PyMedPhys Installation¶

Install Python
Installing PyMedPhys
Installing optional dependencies
Installing the Bleeding Edge version of PyMedPhys

Install Python ¶

In order to make use of the PyMedPhys library, you’ll need Python installed on your workstation. On Windows we recommend that you install the Anaconda Python distribution. Download the latest Anaconda Python 3 (not 2) version from here.

Note

When installing Anaconda make sure to install it for your user only, and tick the option “add to path”.

On Linux or MacOS we recommend not using your system Python and instead managing your Python installation using something like pyenv.

Installing PyMedPhys ¶

Once you have Python you can now install PyMedPhys via pip by typing the following in a terminal or command prompt:

pip install pymedphys

You may need to open and close your terminal if you have only just installed Python.

Installing optional dependencies ¶

Primary library optional dependencies ¶

PyMedPhys has a range of optional dependencies. If while using PyMedPhys as installed above you get ImportErrors you may install the primary optional dependencies for the main library by typing the following:

pip install pymedphys[library]

Labs optional dependencies ¶

If you would like to use some of the experimental libraries within the labs section of PyMedPhys then running the following will install the optional dependencies needed by modules within the labs:

pip install pymedphys[labs]

Difficult optional dependencies ¶

There are two optional dependencies which have some extra complications when installing. shapely can be difficult to install on Windows, and pymssql can be difficult to install on MacOS.

`shapely` for `pymedphys.electronfactors` module ¶

If you wish to use the pymedphys.electronfactors module you will need to install shapely which on MacOS or Linux is as simple as:

pip install shapely

On Windows however you will need to download and install a wheel from the following site – <https://www.lfd.uci.edu/~gohlke/pythonlibs/#shapely>.

`pymssql` for `pymedphys.mosaiq` module ¶

If you wish to use the pymedphys.mosaiq module then you will need to install a version of pymssql that is < 3. On Windows and Linux this is achieved by running:

pip install pymssql<3

On MacOS installing this dependency is a little more involved and can be achieved by first installing both freetds via homebrew and Cython. To do this follow the steps below:

To install homebrew (as described at <https://brew.sh/>):

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

Then to install freetds open a new shell, then run:

brew install freetds

And lastly to install cython run:

pip install cython

Then you will be able to successfully run:

pip install pymssql<3

Installing the Bleeding Edge version of PyMedPhys ¶

If you wish to be able to contribute to PyMedPhys itself you are going to want to instead install PyMedPhys from the master branch on GitHub <https://github.com/pymedphys/pymedphys>. To achieve this follow the OS specific instructions within the contributor tutorials: