Merge pull request #9 from paulromano/generalize-extra-inputs

Generalize ability to specify extra inputs

README.md

@@ -1,6 +1,8 @@
 # WATTS
 
 [![License](https://img.shields.io/badge/license-MIT-green)](https://opensource.org/licenses/MIT)
+[![GitHub Actions build status (Linux)](https://github.com/watts-dev/watts/workflows/CI/badge.svg?branch=development)](https://github.com/watts-dev/watts/actions?query=workflow%3ACI)
+
 
 WATTS (Workflow and Template Toolkit for Simulation) provides a set of Python
 classes that can manage simulation workflows for multiple codes where

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])

examples/example5_multiapps/example5a.py

@@ -18,7 +18,7 @@
 
 moose_app_type = "bison"
 app_dir = os.environ[moose_app_type.upper() + "_DIR"]
-moose_plugin = watts.PluginMOOSE('main.tmpl', supp_inputs=['main_in.e', 'sub.i'])
+moose_plugin = watts.PluginMOOSE('main.tmpl', extra_inputs=['main_in.e', 'sub.i'])
 moose_plugin.moose_exec = app_dir + "/" + moose_app_type.lower() + "-opt"
 moose_result = moose_plugin.workflow(params)
 for key in moose_result.csv_data:

examples/example6_adv_multiapps/example6.py

@@ -39,7 +39,7 @@
 
 # MOOSE Workflow for steady state
 print("Steady-state calculation")
-moose_plugin_ss = watts.PluginMOOSE('MP_ss_griffin.tmpl', n_cpu=40, supp_inputs=['MP_ss_moose.i', 'MP_ss_sockeye.i', '3D_unit_cell_FY21_level-1_bison.e', '3D_unit_cell_FY21_supersimple.e', 'unitcell_nogap_hom_xml_G11_df_MP.xml'])
+moose_plugin_ss = watts.PluginMOOSE('MP_ss_griffin.tmpl', n_cpu=40, extra_inputs=['MP_ss_moose.i', 'MP_ss_sockeye.i', '3D_unit_cell_FY21_level-1_bison.e', '3D_unit_cell_FY21_supersimple.e', 'unitcell_nogap_hom_xml_G11_df_MP.xml'])
 moose_plugin_ss.moose_exec = app_dir + "/" + moose_app_type.lower() + "-opt"
 moose_result_ss = moose_plugin_ss.workflow(params_ss)
 for key in moose_result_ss.csv_data:
@@ -55,7 +55,7 @@
 
 # MOOSE Workflow for Null transient
 print("Null transient calculation")
-moose_plugin_trN = watts.PluginMOOSE('MP_trN_griffin.tmpl', n_cpu=40, show_stdout=False, supp_inputs=['MP_trN_moose.i', 'MP_trN_sockeye.i', 'unitcell_nogap_hom_xml_G11_df_MP.xml'])
+moose_plugin_trN = watts.PluginMOOSE('MP_trN_griffin.tmpl', n_cpu=40, show_stdout=False, extra_inputs=['MP_trN_moose.i', 'MP_trN_sockeye.i', 'unitcell_nogap_hom_xml_G11_df_MP.xml'])
 moose_plugin_trN.moose_exec = app_dir + "/" + moose_app_type.lower() + "-opt"
 moose_result_trN = moose_plugin_trN.workflow(params_trN)
 for key in moose_result_trN.csv_data:
@@ -75,7 +75,7 @@
 
 # MOOSE Workflow for transient
 print("Transient calculation")
-moose_plugin_tr = watts.PluginMOOSE('MP_tr_griffin.tmpl', n_cpu=40, show_stdout=True, supp_inputs=['MP_tr_moose.i', 'MP_tr_sockeye.i', 'unitcell_nogap_hom_xml_G11_df_MP.xml'])
+moose_plugin_tr = watts.PluginMOOSE('MP_tr_griffin.tmpl', n_cpu=40, show_stdout=True, extra_inputs=['MP_tr_moose.i', 'MP_tr_sockeye.i', 'unitcell_nogap_hom_xml_G11_df_MP.xml'])
 moose_plugin_tr.moose_exec = app_dir + "/" + moose_app_type.lower() + "-opt"
 moose_result_tr = moose_plugin_tr.workflow(params_tr)
 for key in moose_result_tr.csv_data:

setup.cfg

@@ -2,7 +2,7 @@
 name = watts
 version = 0.0.1
 author = UChicago Argonne, LLC
-author_email = nstauff@anl.gov
+author_email = watts@anl.gov
 description = Workflow and Template Toolkit for Simulation
 long_description = file: README.md
 long_description_content_type = text/markdown

src/watts/plugin.py

@@ -2,22 +2,32 @@
 # SPDX-License-Identifier: MIT
 
 from abc import ABC, abstractmethod
-import os
 from pathlib import Path
 import shutil
-from typing import Optional
+from typing import Optional, List
 from astropy import units as u
 import copy
 
 from .database import Database
-from .fileutils import cd_tmpdir
+from .fileutils import cd_tmpdir, PathLike
 from .parameters import Parameters
 from .results import Results
 from .template import TemplateModelBuilder
 
 
 class Plugin(ABC):
-    """Class defining the Plugin interface"""
+    """Class defining the Plugin interface
+
+    Parameters
+    ----------
+    extra_inputs
+        Extra (non-templated) input files
+    """
+
+    def __init__(self, extra_inputs: Optional[List[PathLike]] = None):
+        self.extra_inputs = []
+        if extra_inputs is not None:
+            self.extra_inputs = [Path(f).resolve() for f in extra_inputs]
 
     @abstractmethod
     def prerun(self, params):
@@ -61,11 +71,12 @@ def workflow(self, params: Parameters, name='Workflow') -> Results:
         db = Database()
 
         with cd_tmpdir():
+            # Copy extra inputs to temporary directory
+            cwd = Path.cwd()
+            for path in self.extra_inputs:
+                shutil.copy(str(path), str(cwd))  # Remove str() for Python 3.8+
+
             # Run workflow in temporary directory
-            if hasattr(self, 'supp_inputs'):
-                des = os.getcwd()
-                for sifp in self.supp_inputs:
-                    shutil.copy(str(sifp), des)
             self.prerun(params)
             self.run()
             result = self.postrun(params)
@@ -112,7 +123,7 @@ def convert_unit(self, params: Parameters, unit_system: str, unit_temperature: s
 
             if isinstance(params_copy[key], u.quantity.Quantity):
 
-                # Unit conversion for temperature needs to be done separately because 
+                # Unit conversion for temperature needs to be done separately because
                 # astropy uses a different method to convert temperature.
                 # Variables are converted to SI by default.
 
@@ -133,8 +144,12 @@ class TemplatePlugin(Plugin):
     ----------
     template_file
         Path to template file
+    extra_inputs
+        Extra (non-templated) input files
+
     """
-    def  __init__(self, template_file: str):
+    def  __init__(self, template_file: str, extra_inputs: Optional[List[PathLike]] = None):
+        super().__init__(extra_inputs)
         self.model_builder = TemplateModelBuilder(template_file)
 
     def prerun(self, params: Parameters, filename: Optional[str] = None):

src/watts/plugin_moose.py

@@ -3,12 +3,10 @@
 
 from contextlib import redirect_stdout, redirect_stderr
 from datetime import datetime
-import os
 from pathlib import Path
 import shutil
-import subprocess
 import time
-from typing import List
+from typing import List, Optional
 
 import h5py
 import numpy as np
@@ -119,8 +117,8 @@ class PluginMOOSE(TemplatePlugin):
         Whether to display output from stderr when MOOSE is run
     n_cpu
         Number of processors to be used to run MOOSE application
-    supp_inputs
-        List of supplementary input files that are needed for running the MOOSE application
+    extra_inputs
+        List of extra (non-templated) input files that are needed
 
     Attributes
     ----------
@@ -130,16 +128,16 @@ class PluginMOOSE(TemplatePlugin):
     """
 
     def  __init__(self, template_file: str, show_stdout: bool = False,
-                  show_stderr: bool = False, n_cpu: int = 1, supp_inputs: List[str] = []):
-        super().__init__(template_file)
+                  show_stderr: bool = False, n_cpu: int = 1,
+                  extra_inputs: Optional[List[str]] = None):
+        super().__init__(template_file, extra_inputs)
         self._moose_exec = Path('moose-opt')
         self.moose_inp_name = "MOOSE.i"
         self.show_stdout = show_stdout
         self.show_stderr = show_stderr
         if n_cpu < 1:
             raise RuntimeError("The CPU number used to run MOOSE app must be a natural number.")
         self.n_cpu = n_cpu
-        self.supp_inputs = [Path(f).resolve() for f in supp_inputs]
 
     @property
     def moose_exec(self) -> Path:
@@ -206,6 +204,8 @@ def postrun(self, params: Parameters) -> ResultsMOOSE:
         print("Post-run for MOOSE Plugin")
 
         time = datetime.fromtimestamp(self._run_time * 1e-9)
-        inputs = ['MOOSE.i']
+        # Start with non-templated input files
+        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_openmc.py

@@ -6,7 +6,7 @@
 from functools import lru_cache
 from pathlib import Path
 import time
-from typing import Callable, Mapping, List
+from typing import Callable, Mapping, List, Optional
 
 import h5py
 
@@ -103,15 +103,19 @@ class PluginOpenMC(Plugin):
     ----------
     model_builder
         Function that generates an OpenMC model
+    extra_inputs
+        Extra (non-templated) input files
     show_stdout
-        Whether to display output from stdout when SAM is run
+        Whether to display output from stdout when OpenMC is run
     show_stderr
-        Whether to display output from stderr when SAM is run
+        Whether to display output from stderr when OpenMC is run
 
     """
 
-    def __init__(self, model_builder: Callable[[Parameters], None],
+    def __init__(self, model_builder: Optional[Callable[[Parameters], None]] = None,
+                 extra_inputs: Optional[List[PathLike]] = None,
                  show_stdout: bool = False, show_stderr: bool = False):
+        super().__init__(extra_inputs)
         self.model_builder = model_builder
         self.show_stdout = show_stdout
         self.show_stderr = show_stderr
@@ -131,7 +135,8 @@ def prerun(self, params: Parameters) -> None:
 
         print("Pre-run for OpenMC Plugin")
         self._run_time = time.time_ns()
-        self.model_builder(params_copy)
+        if self.model_builder is not None:
+            self.model_builder(params_copy)
 
     def run(self, **kwargs: Mapping):
         """Run OpenMC
@@ -174,8 +179,13 @@ def files_since(pattern, time):
             matches.sort(key=lambda x: x.stat().st_mtime_ns)
             return matches
 
+        # Start with non-templated input files
+        inputs = [Path.cwd() / p.name for p in self.extra_inputs]
+
         # Get generated input files
-        inputs = files_since('*.xml', self._run_time)
+        for path in files_since('*.xml', self._run_time):
+            if path not in inputs:
+                inputs.append(path)
 
         # Get list of all output files
         outputs = ['OpenMC_log.txt']
@@ -185,4 +195,4 @@ def files_since(pattern, time):
         outputs.extend(files_since('statepoint.*.h5', self._run_time))
 
         time = datetime.fromtimestamp(self._run_time * 1e-9)
-        return ResultsOpenMC(params, time, inputs, outputs)
+        return ResultsOpenMC(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)

src/watts/results.py

@@ -107,3 +107,6 @@ def from_hdf5(cls, filename: PathLike):
     def open_folder(self):
         """Open folder containing results"""
         open_file(self.base_path)
+
+    def __repr__(self):
+        return f"<Results{self.plugin}: {self.time}>"