Installation¶
The following are some guidelines for installing NMRPy on a nix system, and are by no means the only way to install a Python package. First be sure to have Python 3 and pip installed. [Pip](https://en.wikipedia.org/wiki/Pip_(package_manager)) is a useful Python package management system. Note: NMRPy will not work using Python 2. On an Ubuntu-like system these can be installed with the following terminal commands:
$ sudo apt-get install python3
$ sudo apt-get install python-pip
Note: the following instructions may require Python C-extensions:
$ sudo apt-get install build-essential python3-dev
…and some other dependencies:
$ sudo apt-get install git libpng12-dev zlib1g-dev libfreetype6-dev tk-dev
Virtual environments¶
Virtual environments are a great way to keep package dependencies separate from your system files. There are several options for setting up your working environment. We will use virtualenvwrapper.
You can install virtualenvwrapper (http://virtualenvwrapper.readthedocs.org/en/latest/), which will take care of managing your virtual environments by maintaining a separate Python site-directory for you.
Install virtualenvwrapper using apt:
$ sudo pip install virtualenv
$ sudo pip install virtualenvwrapper
Add the following to the .bashrc file in your home directory (after the part where PATH is exported!):
export WORKON_HOME="$HOME"/.virtualenvs
source /usr/local/bin/virtualenvwrapper.sh
Then reload your .bashrc settings in the current terminal session:
$ source .bashrc
Make a new virtual environment for working with NMRPy (e.g. nmr), and specify that it use Python 3 (we used Python 3.5):
$ mkvirtualenv -p python3.5 nmr
The new virtual environment will be activated automatically, and this will be indicated in the shell prompt. Eg:
(nmr) user@computer:
If you are not yet familiar with virtual environments we recommend you survey the basic commands (https://virtualenvwrapper.readthedocs.io/en/latest/) before continuing.
Pip¶
The NMRPy code and its dependencies can be installed directly from Github (https://github.com/jeicher/nmrpy) into a virtual environment (if you are currently using one) using pip.
$ pip install git+https://github.com/jeicher/nmrpy.git
Working with NMRPy¶
Though the majority of NMRPy functionality can be used purely in a scripting context and executed by the Python interpreter, it will often need to be used interactively. We suggest two ways to do this:
Ipython¶
Ipython is an interactive Python shell with some useful functionalities like tab-completion. This has been installed by default with NMRPy and can be launched from the command line with:
$ ipython
The Jupyter Notebook¶
For those who prefer a “notebook”-like experience, the Jupyter Notebook may be more appropriate. It can be installed as follows:
$ pip install jupyter
And launched with:
$ jupyter-notebook