Merge pull request #929 from tardis-sn/numba_montecarlo

This is a year worth of work from many people and hopefully will make TARDIS easier to use and develop on. Co-authored-by: Andrew Fullard <[email protected]> Co-authored-by: Jack O'Brien <[email protected]> Co-authored-by: Christian Vogl <[email protected]> Co-authored-by: Andreas Flörs <[email protected]> Co-authored-by: Luke Shingles <[email protected]> Co-authored-by: Alice Harpole <[email protected]> Co-authored-by: Marc Williamson <[email protected]> Co-authored-by: Yssa Camacho <[email protected]> Co-authored-by: Arjun Savel <[email protected]> Co-authored-by: Stuart Archibald <[email protected]> Co-authored-by: Siu Kwan Lam <[email protected]>
tardis-sn · Nov 17, 2020 · 101a493 · 101a493
2 parents 071a48e + d14025e
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diff --git a/docs/development/continuous_integration.rst b/docs/development/continuous_integration.rst
@@ -172,6 +172,9 @@ to paths in Azure:
 See the Azure documentation to learn more about `checking out multiple repositories`_.
 
 
+Azure provides a list of agent hosts that can run the pipeline on a virtual machine. In our pipelines, we
+use the vm_Images: Ubuntu 16.04 and macOs-10.14.
+
 Jobs
 ----
 

diff --git a/docs/development/debug_numba.rst b/docs/development/debug_numba.rst
@@ -0,0 +1,14 @@
+**************************
+Debugging numba_montecarlo
+**************************
+To facilitate more in-depth debugging when interfacing with the `montecarlo_numba`
+module, we provide a set of debugging configurations. PyCharm debugging
+configurations, in addition to related scripts and .yml files, are contained in
+`tardis.scripts.debug`. Currently, these include the ability to run TARDIS
+in asingle-packet mode, with the packet seed identified at debug time.
+`tardis_example_single.yml` is the configuration filethat is used to set up the
+single-packet TARDIS run; `run_numba_single.py` is thePython script that runs
+this .yml file; `run_numba_single.xml` is the PyCharmdebug configuration file
+that can be used in conjunction with the above files.
+
+Note that this method is EXPERIMENTAL.
diff --git a/docs/development/index.rst b/docs/development/index.rst
@@ -11,8 +11,8 @@ to the Astropy team for designing it.
 .. toctree::
     :maxdepth: 2
 
-    running_tests
     issues
+    debug_numba
 
 
 

diff --git a/docs/graphics/numba_comparison_real_quickstart.png b/docs/graphics/numba_comparison_real_quickstart.png
diff --git a/docs/graphics/numba_comparison_virtual_quickstart.png b/docs/graphics/numba_comparison_virtual_quickstart.png
diff --git a/docs/index.rst b/docs/index.rst
@@ -69,6 +69,14 @@ Mission Statement
     Physics overview <physics/index>
     physics/plasma/index
 
+.. toctree::
+    :maxdepth: 2
+    :caption: Testing TARDIS
+    :hidden:
+
+    testing/automated_tests
+    testing/numba
+
 
 .. toctree::
     :maxdepth: 2

diff --git a/docs/running/custom_source.ipynb b/docs/running/custom_source.ipynb
@@ -52,9 +52,10 @@
     "    \n",
     "    def __init__(self, seed, truncation_wavelength):\n",
     "        super().__init__(seed)\n",
+    "        self.rng = np.random.default_rng(seed=seed)\n",
     "        self.truncation_wavelength = truncation_wavelength\n",
     "    \n",
-    "    def create_packets(self, T, no_of_packets,\n",
+    "    def create_packets(self, T, no_of_packets, rng,\n",
     "                       drawing_sample_size=None):\n",
     "        \"\"\"\n",
     "        Packet source that generates a truncated Blackbody source.\n",
@@ -70,11 +71,10 @@
     "            Only wavelengths higher than the truncation wavelength\n",
     "            will be sampled.\n",
     "        \"\"\"\n",
-    "        \n",
-    "        \n",
+    "\n",
     "        # Use mus and energies from normal blackbody source.\n",
-    "        mus = self.create_zero_limb_darkening_packet_mus(no_of_packets)\n",
-    "        energies = self.create_uniform_packet_energies(no_of_packets)\n",
+    "        mus = self.create_zero_limb_darkening_packet_mus(no_of_packets, self.rng)\n",
+    "        energies = self.create_uniform_packet_energies(no_of_packets, self.rng)\n",
     "\n",
     "        # If not specified, draw 2 times as many packets and reject any beyond no_of_packets.\n",
     "        if drawing_sample_size is None:\n",
@@ -86,15 +86,15 @@
     "        \n",
     "        # Draw nus from blackbody distribution and reject based on truncation_frequency.\n",
     "        # If more nus.shape[0] > no_of_packets use only the first no_of_packets.\n",
-    "        nus = self.create_blackbody_packet_nus(T, drawing_sample_size)\n",
+    "        nus = self.create_blackbody_packet_nus(T, drawing_sample_size, self.rng)\n",
     "        nus = nus[nus<truncation_frequency][:no_of_packets]\n",
     "        \n",
     "        \n",
     "        # Only required if the truncation wavelength is too big compared to the maximum \n",
     "        # of the blackbody distribution. Keep sampling until nus.shape[0] > no_of_packets.\n",
     "        while nus.shape[0] < no_of_packets:\n",
     "            additional_nus = self.create_blackbody_packet_nus(\n",
-    "                T, drawing_sample_size\n",
+    "                T, drawing_sample_size, self.rng\n",
     "            )\n",
     "            mask = additional_nus < truncation_frequency\n",
     "            additional_nus = additional_nus[mask][:no_of_packets]\n",
@@ -170,4 +170,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}
diff --git a/tardis/gui/datahandler.py b/tardis/gui/datahandler.py
@@ -39,15 +39,15 @@ class Node(object):
 
     Attributes
     ----------
-        parent: None/Node 
+        parent: None/Node
             The parent of the node.
         children: list of Node
             The children of the node.
-        data: list of string 
+        data: list of string
             The data stored on the node. Can be a key or a value.
-        siblings: dictionary 
-            A dictionary of nodes that are siblings of this node. The 
-            keys are the values of the nodes themselves. This is 
+        siblings: dictionary
+            A dictionary of nodes that are siblings of this node. The
+            keys are the values of the nodes themselves. This is
             used to keep track of which value the user has selected
             if the parent of this node happens to be a key that can
             take values from a list.
@@ -61,18 +61,18 @@ def __init__(self, data, parent=None):
         ----------
             data: list of string
                 The data that is intended to be stored on the node.
-            parent: Node 
-                Another node which is the parent of this node. The 
+            parent: Node
+                Another node which is the parent of this node. The
                 root node has parent set to None.
 
         Note
         ----
-            A leaf node is a node that is the only child of its parent. 
+            A leaf node is a node that is the only child of its parent.
             For this tree this will always be the case. This is because
             the tree stores the key at every node except the leaf node
             where it stores the value for the key. So if in the dictionary
-            the value of a key is another dictionary, then it will 
-            be a node with no leafs. If the key has a value that is a 
+            the value of a key is another dictionary, then it will
+            be a node with no leafs. If the key has a value that is a
             value or a list then it will have one child that is a leaf.
             The leaf can have no children. For example-
 
@@ -86,12 +86,12 @@ def __init__(self, data, parent=None):
                                   val7, val5 and val6 and is currently
                                   set to val5.
 
-            In the tree shown above all quoted values are keys in the 
-            dictionary and are non-leaf nodes in the tree. All values 
-            of the form valx are leaf nodes and are not dictionaries 
+            In the tree shown above all quoted values are keys in the
+            dictionary and are non-leaf nodes in the tree. All values
+            of the form valx are leaf nodes and are not dictionaries
             themselves. If the keys have non-dictionary values then they
             have a leaf attached. And no leaf can have a child.
-        
+
         """
         self.parent = parent
         self.children = []
@@ -105,9 +105,9 @@ def append_child(self, child):
         child.parent = self
 
     def get_child(self, i):
-        """Get the ith child of this node. 
+        """Get the ith child of this node.
 
-        No error is raised if the cild requested doesn't exist. A 
+        No error is raised if the cild requested doesn't exist. A
         None is returned in such cases.
 
         """
@@ -141,7 +141,7 @@ def get_parent(self):
         return self.parent
 
     def get_index_of_self(self):
-        """Returns the number at which it comes in the list of its 
+        """Returns the number at which it comes in the list of its
         parent's children. For root the index 0 is returned.
 
         """
@@ -170,10 +170,10 @@ class TreeModel(QtCore.QAbstractItemModel):
     ----------
         root: Node
             Root node of the tree.
-        disabledNodes: list of Node 
+        disabledNodes: list of Node
             List of leaf nodes that are not editable currently.
-        typenodes: list of Node 
-            List of nodes that correspond to keys that set container 
+        typenodes: list of Node
+            List of nodes that correspond to keys that set container
             types. Look at tardis configuration template. These are the
             nodes that have values that can be set from a list.
 
@@ -184,9 +184,9 @@ def __init__(self, dictionary, parent=None):
 
         Parameters
         ----------
-            dictionary: dictionary            
+            dictionary: dictionary
                 The dictionary that needs to be converted to the tree.
-            parent: None 
+            parent: None
                 Used to instantiate the QAbstractItemModel
 
         """
@@ -267,7 +267,7 @@ def headerData(self, section, orientation, role):
         return None
 
     def index(self, row, column, parent=QtCore.QModelIndex()):
-        """Create a model index for the given row and column. For a 
+        """Create a model index for the given row and column. For a
         tree model, the row is the set of nodes with the same parents and
         the column indexes the data in the node.
 
@@ -315,8 +315,8 @@ def parent(self, index):
         return self.createIndex(parentItem.get_index_of_self(), 0, parentItem)
 
     def rowCount(self, parent=QtCore.QModelIndex()):
-        """The number of rows for a given node. 
-        
+        """The number of rows for a given node.
+
         (The number of rows is just the number of children for a node.)
 
         """
@@ -325,7 +325,7 @@ def rowCount(self, parent=QtCore.QModelIndex()):
         return parentItem.num_hildren()
 
     def setData(self, index, value, role=QtCore.Qt.EditRole):
-        """Set the value as the data at the location pointed by the 
+        """Set the value as the data at the location pointed by the
         index.
 
         """
@@ -360,7 +360,7 @@ def dict_to_tree(self, dictionary, root):
         ----------
             dictionary: dictionary
                 The dictionary that is to be converted to the tree.
-            root: Node 
+            root: Node
                 The root node of the tree.
 
         """
@@ -411,7 +411,7 @@ def tree_from_node(self, dictionary, root):
                     self.typenodes.append(child)
 
     def dict_from_node(self, node):
-        """Take a node and convert the whole subtree rooted at it into a 
+        """Take a node and convert the whole subtree rooted at it into a
         dictionary.
 
         """
@@ -429,7 +429,7 @@ def dict_from_node(self, node):
 
 
 class TreeDelegate(QtWidgets.QStyledItemDelegate):
-    """Create a custom delegate to modify the columnview that displays the 
+    """Create a custom delegate to modify the columnview that displays the
     TreeModel.
 
     """
@@ -457,7 +457,7 @@ def createEditor(self, parent, option, index):
 
     def setModelData(self, editor, model, index):
         """Called when new data id set in the model. This is where the
-        siblings of type nodes are enabled or disabled according to the 
+        siblings of type nodes are enabled or disabled according to the
         new choice made.
 
         """

diff --git a/tardis/gui/interface.py b/tardis/gui/interface.py
@@ -28,15 +28,15 @@
 def show(model):
     """Take an instance of tardis model and display it.
 
-    If IPython functions were successfully imported then QApplication instance 
-    is created using get_app_qt4. This will only create the app instance if 
-    it doesn't already exists. Otherwise it is explicitly started. 
+    If IPython functions were successfully imported then QApplication instance
+    is created using get_app_qt4. This will only create the app instance if
+    it doesn't already exists. Otherwise it is explicitly started.
 
-    Then the mainwindow is created, the model is attached to it and its 
+    Then the mainwindow is created, the model is attached to it and its
     show method is called.
 
     Finally the eventloop is started using IPython functions (which start them
-    consistently) if they were imported. Otherwise it is started explicitly. 
+    consistently) if they were imported. Otherwise it is started explicitly.
 
     """
     if importFailed:

diff --git a/tardis/gui/widgets.py b/tardis/gui/widgets.py
@@ -667,7 +667,7 @@ def change_spectrum_to_spec_virtual_flux_angstrom(self):
 
     def change_spectrum_to_spec_flux_angstrom(self):
         """Change spectrum data back from virtual spectrum. (See the
-            method above)."""
+        method above)."""
         if self.model.runner.spectrum.luminosity_density_lambda is None:
             luminosity_density_lambda = np.zeros_like(
                 self.model.runner.spectrum.wavelength
@@ -946,7 +946,10 @@ def __init__(self, parent, wavelength_start, wavelength_end, tablecreator):
         self.setGeometry(180 + len(self.parent.line_info) * 20, 150, 250, 400)
         self.setWindowTitle(
             "Line Interaction: %.2f - %.2f (A) "
-            % (wavelength_start, wavelength_end,)
+            % (
+                wavelength_start,
+                wavelength_end,
+            )
         )
         self.layout = QtWidgets.QVBoxLayout()
         packet_nu_line_interaction = analysis.LastLineInteraction.from_model(
@@ -1155,8 +1158,10 @@ def __init__(
         self.line_interaction_analysis = line_interaction_analysis
         self.atom_data = atom_data
         self.lines_data = lines_data.reset_index().set_index("line_id")
-        line_interaction_species_group = line_interaction_analysis.last_line_in.groupby(
-            ["atomic_number", "ion_number"]
+        line_interaction_species_group = (
+            line_interaction_analysis.last_line_in.groupby(
+                ["atomic_number", "ion_number"]
+            )
         )
         self.species_selected = sorted(
             line_interaction_species_group.groups.keys()

diff --git a/tardis/io/config_reader.py b/tardis/io/config_reader.py
@@ -239,16 +239,18 @@ class ConfigWriterMixin(HDFWriterMixin):
     """
     Overrides HDFWriterMixin to obtain HDF properties from configuration keys
     """
+
     def get_properties(self):
         data = yaml.dump(self)
-        data = pd.DataFrame(index=[0], data={'config': data})
+        data = pd.DataFrame(index=[0], data={"config": data})
         return data
 
 
 class Configuration(ConfigurationNameSpace, ConfigWriterMixin):
     """
     Tardis configuration class
     """
+
     hdf_name = "simulation"
 
     @classmethod
@@ -358,26 +360,26 @@ def quantity_representer(dumper, data):
 
 def cns_representer(dumper, data):
     """
-    Represents Configuration as dict
+     Represents Configuration as dict
 
-   Parameters
-    ----------
+    Parameters
+     ----------
 
-    dumper :
-        YAML dumper object
+     dumper :
+         YAML dumper object
 
-    data :
-        ConfigurationNameSpace object
+     data :
+         ConfigurationNameSpace object
 
-    Returns
-    -------
+     Returns
+     -------
 
-    yaml dumper representation of Configuration as dict
+     yaml dumper representation of Configuration as dict
 
     """
     return dumper.represent_dict(dict(data))
 
 
 yaml.add_representer(u.Quantity, quantity_representer)
 yaml.add_representer(ConfigurationNameSpace, cns_representer)
-yaml.add_representer(Configuration, cns_representer)
+yaml.add_representer(Configuration, cns_representer)