Removing all wildcard imports (#1252)

* First pass at removing wildcard imports

* run black

* Fixing the rest of the "single line" of wildcard-import files

* Cleaning up wildcard imports and running isort

* Black doesn't like isort

* Removing rest of the wildcard imports

* run black

* Removing pyDOE as required as it (or rather pyDOE3) is now pulled in by smt

Author: ksbeattie

.github/actions/pylint/action.yml

@@ -15,6 +15,6 @@ runs:
       shell: bash
       run: |
         echo '::group::Output of pylint'
-        pylint --rcfile=.pylint/pylintrc --disable=all --enable=E --enable=wrong-import-order,unused-import foqus_lib/
+        pylint --rcfile=.pylint/pylintrc --disable=all --enable=E --enable=wrong-import-order,unused-import,wildcard-import foqus_lib/
         echo '::endgroup::'
 

docs/source/chapt_sm_optimizer/reference/SM_based_optimizer_introduction.rst

@@ -23,12 +23,10 @@ Additional python packages required
 -----------------------------------
 
 1.	Surrogate modeling toolbox - smt: pip install smt
-2.	Experimental design package for python - pyDOE: pip install pyDOE
-3.  Pyomo package for optimization: pip install pyomo
-4.  Mathematical optimization solver ipopt: conda install -c conda-forge ipopt (preferred installation method for Windows users)
+2.  Pyomo package for optimization: pip install pyomo
+3.  Mathematical optimization solver ipopt: conda install -c conda-forge ipopt (preferred installation method for Windows users)
 
 Note: smt package is required to access its Latin hypercube sampling method, which is required to generate samples and re-build surrogate models in each iteration of the algorithm.
-pyDOE package is a requirement within the smt package, which makes its installation necessary.
 
 Framework
 ----------

foqus_lib/foqus.py

@@ -20,11 +20,12 @@
 Keith Beattie, Lawrence Berkeley National Labs, 2020
 """
 
+# Imports
 import argparse
 import json
 import logging
-
-# Imports
+import os
+import shutil
 import signal
 import sys
 import time
@@ -34,7 +35,12 @@
 # FOQUS imports
 import foqus_lib.version.version as ver  # foqus version and other info
 from foqus_lib.framework.listen.listen import foqusListener2
-from foqus_lib.framework.session.session import *
+from foqus_lib.framework.session.session import (
+    generalSettings,
+    makeWorkingDirStruct,
+    makeWorkingDirFiles,
+    session,
+)
 from foqus_lib.gui.make_shortcut import makeShortcut
 
 loadGUI = False

foqus_lib/framework/foqusOptions/optionList.py

@@ -20,7 +20,7 @@
 John Eslick, Carnegie Mellon University, 2014
 """
 
-from foqus_lib.framework.foqusOptions.option import *
+from foqus_lib.framework.foqusOptions.option import option
 
 
 class optionList(dict):

foqus_lib/framework/graph/OptGraphOptim.py

@@ -14,9 +14,6 @@
 #################################################################################
 import numpy
 
-from foqus_lib.framework.graph.edge import *
-from foqus_lib.framework.graph.node import *
-
 
 class optimObj:
     def __init__(self, pycode="", ps=1, failval=1000):

foqus_lib/framework/graph/graph.py

@@ -24,6 +24,7 @@
 import copy
 import logging
 import math
+import os
 import sys
 import threading
 import time
@@ -33,12 +34,12 @@
 import pandas
 
 import foqus_lib.framework.sampleResults.results as resultList
-from foqus_lib.framework.graph.edge import *  # Edge and variable connection classes
-from foqus_lib.framework.graph.node import *  # Node, input var and output var classes
+from foqus_lib.framework.foqusException.foqusException import foqusException
+from foqus_lib.framework.graph.edge import edge
+from foqus_lib.framework.graph.node import Node, NodeEx
 from foqus_lib.framework.graph.nodeModelTypes import nodeModelTypes
-from foqus_lib.framework.graph.nodeVars import *
-from foqus_lib.framework.graph.OptGraphOptim import *  # Objective function calculation class
-from foqus_lib.framework.sim.turbineConfiguration import *
+from foqus_lib.framework.graph.nodeVars import NodeVarList, NodeVarVectorList
+from foqus_lib.framework.sim.turbineConfiguration import TurbineConfiguration
 
 _log = logging.getLogger("foqus." + __name__)
 

foqus_lib/framework/graph/node.py

@@ -28,10 +28,11 @@
 import numpy as np
 
 from foqus_lib.framework.at_dict.at_dict import AtDict
+from foqus_lib.framework.foqusException.foqusException import foqusException
 from foqus_lib.framework.foqusOptions.optionList import optionList
 from foqus_lib.framework.graph.nodeModelTypes import nodeModelTypes
-from foqus_lib.framework.graph.nodeVars import *
-from foqus_lib.framework.pymodel.pymodel import *
+from foqus_lib.framework.graph.nodeVars import NodeVars, NodeVarVector
+from foqus_lib.framework.pymodel.pymodel import pymodel
 from foqus_lib.framework.sim.turbineConfiguration import TurbineInterfaceEx
 
 _logger = logging.getLogger("foqus." + __name__)

foqus_lib/framework/graph/nodeVars.py

@@ -26,7 +26,7 @@
 from collections import OrderedDict
 
 
-from foqus_lib.framework.foqusException.foqusException import *
+from foqus_lib.framework.foqusException.foqusException import foqusException
 from foqus_lib.framework.uq.Distribution import Distribution
 
 ivarScales = [  # list of scaling options for input variables

foqus_lib/framework/optimizer/SM_Optimizer.py

@@ -41,12 +41,9 @@
 from foqus_lib.framework.optimizer.optimization import optimization
 from foqus_lib.framework.uq.SurrogateParser import SurrogateParser
 
-# Check that the required pyomo, pyDOE, and smt packages are available for the surrogate based optimization plugin and import it.
+# Check that the required pyomo and smt packages are available for the surrogate based optimization plugin and import it.
 # If not the Surrogate Based Optimization plug-in will not be available.
-
 try:
-    # add direct imports (in addition to existing wildcard import)
-    # to make pylint happy without affecting the existing runtime behavior
     import pyutilib.subprocess.GlobalData
     from pyomo.environ import (
         ConstraintList,
@@ -57,13 +54,12 @@
     from pyomo.opt import SolverFactory
 
     pyutilib.subprocess.GlobalData.DEFINE_SIGNAL_HANDLERS_DEFAULT = False
-    from pyDOE import *
     from smt.sampling_methods import LHS
 
     packages_available = True
-except ImportError:
-    logging.getLogger("foqus." + __name__).info(
-        "Failed to import the required packages for SM Optimizer solver"
+except ImportError as ie:
+    logging.getLogger("foqus." + __name__).warn(
+        "Failed to import the required packages for SM Optimizer solver: " + str(ie)
     )
     packages_available = False
 

foqus_lib/framework/optimizer/optimization.py

@@ -25,8 +25,6 @@
 
 from foqus_lib.framework.foqusOptions.optionList import optionList
 
-from .problem import *
-
 
 class optimization(threading.Thread):
     """