Merge branch 'master' into unify_unittest_hdfs

.travis.yml

@@ -91,6 +91,7 @@ install:
    - cd $TRAVIS_BUILD_DIR
    - conda env create -f tardis_env27.yml
    - source activate tardis
+   - conda install -y -c conda-forge codecov
    #trouble with building due to segfault at cython (https://github.com/cython/cython/issues/2199)
    #remove if we can get normal cython through conda
    - git clone https://github.com/cython/cython
@@ -104,7 +105,8 @@ script:
     - CC=$COMPILER python setup.py $SETUP_CMD
 
 after_success:
-    - if [[ "$SAVE_COVERAGE" = true ]]; then coveralls; fi
+    - if [[ "$SAVE_COVERAGE" = true ]]; then codecov -t a876d307-9ed5-4f5d-a6c4-e58291ac4111; fi
+
 
 after_failure:
     - cat /home/travis/.pip/pip.log

docs/workflow/development_workflow.rst

@@ -15,6 +15,9 @@ to the Astropy team for designing it.
 
     git_workflow
     release_workflow
+
+.. toctree::
+
     update_refdata
 
 

docs/workflow/update_refdata.rst

@@ -8,9 +8,17 @@ PR open.
 #. clone tardis-refdata (`git clone tardis-refdata`; you need to have git lfs installed) then make a new branch named
     the same as your new tardis feature branch.
 #. Generate new reference data (in your tardis directory and right branch) offline using
-    `python setup.py test --args="--tardis-refdata=<path to refdata repo/with the right branch> --generate-reference"`
+
+    .. code-block:: None
+
+        python setup.py test --args="--tardis-refdata=<path to refdata repo/with the right branch> --generate-reference"
+
 #. Rerun the tests and see if it does not fail using
-    `python setup.py test --args="--tardis-refdata=<path to refdata repo/with the right branch>"`
+
+    .. code-block:: None
+    
+        python setup.py test --args="--tardis-refdata=<path to refdata repo/with the right branch>"
+
 #. Switch to tardis-refdata. Commit the changed ref-data and open a PR on tardis-refdata
 #. Make a copy of the refdata comparer notebook provided in TARDIS-refdata to check if there are
     any unexpected changes in the updated reference data and the previous reference data
@@ -34,4 +42,4 @@ PR open.
         - if [[ $TEST_MODE == 'spectrum' ]]; then git checkout origin/master; fi```
 #. Then make sure that your TARDIS PR passes again.
 #. Then merge your PR to TARDIS master
-#. Congratulations - you updated TARDIS to be better. Have a beer and steak (or Tofu if you are vegetarian/vegan)
+#. Congratulations - you updated TARDIS to be better. Have a beer and steak (or Tofu if you are vegetarian/vegan)

tardis/base.py

@@ -1,6 +1,6 @@
 # functions that are important for the general usage of TARDIS
 
-def run_tardis(config, atom_data=None):
+def run_tardis(config, atom_data=None, simulation_callbacks=[]):
     """
     This function is one of the core functions to run TARDIS from a given
     config object.
@@ -35,6 +35,9 @@ def run_tardis(config, atom_data=None):
         tardis_config = Configuration.from_config_dict(config)
 
     simulation = Simulation.from_config(tardis_config, atom_data=atom_data)
+    for cb in simulation_callbacks:
+        simulation.add_callback(cb)
+
     simulation.run()
 
     return simulation

tardis/montecarlo/base.py

@@ -391,10 +391,10 @@ def from_config(cls, config):
         """
         if config.plasma.disable_electron_scattering:
             logger.warn('Disabling electron scattering - this is not physical')
-            sigma_thomson = 1e-200 / (u.cm ** 2)
+            sigma_thomson = 1e-200 * (u.cm ** 2)
         else:
             logger.debug("Electron scattering switched on")
-            sigma_thomson = 6.652486e-25 / (u.cm ** 2)
+            sigma_thomson = const.sigma_T.cgs
 
         spectrum_frequency = quantity_linspace(
             config.spectrum.stop.to('Hz', u.spectral()),

tardis/montecarlo/tests/test_cmontecarlo.py

@@ -47,6 +47,7 @@
 import pytest
 import numpy as np
 import pandas as pd
+from astropy import constants as const
 from ctypes import (
         CDLL,
         byref,