Add plasma test class

1. BasePlasmaTest defines all the common tests for  different Plasma Setups.
2. Values are compared from a reference HDF file.

tardis/conftest.py

@@ -77,7 +77,8 @@ def pytest_addoption(parser):
     parser.addoption("--less-packets",
                      action="store_true", default=False,
                      help="Run integration tests with less packets.")
-
+    parser.addoption("--plasma-reference", dest="plasma-reference", default=None,
+                     help="folder for plasma reference HDF files")
 
 # -------------------------------------------------------------------------
 # project specific fixtures

tardis/plasma/tests/test_complete_plasmas.py

@@ -1 +1,162 @@
+import os
 
+import pandas as pd
+import pytest
+from pandas.util import testing as pdt
+
+from tardis.io.config_reader import Configuration
+from tardis.simulation import Simulation
+
+
+plasma_ref_path = os.path.expanduser(os.path.expandvars(
+    pytest.config.getvalue('plasma-reference')))
+
+
+class BasePlasmaTest:
+    #Class defining all common tests for different setups of Plasma
+    #This can then be inherited for different Plasma setup
+    @classmethod
+    def setup(cls):
+        pass
+
+    def read_hdf_attr(self, attr):
+        return pd.read_hdf(self.reference_file_path, os.path.join('plasma', attr))
+
+    #GENERAL PROPERTIES
+    def test_beta_rad(self):
+        pdt.assert_almost_equal(self.plasma.beta_rad,
+                                self.read_hdf_attr('beta_rad').values)
+
+    def test_g_electron(self):
+        pdt.assert_almost_equal(self.plasma.g_electron,
+                                self.read_hdf_attr('g_electron').values)
+
+    def test_number_density(self):
+        pdt.assert_almost_equal(
+            self.plasma.number_density, self.read_hdf_attr('number_density'))
+
+    def test_electron_temperature(self):
+        pdt.assert_almost_equal(self.plasma.t_electrons,
+                                self.read_hdf_attr('t_electrons').values)
+
+    #PARTITION PROPERTIES
+    def test_level_boltzmann_factor(self):
+        pdt.assert_almost_equal(
+            self.plasma.level_boltzmann_factor, self.read_hdf_attr('level_boltzmann_factor'))
+
+    def test_lte_partition_function(self):
+        pdt.assert_almost_equal(
+            self.plasma.partition_function, self.read_hdf_attr('partition_function'))
+
+    #ATOMIC PROPERTIES
+    def test_levels_property(self):
+        pdt.assert_almost_equal(
+            self.plasma.excitation_energy, self.read_hdf_attr('excitation_energy'))
+
+    def test_lines_property(self):
+        pdt.assert_almost_equal(self.plasma.lines, self.read_hdf_attr('lines'))
+
+    def test_lines_lower_level_index_property(self):
+        pdt.assert_almost_equal(self.plasma.lines_lower_level_index, self.read_hdf_attr(
+            'lines_lower_level_index').values)
+
+    def test_lines_upper_level_index_property(self):
+        pdt.assert_almost_equal(self.plasma.lines_upper_level_index, self.read_hdf_attr(
+            'lines_upper_level_index').values)
+
+    def test_atomic_mass_property(self):
+        pdt.assert_almost_equal(self.plasma.atomic_mass,
+                                self.read_hdf_attr('atomic_mass'))
+
+    def test_ionization_data_property(self):
+        pdt.assert_almost_equal(
+            self.plasma.ionization_data, self.read_hdf_attr('ionization_data'))
+
+    #ION POPULATION PROPERTIES
+    def test_phi(self):
+        pdt.assert_almost_equal(self.plasma.phi, self.read_hdf_attr('phi'))
+
+    def test_ion_number_density(self):
+        pdt.assert_almost_equal(
+            self.plasma.ion_number_density, self.read_hdf_attr('ion_number_density'))
+
+    def test_electron_densities(self):
+        pdt.assert_almost_equal(
+            self.plasma.electron_densities, self.read_hdf_attr('electron_densities'))
+
+    #LEVEL POPULATION PROPERTIES
+    def test_level_number_density(self):
+        pdt.assert_almost_equal(
+            self.plasma.level_number_density, self.read_hdf_attr('level_number_density'))
+
+    #RADIATIVE PROPERTIES
+    def test_stimulated_emission_factor(self):
+        pdt.assert_almost_equal(self.plasma.stimulated_emission_factor, self.read_hdf_attr(
+            'stimulated_emission_factor').values)
+
+    def test_tau_sobolev(self):
+        pdt.assert_almost_equal(self.plasma.tau_sobolevs,
+                                self.read_hdf_attr('tau_sobolevs'))
+
+    def test_beta_sobolev(self):
+        pdt.assert_almost_equal(self.plasma.beta_sobolev,
+                                self.read_hdf_attr('beta_sobolev').values)
+
+
+@pytest.mark.skipif(not pytest.config.getvalue("plasma-reference"),
+                    reason="Path to Plasma Reference files is not defined")
+class TestLTEPlasma(BasePlasmaTest):
+
+    @classmethod
+    @pytest.fixture(scope="class", autouse=True)
+    def setup(cls):
+        cls.reference_file_path = os.path.join(
+            plasma_ref_path, 'plasma_lte_reference.h5')
+
+        cls.config_path = os.path.join(
+            'tardis', 'plasma', 'tests', 'data', 'plasma_test_config_lte.yml')
+        cls.config = Configuration.from_yaml(cls.config_path)
+        cls.config['atom_data'] = os.path.abspath(os.path.expanduser(os.path.expandvars(
+            pytest.config.getvalue('atomic-dataset'))))
+        cls.sim = Simulation.from_config(cls.config)
+        cls.sim.run()
+        cls.plasma = cls.sim.plasma
+
+
+@pytest.mark.skipif(not pytest.config.getvalue("plasma-reference"),
+                    reason="Path to Plasma Reference files is not defined")
+class TestNLTEPlasma(BasePlasmaTest):
+
+    @classmethod
+    @pytest.fixture(scope="class", autouse=True)
+    def setup(cls):
+        cls.reference_file_path = os.path.join(
+            plasma_ref_path, 'plasma_nlte_reference.h5')
+
+        cls.config_path = os.path.join(
+            'tardis', 'plasma', 'tests', 'data', 'plasma_test_config_nlte.yml')
+        cls.config = Configuration.from_yaml(cls.config_path)
+        cls.config['atom_data'] = os.path.abspath(os.path.expanduser(os.path.expandvars(
+            pytest.config.getvalue('atomic-dataset'))))
+        cls.sim = Simulation.from_config(cls.config)
+        cls.sim.run()
+        cls.plasma = cls.sim.plasma
+
+    #Additional Tests for NLTE Plasma, apart from tests defined in BasePlasmaTest
+    #GENERAL PROPERTIES
+    def test_beta_electron(self):
+        pdt.assert_almost_equal(self.plasma.beta_electron,
+                                self.read_hdf_attr('beta_electron').values)
+
+    def test_selected_atoms(self):
+        pdt.assert_almost_equal(
+            self.plasma.selected_atoms.values, self.read_hdf_attr('selected_atoms').values)
+
+    #ATOMIC PROPERTIES
+    def test_zeta_data_property(self):
+        pdt.assert_almost_equal(
+            self.plasma.zeta_data.values, self.read_hdf_attr('zeta_data').values)
+
+    #ION POPULATION PROPERTIES
+    def test_radiation_field_correction(self):
+        pdt.assert_almost_equal(self.plasma.delta, self.read_hdf_attr('delta'))