Updating configuration name space

docs/configuration/configuration_old.rst

@@ -260,7 +260,7 @@ parameter ``lum_density`` which sets the distance to :math:`\sqrt{\frac{1}{4 \pi
 Config Reader
 ^^^^^^^^^^^^^
 
-The YAML file is read by using a classmethod of the :meth:`~tardis.config_reader.TARDISConfiguration.from_yaml`.
+The YAML file is read by using a classmethod of the :meth:`~tardis.config_reader.Configuration.from_yaml`.
 
 
 

docs/physics/physical_quantities.rst

@@ -30,7 +30,7 @@ and then run your calculation, which is based on your "my_config.yml" file
     import logging
     import warnings
 
-    tardis_config = config_reader.TARDISConfiguration.from_yaml("my_config.yml")
+    tardis_config = config_reader.Configuration.from_yaml("my_config.yml")
     radial1d = model.Radial1DModel(tardis_config)
     simulation.run_radial1d(radial1d)
 

docs/running.rst

@@ -43,7 +43,7 @@ Scripting TARDIS
     from tardis import model, simulation
     from tardis.io import config_reader
 
-    tardis_config = config_reader.TARDISConfiguration.from_yaml('myconfig.yml')
+    tardis_config = config_reader.Configuration.from_yaml('myconfig.yml')
     radial1d_mdl = model.Radial1DModel(tardis_config)
     simulation.run_radial1d(radial1d_mdl)
 

scripts/tardis

@@ -53,7 +53,7 @@ if args.packet_log_file:
     console_handler.setFormatter(packet_logging_formatter)
     logger.addHandler(packet_logging_handler)
 
-tardis_config = config_reader.TARDISConfiguration.from_yaml(args.config_fname)
+tardis_config = config_reader.Configuration.from_yaml(args.config_fname)
 
 radial1d_mdl = model.Radial1DModel(tardis_config)
 

tardis/io/config_reader.py

@@ -17,6 +17,7 @@
 from tardis.util import species_string_to_tuple, parse_quantity, \
     element_symbol2atomic_number
 
+import copy
 
 pp = pprint.PrettyPrinter(indent=4)
 
@@ -28,6 +29,7 @@
                                               'tardis_config_definition.yml')
 #File parsers for different file formats:
 
+
 density_structure_fileparser = {}
 
 inv_ni56_efolding_time = 1 / (8.8 * u.day)
@@ -596,37 +598,125 @@ def calculate_w7_branch85_densities(velocities, time_explosion, time_0=19.999958
     return densities[1:]
 
 
-class TARDISConfigurationNameSpace(object):
-    def __init__(self, config_dict):
-        self.config_dict = config_dict
+class ConfigurationNameSpace(dict):
+    """
+    The configuration name space class allows to wrap a dictionary and adds
+    utility functions for easy access. Accesses like a.b.c are then possible
+
+    Code from http://goo.gl/KIaq8I
+
+    Parameters
+    ----------
+
+    config_dict: ~dict
+        configuration dictionary
+
+    Returns
+    -------
+
+    config_ns: ConfigurationNameSpace
+    """
+
+    marker = object()
+    def __init__(self, value=None):
+        if value is None:
+            pass
+        elif isinstance(value, dict):
+            for key in value:
+                self.__setitem__(key, value[key])
+        else:
+            raise TypeError, 'expected dict'
+
+    def __setitem__(self, key, value):
+        if isinstance(value, dict) and not isinstance(value,
+                                                      ConfigurationNameSpace):
+            value = ConfigurationNameSpace(value)
+
+        if key in self and hasattr(self[key], 'unit'):
+            value = u.Quantity(value, self[key].unit)
+
+        dict.__setitem__(self, key, value)
 
+    def __getitem__(self, key):
+        return super(ConfigurationNameSpace, self).__getitem__(key)
 
     def __getattr__(self, item):
-        if item in self.config_dict:
-            config_item = self.config_dict[item]
-            if isinstance(config_item, dict):
-                setattr(self, item, TARDISConfigurationNameSpace(config_item))
-                return getattr(self, item)
+        if item in self:
+            return self[item]
+        else:
+            super(ConfigurationNameSpace, self).__getattribute__(item)
+
+    __setattr__ = __setitem__
+
+    def __dir__(self):
+        self.keys()
+
+    def get_config_item(self, config_item_string):
+        """
+        Get configuration items using a string of type 'a.b.param'
+
+        Parameters
+        ----------
+
+        config_item_string: ~str
+            string of shape 'section1.sectionb.param1'
+        """
+        config_item_path = config_item_string.split('.')
+
+        if len(config_item_path) == 1:
+            config_item = config_item_path[0]
+
+            if config_item.startswith('item'):
+                return self[config_item_path[0]]
             else:
-                return self.config_dict[item]
+                return self[config_item]
+        elif len(config_item_path) == 2 and\
+                config_item_path[1].startswith('item'):
+            return self[config_item_path[0]][
+                int(config_item_path[1].replace('item', ''))]
+
         else:
-            return super(TARDISConfigurationNameSpace, self).__getattribute__(item)
+            return self[config_item_path[0]].get_config_item(
+                '.'.join(config_item_path[1:]))
+
+    def set_config_item(self, config_item_string, value):
+        """
+        set configuration items using a string of type 'a.b.param'
+
+        Parameters
+        ----------
 
-    def __getitem__(self, item):
-        return self.config_dict.__getitem__(item)
+        config_item_string: ~str
+            string of shape 'section1.sectionb.param1'
 
-    def get(self, k, d=None):
-        return self.config_dict.get(k, d)
+        value:
+            value to set the parameter with it
+        """
 
+        config_item_path = config_item_string.split('.')
+        if len(config_item_path) == 1:
+            self[config_item_path[0]] = value
+        elif len(config_item_path) == 2 and \
+                config_item_path[1].startswith('item'):
+            current_value = self[config_item_path[0]][
+                int(config_item_path[1].replace('item', ''))]
+            if hasattr(current_value, 'unit'):
+                self[config_item_path[0]][
+                    int(config_item_path[1].replace('item', ''))] =\
+                    u.Quantity(value, current_value.unit)
+            else:
+                self[config_item_path[0]][
+                    int(config_item_path[1].replace('item', ''))] = value
 
-    def __repr__(self):
-        return pp.pformat(self.config_dict)
+        else:
+            self[config_item_path[0]].set_config_item(
+                '.'.join(config_item_path[1:]), value)
 
-    def __dir__(self):
-        return self.__dict__.keys() + self.config_dict.keys()
+    def deepcopy(self):
+        return ConfigurationNameSpace(copy.deepcopy(dict(self)))
 
 
-class TARDISConfiguration(TARDISConfigurationNameSpace):
+class Configuration(ConfigurationNameSpace):
     """
     Tardis configuration class
     """
@@ -674,7 +764,7 @@ def from_config_dict(cls, config_dict, atom_data=None, test_parser=False,
         Returns
         -------
 
-        `tardis.config_reader.TARDISConfiguration`
+        `tardis.config_reader.Configuration`
 
         """
 
@@ -903,7 +993,7 @@ def from_config_dict(cls, config_dict, atom_data=None, test_parser=False,
 
 
     def __init__(self, config_dict, atom_data):
-        super(TARDISConfiguration, self).__init__(config_dict)
+        super(Configuration, self).__init__(config_dict)
         self.atom_data = atom_data
         selected_atomic_numbers = self.abundances.index
         if atom_data is not None:

tardis/io/tests/test_config_reader.py

@@ -14,11 +14,11 @@ def data_path(filename):
     return os.path.join(data_dir, 'data', filename)
 
 def test_config_namespace_attribute_test():
-    namespace = config_reader.TARDISConfigurationNameSpace({'param1':1})
+    namespace = config_reader.ConfigurationNameSpace({'param1':1})
     assert namespace.param1 == 1
 
 def test_config_namespace_attribute_test():
-    namespace = config_reader.TARDISConfigurationNameSpace({'param1':1})
+    namespace = config_reader.ConfigurationNameSpace({'param1':1})
     with pytest.raises(AttributeError):
         assert namespace.param2 == 1
 
@@ -74,7 +74,7 @@ class TestParsePaper1Config:
 
     def setup(self):
         #general parsing of the paper config
-        self.config = config_reader.TARDISConfiguration.from_yaml(data_path('paper1_tardis_configv1.yml'),
+        self.config = config_reader.Configuration.from_yaml(data_path('paper1_tardis_configv1.yml'),
                                                                   test_parser=True)
         self.yaml_data = yaml.load(open(data_path('paper1_tardis_configv1.yml')))
 
@@ -121,6 +121,7 @@ def test_spectrum_section(self):
         assert self.config['spectrum']['bins'] == self.yaml_data['spectrum']['num']
 
 
+
     def test_time_explosion(self):
         assert_almost_equal(self.config['supernova']['time_explosion'],
                             13.0 * u.day)
@@ -130,7 +131,7 @@ class TestParseConfigV1ASCIIDensity:
     def setup(self):
         #general parsing of the paper config
         filename = 'tardis_configv1_ascii_density.yml'
-        self.config = config_reader.TARDISConfiguration.from_yaml(data_path(filename),
+        self.config = config_reader.Configuration.from_yaml(data_path(filename),
                                                                   test_parser=True)
         self.yaml_data = yaml.load(open(data_path(filename)))
 
@@ -149,7 +150,7 @@ class TestParseConfigV1ArtisDensity:
     def setup(self):
         #general parsing of the paper config
         filename = 'tardis_configv1_artis_density.yml'
-        self.config = config_reader.TARDISConfiguration.from_yaml(data_path(filename),
+        self.config = config_reader.Configuration.from_yaml(data_path(filename),
                                                                   test_parser=True)
         self.yaml_data = yaml.load(open(data_path(filename)))
 
@@ -176,7 +177,7 @@ def setup(self):
                                                  'filename': 'tardis/io/tests/data/artis_abundances.dat',
                                                  'filetype': 'artis'}
 
-        self.config = config_reader.TARDISConfiguration.from_config_dict(self.yaml_data,
+        self.config = config_reader.Configuration.from_config_dict(self.yaml_data,
                                                                   test_parser=True)
 
 
@@ -199,7 +200,7 @@ def setup(self):
                                                  'filename': 'tardis/io/tests/data/artis_abundances.dat',
                                                  'filetype': 'artis'}
 
-        self.config = config_reader.TARDISConfiguration.from_config_dict(self.yaml_data,
+        self.config = config_reader.Configuration.from_config_dict(self.yaml_data,
                                                                   test_parser=True)
 
 
@@ -221,7 +222,7 @@ def setup(self):
         self.yaml_data['model']['structure']['filename'] = 'tardis/io/tests/data/density.dat'
         self.yaml_data['model']['abundances']['filename'] = 'tardis/io/tests/data/abund.dat'
 
-        self.config = config_reader.TARDISConfiguration.from_config_dict(self.yaml_data,
+        self.config = config_reader.Configuration.from_config_dict(self.yaml_data,
                                                                   test_parser=True)
 
 
@@ -266,8 +267,8 @@ def test_ascii_reader_power_law():
 
     v_inner =  yaml_data['model']['structure']['velocity']['start']
     v_outer =  yaml_data['model']['structure']['velocity']['stop']
-    my_conf = config_reader.TARDISConfiguration.from_yaml(data_path('tardis_configv1_density_power_law_test.yml'),test_parser=True)
-    structure = my_conf.config_dict['structure']
+    my_conf = config_reader.Configuration.from_yaml(data_path('tardis_configv1_density_power_law_test.yml'),test_parser=True)
+    structure = my_conf['structure']
 
     expected_densites = [3.29072513e-14,  2.70357804e-14,  2.23776573e-14,
                          1.86501954e-14,  1.56435277e-14,  1.32001689e-14, 1.12007560e-14,
@@ -294,8 +295,8 @@ def test_ascii_reader_exponential_law():
 
     v_inner =  yaml_data['model']['structure']['velocity']['start']
     v_outer =  yaml_data['model']['structure']['velocity']['stop']
-    my_conf = config_reader.TARDISConfiguration.from_yaml(data_path('tardis_configv1_density_exponential_test.yml'),test_parser=True)
-    structure = my_conf.config_dict['structure']
+    my_conf = config_reader.Configuration.from_yaml(data_path('tardis_configv1_density_exponential_test.yml'),test_parser=True)
+    structure = my_conf['structure']
 
     expected_densites = [5.18114795e-14,  4.45945537e-14,  3.83828881e-14, 3.30364579e-14,  2.84347428e-14,  2.44740100e-14, 2.10649756e-14,  1.81307925e-14,  1.56053177e-14, 1.34316215e-14,  1.15607037e-14,  9.95038990e-15, 8.56437996e-15,  7.37143014e-15,  6.34464872e-15, 5.46088976e-15,  4.70023138e-15,  4.04552664e-15, 3.48201705e-15,  2.99699985e-15]
     expected_unit = 'g / (cm3)'

tardis/io/tests/test_config_validator.py

@@ -121,6 +121,8 @@ def test_default_parser_quantity():
                                return_default=return_default, return_value=return_value)
 
 
+
+
 def test_default_parser_quantity_range():
     example_dic = {'default': ['1 cm', '5 cm'],
                    'help': 'quantity for testing',
@@ -277,7 +279,7 @@ def test_default_parser_string():
     ex = default_parser_helper(example_dic, default, wdefault, value, wvalue, container, mandatory)
 
 
-def test_property_type_bundances():
+def test_property_type_abundances():
     example_dic = {'default': {'He': 0.4, 'Mg': 0.1, 'Pb': 0.5},
                    'help': 'quantity for testing',
                    'mandatory': True,
@@ -296,10 +298,7 @@ def test_property_type_bundances():
                                return_default=return_default, return_value=return_value)
 
 
-#For Debug
-#from tardis.io import config_validator as default_config_parser
-#myconf = default_config_parser.Config.from_yaml('tardis/io/tests/data/tardis_configv1_density_exponential_test.yml','tardis/data/tardis_config_definition.yml')
-#myconf = default_config_parser.Config.from_yaml('tardis/io/tests/data/conf_tes.yml','tardis/io/tests/data/conf_def.yml')
+