Updating black to 26.1.0 and re-running it

cloud/aws/cloudformation/FOQUS_SLM_instance_in_subnet.py

@@ -61,7 +61,6 @@
 from awacs.aws import Allow, Statement, Principal, Policy, Action
 from awacs.sts import AssumeRole
 
-
 # Globals
 # bucket_name:
 #   used by instance cloud-init scripts to grab installers, etc
@@ -76,11 +75,9 @@ def _create_template(
     """returns Template instance"""
     t = Template()
     t.add_version("2010-09-09")
-    t.add_description(
-        """Template to create SLM instance and bind to
+    t.add_description("""Template to create SLM instance and bind to
     passed in Network Interface\
-    """
-    )
+    """)
 
     keyname_param = t.add_parameter(
         Parameter(
@@ -398,7 +395,7 @@ def main():
         usage="USAGE: %prog [vpc_id] [subnet_id] [internet_gateway_id] [network_interface_id] [allocation_id]",
         description=main.__doc__,
     )
-    (options, args) = op.parse_args()
+    options, args = op.parse_args()
     # if len(args) != 1: usage()
     # command = args[0]
     # Ref(VPC)

cloud/aws/foqus_service.py

@@ -18,6 +18,7 @@
 Joshua Boverhof, Lawrence Berkeley National Lab
 
 """
+
 import os, sys
 import traceback
 import win32api

docs/source/_repopath.py

@@ -22,7 +22,6 @@
 from sphinx.application import Sphinx as SphinxApp
 from sphinx.roles import EmphasizedLiteral
 
-
 _logger = logging.getLogger(f"sphinx.ext.{__name__}")
 
 

examples/2020-shmtg/CompDemo/Flowsheet-UQ-SM/MEA_SSM_Part2_files/Ensemble_201008152339/Analysis_201009204103/alamo_surrogate_uq.py

@@ -338,6 +338,6 @@ def interpolate(npts, XX, oid):
     else:
         if y in labels:
             index = labels.index(y)
-(nSamples, inputVectors, nInputs) = getInputData(infileName)
+nSamples, inputVectors, nInputs = getInputData(infileName)
 result = interpolate(nSamples, inputVectors, index)
 genOutputFile(outfileName, result)

examples/2020-shmtg/CompDemo/Flowsheet-UQ-SM/MEA_SSM_Part2_files/Ensemble_201008152339/Analysis_201009204306/alamo_surrogate_uq.py

@@ -338,6 +338,6 @@ def interpolate(npts, XX, oid):
     else:
         if y in labels:
             index = labels.index(y)
-(nSamples, inputVectors, nInputs) = getInputData(infileName)
+nSamples, inputVectors, nInputs = getInputData(infileName)
 result = interpolate(nSamples, inputVectors, index)
 genOutputFile(outfileName, result)

examples/other_files/ML_AI_Plugin/Other_MLAI_Models/mea_column_model_training_jenn.py

@@ -19,7 +19,6 @@
 import pickle
 from types import SimpleNamespace
 
-
 # Example follows the sequence below:
 # 1) Code at end of file to import data and create model
 # 2) Call create_model() to define inputs and outputs

examples/other_files/ML_AI_Plugin/Other_MLAI_Models/mea_column_model_training_smtgenn.py

@@ -19,7 +19,6 @@
 import pickle
 from types import SimpleNamespace
 
-
 # Example follows the sequence below:
 # 1) Code at end of file to import data and create model
 # 2) Call create_model() to define inputs and outputs

foqus_lib/core.py

@@ -15,6 +15,7 @@
 """
 Joshua Boverhof, Lawrence Berkeley National Labs, 2024
 """
+
 import os, shutil, logging
 
 # from foqus_lib.framework.session.session import generalSettings as FoqusSettings

foqus_lib/framework/foqusException/foqusException.py

@@ -18,6 +18,7 @@
 
 John Eslick, Carnegie Mellon University, 2014
 """
+
 import traceback
 
 

foqus_lib/framework/foqusOptions/option.py

@@ -13,7 +13,7 @@
 # "https://github.com/CCSI-Toolset/FOQUS".
 #################################################################################
 """option.py
-     
+
 This is an options class for FOQUS, mainly used for optimization and surrogate
 model plugins.
 

foqus_lib/framework/graph/graph.py

@@ -1877,7 +1877,7 @@ def sear(depth, prevY):
         # rows of A are cycles and columns of A are edges
         # 1 if a edge is in a cycle 0 otherwise
         [A, cycles, cycleEdges] = self.cycleEdgeMatrix()  #
-        (nr, nc) = A.shape
+        nr, nc = A.shape
         if nr == 0:  # no cycles no tear edges and we are done
             return [[[]], 0, 0]
         # There are cycles so find tear edges.

foqus_lib/framework/listen/listen.py

@@ -22,7 +22,6 @@
 John Eslick, Carnegie Mellon University, 2014
 """
 
-
 import copy
 import logging
 import threading

foqus_lib/framework/ml_ai_models/mlaiSearch.py

@@ -12,7 +12,7 @@
 # respectively. This file is also available online at the URL
 # "https://github.com/CCSI-Toolset/FOQUS".
 #################################################################################
-""" mlaiSearch.py
+"""mlaiSearch.py
 
 * This class looks for ml_ai model files and creates a list containing the
   NN model names.

foqus_lib/framework/optimizer/BFGS.py

@@ -12,7 +12,7 @@
 # respectively. This file is also available online at the URL
 # "https://github.com/CCSI-Toolset/FOQUS".
 #################################################################################
-""" #FOQUS_OPT_PLUGIN
+"""#FOQUS_OPT_PLUGIN
 
 Optimization plugins need to have the string "#FOQUS_OPT_PLUGIN" near the
 beginning of the file (see pluginSearch.plugins() for exact character count of
@@ -23,6 +23,7 @@
 
 John Eslick, Carnegie Mellon University, 2014
 """
+
 import logging
 import math
 import time

foqus_lib/framework/optimizer/NLopt.py

@@ -12,7 +12,7 @@
 # respectively. This file is also available online at the URL
 # "https://github.com/CCSI-Toolset/FOQUS".
 #################################################################################
-""" #FOQUS_OPT_PLUGIN
+"""#FOQUS_OPT_PLUGIN
 
 Optimization plugins need to have the string "#FOQUS_OPT_PLUGIN" near the
 beginning of the file (see pluginSearch.plugins() for exact character count of
@@ -25,6 +25,7 @@
 
 John Eslick, Carnegie Mellon University, 2014
 """
+
 import logging
 import math
 import time  # Some of these things are left over from CMA-ES

foqus_lib/framework/optimizer/OptCMA.py

@@ -12,7 +12,7 @@
 # respectively. This file is also available online at the URL
 # "https://github.com/CCSI-Toolset/FOQUS".
 #################################################################################
-""" #FOQUS_OPT_PLUGIN
+"""#FOQUS_OPT_PLUGIN
 
 Optimization plugins need to have the string "#FOQUS_OPT_PLUGIN" near the
 beginning of the file (see pluginSearch.plugins() for exact character count of

foqus_lib/framework/optimizer/PSUADE.py

@@ -12,13 +12,14 @@
 # respectively. This file is also available online at the URL
 # "https://github.com/CCSI-Toolset/FOQUS".
 #################################################################################
-""" #FOQUS_OPT_PLUGIN
+"""#FOQUS_OPT_PLUGIN
 
 Optimization plugins need to have the string "#FOQUS_OPT_PLUGIN" near the
 beginning of the file (see pluginSearch.plugins() for exact character count of
 text).  They also need to have a .py extension and inherit the optimization class.
 
 """
+
 import logging
 
 #

foqus_lib/framework/optimizer/SLSQP.py

@@ -12,7 +12,7 @@
 # respectively. This file is also available online at the URL
 # "https://github.com/CCSI-Toolset/FOQUS".
 #################################################################################
-""" #FOQUS_OPT_PLUGIN
+"""#FOQUS_OPT_PLUGIN
 
 Optimization plugins need to have the string "#FOQUS_OPT_PLUGIN" near the
 beginning of the file (see pluginSearch.plugins() for exact character count of

foqus_lib/framework/optimizer/SM_Optimizer.py

@@ -12,7 +12,7 @@
 # respectively. This file is also available online at the URL
 # "https://github.com/CCSI-Toolset/FOQUS".
 #################################################################################
-""" #FOQUS_OPT_PLUGIN
+"""#FOQUS_OPT_PLUGIN
 
 Optimization plugins need to have the string "#FOQUS_OPT_PLUGIN" near the
 beginning of the file (see pluginSearch.plugins() for exact character count of
@@ -101,9 +101,11 @@ def __init__(self, dat=None):
         optimization.__init__(self, dat)  # base class __init__
 
         # Description of the optimization
-        self.methodDescription = "This solver provides the option to perform mathematical \
+        self.methodDescription = (
+            "This solver provides the option to perform mathematical \
              optimization based on surrogate models developed for the FOQUS \
                  flowsheet"
+        )
         self.available = packages_available  # If plugin is available
         self.description = "Optimization Solver"  # Short description
         self.mp = False  # Can evaluate objectives in parallel?

foqus_lib/framework/optimizer/Sample.py

@@ -12,7 +12,7 @@
 # respectively. This file is also available online at the URL
 # "https://github.com/CCSI-Toolset/FOQUS".
 #################################################################################
-""" #FOQUS_OPT_PLUGIN
+"""#FOQUS_OPT_PLUGIN
 
 Optimization plugins need to have the string "#FOQUS_OPT_PLUGIN" near the
 beginning of the file (see pluginSearch.plugins() for exact character count of

foqus_lib/framework/optimizer/Snobfit.py

@@ -12,7 +12,7 @@
 # respectively. This file is also available online at the URL
 # "https://github.com/CCSI-Toolset/FOQUS".
 #################################################################################
-""" #FOQUS_OPT_PLUGIN
+"""#FOQUS_OPT_PLUGIN
 
 Optimization plugins need to have the string "#FOQUS_OPT_PLUGIN" near the
 beginning of the file (see pluginSearch.plugins() for exact character count of

foqus_lib/framework/optimizer/problem.py

@@ -417,7 +417,7 @@ def calculateObj(self, svlist, nsamples=1):
                         # This is just some error that was caught usually
                         # means failed to converge.
                         fail[i] = True
-            (x, f) = self.get_at_dicts(x, f)
+            x, f = self.get_at_dicts(x, f)
             if self.objtype == self.OBJ_TYPE_EVAL:
                 (
                     res[obj_index],
@@ -474,7 +474,7 @@ def calculateObjVector(self, svlist, nsamples=1):
                         # This is just some error that was caught usually
                         # means failed to converge.
                         fail[i] = True
-            (xvector, fvector) = self.get_at_dicts(xvector, fvector)
+            xvector, fvector = self.get_at_dicts(xvector, fvector)
             if self.objtype == self.OBJ_TYPE_EVAL:
                 (
                     res[obj_index],

foqus_lib/framework/plugins/pluginSearch.py

@@ -12,7 +12,7 @@
 # respectively. This file is also available online at the URL
 # "https://github.com/CCSI-Toolset/FOQUS".
 #################################################################################
-""" pluginSearch.py
+"""pluginSearch.py
 
 * This class looks for plugins and creates a dictionary containing.
   the plugin models.  Plugin objects can be instantiated elsewhere.

foqus_lib/framework/sampleResults/results.py

@@ -240,7 +240,7 @@ def row_to_flow(self, fs, row, filtered=True):
         _log.debug("Row to flowsheet, table row {} dataframe index {}".format(row, idx))
         for col in self.columns:
             try:
-                (io_type, node, var) = col.split(".", 2)
+                io_type, node, var = col.split(".", 2)
             except ValueError:
                 # this would happen for cols with less than two .'s and is
                 # totally fine

foqus_lib/framework/sampleResults/test/results_s3_test.py

@@ -20,6 +20,7 @@
 John Eslick, Carnegie Mellon University, 2014
 See LICENSE.md for license and copyright details.
 """
+
 import json
 import logging
 

foqus_lib/framework/sdoe/nusf_dask.py

@@ -77,7 +77,7 @@ def criterion(
     rand_gen = np.random.default_rng(rand_seed)
 
     def step(
-        mwr_tuple: Tuple[int, List[int], np.ndarray, Union[np.ndarray, None]]
+        mwr_tuple: Tuple[int, List[int], np.ndarray, Union[np.ndarray, None]],
     ) -> Dict:
         mwr, rands, cand_np, hist_np = mwr_tuple
 

foqus_lib/framework/sdoe/test/test_irsf.py

@@ -17,6 +17,7 @@
 
 See LICENSE.md for license and copyright details.
 """
+
 from importlib import resources
 from unittest import result
 

foqus_lib/framework/session/session.py

@@ -20,6 +20,7 @@
 
 John Eslick, Carnegie Mellon University, 2014
 """
+
 import collections
 import copy
 import json

foqus_lib/framework/sim/process_management.py

@@ -19,6 +19,7 @@
 Joshua Boverhof, Lawrence Berkeley National Lab
 
 """
+
 import logging
 
 import psutil

foqus_lib/framework/sim/turbineConfiguration.py

@@ -12,7 +12,7 @@
 # respectively. This file is also available online at the URL
 # "https://github.com/CCSI-Toolset/FOQUS".
 #################################################################################
-""" turbineConfiguration.py
+"""turbineConfiguration.py
 
 * This class contains Turbine configuration profiles and  functions for
   interacting with Turbine
@@ -21,6 +21,7 @@
 
 John Eslick, Carnegie Mellon University, 2014
 """
+
 import configparser
 import importlib
 import json

foqus_lib/framework/sim/turbineLiteDB.py

@@ -17,6 +17,7 @@
 
 John Eslick, Carnegie Mellon University, 2014
 """
+
 import os
 import os.path
 import threading

foqus_lib/framework/sintervectorize/SinterFileVectorize.py

@@ -17,6 +17,7 @@
     to include vector variables.
 
 """
+
 import ast
 import copy
 import json

foqus_lib/framework/surrogate/ACOSSO.py

@@ -12,7 +12,7 @@
 # respectively. This file is also available online at the URL
 # "https://github.com/CCSI-Toolset/FOQUS".
 #################################################################################
-""" #FOQUS_SURROGATE_PLUGIN
+"""#FOQUS_SURROGATE_PLUGIN
 
 Surrogate plugins need to have the string "#FOQUS_SURROGATE_PLUGIN" near the
 beginning of the file (see pluginSearch.plugins() for exact character count of
@@ -25,6 +25,7 @@
 
 John Eslick, Carnegie Mellon University, 2014
 """
+
 import json
 import logging
 import os

foqus_lib/framework/surrogate/ALAMO.py

@@ -12,7 +12,7 @@
 # respectively. This file is also available online at the URL
 # "https://github.com/CCSI-Toolset/FOQUS".
 #################################################################################
-""" #FOQUS_SURROGATE_PLUGIN
+"""#FOQUS_SURROGATE_PLUGIN
 
 Surrogate plugins need to have the string "#FOQUS_SURROGATE_PLUGIN" near the
 beginning of the file (see pluginSearch.plugins() for exact character count of
@@ -30,7 +30,6 @@
 
 """
 
-
 import copy
 import logging
 import math

foqus_lib/framework/surrogate/BSS-ANOVA.py

@@ -12,7 +12,7 @@
 # respectively. This file is also available online at the URL
 # "https://github.com/CCSI-Toolset/FOQUS".
 #################################################################################
-""" #FOQUS_SURROGATE_PLUGIN
+"""#FOQUS_SURROGATE_PLUGIN
 
 Surrogate plugins need to have the string "#FOQUS_SURROGATE_PLUGIN" near the
 beginning of the file (see pluginSearch.plugins() for exact character count of