`pycoco`

v0.9.17

This is the development repo for the python frontend for the core-collapse SNe template code 'CoCo': https://github.com/UoS-SNe/CoCo (my fork is currently https://github.com/RobFirth/CoCo).

CoCo was originally started by Natasha Karpenka, and is currently being updated and maintained by S. Prajs (https://github.com/SzymonPrajs).

A paper, Firth et. al. 2017, is currently in prep.

Extending spectra with "donor" spectra
Implemented a raft of changes that make it easier to interact with the spectral fits and the final templates
fixed a particularly nasty bug (https://github.com/RobFirth/pycoco/issues/28) that was screwing up specphot (via filter resampling)
Updated notebook tarball - (again 17/12/17)
Now available on PyPi and via pip - package available to install as pycocosn
Extending templates now possible with Black Body spectrum, flat and linear
calling CoCo (or reproduced CoCo functions) now more straightforward
Added more test cases to test_pycoco
Travis-CI implemented and Master and dev are passing. Fixed bug with ENVIRONS.
Dependancies now handled in setup.py
Calling all parts of CoCo from pycoco now operational
Migrated to better, and clearer code structure and sub-modules
Mangling now done within python, rather than C++ in CoCo
File I/O and interaction with CoCo LCfit output now operational - 11/01/17
Usage of a SN class now solid
Implementing calls to CoCo LCfit now
Calls to CoCo specfit now implemented
Mangling now stable
Adding tools for calculating magnitude offsets to make it easier to import new data
regeneration of filter list file now possible
added colours and bandpasses for LSST filters
Less dependence on environment variables
installation through setup.py now possible
better handing of CoCo sim outputs
SN position and mu now stored in infofile ./testdata/info/info.dat
dark sky calculations and integration with LSST Throughputs now done
Improved stability
input from astropy tables now more straightforward - better integration with coco.simulate
can now batch fit light curves and spectra from within python

To install:

pip install pycocosn

To install from source:

git clone https://github.com/RobFirth/verbose-enigma.git

then:

cd verbose-enigma
python setup.py install --user

(The --user argument only installs current user only, omitting flag will install for all users on the system if there are appropriate permissions)

NOTE: make sure that the python used to install is the one that you will use with pycoco

Ideally set the following environment variables:

COCO_ROOT_DIR (my default is ~/Code/CoCo/) PYCOCO_FILTER_DIR(my default is ~/Code/CoCo/data/filters/) PYCOCO_DATA_DIR (my default is ~/Code/CoCo/data/) SFD_DIR (my default is ~/data/Dust/sfddata-master/; see below) LSST_THROUGHPUTS (my default is ${HOME}/projects/LSST/throughputs) LSST_THROUGHPUTS_BASELINE (my default is ${LSST_THROUGHPUTS}/baseline)

also pycoco/ and CoCo need to be in your path and pythonpath, i.e.:

 setenv PATH /Users/berto/Code/pycoco/:$PATH

 setenv PYTHONPATH "/Users/berto/Code/pycoco/:$PYTHONPATH

Requirements

python packages

matplotlib
numpy
scipy
astropy
lmfit
sfdmap (https://github.com/kbarbary/sfdmap)

additionally

lsst throughputs (https://github.com/lsst/throughputs; $LSST_THROUGHPUTS points to this directory)

for sfdmap, the environment variable SFD_DIR needs to point at the path to the parent directory of the appropriate dust map files. See the installation instructions here: https://github.com/kbarbary/sfdmap

Known Problems -

If using in an environment (i.e. through (ana)conda) on Mac and you see the following:

~/anaconda3/lib/python3.6/site-packages/pycocosn-0.9.6-py3.6.egg/pycoco/__init__.py in <module>()
     24 from . import extinction
     25 from . import colours
---> 26 from . import utils
     27 from . import errors
     28 from . import kcorr

~/anaconda3/lib/python3.6/site-packages/pycocosn-0.9.6-py3.6.egg/pycoco/utils.py in <module>()
     12 import warnings
     13
---> 14 import matplotlib.pyplot as plt
     15 from astropy import units as u
     16 from astropy.table import Table, Column

~/anaconda3/lib/python3.6/site-packages/matplotlib/pyplot.py in <module>()
    111 ## Global ##
    112
--> 113 _backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()
    114
    115 _IP_REGISTERED = None

~/anaconda3/lib/python3.6/site-packages/matplotlib/backends/__init__.py in pylab_setup(name)
     58     # imports. 0 means only perform absolute imports.
     59     backend_mod = __import__(backend_name, globals(), locals(),
---> 60                              [backend_name], 0)
     61
     62     # Things we pull in from all backends

~/anaconda3/lib/python3.6/site-packages/matplotlib/backends/backend_macosx.py in <module>()
     17
     18 import matplotlib
---> 19 from matplotlib.backends import _macosx
     20
     21 from .backend_agg import RendererAgg, FigureCanvasAgg

RuntimeError: Python is not installed as a framework. The Mac OS X backend will not be able to function correctly if Python is not installed as a framework. See the Python documentation for more information on installing Python as a framework on Mac OS X. Please either reinstall Python as a framework, or try one of the other backends. If you are using (Ana)Conda please install python.app and replace the use of 'python' with 'pythonw'. See 'Working with Matplotlib on OSX' in the Matplotlib FAQ for more information.

you need to swap the default backend.

If you have installed the pip matplotlib, there is a directory in your root called `~/.matplotlib.

Create a file `~/.matplotlib/matplotlibrc there and add the following: backend: TkAgg

RobFirth / pycoco

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