Installation¶
Gcmstools requires Python and a number of third-party packages. Below is a complete list of packages and minium versions:
Python >=3.4 (2.x versions not supported any longer)
Pip >=6.0.6 (might be part of newer Python releases)
Setuptools >=11.3.1
Numpy >=1.9.1
Matplotlib >= 1.4.2
Pandas >=0.15.2
IPython >=2.3.1
PyTables >=3.1.1
Scipy >=0.14.0
Sphinx >=1.2.2 (Optional for documentation.)
numfig is a Sphinx extenstion that is needed to autonumber figures references in the docuementation.
IPython is also a very useful advanced interactive Python interpreter. Examples in this documentation assume that you are using this environment. See the IPython section of Appendix A for more details.
Python¶
The most convenient installation method for third-party Python packages is the
all-in-one Anaconda Python distribution. It combines a large number of
Python packages for scientific data analysis and a program (conda
) for
managing package updates, in addition to many other advanced features. The
Anaconda developers (Continuum Analytics) provide a lot of useful
documentation on installing Anaconda and using conda. There are other
ways to install Python and the third-party packages, but for this
documentation, it will be assumed that your are using Anaconda.
Note
On Mac/Linux, Python is already part of the operating system. Do not try to install these third-party packages into the builtin Python distribution unless you really know what you are doing. You might overwrite an important file, which can cause problems for your system. Confusion between the system and Anaconda Python installation is a common source of problems for beginners, so make sure that your Anaconda Python is “activated” before running the commands in this document. (See the Anaconda documentation for more information on the activation process.)
Learning the usage of all of these Python packages is far beyond the scope of this document. However, excellent documentation for most of the packages as well as full tutorials are easily discovered.
gcmstools¶
There are three installation options for gcmstools: 1) install using conda
(recommended), 2) install using pip
, or 3) install the most recent
development version using git
.
Option 1 (recommended)
If you are using the Anaconda Python distribution, you can use conda
to
install the most recent distribution of gcmstools from Binstar,
Continuum’s package repository.
home>$ conda install -c https://conda.binstar.org/rnelsonchem gcmstools
To uninstall gcmstools from a conda
environment, use the following
command:
home>$ conda remove gcmstools
Option 2
gcmstools can also be installed from the official Python packaging site,
PyPI, using the standard Python installer script pip
. This installation
method will work fine if you have the additional dependencies installed;
otherwise, you may have some problems depending on your platform.
home>$ pip install gcmstools
To uninstall gcmstools using pip
:
home>$ pip uninstall gcmstools
Option 3
The development version of gcmstools is hosted on GitHub. To use this
version, you must install the version-control software Git. gcmstools can
then be downloaded and installed with one pip
command.
home>$ pip install git+https://github.com/rnelsonchem/gcmstools.git
There are advantages and disadvantages with this approach. For example, the GitHub repo will always have the most recent updates and bug fixes; however, these new features might not be as well-tested so you might find new bugs.
To uninstall, use the method described in Option 2