Installation

Note

Requires: Python >=3.5

Tested on macOS El Capitan (10.11.6) - Catalina (10.15.3) and Ubuntu 16.04 - 18.04

How to Install

The Data Tools can currently be installed from the tar file available at the Fermi Science Support Center. Download the tar file to some place on the machine you want it installed on.

One of the easiest and suggested methods of install is to create a virtual environment, which allows you to install the Data Tools requirements without worrying about possible conflicts with other versions of packages you may already have installed. It’s not mandatory to install in a virtual environment, but it could make your life much easier.

Note

One of the requirements for the Data Tools is Basemap, which is a part of the Matplotlib toolkit. Basemap requires the installation of the GEOS C library. If you do not have the library already compiled in a standard place, the Data Tools installation will attempt to compile it for you. There may be cases where this fails. If you encounter such a case, you should follow the instructions on how to compile the GEOS library for basemap here.

To install via pip, navigate to the directory where you want the virtual environment to live and:

$ python3 -m venv gbm
$ source gbm/bin/activate

This will create a new virtual environment called “gbm” and activates the environment.

To install via conda:

$ conda create --name gbm
$ source activate gbm

This will similarly create a new virtual environment and activates it.

It’s also good to ensure you have pip updated:

$ pip3 install --upgrade pip

If you don’t have the GEOS C library (required for Matplotlib Basemap) already installed in a standard location, set your GEOS_DIR environment variable to a path where you would like it installed (and where you have write privileges). For example, if you use bash, you can do something like this:

$ export GEOS_DIR=~/.geos_dir

If you already have the GEOS C library installed in a non-standard location, set GEOS_DIR to that path instead. Then you can install the data tools:

$ pip3 install <path_to_tar>/gbm_data_tools-1.0.2.tar.gz
$ pip3 install ipython
$ pip3 install notebook

The last two lines aren’t mandatory for the Data Tools unless you want to run the Jupyter notebooks provided with the Data Tools (trust us, you do).

If you don’t wish to install via a virtual environment, you are welcome to install with your preferred method, but you may encounter more difficulties, especially if you have existing package installs that conflict with what is required for the Data Tools. Check the requirements.txt for required packages and versions.


How to Uninstall

To uninstall:

$ pip3 uninstall gbm-data-tools

There are also a number of files (documentation, notebooks, etc.) for the tools that are copied into your $HOME/.gbm_data_tools directory. You can delete these files if you wish.

Documentation

On successful installation, you can launch the local HTML documentation by calling:

$ gbm-docs

from the command line.


Launching the Notebooks

If you have installed Jupyter as suggested above, you can run the notebooks provided with the Data Tools. After successful installation, the notebooks can be launched by calling:

$ gbm-demos

from the command line.


Quickstart

To load the Data Tools within your python environment, simply:

import gbm

The Data Tools has several different modules. For example, the data module containing the interfaces to the GBM data files can be loaded by:

from gbm import data

Known Issues

  • On install, Python complains the tar.gz file is not a valid file. This is a known issue with certain browsers, where they download and decompress the file without removing the .gz extension. The easiest fix is to rename the file without the .gz extension and retry the install.

  • When running a notebook in Linux, you observe a similar error:

    %matplotlib notebook
    Warning: Cannot change to a different GUI toolkit: notebook. Using osx instead.
    

    This is due to some backend plotting issue with Jupyter notebook on Linux. Remove the %matplotlib inline in the notebook cell and re-evaluate the cell twice to see the plot.

  • The FTP Data Finders fail with a connection error. This may be due to the underlying OpenSSL library that the Python ftplib uses. You may need to update your OpenSSL library to get this to work. Note that this only appears to be an issue with the FTPS protocol, not the normal FTP protocol.

  • The virtual environment is using your system ipython (or other package) install. This can sometimes happen if you didn’t install ipython (or other package) in the virtual environment. Try installing ipython (or other package) and restart your virtual environment.

  • You observe the following error:

    ImportError: No module named '_tkinter'
    

    This is a situation where Matplotlib is using the tkinter backend for plotting. You would see this error if you don’t have tkinter installed. You don’t need to install tkinter if you don’t want to; instead, you can create a file named matplotlibrc in your working directory that contains the following:

    backend : Agg