CIs error on deprecation warning (#708)

* Raise errors for DeprecationWarnings during CI tests

* Remove ez_setup.py

The version here [generates deprecations](https://app.circleci.com/jobs/github/usnistgov/fipy/2031)
and [ez_setup.py itself is deprecated](pypa/setuptools#581)

* Change "FORTRAN" array ordering to 'F'

Missed in #707

* Update from deprecated Pysparse API

This stuff was deprecated [ages ago](https://sourceforge.net/p/pysparse/git/ci/241a05d7a6e5f0f8ae28c53ac79a2111fe2d7cc0/)

* Switch from itsolvers classes to krylov functions

The itsolvers classes aren't written right (e.g., `solve()` doesn't
return anything) and don't encapsulate anything we care about.
The `krylov` calls are set up the way we expect.

* Raise errors for DeprecationWarnings only in test suite

Raising errors for all of `python setup.py test` causes
errors for deprecations in things we don't control, like versioneer.

* Use legacy absolute tolerance for scipy Krylov solvers

Avoid DeprecationWarning

* Introduce specialized TestProgram to throw Deprecation errors

In Py3k, TestProgram makes it very hard to change DeprecationWarnings
into errors. [TestProgram gives all warnings an action of `default`](https://github.com/python/cpython/blob/master/Lib/unittest/main.py#L84)
which causes [TestRunner to clobber our DeprecationWarning filter](https://github.com/python/cpython/blob/master/Lib/unittest/runner.py#L167)
(passing any other action to TestProgram just causes that action to clobber instead)

* Force Py27 builds on Visual Studio 2015

scikit-fmm (and maybe others) needs VC++ 9.0
https://help.appveyor.com/discussions/problems/26278-organization-build-fails-because-vc-90-is-not-present

* Choose appropriate build environment

[Exclude unwanted build configurations](https://www.appveyor.com/docs/build-configuration/#exclude-configuration-from-the-matrix)

.appveyor.yml

@@ -1,5 +1,9 @@
 # This file was adapted from what's generated by conda-smithy.
 
+image:
+- Visual Studio 2015
+- Visual Studio 2019
+
 environment:
 
   matrix:
@@ -34,6 +38,14 @@ environment:
       CONDA_INSTALL_LOCN: C:\\Miniconda36-x64
       FIPY_SOLVERS: scipy
 
+matrix:
+  exclude:
+    - image: Visual Studio 2015
+      CONDA_PY: 36
+
+    - image: Visual Studio 2019
+      CONDA_PY: 27
+
 # We always use a 64-bit machine, but can build x86 distributions
 # with the TARGET_ARCH variable.
 platform:
@@ -91,7 +103,7 @@ build_script:
 test_script:
     - python setup.py egg_info
     - if defined FIPY_INLINE python setup.py test 1> NUL 2>&1
-    - python setup.py test
+    - python setup.py test --deprecation-errors
     - conda env export
 
 artifacts:

.circleci/config.yml

@@ -78,7 +78,7 @@ commands:
             if [[ ! -z "${FIPY_INLINE}" ]]; then
               << parameters.mpirun >> python setup.py test > /dev/null 2>&1 || true;
             fi
-            << parameters.mpirun >> python setup.py test
+            << parameters.mpirun >> python setup.py test --deprecation-errors
 
       - run:
           name: Output Environment

.travis.yml

@@ -68,6 +68,6 @@ before_script:
       travis_wait 40 $MPIRUN python setup.py test || true;
     fi
 script:
-  - $MPIRUN python setup.py test;
+  - $MPIRUN python setup.py test --deprecation-errors;
 after_success:
   - conda env export

MANIFEST-UNIX.in

@@ -1,5 +1,4 @@
 include *.rst
-include ez_setup.py
 # include MANIFEST MANIFEST.in *.rst
 
 recursive-include documentation *.rst

examples/levelSet/electroChem/matplotlibSurfactantViewer.py

@@ -112,9 +112,9 @@ def _plot(self):
 
         maxX = max(X)
 
-        X = X.reshape(shape, order="FORTRAN")
-        Y = Y.reshape(shape, order="FORTRAN")
-        Z = self.distanceVar.value.reshape(shape, order="FORTRAN")
+        X = X.reshape(shape, order='F')
+        Y = Y.reshape(shape, order='F')
+        Z = self.distanceVar.value.reshape(shape, order='F')
 
         zmin, zmax = self._autoscale(vars=(self.surfactantVar,),
                                      datamin=self._getLimit(('datamin', 'zmin')),

fipy/solvers/pysparse/linearCGSSolver.py

@@ -3,7 +3,7 @@
 
 import sys
 
-from pysparse import itsolvers
+from pysparse.itsolvers import krylov
 
 from fipy.solvers.pysparse.pysparseSolver import PysparseSolver
 
@@ -36,4 +36,4 @@ def __init__(self, precon=None, *args, **kwargs):
         import warnings
         warnings.warn("The Pysparse CGS solver may return incorrect results for some matrices", UserWarning)
         super(LinearCGSSolver, self).__init__(precon=precon, *args, **kwargs)
-        self.solveFnc = itsolvers.cgs
+        self.solveFnc = krylov.cgs

fipy/solvers/pysparse/linearGMRESSolver.py

@@ -1,9 +1,9 @@
 from __future__ import unicode_literals
 __docformat__ = 'restructuredtext'
 
-from fipy.solvers.pysparse.preconditioners import JacobiPreconditioner
-from pysparse import itsolvers
+from pysparse.itsolvers import krylov
 
+from fipy.solvers.pysparse.preconditioners import JacobiPreconditioner
 from fipy.solvers.pysparse.pysparseSolver import PysparseSolver
 
 __all__ = ["LinearGMRESSolver"]
@@ -32,4 +32,4 @@ def __init__(self, precon=JacobiPreconditioner(), *args, **kwargs):
         precon : ~fipy.solvers.pysparse.preconditioners.preconditioner.Preconditioner, optional
         """
         super(LinearGMRESSolver, self).__init__(precon=precon, *args, **kwargs)
-        self.solveFnc = itsolvers.gmres
+        self.solveFnc = krylov.gmres

fipy/solvers/pysparse/linearLUSolver.py

@@ -6,7 +6,7 @@
 
 import os
 
-from pysparse import superlu
+from pysparse.direct import superlu
 
 from fipy.solvers.pysparse.pysparseSolver import PysparseSolver
 from fipy.tools import numerix