landlab

Rough Guide to Python and Landlab Install

Handling Python installs on Linux if you are non-expert can be a confusing and frustrating experience. However, one of us (DEJH) has recently gone through the pain, and offers these thoughts on how to get a Python install capable of running Landlab onto your machine. (As long as your machine is Debian…)

NB: A version of Canopy does exist for linux, but DEJH couldn’t get this to install properly. If you can, this is probably the easier way to go!

What you already have, apt-get, and versioning

Your unix box almost certainly already has a version on Python on it. However, DEJH found it wasn’t the right version in his case. The problem is that the stable Python (and Python package) versions that are maintained through the Debian package repository that apt-get looks at tend not to be up to date. This is problematic, as Landlab needs at least Python 2.7, Numpy 1.8, and Scipy 0.12. NOTE: this is very very old. As of Jan 2020, Landlab will require Python 3 or higher. So first, check your version:

$ python --version

Note the two dashes. If you got 2.7 or higher, congratulations! You win. No further changes to python installs are needed. But if you didn’t, first check whether you can simply update through the package manager:

$ sudo apt-get install -u python
$ python --version

If you’re still seeing a sub-2.7 version number (as I was…), you’re going to need to download the python source and install it manually. Go to the python download site, select the link to the highest version number of Python 2.X available (2.7.6 at time of writing), and download it as a gzipped source tarball. Then:

$ tar -xzf the_downloaded_file.tgz
$ cd the_new_directory
$ ./configure
$ make
$ sudo make install

You should now have Python 2.7! Close the terminal, reopen, and check:

$ python2.7

BUT, it’s highly likely if you just run “python”, you won’t get this version. Check by

$ python --version

again. You can resolve this by messing with your ~/.bashrc profile. Open that file in your favourite text editor, and add at the end:

$ alias python="python2.7"

Restart the terminal again, and check the version number now. Should be right! (You will probably also want to do something similar with ipython, but DEJH didn’t explore that…)

Installing pip

You now have the right version of python, but if you try, e.g., import numpy, you’ll notice you don’t have any packages. This is where pip - the powerful command line Python package manager - comes in.

Get pip by going to the pip site and downloading get_pip.py, which links from that page. Navigate to the folder you downloaded it into, and simply run

$ sudo python get_pip.py

This should give you a trouble free install of pip.

Once you have it, make sure you’re fully up-to-date:

$ pip install --upgrade pip

NB: DO NOT TRY TO INSTALL PIP WITH APT-GET. Pip binds to your Python install, and the binding probably won’t take properly unless you install through your version of Python, as described here. Note that there is a copy of pip you can get with apt-get, but you don’t want it.

Downloading the packages

Now you have pip and it’s bound correctly to your Python install, adding packages should be trouble free:

$ sudo pip install numpy
$ sudo pip install scipy
$ sudo pip install matplotlib
$ sudo pip install sympy
$ sudo pip install netCDF4

Note in future, you can update these packages to new versions by:

$ sudo pip install --upgrade [package_name]

Now test the versions like this:

$ python
>>> import numpy
>>> numpy.__version__

And everything should now be great. You can now continue to install Landlab as you would in the main instructions. e.g., if you have a clone or downloaded copy of Landlab you want to install in developer mode, just navigate to the download’s top level directory and run

$ pip install -e .

and test:

$ python
>>> import landlab
>>> landlab.test()

Or alternatively, just grab the release version using pip, as in the main instructions:

$ pip install landlab

& again, test as above.