Adding geos_ats to docs

Author: cssherman

docs/conf.py

@@ -21,6 +21,7 @@
 python_modules = ('geosx_mesh_tools_package',
                   'geosx_xml_tools_package',
                   'geosx_mesh_doctor',
+                  'geos_ats_package',
                   'hdf5_wrapper_package',
                   'pygeosx_tools_package',
                   'timehistory_package')
@@ -61,7 +62,7 @@
 ]
 
 
-autodoc_mock_imports = ["pygeosx", "pylvarray", "meshio", "lxml", "mpi4py", "h5py"]
+autodoc_mock_imports = ["pygeosx", "pylvarray", "meshio", "lxml", "mpi4py", "h5py", "ats"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:

docs/geos_ats.rst

@@ -0,0 +1,46 @@
+
+GEOS ATS
+==========
+
+The `geos_ats` python package includes tools for managing integrated tests for GEOS.
+It is built using the `Automated Test System <https://ats.readthedocs.io/en/latest/>`_ (ATS) package.
+The available console scripts for this package and its API are described below.
+
+
+run_geos_ats
+----------------
+
+Primary entry point for running integrated tests.
+
+.. argparse::
+   :module: geos_ats.command_line_parsers
+   :func: build_command_line_parser
+   :prog: run_geos_ats
+
+
+.. note::
+    Arguments can be passed to the underlying ATS system with the `--ats` argument.
+
+
+.. note::
+    Other machine-specific options for ATS can be viewed by running `run_geos_ats --ats help`
+
+
+API
+------
+
+
+Restart Check
+^^^^^^^^^^^^^^^
+
+.. automodule:: geos_ats.helpers.restart_check
+    :members:
+
+
+Curve Check
+^^^^^^^^^^^^^^^
+
+.. automodule:: geos_ats.helpers.curve_check
+    :members:
+
+

docs/index.rst

@@ -43,6 +43,8 @@ Packages
 
     hdf5_wrapper
 
+    geos_ats
+
     geosx_mesh_tools
 
     geosx_xml_tools

geos_ats_package/geos_ats/helpers/restart_check.py

@@ -195,21 +195,21 @@ def compareFloatArrays(self, path, arr, base_arr):
         Compares two arrays ARR and BASEARR of floating point values.
         Entries x1 and x2 are  considered equal iff:
 
-            |x1 - x2| <= ATOL * ( 1 + max(|x2|) )
-            - or -
-            |x1 - x2| <= RTOL * |x2|.
+        abs(x1 - x2) <= ATOL * ( 1 + max(abs(x2)) )
+        or
+        abs(x1 - x2) <= RTOL * abs(x2).
 
         To measure the degree of difference a scaling factor q
         is introduced. The goal is now to minimize q such that:
 
-            |x1 - x2| <= ATOL * ( 1 + max(|x2|) ) * q
-            - or -
-            |x1 - x2| <= RTOL * |x2| * q.
+        abs(x1 - x2) <= ATOL * ( 1 + max(abs(x2)) ) * q
+        or
+        abs(x1 - x2) <= RTOL * abs(x2) * q.
 
-        If RTOL * |x2| > ATOL * ( 1 + max(|x2|) )
-            q = |x1 - x2| / (RTOL * |x2|)
+        If RTOL * abs(x2) > ATOL * ( 1 + max(abs(x2)) )
+        q = abs(x1 - x2) / (RTOL * abs(x2))
         else
-            q = |x1 - x2| / ( ATOL * ( 1 + max(|x2|) ) ).
+        q = abs(x1 - x2) / ( ATOL * ( 1 + max(abs(x2)) ) ).
 
         If the maximum value of q over all the
         entries is greater than 1.0 then the arrays are considered
@@ -667,12 +667,11 @@ def findMaxMatchingFile(file_path):
     find and return the path of the greatest matching file/folder or None if no match is found.
 
     FILE_PATH [in]: The pattern to match.
-
+    
     Examples:
-        ".*" will return the file/folder with the greatest name in the current directory.
-
-        "test/plot_*.hdf5" will return the file with the greatest name in the ./test directory
-        that begins with "plot_" and ends with ".hdf5".
+    '.*' will return the file/folder with the greatest name in the current directory.
+    'test/plot_*.hdf5' will return the file with the greatest name in the ./test directory
+    that begins with 'plot' and ends with '.hdf5'.
     """
     file_directory, pattern = os.path.split(file_path)
     if file_directory == "":