**************
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 <https://www.continuum.io/downloads/>`_
to install and/or update these packages.

* `python <http://www.python.org/>`_ versions 3.11 or later
* `numpy <http://www.numpy.org/>`_ version 2.2 or later
* `astropy <http://www.astropy.org/>`_ version 7.1 or later
* `scipy <http://www.scipy.org/>`_ version 1.17 or later
* `healpy <https://healpy.readthedocs.io/en/latest/index.html>`_ version 1.19 or later
* `pandas <https://pandas.pydata.org/>`_ version 2.2 or later
* `requests <https://pillow.readthedocs.io/en/5.3.x/>`_  version 2.18 or later
* `dust_extinction <https://dust-extinction.readthedocs.io/en/latest/>`_ 
* `matplotlib <https://matplotlib.org/>`_ version 3.7 or greater
* `linetools <https://github.com/linetools/linetools>`_  version 0.3.1 or later
* `astropath <https://github.com/FRBs/astropath>`_  version 0.1 or later


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

* `astroquery <https://astroquery.readthedocs.io/en/latest/>`_ v0.4.11 or later
* `datalab-client <https://github.com/noaodatalab/datalab/>`_ v2.20 or later
* `pyvo <https://pyvo.readthedocs.io/en/latest/>`_  version 0.9.2 or later

Extras
------

The following packages are more for builders and not recommended for most users.

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

* `photutils <https://photutils.readthedocs.io/en/stable/>`_  version 1.11.0 or later
* `scikit-image <https://scikit-image.org/>`_  version 0.21.0 or later

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

* `ne2001 <https://github.com/FRBs/ne2001.git>`_  NE2001
* george :: Use pip
* `class <https://github.com/lesgourg/class_public>`_ version 2.7 or greater
* `Aemulator <https://github.com/AemulusProject/Aemulator>`_  pip is broken..
* `hmf_emulator <https://github.com/AemulusProject/hmf_emulator>`_  HMF emulator (requires GSL)

The following are required to build host galaxy objects:

* `pPXF <https://pypi.org/project/ppxf/>`_ version 6.7 or greater
* `pcigale <https://cigale.lam.fr/>`_ version 2025.0

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/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 <https://drive.google.com/drive/folders/1_nu8IiBm0-dnkpoKBcoXyQuqbsrYHNXh?usp=sharing>`_.

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 frb.
	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


.. _download-public:


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.