Update flake8 and docs (#65)

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+extend-exclude =
+    baseclasses/problems/pyFieldPerformance_problem.py

baseclasses/problems/__init__.py

@@ -9,3 +9,20 @@
 from .pyEngine_problem import EngineProblem
 from .pyFieldPerformance_problem import FieldPerformanceProblem
 from .pyLG_problem import LGProblem
+
+__all__ = [
+    "AeroProblem",
+    "TransiProblem",
+    "StructProblem",
+    "AeroStructProblem",
+    "MissionProblem",
+    "MissionProfile",
+    "MissionSegment",
+    "WeightProblem",
+    "FuelCase",
+    "FluidProperties",
+    "ICAOAtmosphere",
+    "EngineProblem",
+    "FieldPerformanceProblem",
+    "LGProblem",
+]

baseclasses/problems/pyAero_problem.py

@@ -266,7 +266,7 @@ def __init__(self, name, **kwargs):
             self.evalFuncs = set(kwargs["funcs"])
 
         # we cast the set to a sorted list, so that each proc can loop over in the same order
-        self.evalFuncs = sorted(list(self.evalFuncs))
+        self.evalFuncs = sorted(self.evalFuncs)
 
         # these are the possible input values
         possibleInputStates = {"mach", "V", "P", "T", "rho", "altitude", "reynolds", "reynoldsLength"}

baseclasses/problems/pyMission_problem.py

@@ -397,13 +397,13 @@ def _checkStateConsistancy(self):
                 pass
             else:
                 if not self.firstSegSet:
-                    setattr(seg, "isFirstStateSeg", True)
+                    seg.isFirstStateSeg = True
                     self.firstSegSet = True
                 # end
                 if seg.isFirstStateSeg:
                     # this is the first segment.
                     # Need to have at least the start alt and V or M
-                    if getattr(seg, "initAlt") is None:
+                    if seg.initAlt is None:
                         raise Error(
                             "%s: Initial altitude must be\
                                      specified for the first non fuel fraction\
@@ -412,11 +412,7 @@ def _checkStateConsistancy(self):
                         )
                     # end
 
-                    if (
-                        (getattr(seg, "initMach") is None)
-                        and (getattr(seg, "initCAS") is None)
-                        and (getattr(seg, "initTAS") is None)
-                    ):
+                    if (seg.initMach is None) and (seg.initCAS is None) and (seg.initTAS is None):
                         raise Error(
                             "%s: One of initCAS,initTAS or initMach needs to be\
                                      specified for the first non fuelfraction\
@@ -430,14 +426,14 @@ def _checkStateConsistancy(self):
 
                 else:
                     prevSeg = self.segments[i - 1]
-                    refAlt = getattr(prevSeg, "finalAlt")
-                    refCAS = getattr(prevSeg, "finalCAS")
-                    refTAS = getattr(prevSeg, "finalTAS")
-                    refMach = getattr(prevSeg, "finalMach")
-                    TASi = getattr(seg, "initTAS")
-                    CASi = getattr(seg, "initCAS")
-                    Mi = getattr(seg, "initMach")
-                    Alti = getattr(seg, "initAlt")
+                    refAlt = prevSeg.finalAlt
+                    refCAS = prevSeg.finalCAS
+                    refTAS = prevSeg.finalTAS
+                    refMach = prevSeg.finalMach
+                    TASi = seg.initTAS
+                    CASi = seg.initCAS
+                    Mi = seg.initMach
+                    Alti = seg.initAlt
                     if CASi is not None:
                         if not CASi == refCAS:
                             raise Error(
@@ -449,7 +445,7 @@ def _checkStateConsistancy(self):
                             )
                         # end
                     else:
-                        setattr(seg, "initCAS", refCAS)
+                        seg.initCAS = refCAS
                     # end
                     if TASi is not None:
                         if not TASi == refTAS:
@@ -462,7 +458,7 @@ def _checkStateConsistancy(self):
                             )
                         # end
                     else:
-                        setattr(seg, "initTAS", refTAS)
+                        seg.initTAS = refTAS
                     # end
                     if Alti is not None:
                         if not Alti == refAlt:
@@ -474,7 +470,7 @@ def _checkStateConsistancy(self):
                             )
                         # end
                     else:
-                        setattr(seg, "initAlt", refAlt)
+                        seg.initAlt = refAlt
                     # end
                     if Mi is not None:
                         if not Mi == refMach:
@@ -486,7 +482,7 @@ def _checkStateConsistancy(self):
                             )
                         # end
                     else:
-                        setattr(seg, "initMach", refMach)
+                        seg.initMach = refMach
                     # end
 
                     # Determine the remaining segment parameters (Alt, Mach, CAS, TAS)
@@ -1056,31 +1052,31 @@ def setMissionData(self, module, segTypeDict, engTypeDict, idx, segIdx):
         """
         set the data for the current segment in the fortran module
         """
-        h1 = getattr(self, "initAlt")
+        h1 = self.initAlt
         if h1 is None:
             h1 = 0.0
-        h2 = getattr(self, "finalAlt")
+        h2 = self.finalAlt
         if h2 is None:
             h2 = 0.0
-        M1 = getattr(self, "initMach")
+        M1 = self.initMach
         if M1 is None:
             M1 = 0.0
-        M2 = getattr(self, "finalMach")
+        M2 = self.finalMach
         if M2 is None:
             M2 = 0.0
-        deltaTime = getattr(self, "segTime")
+        deltaTime = self.segTime
         if deltaTime is None:
             deltaTime = 0.0
         # end
 
-        rangeFraction = getattr(self, "rangeFraction")
+        rangeFraction = self.rangeFraction
         if rangeFraction is None:
             rangeFraction = 1.0
         # end
 
         # Get the fuel-fraction, if provided, then segment is a generic fuel fraction type
-        fuelFraction = getattr(self, "fuelFraction")
-        throttle = getattr(self, "throttle")
+        fuelFraction = self.fuelFraction
+        throttle = self.throttle
         if fuelFraction is None and throttle is None:
             segTypeID = segTypeDict[getattr(self, "phase").lower()]
             fuelFraction = 0.0
@@ -1098,7 +1094,7 @@ def setMissionData(self, module, segTypeDict, engTypeDict, idx, segIdx):
             raise Error(f"engType {self.engType} defined in segment {self.phase} not defined in engTypeDict")
         if self.engType is None:
             self.engType = "None"
-        engTypeID = engTypeDict[getattr(self, "engType")]
+        engTypeID = engTypeDict[self.engType]
 
         module.setmissionsegmentdata(
             idx,

baseclasses/problems/pyStruct_problem.py

@@ -55,7 +55,7 @@ def __init__(self, name, **kwargs):
                 self.evalFuncs = set(kwargs["funcs"])
 
         # we cast the set to a sorted list, so that each proc can loop over in the same order
-        self.evalFuncs = sorted(list(self.evalFuncs))
+        self.evalFuncs = sorted(self.evalFuncs)
 
         # When a solver calls its evalFunctions() it must write the
         # unique name it gives to funcNames.

baseclasses/solvers/__init__.py

@@ -1,2 +1,4 @@
 from .BaseSolver import BaseSolver
 from .pyAero_solver import AeroSolver
+
+__all__ = ["BaseSolver", "AeroSolver"]

baseclasses/testing/__init__.py

@@ -1,2 +1,4 @@
 from .pyRegTest import BaseRegTest, getTol
 from .decorators import require_mpi
+
+__all__ = ["BaseRegTest", "getTol", "require_mpi"]

baseclasses/testing/decorators.py

@@ -4,6 +4,17 @@
 
 
 def require_mpi(func):
+    """A decorator to skip tests unless ``mpi4py`` is available
+
+    Examples
+    --------
+    .. code-block:: python
+
+       @require_mpi
+       def test_mpi4py(self):
+           print(self.comm.rank)
+
+    """
     return base_require(func, "mpi4py")
 
 

baseclasses/utils/__init__.py

@@ -1,3 +1,5 @@
 from .containers import CaseInsensitiveSet, CaseInsensitiveDict
 from .error import Error
 from .py3Util import getPy3SafeString
+
+__all__ = ["CaseInsensitiveSet", "CaseInsensitiveDict", "Error", "getPy3SafeString"]

baseclasses/utils/containers.py

@@ -25,7 +25,7 @@ class CaseInsensitiveDict(MutableMapping):
     --------
     This container preserves the initial capitalization, such that
     any operation which operates on an existing entry will not modify it.
-    This means that add() and update() will NOT update the original capitalization.
+    This means that for example :meth:`__setitem__()` will NOT update the original capitalization.
     """
 
     def __init__(self, *args, **kwargs):
@@ -119,7 +119,7 @@ class CaseInsensitiveSet(MutableSet):
     --------
     This container preserves the initial capitalization, such that
     any operation which operates on an existing entry will not modify it.
-    This means that add() and update() will NOT update the original capitalization.
+    This means that :meth:`add()` and :meth:`update()` will NOT update the original capitalization.
     """
 
     def __init__(self, *args, **kwargs):
@@ -192,7 +192,7 @@ def union(self, d):
         return new_set
 
     def update(self, d):
-        """Just call add() iteratively"""
+        """Just call :meth:`add()` iteratively"""
         for item in d:
             self.add(item)
 

baseclasses/utils/py3Util.py

@@ -6,7 +6,7 @@
 
 
 def getPy3SafeString(string):
-    """Accepts a <string> and makes sure its converted to unicode for python 3.6 and above"""
+    """Accepts a string and makes sure it's converted to unicode for python 3.6 and above"""
 
     if string is None:
         return None

doc/BaseRegTest.rst

@@ -1,12 +1,8 @@
-.. _BaseRegTest:
+Testing
+-------
 
-BaseRegTest
------------
-
-.. currentmodule:: baseclasses.BaseRegTest
-
-.. autoclass:: BaseRegTest
+.. autoclass:: baseclasses.BaseRegTest
     :members:
 
-.. automodule:: baseclasses.BaseRegTest
+.. automodule:: baseclasses.testing
     :members:

doc/BaseSolver.rst

@@ -1,9 +1,5 @@
-.. _BaseSolver:
-
 BaseSolver
 ----------
 
-.. currentmodule:: baseclasses.BaseSolver
-
-.. autoclass:: BaseSolver
+.. autoclass:: baseclasses.BaseSolver
     :members:

doc/index.rst

@@ -3,8 +3,6 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-.. _baseClasses:
-
 ===========
 baseClasses
 ===========
@@ -57,3 +55,9 @@ Or from source, by cloning the repo and then running (from the repo root)::
 
    BaseRegTest
    regression_example
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Utilities
+
+   utils

doc/pyAeroStruct_problem.rst

@@ -1,9 +1,5 @@
-.. _pyAeroStruct_problem:
-
-pyAeroStruct_problem
+AeroStructProblem
 --------------------
 
-.. currentmodule:: baseclasses.pyAeroStruct_problem
-
-.. autoclass:: AeroStructProblem
+.. autoclass:: baseclasses.AeroStructProblem
     :members:

doc/pyAero_problem.rst

@@ -1,9 +1,5 @@
-.. _pyAero_problem:
+AeroProblem
+-----------
 
-pyAero_problem
---------------
-
-.. currentmodule:: baseclasses.pyAero_problem
-
-.. autoclass:: AeroProblem
+.. autoclass:: baseclasses.AeroProblem
     :members:

doc/pyAero_solver.rst

@@ -1,9 +1,7 @@
-.. _pyAero_solver:
+AeroSolver
+----------
 
-pyAero_solver
--------------
-
-.. currentmodule:: baseclasses.pyAero_solver
+.. currentmodule:: baseclasses
 
 .. autoclass:: AeroSolver
     :members:

doc/pyMission_problem.rst

@@ -1,13 +1,9 @@
-.. _pyMission_problem:
+MissionProblem
+--------------
 
-pyMission_problem
------------------
-
-.. currentmodule:: baseclasses.pyMission_problem
-
-.. autoclass:: MissionProblem
+.. autoclass:: baseclasses.MissionProblem
     :members:
-.. autoclass:: MissionProfile
+.. autoclass:: baseclasses.MissionProfile
     :members:
-.. autoclass:: MissionSegment
+.. autoclass:: baseclasses.MissionSegment
     :members:

doc/pyStruct_problem.rst

@@ -1,9 +1,5 @@
-.. _pyStruct_problem:
+StructProblem
+-------------
 
-pyStruct_problem
-----------------
-
-.. currentmodule:: baseclasses.pyStruct_problem
-
-.. autoclass:: StructProblem
+.. autoclass:: baseclasses.StructProblem
     :members:

doc/pyWeight_problem.rst

@@ -1,9 +1,5 @@
-.. _pyWeight_problem:
-
-pyWeight_problem
+WeightProblem
 ----------------
 
-.. currentmodule:: baseclasses.pyWeight_problem
-
-.. autoclass:: WeightProblem
+.. autoclass:: baseclasses.WeightProblem
     :members: