Fipy

--------------------------

Fixes
-----

- `502 <https://github.com/usnistgov/fipy/issues/502>`_:
gmane is defunct

--------------------------

--------------------------

Pulls
-----

- remove `recvobj` from calls to `allgather`, require `sendobj`
(`492 <https://github.com/usnistgov/fipy/pull/492>`_)
- restore trailing whitespace to expected output of pysparse matrix
tests
(`485 <https://github.com/usnistgov/fipy/pull/485>`_)
- Format version string for pep 440
(`483 <https://github.com/usnistgov/fipy/pull/483>`_)
- Provide some documentation for what `_faceToCellDistanceRatio` is
and why it's scalar
(`481 <https://github.com/usnistgov/fipy/pull/481>`_)
- Strip all trailing white spaces and empty lines at EOF for `.py` and
`.r`?
(`479 <https://github.com/usnistgov/fipy/pull/479>`_)
Thanks to `pya <https://github.com/pya>`_.
- `fipy/meshes/uniformGrid3D.py`: fix `_cellToCellIDs` and more
`concatenate()` calls
(`478 <https://github.com/usnistgov/fipy/pull/478>`_)
Thanks to `pkgw <https://github.com/pkgw>`_.
- Remove incorrect `axis` argument to `concatenate`
(`477 <https://github.com/usnistgov/fipy/pull/477>`_)
- Updated to NumPy 1.10
(`472 <https://github.com/usnistgov/fipy/pull/472>`_)
Thanks to `pya <https://github.com/pya>`_.
- Some spelling corrections
(`471 <https://github.com/usnistgov/fipy/pull/471>`_)
Thanks to `pkgw <https://github.com/pkgw>`_.
- Sort entry points by package name before testing.
(`469 <https://github.com/usnistgov/fipy/pull/469>`_)
- Update import syntax in examples
(`466 <https://github.com/usnistgov/fipy/pull/466>`_)
- Update links to prerequisites
(`465 <https://github.com/usnistgov/fipy/pull/465>`_)
- Correct implementation of `examples.cahnHilliard.mesh2DCoupled`. Fixes
?
(`463 <https://github.com/usnistgov/fipy/pull/463>`_)
- Fix typeset analytical solution
(`460 <https://github.com/usnistgov/fipy/pull/460>`_)
- Clear `pdflatex` build errors by removing :term:`Python` from heading
(`459 <https://github.com/usnistgov/fipy/pull/459>`_)
- purge gist from viewers and optional module lists in `setup.py`
(`456 <https://github.com/usnistgov/fipy/pull/456>`_)
- Remove deprecated methods that duplicate NumPy ufuncs
(`454 <https://github.com/usnistgov/fipy/pull/454>`_)
- Remove deprecated Gmsh importers
(`452 <https://github.com/usnistgov/fipy/pull/452>`_)
- Remove deprecated getters and setters
(`450 <https://github.com/usnistgov/fipy/pull/450>`_)
- Update links for FiPy developers
(`448 <https://github.com/usnistgov/fipy/pull/448>`_)
- Render appropriately if in IPython notebook
(`447 <https://github.com/usnistgov/fipy/pull/447>`_)
- Plot contour in proper axes
(`446 <https://github.com/usnistgov/fipy/pull/446>`_)
- Robust Gmsh version checking with `distutils.version.StrictVersion`
(`442 <https://github.com/usnistgov/fipy/pull/442>`_)
- compare gmsh versions as tuples, not floats
(`441 <https://github.com/usnistgov/fipy/pull/441>`_)
- Corrected two tests
(`439 <https://github.com/usnistgov/fipy/pull/439>`_)
Thanks to `alfrenardi <https://github.com/alfrenardi>`_.
- Issue426 fix robin example typo
(`431 <https://github.com/usnistgov/fipy/pull/431>`_)
Thanks to `raybsmith <https://github.com/raybsmith>`_.
- Issue426 fix robin example analytical solution
(`429 <https://github.com/usnistgov/fipy/pull/429>`_)
Thanks to `raybsmith <https://github.com/raybsmith>`_.
- Force `MatplotlibViewer` to display
(`428 <https://github.com/usnistgov/fipy/pull/428>`_)
- Allow for 2 periodic axes in 3D
(`424 <https://github.com/usnistgov/fipy/pull/424>`_)
- Bug with Matplotlib 1.4.0 is fixed
(`419 <https://github.com/usnistgov/fipy/pull/419>`_)

Fixes
-----

- `498 <https://github.com/usnistgov/fipy/issues/498>`_:
nonlinear source term
- `496 <https://github.com/usnistgov/fipy/issues/496>`_:
`scipy.LinearBicgstabSolver` doesn't take arguments
- `494 <https://github.com/usnistgov/fipy/issues/494>`_:
Gmsh call errors
- `493 <https://github.com/usnistgov/fipy/issues/493>`_:
`Reviewable.io` has read-only access, can't leave comments
- `491 <https://github.com/usnistgov/fipy/issues/491>`_:
`globalValue` raises error from mpi4py
- `484 <https://github.com/usnistgov/fipy/issues/484>`_:
Pysparse tests fail
- `482 <https://github.com/usnistgov/fipy/issues/482>`_:
FiPy development version string not compliant with PEP 440
- `476 <https://github.com/usnistgov/fipy/issues/476>`_:
`setuptools` 18.4 breaks test suite
- `475 <https://github.com/usnistgov/fipy/issues/475>`_:
`Grid3D` broken by numpy 1.10
- `470 <https://github.com/usnistgov/fipy/issues/470>`_:
`Mesh3D` `cellToCellIDs` is broken
- `467 <https://github.com/usnistgov/fipy/issues/467>`_:
Out-of-sequence Viewer imports
- `462 <https://github.com/usnistgov/fipy/issues/462>`_:
GMSH version >= 2.10 incorrectly read by `gmshMesh.py`
- `455 <https://github.com/usnistgov/fipy/issues/455>`_:
`setup.py` gist warning
- `445 <https://github.com/usnistgov/fipy/issues/445>`_:
`DendriteViewer` puts contours over color bar
- `443 <https://github.com/usnistgov/fipy/issues/443>`_:
`MatplotlibViewer` still has problems in IPython notebook
- `440 <https://github.com/usnistgov/fipy/issues/440>`_:
Use github API to get nicely formatted list of issues
- `438 <https://github.com/usnistgov/fipy/issues/438>`_:
Failed tests on Mac OS X
- `437 <https://github.com/usnistgov/fipy/issues/437>`_:
Figure misleading in `examples.cahnHilliard.mesh2DCoupled`
- `433 <https://github.com/usnistgov/fipy/issues/433>`_:
Links to prerequisites are broken
- `430 <https://github.com/usnistgov/fipy/issues/430>`_:
Make develop the default branch on Github
- `427 <https://github.com/usnistgov/fipy/issues/427>`_:
`MatplotlibViewer` don't display
- `425 <https://github.com/usnistgov/fipy/issues/425>`_:
Links for Warren and Guyer are broken on the web page
- `421 <https://github.com/usnistgov/fipy/issues/421>`_:
The "limits" argument for `Matplotlib2DGridViewer` does not function
- `416 <https://github.com/usnistgov/fipy/issues/416>`_:
Updates to reflect move to Github

--------------------------

--------------------------

Fixes
-----

- `415 <https://github.com/usnistgov/fipy/issues/415>`_:
`MatplotlibGrid2DViewer` error with Matplotlib version 1.4.0
- `414 <https://github.com/usnistgov/fipy/issues/414>`_:
`PeriodicGrid3D` supports Only 1 axes of periodicity or all 3, not 2
- `413 <https://github.com/usnistgov/fipy/issues/413>`_:
Remind users of different types of conservation equations
- `412 <https://github.com/usnistgov/fipy/issues/412>`_:
Pickling Communicators is unnecessary for Grids
- `408 <https://github.com/usnistgov/fipy/issues/408>`_:
Implement `PeriodicGrid3D`
- `407 <https://github.com/usnistgov/fipy/issues/407>`_:
Strange deprecation loop in reshape()
- `404 <https://github.com/usnistgov/fipy/issues/404>`_:
package never gets uploaded to PyPI
- `401 <https://github.com/usnistgov/fipy/issues/401>`_:
Vector equations are broken when `sweep` is used instead of `solve`.
- `295 <https://github.com/usnistgov/fipy/issues/295>`_:
Gmsh version must be >= 2.0 errors on `zizou`

------------------------

------------------------

The significant changes since version 3.0 are:

- Level sets are now handled by :ref:`LSMLIBDOC` or :ref:`SCIKITFMM`
solver libraries. These libraries are orders of magnitude faster than the
original, :term:`Python`-only prototype.
- The :term:`Matplotlib` :func:`streamplot()` function can be used to display
vector fields.
- Version control was switched to the Git_ distributed version control
system. This system should make it much easier for :term:`FiPy` users to
participate in development.

.. _Git: https://github.com/usnistgov/fipy

Fixes
-----

- `398 <https://github.com/usnistgov/fipy/issues/398>`_:
Home page needs out-of-NIST redirects
- `397 <https://github.com/usnistgov/fipy/issues/397>`_:
Switch to `sphinxcontrib-bibtex`
- `396 <https://github.com/usnistgov/fipy/issues/396>`_:
enable google analytics
- `395 <https://github.com/usnistgov/fipy/issues/395>`_:
Documentation change for Ubuntu install
- `393 <https://github.com/usnistgov/fipy/issues/393>`_:
`CylindricalNonUniformGrid2D` doesn't make a `FaceVariable` for
`exteriorFaces`
- `392 <https://github.com/usnistgov/fipy/issues/392>`_:
`exit_nist.cgi` deprecated
- `391 <https://github.com/usnistgov/fipy/issues/391>`_:
Péclet inequalities have the wrong sign
- `388 <https://github.com/usnistgov/fipy/issues/388>`_:
Windows 64 and numpy's `dtype=int`
- `384 <https://github.com/usnistgov/fipy/issues/384>`_:
Add support for Matplotlib `streamplot`
- `382 <https://github.com/usnistgov/fipy/issues/382>`_:
Neumann boundary conditions not clearly documented
- `381 <https://github.com/usnistgov/fipy/issues/381>`_:
numpy 1.7.1 test failures with `physicalField.py`
- `377 <https://github.com/usnistgov/fipy/issues/377>`_:
`VanLeerConvectionTerm` MinMod slope limiter is broken
- `376 <https://github.com/usnistgov/fipy/issues/376>`_:
testing `CommitTicketUpdater`
- `375 <https://github.com/usnistgov/fipy/issues/375>`_:
NumPy 1.7.0 doesn't have `_formatInteger`
- `373 <https://github.com/usnistgov/fipy/issues/373>`_:
Bug with numpy 1.7.0
- `372 <https://github.com/usnistgov/fipy/issues/372>`_:
convection problem with cylindrical grid
- `371 <https://github.com/usnistgov/fipy/issues/371>`_:
`examples/phase/binary.py` has problems
- `370 <https://github.com/usnistgov/fipy/issues/370>`_:
FIPY_DISPLAY_MATRIX is broken
- `368 <https://github.com/usnistgov/fipy/issues/368>`_:
Viewers don't inline well in IPython notebook
- `367 <https://github.com/usnistgov/fipy/issues/367>`_:
Change documentation to promote use of stackoverflow
- `366 <https://github.com/usnistgov/fipy/issues/366>`_:
`unOps` can't be pickled
- `365 <https://github.com/usnistgov/fipy/issues/365>`_:
Rename communicator instances
- `364 <https://github.com/usnistgov/fipy/issues/364>`_:
Parallel bug in non-uniform grids and conflicting mesh class and
factory function names
- `360 <https://github.com/usnistgov/fipy/issues/360>`_:
NIST CSS changed
- `356 <https://github.com/usnistgov/fipy/issues/356>`_:
link to mailing list is wrong
- `353 <https://github.com/usnistgov/fipy/issues/353>`_:
Update Ohloh to point at git repo
- `352 <https://github.com/usnistgov/fipy/issues/352>`_:
`getVersion()` fails on Py3k
- `350 <https://github.com/usnistgov/fipy/issues/350>`_:
Gmsh importer can't read mesh elements with no tags
- `347 <https://github.com/usnistgov/fipy/issues/347>`_:
Include mailing list activity frame on front page
- `339 <https://github.com/usnistgov/fipy/issues/339>`_:
Fix for test failures on `loki`
- `337 <https://github.com/usnistgov/fipy/issues/337>`_:
Clean up interaction between dependencies and installation process
- `336 <https://github.com/usnistgov/fipy/issues/336>`_:
`fipy.test()` and `fipy/test.py` clash
- `334 <https://github.com/usnistgov/fipy/issues/334>`_:
Make the citation links go to the DOI links
- `333 <https://github.com/usnistgov/fipy/issues/333>`_:
Web page links seem to be broken
- `331 <https://github.com/usnistgov/fipy/issues/331>`_:
Assorted errors
- `330 <https://github.com/usnistgov/fipy/issues/330>`_:
`faceValue` as `FaceCenters` gives inline failures
- `329 <https://github.com/usnistgov/fipy/issues/329>`_:
Gmsh background mesh doesn't work in parallel
- `326 <https://github.com/usnistgov/fipy/issues/326>`_:
`Gmsh2D` does not respect background mesh
- `323 <https://github.com/usnistgov/fipy/issues/323>`_:
`getFaceCenters()` should return a `FaceVariable`
- `319 <https://github.com/usnistgov/fipy/issues/319>`_:
Explicit convection terms should fail when the equation has no
`TransientTerm` `(dt=None)`
- `318 <https://github.com/usnistgov/fipy/issues/318>`_:
FiPy will not import
- `311 <https://github.com/usnistgov/fipy/issues/311>`_:
LSMLIB refactor
- `305 <https://github.com/usnistgov/fipy/issues/305>`_:
`mpirun -np 2 python -Wd setup.py test --trilinos` hanging on
sandbox under buildbot
- `297 <https://github.com/usnistgov/fipy/issues/297>`_:
Remove deprecated gist and gnuplot support
- `291 <https://github.com/usnistgov/fipy/issues/291>`_:
efficiency_test chokes on `liquidVapor2D.py`
- `289 <https://github.com/usnistgov/fipy/issues/289>`_:
`diffusionTerm._test()` requires Pysparse
- `287 <https://github.com/usnistgov/fipy/issues/287>`_:
move FiPy to distributed version control
- `275 <https://github.com/usnistgov/fipy/issues/275>`_:
`mpirun -np 2 python setup.py test --no-pysparse` hangs on `bunter`
- `274 <https://github.com/usnistgov/fipy/issues/274>`_:
Epetra `Norm2` failure in parallel
- `272 <https://github.com/usnistgov/fipy/issues/272>`_:
Error adding meshes
- `269 <https://github.com/usnistgov/fipy/issues/269>`_:
Rename `GridXD`
- `255 <https://github.com/usnistgov/fipy/issues/255>`_:
numpy 1.5.1 and masked arrays
- `253 <https://github.com/usnistgov/fipy/issues/253>`_:
Move the mail archive link to a more prominent place on web page.
- `245 <https://github.com/usnistgov/fipy/issues/245>`_:
Fix `fipy.terms._BinaryTerm` test failure in parallel
- `228 <https://github.com/usnistgov/fipy/issues/228>`_:
`--pysparse` configuration should never attempt MPI imports
- `225 <https://github.com/usnistgov/fipy/issues/225>`_:
Windows interactive plotting mostly broken
- `209 <https://github.com/usnistgov/fipy/issues/209>`_:
add Rhie-Chow correction term in stokes cavity example
- `180 <https://github.com/usnistgov/fipy/issues/180>`_:
broken arithmetic face to cell distance calculations
- `128 <https://github.com/usnistgov/fipy/issues/128>`_:
Trying to "solve" an integer `CellVariable` should raise an error
- `123 <https://github.com/usnistgov/fipy/issues/123>`_:
`numerix.dot` doesn't support tensors
- `103 <https://github.com/usnistgov/fipy/issues/103>`_:
`subscriber()._markStale()` `AttributeError`
- `61 <https://github.com/usnistgov/fipy/issues/61>`_:
Move `ImplicitDiffusionTerm().solve(var) == 0` "failure" from
`examples.phase.simple` to `examples.diffusion.mesh1D`?

--------------------------

--------------------------

Fixes
-----

- `346 <https://github.com/usnistgov/fipy/issues/346>`_:
text in `trunk/examples/convection/source.py`
is out of date
- `342 <https://github.com/usnistgov/fipy/issues/342>`_:
sign issues for equation with transient, convection and implicit
terms
- `338 <https://github.com/usnistgov/fipy/issues/338>`_:
SvnToGit clean up

------------------------

------------------------

The bump in major version number reflects more on the substantial increase
in capabilities and ease of use than it does on a break in compatibility
with FiPy 2.x. Few, if any, changes to your existing scripts should be
necessary.

The significant changes since version 2.1 are:

- :ref:`CoupledEquations` are now supported.
- A more robust mechanism for specifying :ref:`BoundaryConditions` is now
used.
- Most :class:`~fipy.meshes.mesh.Mesh`\es can be partitioned by
:ref:`MeshingWithGmsh`.
- :ref:`PYAMG` and :ref:`SCIPY` have been added to the :ref:`SOLVERS`.
- FiPy is capable of running under :term:`Python 3`.
- "getter" and "setter" methods have been pervasively changed to Python
properties.
- The test suite now runs much faster.
- Tests can now be run on a full install using `fipy.test()`.
- The functions of the :mod:`~fipy.tools.numerix` module are no longer
included in the :mod:`fipy` namespace. See
:mod:`examples.updating.update2_0to3_0` for details.
- Equations containing a :class:`~fipy.terms.transientTerm.TransientTerm`,
must specify the timestep by passing a ``dt=`` argument when calling
:meth:`~fipy.terms.term.Term.solve` or :meth:`~fipy.terms.term.Term.sweep`.

.. warning::

:term:`FiPy` 3 brought unavoidable syntax changes from :term:`FiPy` 2.
Please see :mod:`examples.updating.update2_0to3_0` for guidance on the
changes that you will need to make to your :term:`FiPy` 2.x scripts.

Fixes
-----

- `332 <https://github.com/usnistgov/fipy/issues/332>`_:
Inline failure on Ubuntu x86_64
- `324 <https://github.com/usnistgov/fipy/issues/324>`_:
constraining values with `ImplicitSourceTerm` not documented?
- `317 <https://github.com/usnistgov/fipy/issues/317>`_:
`gmshImport` tests fail on Windows due to shared file
- `316 <https://github.com/usnistgov/fipy/issues/316>`_:
changes to `gmshImport.py` caused `--inline` problems
- `313 <https://github.com/usnistgov/fipy/issues/313>`_:
Gmsh I/O
- `307 <https://github.com/usnistgov/fipy/issues/307>`_:
Failures on sandbox under buildbot
- `306 <https://github.com/usnistgov/fipy/issues/306>`_:
Add in parallel buildbot testing on more than 2 processors
- `302 <https://github.com/usnistgov/fipy/issues/302>`_:
`CellVariable.min()` broken in parallel
- `301 <https://github.com/usnistgov/fipy/issues/301>`_:
`Epetra.PyComm()` broken on Debian
- `300 <https://github.com/usnistgov/fipy/issues/300>`_:
`examples/cahnHilliard/mesh2D.py` broken with -- trilinos
- `299 <https://github.com/usnistgov/fipy/issues/299>`_:
Viewers not working when plotting meshes with zero cells in parallel
- `298 <https://github.com/usnistgov/fipy/issues/298>`_:
Memory consumption growth with repeated meshing, especially with
Gmsh
- `294 <https://github.com/usnistgov/fipy/issues/294>`_:
`--pysparse --inline` failures
- `293 <https://github.com/usnistgov/fipy/issues/293>`_:
`python examples/cahnHilliard/sphere.py --inline` segfaults on OS X
- `292 <https://github.com/usnistgov/fipy/issues/292>`_:
two `--scipy` failures
- `290 <https://github.com/usnistgov/fipy/issues/290>`_:
Improve test reporting to avoid inconsequential buildbot failures
- `288 <https://github.com/usnistgov/fipy/issues/288>`_:
gmsh importer and gmsh tests don't clean up after themselves
- `286 <https://github.com/usnistgov/fipy/issues/286>`_:
get running in Py3k
- `285 <https://github.com/usnistgov/fipy/issues/285>`_:
remove deprecated `viewers.make()`
- `284 <https://github.com/usnistgov/fipy/issues/284>`_:
remove deprecated `Variable.transpose()`
- `281 <https://github.com/usnistgov/fipy/issues/281>`_:
remove deprecated `NthOrderDiffusionTerm`
- `280 <https://github.com/usnistgov/fipy/issues/280>`_:
remove deprecated `diffusionTerm=` argument to `ConvectionTerm`
- `277 <https://github.com/usnistgov/fipy/issues/277>`_:
remove deprecated `steps=` from Solver
- `273 <https://github.com/usnistgov/fipy/issues/273>`_:
Make `DiffusionTermNoCorrection` the default
- `270 <https://github.com/usnistgov/fipy/issues/270>`_:
tests take *too* long!!!
- `267 <https://github.com/usnistgov/fipy/issues/267>`_:
Reduce the run times for chemotaxis tests
- `264 <https://github.com/usnistgov/fipy/issues/264>`_:
HANG in parallel test of `examples/chemotaxis/input2D.py` on some
configurations
- `261 <https://github.com/usnistgov/fipy/issues/261>`_:
`GmshImport` should read element colors
- `260 <https://github.com/usnistgov/fipy/issues/260>`_:
`GmshImport` should support all element types
- `259 <https://github.com/usnistgov/fipy/issues/259>`_:
Introduce `mesh.x` as shorthand for `mesh.cellCenters[0]` etc
- `258 <https://github.com/usnistgov/fipy/issues/258>`_:
`GmshExport` is not tested and does not work
- `252 <https://github.com/usnistgov/fipy/issues/252>`_:
Include Benny's improved interpolation patch
- `250 <https://github.com/usnistgov/fipy/issues/250>`_:
TeX is wrong in `examples.phase.quaternary`
- `247 <https://github.com/usnistgov/fipy/issues/247>`_:
`diffusionTerm(var=var1).solver(var=var0)` should fail sensibly
- `243 <https://github.com/usnistgov/fipy/issues/243>`_:
close out reconstrain branch
- `242 <https://github.com/usnistgov/fipy/issues/242>`_:
update documentation
- `240 <https://github.com/usnistgov/fipy/issues/240>`_:
Profile and merge reconstrain branch
- `237 <https://github.com/usnistgov/fipy/issues/237>`_:
`--Trilinos --no-pysparse` uses Pysparse?!?
- `236 <https://github.com/usnistgov/fipy/issues/236>`_:
anisotropic diffusion and constraints don't mix
- `235 <https://github.com/usnistgov/fipy/issues/235>`_:
changed constraints don't propagate
- `231 <https://github.com/usnistgov/fipy/issues/231>`_:
`factoryMeshes.py` not up to date with respect to keyword arguments
- `223 <https://github.com/usnistgov/fipy/issues/223>`_:
mesh in FiPy name space
- `218 <https://github.com/usnistgov/fipy/issues/218>`_:
Absence of `enthought.tvtk` causes test failures
- `216 <https://github.com/usnistgov/fipy/issues/216>`_:
Fresh FiPy gives "`ImportError: No viewers found`"
- `213 <https://github.com/usnistgov/fipy/issues/213>`_:
PyPI is failing
- `206 <https://github.com/usnistgov/fipy/issues/206>`_:
`gnuplot1d` gives error on plot of `FaceVariable`
- `205 <https://github.com/usnistgov/fipy/issues/205>`_:
wrong cell to cell normal in periodic meshes
- `203 <https://github.com/usnistgov/fipy/issues/203>`_:
Give helpful error on - or / of meshes
- `202 <https://github.com/usnistgov/fipy/issues/202>`_:
mesh manipulation of periodic meshes leads to errors
- `201 <https://github.com/usnistgov/fipy/issues/201>`_:
Use physical velocity in the manual/FAQ
- `200 <https://github.com/usnistgov/fipy/issues/200>`_:
FAQ gives bad guidance for anisotropic diffusion
- `195 <https://github.com/usnistgov/fipy/issues/195>`_:
term multiplication changes result
- `163 <https://github.com/usnistgov/fipy/issues/163>`_:
Default time steps should be infinite
- `162 <https://github.com/usnistgov/fipy/issues/162>`_:
remove ones and zeros from `numerix.py`
- `130 <https://github.com/usnistgov/fipy/issues/130>`_:
tests should be run with `fipy.tests()`
- `86 <https://github.com/usnistgov/fipy/issues/86>`_:
Grids should take `Lx`, `Ly`, `Lz` arguments
- `77 <https://github.com/usnistgov/fipy/issues/77>`_:
`CellVariable.hasOld()` should set `self.old`
- `44 <https://github.com/usnistgov/fipy/issues/44>`_:
Navier-Stokes

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