Rc1.4.0 (#607)

* modified version

* sphinx doc fixes (some circular imports and string formatting)

doc/source/_templates/layout.html

@@ -104,11 +104,12 @@
      style="height:1in;"> A Python toolkit for computational methods and simulation</p>
     <div class="btn-group" role="group">
       <a class="btn btn-success"
-          href="https://github.com/erdc-cm/proteus/archive/1.3.3.tar.gz">
+          href="https://github.com/erdc-cm/proteus/archive/1.4.0.tar.gz">
             <span class="glyphicon glyphicon-download"></span> Download
       </a>
       <button type="button" class="btn btn-success dropdown-toggle" data-toggle="dropdown"><span class="caret"></span></button>
       <ul class="dropdown-menu">
+        <li><a https://github.com/erdc-cm/proteus/archive/1.4.0.tar.gz">Version 1.4.0</a></li>
         <li><a https://github.com/erdc-cm/proteus/archive/1.3.3.tar.gz">Version 1.3.3</a></li>
         <li><a https://github.com/erdc-cm/proteus/archive/1.3.2.tar.gz">Version 1.3.2</a></li>
         <li><a https://github.com/erdc-cm/proteus/archive/1.3.1.tar.gz">Version 1.3.1</a></li>

proteus/Isosurface.pyx

@@ -2,9 +2,6 @@
 #cython: embedsignature=True
 """
 AuxiliaryVariables subclasses for extracting isosurfaces and contours
-
-.. inheritance-diagram:: proteus.Isosurface
-   :parts: 1
 """
 from collections import defaultdict, OrderedDict
 from itertools import product

proteus/MeshTools.py

@@ -6261,7 +6261,7 @@ def genMeshWithTetgen(polyfile,
    nbase : int
 
    Returns
-    -------
+   --------
    mesh : :class:`proteus.MeshTools.TetrahedralMesh`
        Simplex mesh
    """
@@ -6277,10 +6277,6 @@ def genMeshWithTetgen(polyfile,
                                 base=nbase)
    return mesh
 
-
-from proteus import default_n as dn
-from proteus import default_p as dp
-
 class MeshOptions:
     """
     Mesh options for the domain

proteus/NonlinearSolvers.py

@@ -635,7 +635,7 @@ def solve(self,u,r=None,b=None,par_u=None,par_r=None):
 
 class ExplicitLumpedMassMatrixShallowWaterEquationsSolver(Newton):
     """
-     This is a fake solver meant to be used with optimized code
+    This is a fake solver meant to be used with optimized code
     A simple iterative solver that is Newton's method
     if you give it the right Jacobian
     """
@@ -669,7 +669,7 @@ def solve(self,u,r=None,b=None,par_u=None,par_r=None):
 
 class ExplicitConsistentMassMatrixShallowWaterEquationsSolver(Newton):
     """
-     This is a fake solver meant to be used with optimized code
+    This is a fake solver meant to be used with optimized code
     A simple iterative solver that is Newton's method
     if you give it the right Jacobian
     """
@@ -2356,6 +2356,7 @@ class EikonalSolver:
        FMMEikonalSolver
        FSWEikonalSolver
 
+
     """
 #    TODO Feb 20
 #      Debug change in use truncation approach for positive and negative solutions

proteus/TransportCoefficients.py

@@ -9768,7 +9768,6 @@ def evaluate(self,t,c):
                                                         c[('dr',1,0)],
                                                         c[('dr',1,1)])
 
-from proteus import FemTools
 class ConservativeHeadRichardsMualemVanGenuchtenBlockHetV2withUpwind(TC_base):
     """
     version of Re where element material type id's used in evals

proteus/__init__.py

@@ -9,7 +9,7 @@
     import pkgutil
     __path__ = pkgutil.extend_path(__path__, __name__)
 
-__version__ = '1.3.3.dev0'
+__version__ = '1.4.0'
 
 __all__ = ["Archiver",
            "Domain",

setup.py

@@ -39,7 +39,7 @@
         break
 
 setup(name='proteus',
-      version='1.3.3.dev0',
+      version='1.4.0',
       description='Python tools for multiphysics modeling',
       author='The Proteus Developers',
       author_email='[email protected]',