Replace Comparison values in Plasma Unit Tests with reference HDF file

.travis.yml

@@ -72,6 +72,8 @@ 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 lfs pull --include="atom_data/kurucz_cd23_chianti_H_He.h5" origin; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then git lfs pull --include="plasma_reference/" origin; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then cd $TRAVIS_BUILD_DIR; fi

tardis/io/util.py

@@ -282,6 +282,8 @@ def get_properties(self):
         data['atom_data_uuid'] = self.atomic_data.uuid1
         if 'atomic_data' in data:
             data.pop('atomic_data')
+        if 'nlte_data' in data:
+            data.pop('nlte_data')
         return data
 
     def to_hdf(self, file_path, path='', name=None, collection=None):

tardis/plasma/properties/nlte.py

@@ -60,7 +60,7 @@ def calculate(level_boltzmann_factor,
         helium_population.ix[0,0] = 0.0
         #He II excited states
         he_two_population = level_boltzmann_factor.ix[2,1].mul(
-            (g.ix[2,1].ix[0]**(-1)))
+            (g.ix[2,1].ix[0]**(-1.0)))
         helium_population.ix[1].update(he_two_population)
         #He II ground state
         helium_population.ix[1,0] = 1.0

tardis/plasma/properties/partition_function.py

@@ -169,7 +169,7 @@ def _main_nlte_calculation(
                 else:
                     collision_matrix = nlte_data.get_collision_matrix(
                             species, t_electrons
-                            ) * previous_electron_densities.values
+                            ) * previous_electron_densities
             else:
                 collision_matrix = r_ul_matrix.copy()
                 collision_matrix.fill(0.0)

tardis/plasma/tests/data/plasma_base_test_config.yml

@@ -0,0 +1,42 @@
+tardis_config_version: v1.0
+
+supernova:
+    luminosity_requested: 2.8e9 solLum
+    time_explosion: 13 day
+
+atom_data: kurucz_atom_pure_simple.h5
+
+model:
+
+    structure:
+        type: specific
+
+        velocity:
+            start: 1.1e4 km/s
+            stop: 2.0e4 km/s
+            num: 20
+
+        density:
+            type: branch85_w7
+
+    abundances:
+        type: uniform
+        He: 1
+
+plasma:
+    ionization: lte
+    excitation: lte
+    radiative_rates_type: dilute-blackbody
+    line_interaction_type: macroatom
+
+montecarlo:
+    seed: 23111963
+    no_of_packets : 1.0e+5
+    iterations: 10
+    last_no_of_packets: 1.0e+5
+    no_of_virtual_packets: 5
+
+spectrum:
+    start: 500 angstrom
+    stop: 20000 angstrom
+    num: 10000