fixed some of the doc problems

docs/conf.py

@@ -41,6 +41,26 @@
 # Load all of the global Astropy configuration
 from astropy_helpers.sphinx.conf import *
 
+#extensions = [
+#    'sphinx.ext.autodoc',
+#    'sphinx.ext.intersphinx',
+#    'sphinx.ext.todo',
+#    'sphinx.ext.coverage',
+#    'sphinx.ext.pngmath',
+#    'sphinx.ext.inheritance_diagram',
+#    'astropy_helpers.sphinx.ext.numpydoc',
+#    'astropy_helpers.sphinx.ext.astropyautosummary',
+#    'astropy_helpers.sphinx.ext.automodsumm',
+#    'astropy_helpers.sphinx.ext.automodapi',
+#    'astropy_helpers.sphinx.ext.tocdepthfix',
+#    'astropy_helpers.sphinx.ext.doctest',
+#    'astropy_helpers.sphinx.ext.changelog_links',
+#    'astropy_helpers.sphinx.ext.viewcode',  # Use patched version of viewcode
+#    'astropy_helpers.sphinx.ext.smart_resolver'
+#    ]
+extensions.pop(extensions.index('astropy_helpers.sphinx.ext.automodsumm'))
+extensions.pop(extensions.index('astropy_helpers.sphinx.ext.automodapi'))
+
 # Get configuration information from setup.cfg
 from distutils import config
 conf = config.ConfigParser()

docs/getting_started.rst

@@ -0,0 +1,15 @@
+***************
+Getting started
+***************
+
+The first useful thing is to create a lightcurve model for a Ni56 powered
+explosion. Here the values for the different are given in units of solar
+masses::
+
+    >>> from tardisnuclear import models
+    >>> sn_model = models.make_bolometric_model(ni56=1.0)
+    >>> sn_model
+    <BolometricLightCurve(ni56=1.0)>
+
+It is however very likely that this will fail due to the inavailabilty of the
+necessary nuclear data. The nuclear data.

docs/index.rst

@@ -1,13 +1,18 @@
-Documentation
-=============
+TARDIS Nuclear
+==============
 
-This is an affiliated package for the AstroPy package. The documentation for
-this package is here:
+TARDIS Nuclear is a framework to calculate the energy budget from nuclear
+decay in supernovae. It is a companion package to the TARDIS SN radiative
+transfer code and in the future these packages are intended to work together.
+Furthermore, this code can be used to calculate simple bolometric lightcurves.
 
 .. toctree::
-  :maxdepth: 2
+    :maxdepth: 2
+
+    install.rst
+    getting_started.rst
+
+
+
 
-  packagename/index.rst
 
-.. note:: Do not edit this page - instead, place all documentation for the
-          affiliated package inside ``packagename/``

docs/install.rst

@@ -0,0 +1,10 @@
+************
+Installation
+************
+
+``tardisnuclear`` has several dependencies that are easiest installed via
+ `Anaconda <http://continuum.io/downloads>`_ and all further instructions will
+ assume that you use that for your installation. The first package that needs
+ to be installed is pyne::
+
+    conda install -c cyclus -c pyne pyne=0.5.0

tardisnuclear/io/read_henke.py

@@ -0,0 +1,15 @@
+import requests
+from bs4 import BeautifulSoup
+
+base_url = 'http://henke.lbl.gov/cgi-bin/pert_cgi.pl'
+
+
+def get_photo_absorption_cross_section(element_code, energy):
+    data = requests.get(base_url, data=dict(
+        Element=element_code, Energy=energy))
+    bs = BeautifulSoup(data.text)
+    for item in bs.find_all('li'):
+        if item.text.startswith('Photo'):
+            return float(item.text.split(':')[1].strip().replace('cm^2/g', ''))
+
+

tardisnuclear/io/tests/__init__.py

@@ -0,0 +1 @@
+

tardisnuclear/io/tests/test_henke.py

@@ -0,0 +1,4 @@
+
+
+def test_henke_fe():
+    pass

tardisnuclear/models/__init__.py

@@ -0,0 +1 @@
+__author__ = 'wkerzend'

tardisnuclear/models/base.py

@@ -0,0 +1,77 @@
+import numpy as np
+
+from astropy.modeling import FittableModel, Parameter
+from astropy import units as u
+from pyne import nucname
+
+from tardisnuclear.ejecta import Ejecta, msun_to_cgs
+from tardisnuclear.rad_trans import SimpleLateTime
+from tardisnuclear.nuclear_data import NuclearData
+
+mpc_to_cm = u.Mpc.to(u.cm)
+
+class BaseBolometricLightCurve(FittableModel):
+    inputs = ('epoch', )
+    outputs = ('luminosity', )
+
+    def __init__(self, **kwargs):
+        super(BaseBolometricLightCurve, self).__init__(**kwargs)
+        self._init_ejecta(kwargs)
+        nuclear_data = NuclearData(self.ejecta.get_all_children_nuc_name())
+        self.rad_trans = SimpleLateTime(self.ejecta, nuclear_data)
+
+    def _init_ejecta(self, isotope_dict):
+        titled_isotope_dict = {name.title():value * u.Msun
+                               for name, value in isotope_dict.items()}
+        self.ejecta = Ejecta.from_masses(**titled_isotope_dict)
+
+    def _update_ejecta(self, isotope_masses):
+        assert len(isotope_masses) == len(self.param_names)
+        total_mass = np.sum(isotope_masses)
+        self.ejecta.mass_g = total_mass * msun_to_cgs
+        for isotope_name, isotope_mass in zip(self.param_names, isotope_masses):
+            self.ejecta[isotope_name.title()] = isotope_mass / total_mass
+
+    def evaluate(self, epoch, *args):
+        self._update_ejecta(args)
+        return self.rad_trans.total_bolometric_light_curve(epoch)
+
+
+def make_bolometric_model(**kwargs):
+    """
+    Make a bolometric lightcurve model
+    :param kwargs:
+    :return:
+    """
+    class_dict = {}
+    class_dict['__init__'] = BaseBolometricLightCurve.__init__
+    init_kwargs = {}
+    for isotope_name in kwargs:
+        if not nucname.isnuclide(isotope_name):
+            raise ValueError('{0} is not a nuclide name')
+        class_dict[isotope_name.lower()] = Parameter()
+        init_kwargs[isotope_name.lower()] = kwargs[isotope_name]
+    BolometricLightCurve = type('BolometricLightCurve',
+                                (BaseBolometricLightCurve, ), class_dict)
+
+    return BolometricLightCurve(**init_kwargs)
+
+class RSquared(FittableModel):
+    inputs = ('luminosity', )
+    outputs = ('luminosity_density', )
+
+    #Distance in Mpc
+    distance = Parameter()
+
+
+    def evaluate(self, luminosity, distance):
+        return luminosity / (4 * np.pi * (distance * mpc_to_cm)**2)
+
+
+class BolometricChi2Likelihood(FittableModel):
+
+    inputs = ('luminosity_density', )
+    outputs = ('log_likelihood')
+
+    def __init__(self, epochs, ):
+        pass

tardisnuclear/models/supernova.py

@@ -0,0 +1,5 @@
+from astropy import modeling
+
+class BaseHomologousRadial1D(object):
+    def __init__(self, abundances, densities):
+        pass