How to install SciPy stack with pip and homebrew?

Question

I'm trying to install the basic scipy stack (numpy, scipy, matplotlib, pandas, sympy, ipython, nose) into a virtualenv; currently, I'm using OSX Mountain Lion. From the installation pages for these packages, as well as various threads here and around the web, it seems that pandas, sympy, and nose can be installed easily with just pip (although some list numpy/scipy/etc. as dependencies).

However, there seems to be conflicting and kind of convoluted instructions for properly installing numpy, scipy, matplotlib, and, to a certain extent, ipython*. Installing solely with pip doesn't seem to be the proper way to install these packages; it seems that some dependencies need to be installed with homebrew, but various places list different packages to brew install before pip installing numpy/scipy/etc. Is there a comprehensive and current list of package dependencies that need to be installed with homebrew before pip installing numpy, scipy, and matplotlib?

Just as a note, I've looked at tapping homebrew/python for installing numpy, scipy, and matplotlib properly with homebrew, but I want to install into a virtualenv and I don't think I can use homebrew to do that.

Any help would be greatly appreciated; thanks in advance!

*Also, for ipython, the installation page says that pip install ipython[all] should be sufficient, but some other sources (http://www.coderstart.com/setup/python-setup.html; http://www.lowindata.com/2013/installing-scientific-python-on-mac-os-x/) seem to suggest that the qt, pyqt, and zmq packages need to be brew installed first before pip installing ipython; are the homebrew installation necessary or is it fine to just pip install according to the ipython installation page?

Answer 1

Answering my own question here, but hopefully this is helpful; feel free to correct if there are any mistakes. The original version is a gigantic wall of text, so I've added a tl;dr to the top with just the steps to hopefully make the process more clear.

tl;dr: In terminal/bash, go into a virtualenv (if you want to install into one) and enter these commands in order. This is tested for OSX Mountain Lion.

pip install numpy
brew install gcc
pip install scipy
brew install freetype
pip install matplotlib
pip install nose
pip install pandas
pip install sympy
pip install ipython[all]
brew install pyqt
brew install qt
brew install sip
echo "export PYTHONPATH=/usr/local/lib/python2.7/site-packages:$PYTHONPATH" >> ~/.bash_profile
source ~/.bash_profile

*Notes: brew installing pyqt might already install qt and sip; if it does, no need to install qt and sip after installing pyqt. For the second to last line, might be be more reliable to directly c/p that line into ~/.bash_profile, since it might need to be at the top of the ~/.bash_profile contents. Also, brew install pandoc is optional, but necessary for ipython notebook's nbconvert command work properly.

edit 10/13/14 [see edit at bottom]: editing PYTHONPATH in ~/.bash_profile forces virtual environments to inherit global packages; if you want to be able to make isolated environments, don't do the last two steps. Instead, assuming virtualenvwrapper is installed, edit the local postactivate and predeactivate scripts in the bin directory under the virtualenv that contains the scipy stuff.

In postactivate, enter:

export PYTHONPATH=/usr/local/lib/python2.7/site-packages:$PYTHONPATH 

In predeactivate, enter:

unset PYTHONPATH

This should edit PYTHONPATH when when the virtualenv with scipy stuff is activated so that ipython qtconsole works, but should reset PYTHONPATH when the virtualenv is deactivated, so that other virtualenvs are not affected by PYTHONPATH changes.

---

Below is the long narrative version.

Anyway, from some trial and error after I originally posted the question, I found that the following steps work; I used the two sets of instructions that I linked above as general guides, and this was tested on OSX Mountain Lion.

After activating the virtualenv in which the packages are going to be installed, first pip install numpy; this should work as expected and numpy should be installed (note that numpy should be installed first since a lot of the other packages in the scipy stack depend on numpy).

Now, before installing scipy, several sources note that gfortran (this seems to be the most common, but I think any fortran compiler should work) needs to be installed; brew install gfortran returns an error that says that gcc now includes gfortran so the gfortran formula is deprecated. Hence, we brew install gcc (note that even though xcode command line tools, which is generally installed before homebrew, already includes gcc, its version of gcc somehow doesn't work or doesn't include gfortran). After installing gcc, pip install scipy works as expected, and scipy should be installed. Quick aside: brew install gcc installs gcc as well as a bunch of dependencies, namely cloog, gcc, gmp, isl, libmpc, mpfr. [These should all be installed into /usr/local/Cellar, which is the default install location for homebrew.]

For installing matplotlib, freetype needs to be installed first, so we brew install freetype; this should install freetype and libpng, which seems to be a freetype dependency. Afterwards, pip install matplotlib works as expected, installing matplotlib successfully. Note that matplotlib installs with mock (needed to run matplotlib test suite), pyparsing (required for mathtext support), python-dateutil (required for date axis support), six (no reason given) along with it. [These should all be installed, along with any other pip install within a virtualenv, into the site-packages directory within the virtualenv.]

Installing nose, sympy, and pandas simply require pip installing, as they don't have any dependencies that need to be brew installed. However, of these, note that at least pandas depends on numpy, so installing pandas (not sure about the others) after installing numpy is probably preferred. Also, note that pandas installs with pytz (for time zone calculations).

Installing ipython is pretty simple, but setting it up is a little more convoluted. As a heads up, ipython can be used with both a qt console and something called ipython notebook, which have various benefits. You can choose to just install ipython with pip install ipython and install optional dependencies later on as needed, but I installed all the main optional dependencies with pip install ipython[all]. This installs ipython, along with a lot of other packages dependencies (installs with backports.ssl-match-hostname (from tornado), certifi (from tornado), docutils (from sphinx), gnureadline, ipython, jinja2, markupsafe (from jinja2), numpydoc (from ipython[all]), pygments, pyzmq, sphinx, tornado). This should be a good foundation for ipython to use both the standard ipython shell, the qt console, and the ipython notebook. However, it's not fully set up if you want to use either the qt console or the notebook.

To use the qt console, the pyqt, qt, and sip packages must be brew installed, as these are dependencies that cannot be installed with pip; from experience, brew install pyqt seems to install all three packages, but individually installing the three might be a safer bet. After doing this, go into ~/.bash_profile and add the line 'export PYTHONPATH=/usr/local/lib/python2.7/site-packages:$PYTHONPATH' to it; then 'source ~/.bash_profile' in terminal to reload the shell. This should successfully allow the qt console to be launched. [I'm not totally sure why this line needs to be added, since I had already edited the PATH variable to put /usr/local/bin before /usr/bin, but perhaps qt/pyqt/sip were still trying to link themselves with the system default python instead of homebrew installed python.]

The notebook seems to work fine out of the box as far as I've seen, but there's one thing of note: in order to use nbconvert (converting the notebook to different file formats), the pandoc package must be installed, presumably with homebrew. Like qt/pyqt/sip, it can't be installed with pip which is why it wasn't installed with pip install ipython[all].

edit 10/13/14: So apparently, editing PYTHONPATH will nullify empty virtual environments, making global packages also available in a virtualenv (how to isolate virtualenv from local dist-packages?); this, for the most part, defeats the purpose of a virtualenv, assuming that you want to a fresh environment, but is necessary for ipython qtconsole to work correctly.

The fix is to edit (assuming virtualenvwrapper is installed) the local postactivate and predeactivate scripts in the bin file of your virtualenv. In postactivate, enter the line "export PYTHONPATH=/usr/local/lib/python2.7/site-packages:$PYTHONPATH; in predeactivate, enter the line "reset PYTHONPATH". Don't do the last two steps of the original sequence, or delete the line that was added to ~/bash_profile. This should make it so that the changes to PYTHONPATH are made only when the virtualenv with our installed packages is activated, so that qtconsole works, but are reset before the virtualenv deactivates, so that other environments are not affected.

Answer 2

I'm on OSX 10.9, but I had good luck following these instructions and get roughly the same environment that you outlined above http://hackercodex.com/guide/python-development-environment-on-mac-osx/

Hope this helps