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Installation

Installation should be relatively easy, but it may break down depending on your compiler.

Installation requires astroquery and specutils. These can be pip installed:

pip install astroquery
pip install https://github.com/astropy/specutils/archive/master.zip

Compiling RADEX

This command should install the python-wrapped-fortran version of RADEX:

$ python setup.py install_radex install_myradex install

If it doesn't work, there are a number of ways things could have gone wrong.

If you try to import pyradex and see the error:

ImportError: No module named radex

that means that the "shared object" file radex.so (which is what python actually imports) never got built. In this case, you should have seen an error message at the python setup.py install_radex step. At this point, look in the radex_build.log file - it may contain useful information.

I don't know how general this advice is, but for installation on 2 macs and 1 linux machine, the trick was using the right gfortran versions with the right flags.

If you're using mac-native compilers (e.g., gcc-4.2 from Xcode), you can use the -arch flags. I used this really long command to make sure everything got set right:

FFLAGS='-arch i686 -arch x86_64 -fPIC' CFLAGS='-fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -O2' LDFLAGS='-arch i686 -arch x86_64 -undefined dynamic_lookup -bundle' python setup.py install_radex

If you're using a different compiler, say from hpc.sourceforge.net, you need a different set of flags, and you need to make sure that gcc --version and gfortran --version match.

FFLAGS='-m64 -fPIC' CFLAGS='-fno-strict-aliasing -fno-common -dynamic -m64 -g -O2' LDFLAGS='-m64 -undefined dynamic_lookup -bundle' python setup.py install_radex install

Note that if you're using a 32 bit machine or 32 bit python, you should use -m32 instead of -m64 in those flags.

You may also need to set your C_INCLUDE_PATH, e.g.:

C_INCLUDE_PATH /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk/usr/include

(I didn't have to do this, but someone else did - the error that pointed us in this direction was that stdio.h couldn't be found)

For linux, the build failed with gcc-4.0.1 but succeeded with gcc-4.3.6, which suggests that gcc>=4.2 might be required (since gcc-4.2 worked on a mac).

Environment Setup

The shell environmental variable RADEX_DATAPATH should be set to the directory in which you store collision rate data files. You can also use the datapath keyword argument to specify the path during initialization of the RADEX object.

Installation Troubles

If you still cannot install pyradex given the above information, please post on the issues page, and include the following information:

  • python version
  • numpy version
  • astropy version
  • gfortran version

e.g.:

$ python -c "import sys, astropy, numpy; print(sys.version); print(numpy.__version__,astropy.__version__)"
2.7.2 (v2.7.2:8527427914a2, Jun 11 2011, 15:22:34)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)]
('1.6.1', '0.3.dev6331')

$ gfortran --version
GNU Fortran (GCC) 4.2.3
Copyright (C) 2007 Free Software Foundation, Inc.