Relocate test_w7.py and add documentation.

- Some changes are made in setup() method of the
  integration test - the description about it is
  now updated in the block comments.

tardis/tests/w7_13d/test_w7.py → tardis/tests/test_w7.py

@@ -1,9 +1,18 @@
+import os
+import yaml
 import pytest
 import numpy as np
-import tardis
 import numpy.testing as nptesting
 from astropy import units as u
-import os
+
+import tardis
+from tardis.simulation.base import Simulation
+from tardis.model import Radial1DModel
+from tardis.io.config_reader import Configuration
+
+
+def w7_path(fname):
+    return os.path.join(tardis.__path__[0], 'tests', 'w7_13d', fname)
 
 
 @pytest.mark.skipif(not pytest.config.getoption("--run-slow"),
@@ -16,18 +25,55 @@ class TestW7:
     @classmethod
     @pytest.fixture(scope="class", autouse=True)
     def setup(self):
-        self.w7_config_filepath = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'tardis_w7.yml')
-        self.atom_data_filepath = os.path.realpath('/tmp/kurucz_cd23_chianti_H_He.h5')
-        self.obtained_w7_radial1d_model = tardis.run_tardis(config=self.w7_config_filepath,
-                                                            atom_data=self.atom_data_filepath)
-
+        """
+        This method does an initial setup of making the configuration and performing
+        a single run of this integration test from Stratified W7 setup.
+        """
+
+        # First we check whether the config file does even exist at the desired path.
+        assert os.path.exists(w7_path('tardis_w7.yml')), ('%s config file does not exist' %
+                                                          w7_path('tardis_w7.yml'))
+
+        # The available config file does not have the filepaths of atom data file,
+        # densities and abundances profile files as desired. We form a dictionary
+        # from the config file and tweak those parameters - putting the filepaths
+        # of these three files at proper places.
+        self.config_yaml = yaml.load(open(w7_path('tardis_w7.yml')))
+
+        # Remaining assertions are made here - each for atom data file, abundances
+        # profile file and densities profile file.
+        assert os.path.exists('/tmp/kurucz_cd23_chianti_H_He.h5'), ('%s atom data file does not exist' %
+                                                                    w7_path('tardis_w7.yml'))
+
+        assert os.path.exists(w7_path('tardis_w7_13d_abundances.dat')), ('%s abundances profile file does not exist' %
+                                                                         w7_path('tardis_w7.yml'))
+
+        assert os.path.exists(w7_path('tardis_w7_13d_densities.dat')), ('%s densities profile file does not exist' %
+                                                                        w7_path('tardis_w7.yml'))
+
+        self.config_yaml['atom_data'] = '/tmp/kurucz_cd23_chianti_H_He.h5'
+        self.config_yaml['model']['abundances']['filename'] = w7_path('tardis_w7_13d_abundances.dat')
+        self.config_yaml['model']['structure']['filename'] = w7_path('tardis_w7_13d_densities.dat')
+
+        # The configuration hence obtained will be having appropriate file paths.
+        tardis_config = Configuration.from_config_dict(self.config_yaml)
+
+        # We now do a run with the prepared configuration and get radial1d model.
+        self.obtained_w7_radial1d_model = Radial1DModel(tardis_config)
+        self.simulation = Simulation(tardis_config)
+        self.simulation.legacy_run_simulation(self.obtained_w7_radial1d_model)
+
+        # The benchmark data against which assertions are to be made is ingested
+        # from an already available compressed binary (.npz). This will return a
+        # dictionary of numpy.ndarrays and the latter will also return dictionary
+        # of numpy.ndarrays - difference is, they were astropy quantities earlier.
         self.expected_w7_ndarrays = np.load(
-            os.path.join(os.path.dirname(os.path.realpath(__file__)), 'expected_ndarrays.npz')
-        )
+            os.path.join(os.path.dirname(w7_path('expected_ndarrays.npz'))
+        ))
 
         self.expected_w7_astropy_quantities = np.load(
-            os.path.join(os.path.dirname(os.path.realpath(__file__)), 'expected_quantities.npz')
-        )
+            os.path.join(os.path.dirname(w7_path('expected_quantities.npz'))
+        ))
 
     def test_j_estimators(self):
         np.testing.assert_allclose(