Documentation/sbachmei/mic 5097 5221 concepts (#471)

docs/source/concepts/lifecycle.rst

@@ -34,7 +34,8 @@ during a simulation.
    * - | :ref:`Main Loop <lifecycle_main_loop>`
      - | The core logic (as encoded in the simulation components) is executed.
    * - | :ref:`Simulation End <lifecycle_simulation_end>`
-     - | The population state is finalized and results are tabulated.
+     - | The population state is finalized and results are tabulated and written
+       | to disk.
 
 The simulation itself maintains a formal representation of its internal
 execution state using the tools in the :mod:`~vivarium.framework.lifecycle`
@@ -197,4 +198,4 @@ simulation end. It is split into two states.  During the first, the
 signal that the event loop has finished and the
 :ref:`state table <population_concept>` is final. At this point, final
 simulation outputs are safe to compute. The second state is *report* in
-which the simulation will accumulate all final outputs and return them.
+which the simulation will accumulate all final outputs and write them to disk.

docs/source/concepts/model_specification/index.rst

@@ -4,6 +4,16 @@
 The Model Specification
 =======================
 
+.. contents::
+   :depth: 2
+   :local:
+   :backlinks: none
+
+.. toctree::
+   :hidden:
+
+   yaml_basics
+
 A :term:`model specification <Model Specification>` is a complete representation
 of a :mod:`vivarium` simulation formatted as a yaml file.
 
@@ -19,10 +29,11 @@ Each of these blocks is delineated by a top-level key in the yaml file:
 You can find a short intro to yaml basics
 :ref:`here <model_specification_yaml_concept>`.
 
-.. contents::
-   :depth: 2
-   :local:
-   :backlinks: none
+The Plugins Block
+-----------------
+
+.. todo::
+   describe plugins
 
 The Components Block
 --------------------
@@ -85,7 +96,30 @@ call on either of the above yaml components block examples would be a list
 containing three instantiated objects: a population object, a mortality object,
 and a diarrhea disease model.
 
-.. toctree::
-   :hidden:
+The Configuration Block
+-----------------------
 
-   yaml_basics
+The configuration block of the model specification file contains any information
+necessary to configure the simulation to run, including (among other things) 
+key columns to be used for common random number generation, the simulation 
+start and end times, step size, and the population size.
+
+.. code-block:: yaml
+
+    configuration:
+        randomness:
+            key_columns: ['entrance_time', 'age']
+        time:
+            start:
+                year: 2022
+                month: 1
+                day: 1
+            end:
+                year: 2026
+                month: 12
+                day: 31
+            step_size: 0.5  # Days
+        population:
+            population_size: 100_000
+            age_start: 0
+            age_end: 5