As simpler run_tardis

docs/physics/physical_quantities.rst

@@ -12,7 +12,7 @@ inspect the model properties.
 
 
 Runing in interactive Python session
-------------------------------
+------------------------------------
 
 With iPython installed launch a session using
 
@@ -25,10 +25,9 @@ and then run your calculation, which is based on your "my_config.yml" file
 .. code-block:: python
 
     from tardis import run_tardis
-    import yaml
 
-    configuration_dict = yaml.load(open('myconfig.yml')
-    model = run_tardis(configuration_dict)
+
+    model = run_tardis('myconfig.yml')
 
 
 If all goes well, the simulation should run as usual. Afterwards, the

docs/running.rst

@@ -7,8 +7,8 @@ Running TARDIS
 To run TARDIS requires two files. The atomic database (for more info refer to :ref:`atomic-data`) and a
 configuration file (more info at :ref:`config-file`).
 
-Simple Example
-==============
+Running TARDIS in the commandline
+=================================
 
 After installing TARDIS just download the example directory `<https://www.dropbox.com/s/svvyr5i7m8ouzdt/tardis_example.tar.gz>`_
 and run TARDIS with:
@@ -28,25 +28,33 @@ Then plot the output_spectrum.dat with your favourite plotting program. Here's a
 .. code-block:: python
 
     ipython --pylab
-    tardis_spec = loadtxt('output_spectrum.dat')
-    plot(tardis_spec[:,0], tardis_spec[:,1])
+    >>> tardis_spec = loadtxt('output_spectrum.dat')
+    >>> plot(tardis_spec[:,0], tardis_spec[:,1])
 
 
 More atomic datasets can be downloaded from :ref:`atomic-data-download`.
 
 
-Scripting TARDIS
-================
+
+
+Running TARDIS interactively
+============================
+
+To get more information from each run of TARDIS one can run it interactively and
+have full access to the model properties
 
 .. code-block:: python
-    from tardis import run_tardis
-    import yaml
 
-    configuration_dict = yaml.load(open('myconfig.yml')
-    model = run_tardis(configuration_dict)
+    >>> from tardis import run_tardis
+    >>> model = run_tardis('myconfig.yml')
+
+This model can then be used for inspecting the run as described
+:ref:`physical_quantities`
+
 
 Graphical User Interface
 ========================
 
-A graphical user interface is being developed for this code using QT. We envision to have this available in the next few minor releases.
+A graphical user interface is being developed for this code using QT.
+We envision to have this available in the next few minor releases.
 

setup.py

@@ -34,9 +34,10 @@
 URL = metadata.get('url', 'http://astropy.org')
 
 # Get the long description from the package's docstring
-__import__(PACKAGENAME)
-package = sys.modules[PACKAGENAME]
-LONG_DESCRIPTION = package.__doc__
+#__import__(PACKAGENAME)
+#package = sys.modules[PACKAGENAME]
+#LONG_DESCRIPTION = package.__doc__
+LONG_DESCRIPTION = ""
 
 # Store the package name in a built-in variable so it's easy
 # to get from other parts of the setup infrastructure

tardis/__init__.py

@@ -7,6 +7,7 @@
 from ._astropy_init import *
 # ----------------------------------------------------------------------------
 
+from tardis.base import run_tardis
 
 logger = logging.getLogger('tardis')
 logger.setLevel(logging.INFO)

tardis/base.py

@@ -0,0 +1,46 @@
+#functions that are important for the general usage of TARDIS
+
+import yaml
+
+from tardis.io import config_reader
+from tardis import model, simulation, atomic
+
+
+def run_tardis(config, atom_data=None):
+    """
+    This function is one of the core functions to run TARDIS from a given
+    config object.
+
+    It will return a model object containing
+
+    Parameters
+    ----------
+
+    config: ~str or ~dict
+        filename of configuration yaml file or dictionary
+
+    atom_data: ~str or ~tardis.atomic.AtomData
+        if atom_data is a string it is interpreted as a path to a file storing
+        the atomic data. Atomic data to use for this TARDIS simulation. If set to None, the
+        atomic data will be loaded according to keywords set in the configuration
+        [default=None]
+    """
+
+    try:
+        config_dict = yaml.load(open(config))
+    except TypeError:
+        config_dict = config
+
+    if atom_data is not None:
+        try:
+            atom_data = atomic.AtomData.from_hdf5(atom_data)
+        except TypeError:
+            atom_data = atom_data
+
+    tardis_config = config_reader.Configuration.from_config_dict(
+        config_dict, atom_data=atom_data)
+    radial1d_mdl = model.Radial1DModel(tardis_config)
+
+    simulation.run_radial1d(radial1d_mdl)
+
+    return radial1d_mdl

tardis/io/config_reader.py

@@ -772,7 +772,7 @@ class Configuration(ConfigurationNameSpace):
     @classmethod
     def from_yaml(cls, fname, test_parser=False):
         try:
-            yaml_dict = yaml.load(file(fname))
+            yaml_dict = yaml.load(open(fname))
         except IOError as e:
             logger.critical('No config file named: %s', fname)
             raise e

tardis/tests/test_tardis_full.py

@@ -9,6 +9,8 @@
 import os
 
 
+from tardis import run_tardis
+
 def data_path(fname):
     return os.path.join(tardis.__path__[0], 'tests', 'data', fname)
 
@@ -31,9 +33,7 @@ def setup(self):
         self.config_yaml = yaml.load(open('tardis/io/tests/data/tardis_configv1_verysimple.yml'))
         self.config_yaml['atom_data'] = self.atom_data_filename
 
-        self.config = Configuration.from_config_dict(self.config_yaml)
-        self.model = model.Radial1DModel(self.config)
-        simulation.run_radial1d(self.model)
+        self.model = run_tardis(self.config_yaml)
 
 
     def test_spectrum(self):