Merge 9a49ca9 into d6a2ac0

.travis.yml

@@ -74,8 +74,12 @@ 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
+    # Use the following to get the ref-data from the master; 
     - if [[ $TEST_MODE == 'spectrum' ]]; then git fetch origin; fi
     - if [[ $TEST_MODE == 'spectrum' ]]; then git checkout origin/master; fi
+    # Use the following to get the ref-data from a specific pull request; 
+    # - if [[ $TEST_MODE == 'spectrum' ]]; then git fetch origin pull/10/head:formalintegral-ref; fi
+    # - if [[ $TEST_MODE == 'spectrum' ]]; then git checkout formalintegral-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

tardis/tests/test_tardis_full_formal_integral.py

@@ -0,0 +1,89 @@
+import os
+import pytest
+import numpy as np
+import numpy.testing as npt
+from astropy import units as u
+from astropy.tests.helper import assert_quantity_allclose
+
+from tardis.simulation.base import Simulation
+from tardis.io.config_reader import Configuration
+
+
+config_line_modes = ['downbranch', 'macroatom']
+
+
+@pytest.fixture(scope='module', params=config_line_modes)
+def config(request):
+    config = Configuration.from_yaml(
+        'tardis/io/tests/data/tardis_configv1_verysimple.yml')
+
+    config["plasma"]["line_interaction_type"] = request.param
+    config["montecarlo"]["no_of_packets"] = 4.0e+4
+    config["montecarlo"]["last_no_of_packets"] = 1.0e+5
+    config["montecarlo"]["no_of_virtual_packets"] = 0
+    config["spectrum"]["method"] = "integrated"
+
+    return config
+
+
+class TestRunnerSimpleFormalInegral():
+    """
+    Very simple run with the formal integral spectral synthesis method
+    """
+    name = 'test_runner_simple_integral'
+
+    @pytest.fixture(scope="class")
+    def runner(
+            self, config, atomic_data_fname,
+            tardis_ref_data, generate_reference):
+        config.atom_data = atomic_data_fname
+
+        self.name = (self.name +
+                     "_{:s}".format(config.plasma.line_interaction_type))
+
+        simulation = Simulation.from_config(config)
+        simulation.run()
+
+        if not generate_reference:
+            return simulation.runner
+        else:
+            simulation.runner.hdf_properties = [
+                    'j_blue_estimator',
+                    'spectrum',
+                    'spectrum_integrated'
+                    ]
+            simulation.runner.to_hdf(
+                    tardis_ref_data,
+                    '',
+                    self.name)
+            pytest.skip(
+                    'Reference data was generated during this run.')
+
+    @pytest.fixture(scope='class')
+    def refdata(self, tardis_ref_data):
+        def get_ref_data(key):
+            return tardis_ref_data[os.path.join(
+                    self.name, key)]
+        return get_ref_data
+
+    def test_j_blue_estimators(self, runner, refdata):
+        j_blue_estimator = refdata('j_blue_estimator').values
+
+        npt.assert_allclose(
+                runner.j_blue_estimator,
+                j_blue_estimator)
+
+    def test_spectrum(self, runner, refdata):
+        luminosity = u.Quantity(refdata('spectrum/luminosity'), 'erg /s')
+
+        assert_quantity_allclose(
+            runner.spectrum.luminosity,
+            luminosity)
+
+    def test_spectrum_integrated(self, runner, refdata):
+        luminosity = u.Quantity(
+                refdata('spectrum_integrated/luminosity'), 'erg /s')
+
+        assert_quantity_allclose(
+            runner.spectrum_integrated.luminosity,
+            luminosity)