Assorted fixes while supporting PETSc

.appveyor.yml

@@ -64,8 +64,9 @@ install:
     - cmd: conda.exe config --add channels conda-forge
 
     # Configure the VM.
-    - cmd: if "%TARGET_ARCH%" == "x64" if "%CONDA_PY%" == "27" conda.exe install --quiet --name root --only-deps python=2.7 fipy
-    - cmd: if "%TARGET_ARCH%" == "x64" if "%CONDA_PY%" == "36" conda.exe install --quiet --name root --only-deps python=3.6 fipy
+    - cmd: if "%TARGET_ARCH%" == "x64" if "%CONDA_PY%" == "27" conda.exe install --quiet --name root python=2.7 fipy
+    - cmd: if "%TARGET_ARCH%" == "x64" if "%CONDA_PY%" == "36" conda.exe install --quiet --name root python=3.6 fipy "gmsh<4.0"
+    - cmd: conda.exe remove --quiet --force fipy
     # FIXME: fipy recipe on conda-forge doesn't have gmsh compatible with Python 2.7
     - ps: |
         $ErrorActionPreference = "Stop";

.circleci/config.yml

@@ -36,7 +36,7 @@ commands:
       - run:
           name: Create Conda Environment
           command: |
-            conda create -v --quiet --prefix << parameters.condaenv >> --show-channel-urls --channel conda-forge --only-deps << parameters.packages >>
+            conda create -v --quiet --prefix << parameters.condaenv >> --show-channel-urls --channel conda-forge << parameters.packages >> "gmsh<4.0"
             source activate ~/project/<< parameters.condaenv >>
             pip install future
             pip install scikit-fmm

.travis.yml

@@ -41,7 +41,7 @@ before_install:
   - hash -r
   - conda config --set always_yes yes --set changeps1 no
   - conda update -q conda
-  - conda create --quiet --name test-environment --show-channel-urls --channel conda-forge --only-deps python=$TRAVIS_PYTHON_VERSION fipy;
+  - conda create --quiet --name test-environment --show-channel-urls --channel conda-forge python=$TRAVIS_PYTHON_VERSION fipy "gmsh<4.0";
   - source activate test-environment
   # Useful for debugging any issues with conda
   - conda info -a

INSTALLATION.rst

@@ -124,7 +124,7 @@ Recommended Method
 .. _Linux: http://www.linux.org/
 .. _Windows: http://www.microsoft.com/windows/
 .. |CondaForge|    image:: https://anaconda.org/conda-forge/fipy/badges/installer/conda.svg
-.. _CondaForge:    https://anaconda.org/guyer/fipy
+.. _CondaForge:    https://anaconda.org/conda-forge/fipy
 
 
 --------------
@@ -256,6 +256,8 @@ Gmsh
 http://www.geuz.org/gmsh/
 
 :term:`Gmsh` is an application that allows the creation of irregular meshes.
+When running in parallel, :term:`FiPy` requires a version of :term:`Gmsh`
+>= 2.5 and < 4.0.
 
 SciPy
 =====

README.rst

@@ -169,7 +169,7 @@ or a
 .. |PyPI|          image:: https://img.shields.io/pypi/v/fipy.svg
 .. _PyPI:          https://pypi.python.org/pypi/FiPy
 .. |CondaForge|    image:: https://anaconda.org/conda-forge/fipy/badges/installer/conda.svg
-.. _CondaForge:    https://anaconda.org/guyer/fipy
+.. _CondaForge:    https://anaconda.org/conda-forge/fipy
 .. |Depsy|         image:: http://depsy.org/api/package/pypi/FiPy/badge.svg
 .. _Depsy:         http://depsy.org/package/python/FiPy
 .. |Codacy|         image:: https://api.codacy.com/project/badge/Grade/d02921bb54b14e88a1e2e1f5520133f4

_setup/upload_products.py

@@ -29,13 +29,17 @@ def finalize_options (self):
 
     def run(self):
         if self.pdf:
+            fname = 'dist/fipy-%s.pdf' % self.distribution.metadata.get_version()
             print("setting permissions of manual...")
             os.system('chmod -R g+w documentation/_build/latex/fipy.pdf')
 
             print("linking manual to `dist/`...")
             os.system('mkdir dist/')
-            os.system('ln -f documentation/_build/latex/fipy.pdf dist/fipy-%s.pdf'%self.distribution.metadata.get_version())
+            os.system('ln -f documentation/_build/latex/fipy.pdf %s' % fname)
 
+            print("uploading pdf...")
+            os.system('rsync -pgoDLC -e ssh %s %s/download/' % (fname, os.environ['FIPY_WWWHOST']))
+
         if self.html:
             print("setting group and ownership of web pages...")
             os.system('chmod -R g+w documentation/_build/html/')
@@ -46,21 +50,20 @@ def run(self):
             os.system('rsync -rlpgoDLC -e ssh %s %s' % ('documentation/_build/html/', os.environ['FIPY_WWWHOST']))
 
         if self.tarball:
-            file = 'dist/FiPy-%s.tar.gz' % self.distribution.metadata.get_version()
-            print("setting permissions for %s ..." % file)
-            os.system('chmod -R g+w %s' % file)
+            fname = 'dist/FiPy-%s.tar.gz' % self.distribution.metadata.get_version()
+            print("setting permissions for %s ..." % fname)
+            os.system('chmod -R g+w %s' % fname)
 
             print("uploading tarball...")
-            os.system('rsync -pgoDLC -e ssh %s %s/download/' % (file, os.environ['FIPY_WWWHOST']))
+            os.system('rsync -pgoDLC -e ssh %s %s/download/' % (fname, os.environ['FIPY_WWWHOST']))
 
         if self.winzip:
-            file = 'dist/FiPy-%s.win32.zip' % self.distribution.metadata.get_version()
-            print("setting permissions for %s ..." % file)
-            os.system('chmod -R g+w %s' % file)
+            fname = 'dist/FiPy-%s.win32.zip' % self.distribution.metadata.get_version()
+            print("setting permissions for %s ..." % fname)
+            os.system('chmod -R g+w %s' % fname)
 
             print("uploading winzip...")
-            os.system('rsync -pgoDLC -e ssh %s %s/download/' % (file, os.environ['FIPY_WWWHOST']))
+            os.system('rsync -pgoDLC -e ssh %s %s/download/' % (fname, os.environ['FIPY_WWWHOST']))
 
-        if self.pdf or self.tarball or self.winzip:
-            print("activating web pages...")
-            os.system(os.environ['FIPY_WWWACTIVATE'])
+        print("activating web pages...")
+        os.system(os.environ['FIPY_WWWACTIVATE'])

documentation/USAGE.rst

@@ -196,9 +196,10 @@ package.
 
    If present, causes the graphical display of the solution matrix of each
    equation at each call of :meth:`~Term.solve` or :meth:`~Term.sweep`.
-   Setting the value to "``terms``," causes the display of the matrix for each
+   Setting the value to "``terms``" causes the display of the matrix for each
    :class:`Term` that composes the equation. Requires the :term:`Matplotlib`
-   package.
+   package. Setting the value to "``print``" causes the matrix to be
+   printed to the console.
 
 .. envvar:: FIPY_INLINE
 

documentation/_templates/index.html

@@ -69,7 +69,7 @@ <h1>FiPy: A Finite Volume PDE Solver Using Python</h1>
   <a href="https://github.com/usnistgov/fipy"><img src="https://img.shields.io/github/contributors/usnistgov/fipy.svg" alt="GitHub"></img></a>
   <a href="https://pypi.python.org/pypi/FiPy"><img src="https://img.shields.io/pypi/v/fipy.svg" alt="PyPi"></img></a>
   <a class="badge-align" href="https://www.codacy.com/app/tkphd/fipy?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=usnistgov/fipy&amp;utm_campaign=Badge_Grade"><img src="https://api.codacy.com/project/badge/Grade/d02921bb54b14e88a1e2e1f5520133f4"/></a>
-  <a href="https://anaconda.org/guyer/fipy"><img src="https://anaconda.org/conda-forge/fipy/badges/installer/conda.svg" alt="CondaForge"></img></a>
+  <a href="https://anaconda.org/conda-forge/fipy"><img src="https://anaconda.org/conda-forge/fipy/badges/installer/conda.svg" alt="CondaForge"></img></a>
   <a href="https://mybinder.org/v2/gh/usnistgov/fipy/master?filepath=examples%2Findex.ipynb"><img src="https://mybinder.org/badge.svg" alt="Binder"></img></a>
   <br>
   <!-- Community Badges -->

examples/cahnHilliard/mesh2DCoupled.py

@@ -1,5 +1,14 @@
 r"""Solve the Cahn-Hilliard problem in two dimensions.
 
+.. warning:: This formulation has
+   `serious performance problems`_
+   and is **not automatically tested**.  Specifically, for non-trivial mesh
+   sizes, :term:`PySparse` requires enormous amounts of memory,
+   :term:`Trilinos` cannot solve the coupled form, and :term:`PETSc` cannot
+   solve the vector form.
+
+.. _serious performance problems: https://github.com/usnistgov/fipy/issues/378
+
 The spinodal decomposition phenomenon is a spontaneous separation of
 an initially homogeneous mixture into two distinct regions of different
 properties (spin-up/spin-down, component A/component B). It is a

examples/cahnHilliard/tanh1D.py

@@ -139,10 +139,10 @@
 ...     if __name__ == '__main__':
 ...         diff = abs(answer - numerix.array(var))
 ...         maxarg = numerix.argmax(diff)
-...         print('maximum error:', diff[maxarg])
+...         print('maximum error: {}'.format(diff[maxarg]))
 ...         print('element id:', maxarg)
-...         print('value at element ', maxarg, ' is ', var[maxarg])
-...         print('solution value', answer[maxarg])
+...         print('value at element {} is {}'.format(maxarg, var[maxarg]))
+...         print('solution value: {}'.format(answer[maxarg]))
 ... 
 ...         viewer.plot()
 

examples/cahnHilliard/test.py

@@ -8,7 +8,7 @@ def _suite():
             'mesh2D',
             'mesh3D',
             'sphere',
-            'mesh2DCoupled',
+#             'mesh2DCoupled',  # FIXME: this test is [borked](https://github.com/usnistgov/fipy/issues/378)
         ), base = __name__)
 
 if __name__ == '__main__':

examples/chemotaxis/input.py

@@ -4,113 +4,114 @@
 
 Here are some test cases for the model.
 
-    >>> from builtins import range
-    >>> for i in range(28):
-    ...     for var, eqn in eqs:
-    ...         var.updateOld()
-    ...     for var, eqn in eqs:
-    ...         eqn.solve(var, dt = 1.0)
-
-    >>> accuracy = 1e-2
-    >>> print(KMVar.allclose(params['KM'], atol = accuracy))
-    1
-    >>> print(TMVar.allclose(params['TM'], atol = accuracy))
-    1
-    >>> print(TCVar.allclose(params['TC'], atol = accuracy))
-    1
-    >>> print(P2Var.allclose(params['P2'], atol = accuracy))
-    1
-    >>> print(P3Var.allclose(params['P3'], atol = accuracy))
-    1
-    >>> print(KCVar.allclose(params['KC'], atol = accuracy))
-    1
-
+>>> from __future__ import division
+
+>>> from builtins import input
+>>> from builtins import range
+>>> from examples.chemotaxis.parameters import parameters
+>>> from fipy import CellVariable, Grid1D, TransientTerm, DiffusionTerm, ImplicitSourceTerm, Viewer, numerix
+
+>>> params = parameters['case 2']
+
+>>> nx = 50
+>>> dx = 1.
+>>> L = nx * dx
+
+>>> mesh = Grid1D(nx=nx, dx=dx)
+
+>>> shift = 1.
+
+>>> KMVar = CellVariable(mesh=mesh, value=params['KM'] * shift, hasOld=1)
+>>> KCVar = CellVariable(mesh=mesh, value=params['KC'] * shift, hasOld=1)
+>>> TMVar = CellVariable(mesh=mesh, value=params['TM'] * shift, hasOld=1)
+>>> TCVar = CellVariable(mesh=mesh, value=params['TC'] * shift, hasOld=1)
+>>> P3Var = CellVariable(mesh=mesh, value=params['P3'] * shift, hasOld=1)
+>>> P2Var = CellVariable(mesh=mesh, value=params['P2'] * shift, hasOld=1)
+>>> RVar = CellVariable(mesh=mesh, value=params['R'], hasOld=1)
+
+>>> PN = P3Var + P2Var
+
+>>> KMscCoeff = params['chiK'] * (RVar + 1) * (1 - KCVar - KMVar.cellVolumeAverage)
+>>> KMspCoeff = params['lambdaK'] / (1 + PN / params['kappaK'])
+>>> KMEq = TransientTerm() - KMscCoeff + ImplicitSourceTerm(KMspCoeff)
+
+>>> TMscCoeff = params['chiT'] * (1 - TCVar - TMVar.cellVolumeAverage)
+>>> TMspCoeff = params['lambdaT'] * (KMVar + params['zetaT'])
+>>> TMEq = TransientTerm() - TMscCoeff + ImplicitSourceTerm(TMspCoeff)
+
+>>> TCscCoeff = params['lambdaT'] * (TMVar * KMVar).cellVolumeAverage
+>>> TCspCoeff = params['lambdaTstar']
+>>> TCEq = TransientTerm() - TCscCoeff + ImplicitSourceTerm(TCspCoeff)
+
+>>> PIP2PITP = PN / (PN / params['kappam'] + PN.cellVolumeAverage / params['kappac'] + 1) + params['zetaPITP']
+
+>>> P3spCoeff = params['lambda3'] * (TMVar + params['zeta3T'])
+>>> P3scCoeff = params['chi3'] * KMVar * (PIP2PITP / (1 + KMVar / params['kappa3']) + params['zeta3PITP']) + params['zeta3']
+>>> P3Eq = TransientTerm() - DiffusionTerm(params['diffusionCoeff']) - P3scCoeff + ImplicitSourceTerm(P3spCoeff)
+
+>>> P2scCoeff = scCoeff = params['chi2'] + params['lambda3'] * params['zeta3T'] * P3Var
+>>> P2spCoeff = params['lambda2'] * (TMVar + params['zeta2T'])
+>>> P2Eq = TransientTerm() - DiffusionTerm(params['diffusionCoeff']) - P2scCoeff + ImplicitSourceTerm(P2spCoeff)
+
+>>> KCscCoeff = params['alphaKstar'] * params['lambdaK'] * (KMVar / (1 + PN / params['kappaK'])).cellVolumeAverage
+>>> KCspCoeff = params['lambdaKstar'] / (params['kappaKstar'] + KCVar)
+>>> KCEq = TransientTerm() - KCscCoeff + ImplicitSourceTerm(KCspCoeff)
+
+>>> eqs = ((KMVar, KMEq), (TMVar, TMEq), (TCVar, TCEq), (P3Var, P3Eq), (P2Var, P2Eq), (KCVar, KCEq))
+
+>>> if __name__ == '__main__':
+...     steps = 100
+... else:
+...     steps = 28
+
+>>> for i in range(steps):
+...     for var, eqn in eqs:
+...         var.updateOld()
+...     for var, eqn in eqs:
+...         eqn.solve(var, dt=1.)
+
+>>> accuracy = 1e-2
+>>> print(KMVar.allclose(params['KM'], atol=accuracy))
+1
+>>> print(TMVar.allclose(params['TM'], atol=accuracy))
+1
+>>> print(TCVar.allclose(params['TC'], atol=accuracy))
+1
+>>> print(P2Var.allclose(params['P2'], atol=accuracy))
+1
+>>> print(P3Var.allclose(params['P3'], atol=accuracy))
+1
+>>> print(KCVar.allclose(params['KC'], atol=accuracy))
+1
+
+>>> PNView = PN / PN.cellVolumeAverage
+>>> PNView.name = 'PN'
+
+>>> KMView = KMVar / KMVar.cellVolumeAverage
+>>> KMView.name = 'KM'
+
+>>> TMView = TMVar / TMVar.cellVolumeAverage
+>>> TMView.naem = 'TM'
+
+>>> RVar[:] = params['S'] + (1 + params['S']) * params['G'] * numerix.cos((2 * numerix.pi * mesh.cellCenters[0]) / L)
+
+>>> if __name__ == '__main__':
+...     KMViewer = Viewer((PNView, KMView, TMView), title = 'Gradient Stimulus: Profile')
+...
+...     for i in range(100):
+...         for var, eqn in eqs:
+...             var.updateOld()
+...         for var, eqn in eqs:
+...             eqn.solve(var, dt=0.1)
+...
+...         KMViewer.plot()
+...
+...     input("finished")
 """
-from __future__ import division
 from __future__ import unicode_literals
 
-from builtins import range
-from examples.chemotaxis.parameters import parameters
-
-from fipy import input
-from fipy import CellVariable, Grid1D, TransientTerm, DiffusionTerm, ImplicitSourceTerm, Viewer
-
-params = parameters['case 2']
-
-nx = 50
-dx = 1.
-L = nx * dx
-
-mesh = Grid1D(nx = nx, dx = dx)
-
-shift = 1.
-
-KMVar = CellVariable(mesh = mesh, value = params['KM'] * shift, hasOld = 1)
-KCVar = CellVariable(mesh = mesh, value = params['KC'] * shift, hasOld = 1)
-TMVar = CellVariable(mesh = mesh, value = params['TM'] * shift, hasOld = 1)
-TCVar = CellVariable(mesh = mesh, value = params['TC'] * shift, hasOld = 1)
-P3Var = CellVariable(mesh = mesh, value = params['P3'] * shift, hasOld = 1)
-P2Var = CellVariable(mesh = mesh, value = params['P2'] * shift, hasOld = 1)
-RVar = CellVariable(mesh = mesh, value = params['R'], hasOld = 1)
-
-PN = P3Var + P2Var
-
-KMscCoeff = params['chiK'] * (RVar + 1) * (1 - KCVar - KMVar.cellVolumeAverage)
-KMspCoeff = params['lambdaK'] / (1 + PN / params['kappaK'])
-KMEq = TransientTerm() - KMscCoeff + ImplicitSourceTerm(KMspCoeff)
-
-TMscCoeff = params['chiT'] * (1 - TCVar - TMVar.cellVolumeAverage)
-TMspCoeff = params['lambdaT'] * (KMVar + params['zetaT'])
-TMEq = TransientTerm() - TMscCoeff + ImplicitSourceTerm(TMspCoeff)
-
-TCscCoeff = params['lambdaT'] * (TMVar * KMVar).cellVolumeAverage
-TCspCoeff = params['lambdaTstar']
-TCEq = TransientTerm() - TCscCoeff + ImplicitSourceTerm(TCspCoeff)
-
-PIP2PITP = PN / (PN / params['kappam'] + PN.cellVolumeAverage / params['kappac'] + 1) + params['zetaPITP']
-
-P3spCoeff = params['lambda3'] * (TMVar + params['zeta3T'])
-P3scCoeff = params['chi3'] * KMVar * (PIP2PITP / (1 + KMVar / params['kappa3']) + params['zeta3PITP']) + params['zeta3']
-P3Eq = TransientTerm() - DiffusionTerm(params['diffusionCoeff']) - P3scCoeff + ImplicitSourceTerm(P3spCoeff)
-
-P2scCoeff = scCoeff = params['chi2'] + params['lambda3'] * params['zeta3T'] * P3Var
-P2spCoeff = params['lambda2'] * (TMVar + params['zeta2T'])
-P2Eq = TransientTerm() - DiffusionTerm(params['diffusionCoeff']) - P2scCoeff + ImplicitSourceTerm(P2spCoeff)
-
-KCscCoeff = params['alphaKstar'] * params['lambdaK'] * (KMVar / (1 + PN / params['kappaK'])).cellVolumeAverage
-KCspCoeff = params['lambdaKstar'] / (params['kappaKstar'] + KCVar)
-KCEq = TransientTerm() - KCscCoeff + ImplicitSourceTerm(KCspCoeff)
-
-eqs = ((KMVar, KMEq), (TMVar, TMEq), (TCVar, TCEq), (P3Var, P3Eq), (P2Var, P2Eq), (KCVar, KCEq))
+__docformat__ = 'restructuredtext'
 
 if __name__ == '__main__':
-
-    v1 = KMVar / KMVar.cellVolumeAverage
-    v2 = PN / PN.cellVolumeAverage
-    v3 = TMVar / TMVar.cellVolumeAverage
-    v1.setName('KM')
-    v2.setName('PN')
-    v3.setName('TM')
-
-    KMViewer = Viewer((v1, v2, v3), title = 'Gradient Stimulus: Profile')
-
-    KMViewer.plot()
-
-    for i in range(100):
-        for var, eqn in eqs:
-            var.updateOld()
-        for var, eqn in eqs:
-            eqn.solve(var, dt = 1.)
-
-    RVar[:] = params['S'] + (1 + params['S']) * params['G'] * cos((2 * pi * mesh.cellCenters[0]) / L)
-
-    for i in range(100):
-        for var, eqn in eqs:
-            var.updateOld()
-        for var, eqn in eqs:
-            eqn.solve(var, dt = 0.1)
-        KMViewer.plot()
-
-    KMViewer.plot()
-
-    input("finished")
+    import fipy.tests.doctestPlus
+    exec(fipy.tests.doctestPlus._getScript())