Change PluginPyARC to use extra_inputs

doc/source/user/usage.rst

@@ -56,15 +56,16 @@ added to WATTS and are available for your use.
 MOOSE Plugin
 ~~~~~~~~~~
 
-The :class:`~watts.PluginMOOSE` class enables MOOSE simulations using a templated
-input file. This is demonstrated here for a SAM application, but other examples based on BISON are also available. 
-For MOOSE codes such as SAM or BISON that use text-based input files, WATTS relies on
-the `Jinja <https://jinja.palletsprojects.com>`_ templating engine for handling
-templated variables and expressions. The templated input file looks like a
-normal MOOSE input file where some values have been replaced with
-**variables**, which are denoted by ``{{`` and ``}}`` pairs and get replaced
-with actual values when the template is *rendered*. For example, a templated
-input file might look as follows:
+The :class:`~watts.PluginMOOSE` class enables MOOSE simulations using a
+templated input file. This is demonstrated here for a SAM application, but other
+examples based on BISON are also available. For MOOSE codes such as SAM or BISON
+that use text-based input files, WATTS relies on the `Jinja
+<https://jinja.palletsprojects.com>`_ templating engine for handling templated
+variables and expressions. The templated input file looks like a normal MOOSE
+input file where some values have been replaced with **variables**, which are
+denoted by ``{{`` and ``}}`` pairs and get replaced with actual values when the
+template is *rendered*. For example, a templated input file might look as
+follows:
 
 .. code-block:: jinja
 
@@ -81,8 +82,9 @@ If the templated input file is ``sam_template.inp``, the SAM code will rely the
 
     moose_plugin = watts.PluginMOOSE('sam_template.inp')
 
-The MOOSE plugin provides the option to specify supplementary input files (in `supp_inputs` option) that 
-will be copied together with the templated input file (mesh or cross-section files).
+The MOOSE plugin provides the option to specify non-templated input files (in
+`extra_inputs` option) that will be copied together with the templated input
+file (mesh or cross-section files).
 
 The SAM executable defaults to ``sam-opt`` (assumed to be present on your
 :envvar:`PATH`) but can also be specified explicitly with the
@@ -163,7 +165,7 @@ PyARC Plugin
 ~~~~~~~~~~~~~
 
 The :class:`~watts.PluginPyARC` class handles PyARC execution in a similar
-manner to the :class:`~watts.PluginSAM` class for SAM. PyARC use text-based 
+manner to the :class:`~watts.PluginSAM` class for SAM. PyARC use text-based
 input files which can be templated as follows:
 
 .. code-block:: jinja
@@ -176,15 +178,15 @@ input files which can be templated as follows:
 
 If the templated input file is `pyarc_template`, then the PyARC plugin can be instantiated with following command line::
 
-    pyarc_plugin = watts.PluginPyARC('pyarc_template', show_stdout=True, supp_inputs=['lumped_test5.son'])
+    pyarc_plugin = watts.PluginPyARC('pyarc_template', show_stdout=True, extra_inputs=['lumped_test5.son'])
 
 The path to PyARC directory must be specified explicitly with the
 :attr:`~watts.PluginPyARC.pyarc_exec` attribute::
 
     pyarc_plugin.pyarc_exec  = "/path/to/PyARC"
 
-To execute PyARC, the :meth:`~watts.PluginPyARC.workflow` method is called 
-the same way as other Plugins. 
+To execute PyARC, the :meth:`~watts.PluginPyARC.workflow` method is called
+the same way as other Plugins.
 
 Results
 +++++++

examples/example1c_PyARC/example1c.py

@@ -15,7 +15,7 @@
 
 # PyARC Workflow
 
-pyarc_plugin = watts.PluginPyARC('pyarc_template', show_stdout=True, supp_inputs=['lumped_test5.son']) # show all the output
+pyarc_plugin = watts.PluginPyARC('pyarc_template', show_stdout=True, extra_inputs=['lumped_test5.son']) # show all the output
 pyarc_result = pyarc_plugin.workflow(params)
 for key in pyarc_result.results_data:
     print(key, pyarc_result.results_data[key])

src/watts/plugin_moose.py

@@ -205,7 +205,7 @@ def postrun(self, params: Parameters) -> ResultsMOOSE:
 
         time = datetime.fromtimestamp(self._run_time * 1e-9)
         # Start with non-templated input files
-        inputs = [Path.cwd() / p.name for p in self.extra_inputs]
+        inputs = [p.name for p in self.extra_inputs]
         inputs.append('MOOSE.i')
         outputs = [p for p in Path.cwd().iterdir() if p.name not in inputs]
-        return ResultsMOOSE(params, time, inputs, outputs)
+        return ResultsMOOSE(params, time, inputs, outputs)

src/watts/plugin_pyarc.py

@@ -6,7 +6,7 @@
 import os
 import tempfile
 import time
-from typing import Mapping, List
+from typing import Mapping, List, Optional
 
 import h5py
 import sys
@@ -62,7 +62,7 @@ def _save_PyARC(self, user_object) -> dict:
         results_data["persent_sens"] = user_object.results_kuq_persent
         results_data["gamsor"] = user_object.results_power_gamsor
         results_data["dassh"] = user_object.results_dassh
-        # TODO - this is minimum information that can be brought back easily. 
+        # TODO - this is minimum information that can be brought back easily.
         # More should be returned but will require work on PyARC.
         return results_data
 
@@ -98,12 +98,12 @@ class PluginPyARC(TemplatePlugin):
     template_file
         Templated PyARC input
     show_stdout
-        Whether to display output from stdout when SAM is run
+        Whether to display output from stdout when PyARC is run
     show_stderr
-        Whether to display output from stderr when SAM is run
-    supp_inputs
-        List of supplementary input files that are needed for running PyARC
-    
+        Whether to display output from stderr when PyARC is run
+    extra_inputs
+        List of extra (non-templated) input files that are needed
+
     Attributes
     ----------
     pyarc_exec
@@ -112,13 +112,13 @@ class PluginPyARC(TemplatePlugin):
     """
 
     def  __init__(self, template_file: str, show_stdout: bool = False,
-                  show_stderr: bool = False, supp_inputs: List[str] = []):
-        super().__init__(template_file)
+                  show_stderr: bool = False,
+                  extra_inputs: Optional[List[str]] = None):
+        super().__init__(template_file, extra_inputs)
         self._pyarc_exec = Path(os.environ.get('PyARC_DIR', 'PyARC.py'))
         self.pyarc_inp_name = "pyarc_input.son"
         self.show_stdout = show_stdout
         self.show_stderr = show_stderr
-        self.supp_inputs = [Path(f).resolve() for f in supp_inputs]
 
     @property
     def pyarc_exec(self) -> Path:
@@ -178,7 +178,7 @@ def postrun(self, params: Parameters) -> ResultsPyARC:
         print("Post-run for PyARC Plugin")
 
         time = datetime.fromtimestamp(self._run_time * 1e-9)
-        inputs = [p.name for p in self.supp_inputs]
+        inputs = [p.name for p in self.extra_inputs]
         inputs.append(self.pyarc_inp_name)
         outputs = [p for p in Path.cwd().iterdir() if p.name not in inputs]
         return ResultsPyARC(params, time, inputs, outputs, self.pyarc.user_object)