The final carsus merge

.travis.yml

@@ -72,13 +72,16 @@ before_install:
     - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs install --skip-smudge; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then git clone $TARDIS_REF_DATA_URL $HOME/tardis-refdata; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then cd $HOME/tardis-refdata; fi
-    - if [[ $TEST_MODE == 'spectrum' ]]; then git fetch origin pull/2/head:plasma-ref2; fi
-    - if [[ $TEST_MODE == 'spectrum' ]]; then git checkout plasma-ref2; fi
+    - if [[ $TEST_MODE == 'spectrum' ]]; then git fetch origin pull/3/head:carsus-ref; fi
+    - if [[ $TEST_MODE == 'spectrum' ]]; then git checkout carsus-ref; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs pull --include="atom_data/kurucz_cd23_chianti_H_He.h5" origin; fi
+    - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs pull --include="atom_data/chianti_He.h5" origin; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs pull --include="plasma_reference/" origin; fi
+    - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs pull --include="unit_test_data.h5" origin; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then cd $TRAVIS_BUILD_DIR; fi
 
 install:
+   - cd $TRAVIS_BUILD_DIR
    - conda env create -f tardis_env27.yml
    - source activate tardis
 

docs/atomic/atomic_data_description.rst

@@ -3,7 +3,7 @@
 ******************************
 Atomic Data Format Description
 ******************************
-.. currentmodule:: tardis.atomic
+.. currentmodule:: tardis.io.atomic
 
 
 The atomic data for tardis is stored in `hdf5 files <http://www.h5py.org/>`_. TARDIS ships with a
@@ -205,7 +205,7 @@ Macro Atom References
 The Atom Data Class
 -------------------
 
-Atom Data is stored inside TARDIS in the :class:`AtomData`-class. The class method :func:`AtomData.from_hdf5` will
+Atom Data is stored inside TARDIS in the :class:`AtomData`-class. The class method :func:`AtomData.from_hdf` will
 instantiate a new `AtomData`-class from an HDF5 file. If none is given it will automatically
 take the default HDF5-dataset shipped with TARDIS. A second function :func:`AtomData.prepare_atom_data`
 will cut the levels and lines data to only the required atoms and ions. In addition, it will create the intricate system
@@ -225,4 +225,4 @@ TO BE BETTER DOCUMENTED ...
 
 
 
-.. automodapi:: tardis.atomic
+.. automodapi:: tardis.io.atomic

docs/physics/plasma.rst

@@ -45,8 +45,9 @@ setting `BasePlasma.beta_rad` to :math:`\frac{1}{k_\textrm{B}T_\textrm{rad}}`.
 Here's an example how to instantiate a simple base plasma::
 
 
-    >>> from tardis import atomic, plasma
-    >>> atom_data = atomic.AtomData.from_hdf5()
+    >>> from tardis import plasma
+    >>> from tardis.io import atomic
+    >>> atom_data = atomic.AtomData.from_hdf()
     >>> my_plasma = plasma.BasePlasma({'Fe':0.5, 'Ni':0.5}, 10000, 1e-13, atom_data)
     >>> print my_plasma.abundances
     atomic_number abundance_fraction number_density

docs/physics/plasma/plasma_plots/lte_ionization_balance.py

@@ -1,7 +1,8 @@
 import os
 from matplotlib import pyplot as plt
 from matplotlib import colors
-from tardis import atomic, plasma_array, util
+from tardis import util
+from tardis.io import atomic
 import numpy as np
 import pandas as pd
 from astropy import units as u
@@ -18,7 +19,7 @@
 atom_fname = os.path.join(os.path.dirname(atomic.__file__), 'data', 'atom_data.h5')
 
 # reading in the HDF5 File
-atom_data = atomic.AtomData.from_hdf5(atom_fname)
+atom_data = atomic.AtomData.from_hdf(atom_fname)
 
 #The atom_data needs to be prepared to create indices. The Class needs to know which atomic numbers are needed for the
 #calculation and what line interaction is needed (for "downbranch" and "macroatom" the code creates special tables)
@@ -27,7 +28,12 @@
 #Initializing the NebularPlasma class using the from_abundance class method.
 #This classmethod is normally only needed to test individual plasma classes
 #Usually the plasma class just gets the number densities from the model class
-lte_plasma = plasma_array.BasePlasmaArray.from_abundance({'Si':1.0}, 1e-14*u.g/u.cm**3, atom_data, 10*u.day)
+assert True, (
+        'This script needs a proper rewrite and should use the new'
+        '"assemble_plasma" function.')
+# TODO: Uncomment and fix the next line
+# lte_plasma = assemble_plasma({'Si':1.0}, 1e-14*u.g/u.cm**3, atom_data, 10*u.day)
+lte_plasma = None
 lte_plasma.update_radiationfield([10000], [1.0])
 
 #Initializing a dataframe to store the ion populations  and level populations for the different temperatures
@@ -79,4 +85,4 @@
 ax2.set_ylabel('Number Density Fraction')
 cb.set_label('T [K]')
 
-plt.show()
+plt.show()

docs/physics/plasma/plasma_plots/nebular_ionization_balance.py

@@ -1,7 +1,8 @@
 import os
 
 from matplotlib import colors
-from tardis import atomic, plasma_array, util
+from tardis import util
+from tardis.io import atomic
 from matplotlib import pyplot as plt
 
 import numpy as np
@@ -19,7 +20,7 @@
 atom_fname = os.path.expanduser('~/.tardis/si_kurucz.h5')
 
 # reading in the HDF5 File
-atom_data = atomic.AtomData.from_hdf5(atom_fname)
+atom_data = atomic.AtomData.from_hdf(atom_fname)
 
 #The atom_data needs to be prepared to create indices. The Class needs to know which atomic numbers are needed for the
 #calculation and what line interaction is needed (for "downbranch" and "macroatom" the code creates special tables)
@@ -109,4 +110,4 @@
 ax2.set_ylabel('Number Density Fraction')
 cb.set_label('T [K]')
 
-plt.show()
+plt.show()