. 100% |###############################################################################################################| Time: 0:00:00 184.07 kB/s
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Extracting packages ...
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#
# To activate this environment, use:
# $ source activate points471
#
# To deactivate this environment, use:
# $ source deactivate
#
At this pont we are ready to roll with our new environment. So to activate it we follow the directions in the last set of lines above:
~/D/g/G/G/4/points ❯❯❯ source activate points471
discarding /home/serge/anaconda2/bin from PATH
prepending /home/serge/anaconda2/envs/points471/bin to PATH
(points471)~/D/g/G/G/4/points ❯❯❯
Notice how my prompt has now changed to indicate I am using the (points461) environment.
I can check to see where the search path leads to when issuing a command like calling jupyter:
(points471)~/D/g/G/G/4/points ❯❯❯ which jupyter
/home/serge/anaconda2/envs/points471/bin/jupyter
So we see that the search path points to the conda environment that is currently active.
Installing PySAL into the Conda Environment
We relied on conda to install most of the packages we will need to analyze point patterns. There are a few additional packages that are not currently part of conda that we need. We would also like to install an experimental version of PySAL which differs from the one in the conda system.
Installing folium
(points471)~/D/g/G/G/4/points ❯❯❯ pip install folium ⏎
Collecting folium
Requirement already satisfied (use --upgrade to upgrade): Jinja2 in /home/serge/anaconda2/envs/points471/lib/python2.7/site-packages (from folium)
Requirement already satisfied (use --upgrade to upgrade): MarkupSafe in /home/serge/anaconda2/envs/points471/lib/python2.7/site-packages (from Jinja2->folium)
Installing collected packages: folium
Successfully installed folium-0.2.0
You are using pip version 7.1.2, however version 8.1.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Installing the custom PySAL Branch
Work on the new point pattern module in PySAL is happening in the points_contrib branch. To install it in our conda environment we do:
(points471)~/D/g/G/G/4/points ❯❯❯ pip install https://github.com/sjsrey/pysal/archive/points_contrib.zip ⏎
Collecting https://github.com/sjsrey/pysal/archive/points_contrib.zip
Downloading https://github.com/sjsrey/pysal/archive/points_contrib.zip
| 20.4MB 17.5MB/s
Installing collected packages: PySAL
Running setup.py install for PySAL
Successfully installed PySAL-1.11.1
You are using pip version 7.1.2, however version 8.1.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
(points471)~/D/g/G/G/4/points ❯❯❯
One last test to make sure we have the correct version of PySAL:
(points471)~/D/g/G/G/4/points ❯❯❯ ipython ⏎
Python 2.7.11 |Continuum Analytics, Inc.| (default, Dec 6 2015, 18:08:32)
Type "copyright", "credits" or "license" for more information.
IPython 4.1.2 -- An enhanced Interactive Python.
? -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help -> Python's own help system.
object? -> Details about 'object', use 'object??' for extra details.
In [1]: import pysal
In [2]: pysal.version
Out[2]: '1.11.1'
In [3]:
You should see version 1.11.1. If not, it means you likely haven't activated the conda environment and instead are using your base anaconda install. Activate your environment as explained above, if this is the case.
Introduction to Point Patterns in PySAL
We are now in a position to begin exploring point pattern analysis in PySAL. In this session we will look at two notebooks:
Once you are done with this session you can either close the terminal you were working in or deactivate the environment:
(points471)~/D/g/G/G/4/points ❯❯❯ source deactivate
discarding /home/serge/anaconda2/envs/points471/bin from PATH
~/D/g/G/G/4/points ❯❯❯