Tag: scipy

Doing science with Python 3

Up until recently, I basically ignored Python 3 in my day-to-day Python practice. Sure, I listened to some podcasts and read some articles, but Python 2.7 is doing everything I want, so why add another item to the load of things to think about? Turns out, I’m currently writing a little library, and the question arises, should I support Python 3? If yes, how, and how hard is it? Or maybe I can claim that the scientific Python tool set is not quite ready for Python 3 and can ignore it for a little longer?

Well, no such luck — once I went ahead and installed it to see for myself, Python 3 with the packages I use most intensely turned out to be astonishingly well-behaved. Here is how I proceeded, both for my own records and in case this is useful for someone.

0. Background

System before install: Apple OS X 10.6.8 (Snow Leopard) with Python 2.7.5 from python.org installed as the default Python. I use Doug Hellmann’s virtualenvwrapper to manage my virtual environments, but up to now I didn’t use –no-site-packages, and some packages (scipy, for example) are installed globally. As far as easily possible, packages are installed with pip. However, the underlying shared libraries that are prerequisites for some of the scientific Python packages [1] are mostly managed with Homebrew.

Intended situation after install:

  • Python 2.7.5 remains the default Python
  • Python 3.3.3 available via the python3 command
  • A whole virtual environment using python3, with all the most common science tools

1. Install Python 3 from python.org

I downloaded the DMG file called Python 3.3.3 Mac OS X 64-bit/32-bit x86-64/i386 Installer (for Mac OS X 10.6 and later) and ran it. This didn’t overwrite the python command. Python 3 is, as expected, in /Library/Frameworks/Python.framework/Versions/3.3/, and the python3 executable is symlinked to /usr/local/bin/python3.

2. Install pip for Python 3

The easiest way, I believe:

curl http://python-distribute.org/distribute_setup.py | python3
curl https://raw.github.com/pypa/pip/master/contrib/get-pip.py | python3

3. Set up the virtual environment

I installed the virtualenv libraries for Python 3 rather than trying to use those for Python 2.7.5. (Python3 comes with its own tool to manage virtual environments, pyvenv, but I prefer to continue using my existing Python2.7 virtual environments rather than learn at this stage how the new tool works.)

/Library/Frameworks/Python.framework/Versions/3.3/bin/pip install virtualenv
/Library/Frameworks/Python.framework/Versions/3.3/bin/pip install virtualenvwrapper
/Library/Frameworks/Python.framework/Versions/3.3/bin/virtualenv --no-site-packages -p /usr/local/bin/python3 --distribute .virtualenvs/science3
workon science3
which pip
/Users/[username]/.virtualenvs/science3/bin/pip

The last command is to check that the pip command is indeed the one in our new virtual environment.

4. Get installing

pip install numpy
pip install pyzmq
pip install tornado
pip install jinja2
pip install ipython
pip install GDAL
pip install pyproj
pip instal h5py
pip install netcdf4
pip install matplotlib
...

Note that most of these require shared libraries to be installed beforehand. pyzmq requires zeromq for example; pyzmq, tornado and jinja2 are required for iPython (which is called afterwards as ipython3). The Geospatial Data Abstraction Library can be quite tricky to compile if you need support for many scientific data file formats (the HDF family, netCDF, ….), but luckily it doesn’t care if it is bound into Python 2 or Python 3.   Matplotlib will also install some prerequisites.

In the end, the following Python 3 packages are installed via pip:

(science3)$ pip freeze
Cython==0.19.2
GDAL==1.10.0
Jinja2==2.7.1
MarkupSafe==0.18
basemap==1.0.3
h5py==2.2.0
ipython==1.1.0
matplotlib==1.3.1
netCDF4==1.0.7
nose==1.3.0
numpy==1.8.0
pyparsing==2.0.1
pyproj==1.9.3
python-dateutil==2.2
pyzmq==14.0.0
readline==6.2.4.1
scikit-image==0.9.3
scikit-learn==0.14.1
scipy==0.13.1
six==1.4.1
tornado==3.1.1

5. What didn’t quite work

There were two glitches, one to do with the Matplotlib Basemap toolkit, the other with scipy.

The Basemap package from mpl_toolkits is a 120 MB download. That’s why I keep a version (not the newest one) saved locally and install from there:

pip install basemap-1.0.3.tar.gz

On a sidenote, this and some package installs (mostly those with code hosted in Google Code) came back with this warning:

You are installing a potentially insecure and unverifiable file. Future versions of pip will default to disallowing insecure files.

It installed fine, but importing Basemap (“from mpl_toolkits.basempap import Basemap”) fails with the error “ValueError: level must be >= 0”. Some googling shows that this has happened for a few Python packages with Python 3.3.3. Maybe upgrading the Basemap toolkit to the newest version will fix it. Right now this isn’t the highest priority.

As for scipy, the issue was quite different: A C code file (implementing a highly specialized numerical linear algebra algorithm — unsymmetric multifrontal sparse LU factorization) refused to compile (_umfpack_wrap.c). I am doubtful the issue even has anything to do with Python 3. In any event, I had been using a binary scipy package with Python 2.7, so I wouldn’t have seen the issue.

The solution was provided on a mailing list, to remove  UMFPACK altogether (“export UMFPACK=None”), and indeed scipy installed just fine without it. There is a related issue open for scipy on Github.

6. Conclusions

Python 3 feels just like Python always did! I don’t think the upgrade will change my way I go about designing software in Python, which is a relief. I made an iPython3 Notebook showing off some basic tasks (“open some weird scientific data files, read some metadata, plot the contents”).

[1] The top of my list consists of zeromq for iPython; gdal, geos, proj and maybe udunits for projected geospatial data; libpng, libtiff, libgeotiff for imagery; hdf4, hdf5, netcdf to access the scientific file formats I use most often — your list may be slightly different.