Fermipy is only compatible with Science Tools v10r0p5 or later. If you are using an earlier version, you will need to download and install the latest version from the FSSC. Note that it is recommended to use the non-ROOT binary distributions of the Science Tools.

These instructions assume that you already have a local installation of the Fermi Science Tools (STs). For more information about installing and setting up the STs see Installing the Fermi Science Tools. If you are running at SLAC you can follow the Running at SLAC instructions. For Unix/Linux users we currently recommend following the Installing with Anaconda Python instructions. For OSX users we recommend following the Installing with pip instructions. The Installing with Docker instructions can be used to install the STs on OSX and Linux machines that are new enough to support Docker. To install the development version of Fermipy follow the Installing Development Versions instructions.

Installing the Fermi Science Tools

The Fermi STs are a prerequisite for fermipy. To install the STs we recommend using one of the non-ROOT binary distributions available from the FSSC. The following example illustrates how to install the binary distribution on a Linux machine running Ubuntu Trusty:

$ curl -OL
$ tar xzf ScienceTools-v10r0p5-fssc-20150518-x86_64-unknown-linux-gnu-libc2.19-10-without-rootA.tar.gz
$ export FERMI_DIR=ScienceTools-v10r0p5-fssc-20150518-x86_64-unknown-linux-gnu-libc2.19-10-without-rootA/x86_64-unknown-linux-gnu-libc2.19-10
$ source $FERMI_DIR/

More information about installing the STs as well as the complete list of the available binary distributions is available on the FSSC software page.

Installing with pip

These instructions cover installation with the pip package management tool. This will install fermipy and its dependencies into the python distribution that comes with the Fermi Science Tools. First verify that you’re running the python from the Science Tools

$ which python

If this doesn’t point to the python in your Science Tools install (i.e. it returns /usr/bin/python or /usr/local/bin/python) then the Science Tools are not properly setup.

Before starting the installation process, you will need to determine whether you have setuptools and pip installed in your local python environment. You may need to install these packages if you are running with the binary version of the Fermi Science Tools distributed by the FSSC. The following command will install both packages in your local environment:

$ curl | python -

Check if pip is correctly installed:

$ which pip

Once again, if this isn’t the pip in the Science Tools, something went wrong. Now install fermipy by running

$ pip install fermipy

To run the ipython notebook examples you will also need to install jupyter notebook:

$ pip install jupyter

Finally, check that fermipy imports:

$ python
Python 2.7.8 (default, Aug 20 2015, 11:36:15)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from fermipy.gtanalysis import GTAnalysis
>>> help(GTAnalysis)

Installing with Anaconda Python


The following instructions have only been verified to work with binary Linux distributions of the Fermi STs. If you are using OSX or you have installed the STs from source you should follow the Installing with pip thread above.

These instructions cover how to use fermipy with a new or existing anaconda python installation. These instructions assume that you have already downloaded and installed the Fermi STs from the FSSC and you have set the FERMI_DIR environment variable to point to the location of this installation.

If you already have an existing anaconda python installation then fermipy can be installed from the conda-forge channel as follows:

$ conda config --append channels conda-forge
$ conda install fermipy

If you do not have an anaconda installation, the script can be used to create a minimal anaconda installation from scratch. First download and source the script from the fermipy repository:

$ curl -OL
$ source

If you do not already have anaconda python installed on your system this script will create a new installation under $HOME/miniconda. If you already have anaconda installed and the conda command is in your path the script will use your existing installation. After running fermipy can be installed with conda:

$ conda install fermipy

Once fermipy is installed you can initialize the ST/fermipy environment by running

$ curl -OL
$ source

If you installed fermipy in a specific conda environment you should switch to this environment before running the script:

$ source activate fermi-env
$ source

Installing with Docker


This method for installing the STs is currently experimental and has not been fully tested on all operating systems. If you encounter issues please try either the pip- or anaconda-based installation instructions.

Docker is a virtualization tool that can be used to deploy software in portable containers that can be run on any operating system that supports Docker. Before following these instruction you should first install docker on your machine following the installation instructions for your operating system. Docker is currently supported on the following operating systems:

  • macOS 10.10.3 Yosemite or later
  • Ubuntu Precise 12.04 or later
  • Debian 8.0 or later
  • RHEL7 or later
  • Windows 10 or later

Note that Docker is not supported by RHEL6 or its variants (CentOS6, Scientific Linux 6).

These instructions describe how to create a docker-based ST installation that comes preinstalled with anaconda python and fermipy. The installation is fully contained in a docker image that is roughly 2GB in size. To see a list of the available images go to the fermipy Docker Hub page. Images are tagged with the release version of the STs that was used to build the image (e.g. 11-05-00). The latest tag points to the image for the most recent ST release.

To install the latest image first download the image file:

$ docker pull fermipy/fermipy

Now switch to the directory where you plan to run your analysis and execute the following command to launch a docker container instance:

$ docker run -it --rm -p 8888:8888 -v $PWD:/workdir -w /workdir fermipy/fermipy

This will start an ipython notebook server that will be attached to port 8888. Once you start the server it will print a URL that you can use to connect to it with the web browser on your host machine. The -v $PWD:/workdir argument mounts the current directory to the working area of the container. Additional directories may be mounted by adding more volume arguments -v with host and container paths separated by a colon.

The same docker image may be used to launch python, ipython, or a bash shell by passing the command as an argument to docker run:

$ docker run -it --rm -v $PWD:/workdir -w /workdir fermipy/fermipy ipython
$ docker run -it --rm -v $PWD:/workdir -w /workdir fermipy/fermipy python
$ docker run -it --rm -v $PWD:/workdir -w /workdir fermipy/fermipy /bin/bash

By default interactive graphics will not be enabled. The following commands can be used to enable X11 forwarding for interactive graphics on an OSX machine. This requires you to have installed XQuartz 2.7.10 or later. First enable remote connections by default and start the X server:

$ defaults write org.macosforge.xquartz.X11 nolisten_tcp -boolean false
$ open -a XQuartz

Now check that the X server is running and listening on port 6000:

$ lsof -i :6000

If you don’t see X11 listening on port 6000 then try restarting XQuartz.

Once you have XQuartz configured you can enable forwarding by setting DISPLAY environment variable to the IP address of the host machine:

$ export HOST_IP=`ifconfig en0 | grep "inet " | cut -d " " -f2`
$ xhost +local:
$ docker run -it --rm -e DISPLAY=$HOST_IP:0 -v $PWD:/workdir -w /workdir fermipy ipython

Installing Development Versions

The instructions describe how to install development versions of Fermipy. Before installing a development version we recommend first installing a tagged release following the Installing with pip or Installing with Anaconda Python instructions above.

The development version of Fermipy can be installed by running pip install with the URL of the git repository:

$ pip install git+

This will install the most recent commit on the master branch. Note that care should be taken when using development versions as features/APIs under active development may change in subsequent versions without notice.

Running at SLAC

This section provides specific installation instructions for running in the SLAC computing environment. We suggest to follow these instruction if you are running Fermipy at SLAC. You will create your own conda installation in this way you will not depend on old version of programs present in the SLAC machines. First grab the installation and setup scripts from the fermipy github repository:

$ curl -OL
$ curl -OL

Now choose an installation path. This should be a new directory (e.g. $HOME/anaconda) that has at least 2-4 GB available. We will assign this location to the CONDABASE environment variable which is used by the setup script to find the location of your python installation. To avoid setting this every time you log in it’s recommended to set CONDABASE into your .bashrc file.

Now run the following commands to install anaconda and fermipy. This will take about 5-10 minutes.

$ export CONDABASE=<path to install directory>

Once anaconda is installed you will initialize your python and ST environment by running the slacsetup function in This function will set the appropriate environment variables needed to run the STs and python.

$ source
$ slacsetup

For convenience you can also copy this function into your .bashrc file so that it will automatically be available when you launch a new shell session. By default the function will setup your environment to point to a recent version of the STs and the installation of python in CONDABASE. If CONDABASE is not defined then it will use the installation of python that is packaged with a given release of the STs. The slacsetup function takes two optional arguments which can be used to override the ST version or python installation path.

# Use ST 10-00-05
$ slacsetup 10-00-05
# Use ST 11-01-01 and python distribution located at <PATH>
$ slacsetup 11-01-01 <PATH>

The installation script only installs packages that are required by fermipy and the STs. Once you’ve initialized your shell environment you are free to install additional python packages with the conda package manager tool with conda install <package name>. Packages that are not available on conda can also be installed with pip.

conda can also be used to upgrade packages. For instance you can upgrade fermipy to the newest version with the conda update command:

$ conda update fermipy

You can verify that the installation has succeeded by importing GTAnalysis:

$ python
Python 2.7.8 |Anaconda 2.1.0 (64-bit)| (default, Aug 21 2014, 18:22:21)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: and
>>> from fermipy.gtanalysis import GTAnalysis


By default installing fermipy with pip or conda will get the latest tagged released available on the PyPi package respository. You can check your currently installed version of fermipy with pip show:

$ pip show fermipy

or conda info:

$ conda info fermipy

To upgrade your fermipy installation to the latest version run the pip installation command with --upgrade --no-deps (remember to also include the --user option if you’re running at SLAC):

$ pip install fermipy --upgrade --no-deps
Collecting fermipy
Installing collected packages: fermipy
  Found existing installation: fermipy 0.6.6
    Uninstalling fermipy-0.6.6:
      Successfully uninstalled fermipy-0.6.6
Successfully installed fermipy-0.6.7

If you installed fermipy with conda the equivalent command is:

$ conda update fermipy

Developer Installation

These instructions describe how to install fermipy from its git source code repository using the script. Installing from source can be useful if you want to make your own modifications to the fermipy source code. Note that non-developers are recommended to install a tagged release of fermipy following the Installing with pip or Installing with Anaconda Python instructions above.

First clone the fermipy git repository and cd to the root directory of the repository:

$ git clone
$ cd fermipy

To install the latest commit in the master branch run install from the root directory:

# Install the latest commit
$ git checkout master
$ python install --user

A useful option if you are doing active code development is to install your working copy of the package. This will create an installation in your python distribution that is linked to the copy of the code in your local repository. This allows you to run with any local modifications without having to reinstall the package each time you make a change. To install your working copy of fermipy run with the develop argument:

# Install a link to your source code installation
$ python develop --user

You can later remove the link to your working copy by running the same command with the --uninstall flag:

# Install a link to your source code installation
$ python develop --user --uninstall

Specific release tags can be installed by running git checkout before running the installation command:

# Checkout a specific release tag
$ git checkout X.X.X
$ python install --user

To see the list of available release tags run git tag.


If you get an error about importing matplotlib (specifically something about the macosx backend) you might change your default backend to get it working. The customizing matplotlib page details the instructions to modify your default matplotlibrc file (you can pick GTK or WX as an alternative). Specifically the TkAgg and macosx backends currently do not work on OSX if you upgrade matplotlib to the version required by fermipy. To get around this issue you can switch to the Agg backend at runtime before importing fermipy:

>>> import matplotlib
>>> matplotlib.use('Agg')

However note that this backend does not support interactive plotting.

If you are running OSX El Capitan or newer you may see errors like the following:

dyld: Library not loaded

In this case you will need to disable the System Integrity Protections (SIP). See here for instructions on disabling SIP on your machine.

In some cases the script will fail to properly install the fermipy package dependecies. If installation fails you can try running a forced upgrade of these packages with pip install --upgrade:

$ pip install --upgrade --user numpy matplotlib scipy astropy pyyaml healpy wcsaxes ipython jupyter