From c0b2efbb45fb89fd351d1c6d3aa6541d016a36e9 Mon Sep 17 00:00:00 2001
From: Rory Barnes <rory@proxima.astro.washington.edu>
Date: Fri, 21 Jun 2024 14:26:07 -0700
Subject: [PATCH] Updated docs for testing and adding primary variables (Thanks
 David and Sam!)

---
 docs/primaryvariable.rst | 26 ++++++++++++++++++++++++++
 docs/tests.rst           | 12 ++++++++++--
 2 files changed, 36 insertions(+), 2 deletions(-)

diff --git a/docs/primaryvariable.rst b/docs/primaryvariable.rst
index 1ed5a7b49..ac876c2ff 100644
--- a/docs/primaryvariable.rst
+++ b/docs/primaryvariable.rst
@@ -167,6 +167,10 @@ block of code that initializes the other pieces of the UPDATE struct.
            malloc(update[iBody].iNumPrimaryVariable * sizeof(int));
         control->Evolve.tmpUpdate[iBody].iaBody[iVar] =
            malloc(update[iBody].iNumPrimaryVariable * sizeof(int *));
+        for (iSubStep=0; iSubStep < 4; iSubStep++) {
+          control->Evolve.daDerivProc[iSubStep][iBody][iVar] =
+              malloc(update[iBody].iNumEqns[iVar] * sizeof(double));
+        }
       }
 
       // Now allocate memory for the number of processes that affect this variable
@@ -192,6 +196,28 @@ variable.
   assign a new value to this variable, you will overwrite the primary variable's
   derivative (which would be bad!).
 
+We then need to add some lines to ```module.c```. In InitializeModule, add
+
+.. code-block:: bash  
+
+module->fnFinalizeUpdatePhysics =
+        malloc(iNumBodies * sizeof(fnFinalizeUpdateCarbManModule));
+
+and in FinalizeModule, add
+
+.. code-block:: bash
+
+  module->fnFinalizeUpdatePhysics[iBody] =
+        malloc(iNumModules * sizeof(fnFinalizeUpdateCarbManModule));
+
+and
+
+.. code-block:: bash
+
+ module->fnFinalizeUpdatePhysics[iBody][iModule]   = &FinalizeUpdateNULL; 
+
+Please add them next to the other similar statements
+
 Next we need to add code to the module file, physics.c in this example, for
 which this primary variable will be added. First add a new function that
 continues the initialization process:
diff --git a/docs/tests.rst b/docs/tests.rst
index 14e943d51..c22b6630a 100644
--- a/docs/tests.rst
+++ b/docs/tests.rst
@@ -16,7 +16,10 @@ further enabling confidence in the code's accuracy.
 Test scripts live in the :code:`tests/` directory and are executed automatically 
 on every pull request with GitHub Actions. To perform the tests, we use :code:`pytest`, which will
 find all Python files with the word :code:`test` somewhere in their name (side note:
-if it's not meant to be a test, don't put :code:`test` in the file name!).
+if it's not meant to be a test, don't put :code:`test` in the file name!). Under the :code:`tests`
+directory are subdirectories whose names consists of VPLanet modules, e.g. BINARY and AtmescEqtideStellar.
+These subdirectories contain the tests available for the module combinations of the subdirectory name.
+
 
 The VPLanet team has made it easy to add or revise tests. Inside the :code:`tests/` directory
 is a file called :code:`maketest.py`, which will generate a unit test from a set of valid infiles.
@@ -24,7 +27,12 @@ So a typical procedure to create a new test is to:
 
 - Create a simulation that executes previously untested functionality
 - Verify the results are accurate! (Obvious, we know, but please don't forget!)
-- Copy the .in files t
+- Create a subdirectory with a unique name for your test. 
+- Copy the .in files for your test into your new subdirectory
+- cd to the :code:`tests` directory and run ```python maketest.py <modules/subdir>```, which the 
+  argument is the relative to path to your new test
+- Commit your .in files and the new :code:`test_<subdir>.py" file to the repository
+- Issue a PR!
 
 These unit tests not only ensure new modification don't break parts of the code
 that already work. In addition, they are used to compute the fraction of the code