Python code dependencies

Summary of dependencies

The packages required for the Python code are:

• Python
• NumPy
• Matplotlib
• h5py
• Astropy

Overview

How you install these depends on your operating system, whether you are an existing Python user, and whether you use package managers. To find out whether any of these are already installed, start up a Python prompt by typing python on the command line, then try the following commands:

import numpy
import matplotlib
import h5py
import astropy

If you see this:

>>> import numpy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named numpy
>>>

then the module is not installed. If you see this

>>> import numpy
>>>

then the module is already installed.

Linux

Numpy, Matplotlib, and h5py should be available in most major Linux package managers. If Astropy is not available, you can easily install it from source. To do this, go to the Astropy homepage and download the latest stable version. Then, expand the tar file and install using:

tar xvzf astropy-x.x.tar.gz
cd astropy-x.x
python setup.py install

Finally, check that Astropy imports cleanly:

~> python
Python 2.7.2 (default, Aug 19 2011, 20:41:43) [GCC] on linux2
Type "help", "copyright", "credits" or "license" for more information.
 >>> import astropy
 >>>

MacOS X

MacPorts

If you are installing Python for the first time, we strongly recommend the use of MacPorts to install a full Python distribution. If you would like to do this, follow these instructions to get set up. Once you have your Python distribution installed, make sure all the dependencies for Hyperion are installed:

sudo port selfupdate
sudo port install py27-numpy py27-matplotlib py27-h5py py27-astropy

If this works, you are all set, and you can move on to the actual Hyperion installation instructions.

System/python.org Python

Numpy and Matplotlib

If you do not want to use MacPorts, the easiest way to install the two first dependencies is to download and install the MacOS X dmg files for NumPy and Matplotlib. Use the links at the top of this section to get the latest dmg files from the different websites. You can of course also install these from source, but this is beyond the scope of this documentation.

Note

If you get an error saying x can’t be installed on this disk. x requires Python 2.7 from www.python.org to install, then this means you are probably just using the system Python installation. Go to www.python.org and download the 2.7.2 version of Python, install, and try installing the packages again.

Check that the packages import correctly:

$ python
Python 2.7.2 (default, Jan 31 2012, 22:38:06)
[GCC 4.2.1 (Apple Inc. build 5646)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> import matplotlib
>>>

If any of the packages are incorrectly installed, they will not import cleanly as above.

h5py

Once Numpy and Matplotlib are installed, you will need to install h5py. First, you will need to install the HDF5 library. Note that for the Fortran code, you also need to install the HDF5 library, but here we need to create a clean installation without the fortran bindings, or else h5py will not install properly. Make sure that you perform the following installation in a different directory from before, to avoid overwriting any files.

To install the plain HDF5 library download the source code from the latest HDF5 downloads (choose the hdf5-x.x.x.tar.gz file), then expand the source code:

tar xvzf hdf5-x.x.x.tar.gz
cd hdf5-x.x.x

and carry out the installation:

./configure --prefix=/usr/local/hdf5
make
sudo make install

Now, download the latest h5py-x.x.x.tar.gz package from the h5py website, and do:

tar xvzf h5py-x.x.x.tar.gz
cd h5py-x.x.x
python setup.py build --api=18 --hdf5=/usr/local/hdf5
python setup.py install

Now, go back to your home directory, and check that h5py imports cleanly:

$ python
Python 2.7.2 (default, Jan 31 2012, 22:38:06)
[GCC 4.2.1 (Apple Inc. build 5646)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import h5py
>>>

Astropy

Finally, if needed, install Astropy by going to the Astropy homepage and downloading the latest stable version. Then, expand the tar file and install using:

tar xvzf astropy-x.x.tar.gz
cd astropy-x.x
python setup.py install

Finally, check that Astropy imports cleanly:

$ python
Python 2.7.2 (default, Jan 31 2012, 22:38:06)
[GCC 4.2.1 (Apple Inc. build 5646)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import astropy
>>>