Installing frb

This document describes how to install the frb repository.

Installing Dependencies

We have and will continue to keep the number of dependencies low. There are a few standard packages that must be installed and one package linetools under review for astropy affiliated status.

In general, we recommend that you use Anaconda for the majority of these installations.

Detailed installation instructions are presented below:

Python Dependencies

frb depends on the following list of Python packages.

We recommend that you use Anaconda to install and/or update these packages.

If you are using Anaconda, you can check the presence of these packages with:

conda list "^python|numpy|astropy|scipy|pandas"

If the packages have been installed, this command should print out all the packages and their version numbers.

The following packages are required to access surveys (e.g. SDSS, DES) for data that may be associated to an FRB:

The following package(s) is/are required to access FRB galaxy spectra:

The following package is required to map a slit onto a finder chart (frb.figures.finder):

The following are required to use our KCWI datacube handling tools:

The following are required to run some of the halo codes:

The following are required to build host galaxy objects:

  • pPXF version 6.7 or greater
  • pcigale version 2018.0.1 to 2020.0 (cannot yet accommodate 2022.0 or greater)

The following is required to run the code in dm_kde:

  • asymmetric_kde <https://github.com/tillahoffmann/asymmetric_kde> no versioning

The following is required to run the MCMC DM code in dm.mcmc.py:

  • numba <https://github.com/https://github.com/numba/numba> version >= 0.50

For pPXF, you will also likely need to modify the standard install to use the Chabrier libraries. See the InstallNotes in this Google Drive.

The following are required for using functions in halos.photoz.py:

  • threedhst <https://github.com/gbrammer/threedhst> version >= 0.1.dev0
  • progressbar2 :: Use pip
  • pathos :: Use pip

Our CIGALE wrappers use custom filter files not provided by their current release (e.g DES, Pan-STARRS). See the instructions for adding those as needed.

Installing frb

Presently, you must download the code from github:

#go to the directory where you would like to install specdb.
git clone https://github.com/FRBs/FRB.git

From there, you can build and install with:

cd FRB
python setup.py install  # or use develop

This should install the package and scripts. Make sure that your PATH includes the standard location for Python scripts (e.g. ~/anaconda/bin)

Adding additional CIGALE filter files

We have had to add new filters to CIGALE (e.g. from DES and Pan-STARRS). You can find these filter files in frb.data.analysis.CIGALE. If you use any of those surveys, our wrappers will not work without them.

Here are the steps to update CIGALE:

  • cd frb/data/analysis/CIGALE
  • Add any desired filter into your CIGALE code base with: pcigale-filters add file.dat

Note that DECaLs uses the BASS and MzLS data files.

EAZY setup

In order to perform photo-z estimation with EAZY using our wrappers, the following changes need to be made.

  • Add an environment variable EAZYDIR that points to your EAZY installation. Add this to your bashrc:

    export EAZYDIR="/path/to/eazy-photoz/"

  • Locate the templates folder in $EAZYDIR and edit the paths present in *.spectra.param. Replace all SED file paths with the absolute paths. For instance, in $EAZYDIR/templates/eazy_v1.3.spectra.param, replace:

    templates/EAZY_v1.1_lines/eazy_v1.1_sed1.dat

with:

/path/to/eazy-photoz/templates/EAZY_v1.1_lines/eazy_v1.1_sed1.dat

pPXF

Our pPXF wrapper currently uses an older version of the code (v 6.7.17) and a few custom files. Contact JXP if you wish to use this.