version-3_1_1

• [closed] GMSH version >= 2.10 incorrectly read by gmshMesh.py #462
• [closed] setup.py gist warning #455
• [bug][viewers] DendriteViewer puts contours over color bar #445
• [bug][viewers] MatplotlibViewer still has problems in IPython notebook #443
• [closed] Use github API to get nicely formatted list of issues #440
• [closed] Failed tests on Mac OS X #438
• [examples] Figure misleading in examples.cahnHilliard.mesh2DCoupled #437
• [bug][documentation][installation] Links to prerequisites are broken #433
• [closed] Make devlop the default branch on Github #430
• [bug][viewers] MatplotlibViewer don't display #427
• [bug][documentation] Links for Warren and Guyer are broken on the web page #425
• [bug][viewers] The "limits" argument for Matplotlib2DGridViewer does not function #421
• [enhancement] Updates to reflect move to Github #416
• [bug][viewers] MatplotlibGrid2DViewer error with Matplotlib version 1.4.0 #415
• [enhancement][meshes] Implement PeriodicGrid3D #408
• [boundaryConditions][bug][invalid] FiPy self-test fails #405
• [bug][installation] package never gets uploaded to PyPI #404
• [boundaryConditions][bug] both insight and internal #403
• [boundaryConditions][bug] do n't have to take a look overly far #402
• [boundaryConditions][bug] Vector equations are broken when sweep is used instead of solve. #401
• [documentation][task] Home page needs out-of-NIST redirects #398
• [documentation][duplicate][enhancement] Switch to sphinxcontrib-bibtex #397
• [documentation][enhancement] enable google analytics #396
• [bug][documentation] Documentation change for Ubuntu install #395
• [bug][meshes] CylindricalNonUniformGrid2D doesn't make a FaceVariable for exteriorFaces #393
• [bug][documentation] exit_nist.cgi deprecated #392
• [bug][documentation] Peclet inequalities have the wrong sign #391
• [bug][invalid] test ticket #389
• [bug][numerix] Windows 64 and numpy's dtype=int #388
• [enhancement][viewers] Add support for Matplotlib streamplot #384
• [boundaryConditions][bug] Neumann boundary conditions not clearly documented #382
• [boundaryConditions][bug] numpy 1.7.1 test failures with physicalField.py #381
• [bug][terms] VanLeerConvectionTerm MinMod slope limiter is broken #377
• [bug] testing CommitTicketUpdater #376
• [bug][numerix] NumPy 1.7.0 doesn't have _formatInteger #375
• [bug][numerix] Bug with numpy 1.7.0 #373
• [bug][meshes] convection problem with cylindrical grid #372
• [bug][examples] examples/phase/binary.py has problems #371
• [bug][terms] FIPY_DISPLAY_MATRIX is broken #370
• [bug][viewers] Viewers don't inline well in IPython notebook #368
• [documentation][enhancement] Change documentation to promote use of stackoverflow #367
• [bug][variables] unOps can't be pickled #366
• [enhancement][parallel] Rename communicator instances #365
• [bug][meshes] Parallel bug in non-uniform grids and conflicting mesh class and factory function names #364
• [bug][invalid][meshes] Using Popen('gmsh ...', shell=True) rather than shell=False security danger #362
• [bug][documentation] NIST CSS changed #360
• [enhancement][variables][wontfix] constrain should return a handle to the constraint for later deletion #357
• [bug][documentation] link to mailing list is wrong #356
• [documentation][task] Update Ohloh to point at git repo #353
• [bug] getVersion() fails on Py3k #352
• [bug][meshes] Gmsh importer can't read mesh elements with no tags #350
• [documentation][enhancement] Include mailing list activity frame on front page #347
• [bug][examples] text in trunk/examples/convection/source.py is out of date #346
• [bug][terms][wontfix] segfault on loki #344
• [bug][terms][wontfix] multiplying equation by "x" changes the solution #343
• [bug][terms] sign issues for equation with transient, convection and implicit terms #342
• [bug] Fix for test failures on loki #339
• [bug][documentation] SvnToGit clean up #338
• [enhancement][installation] Clean up interaction between dependencies and installation process #337
• [documentation][enhancement] Make the citation links go to the DOI links #334
• [bug][documentation] Web page links seem to be broken #333
• [bug][tests] Inline failure on Ubuntu x86_64 #332
• [bug] Assorted errors #331
• [--inline][bug] faceValue as FaceCenters gives inline failures #330
• [bug][meshes] Gmsh background mesh doesn't work in parallel #329
• [bug][io] Gmsh2D does not respect background mesh #326
• [documentation][enhancement] constraining values with ImplictSourceTerm not documented? #324
• [bug][meshes] getFaceCenters() should return a FaceVariable #323
• [bug][terms] Explicit convetion terms should fail when the equation has no TransientTerm (dt=None) #319
• [bug][solvers] FiPy will not importy #318
• [bug][meshes] gmshImport tests fail on Windows due to shared file #317
• [--inline][bug] changes to gmshImport.py caused --inline problems #316
• [bug][io] Gmsh I/O #313
• [enhancement] LSMLIB refactor #311
• [bug][tests] Failures on sandbox under buildbot #307
• [task][tests] Add in parallel buildbot testing on more than 2 processors #306
• [bug][parallel] cellVariable.min() broken in parallel #302
• [bug][installation] Epetra.PyComm() broken on Debian #301
• [bug][examples] examples/cahnHilliard/mesh2D.py broken with -- trilinos #300
• [bug] Viewers not working when plotting meshes with zero cells in parallel #299
• [bug][meshes] Memory consumption growth with repeated meshing, especially with Gmsh #298
• [deprecations][task] Remove deprecated gist and gnuplot support #297
• [task][tests][wontfix] Windows for release 3.0 #296
• [bug] Gmsh version must be >= 2.0 errors on zizou #295
• [--inline][bug] --pysparse --inline failures #294
• [--inline][bug] python examples/cahnHilliard/sphere.py --inline segfaults on OS X #293
• [bug][solvers] two --scipy failures #292
• [bug][tests] efficiency_test chokes on liquidVapor2D.py #291
• [enhancement][tests] Improve test reporting to avoid inconsequential buildbot failures #290
• [bug][tests] diffusionTerm._test() requires PySparse #289
• [bug][viewers] gmsh importer and gmsh tests don't clean up after themselves #288
• [documentation][task] move FiPy to distributed version control #287
• [task] get running in Py3k #286
• [deprecations][enhancement] remove deprecated viewers.make() #285
• [deprecations][enhancement] remove deprecated Variable.transpose() #284
• [deprecations][enhancement] remove deprecated getters and setters #282
• [deprecations][enhancement] remove deprecated NthOrderDiffusionTerm #281
• [deprecations][enhancement] remove deprecated diffusionTerm= argument to ConvectionTerm #280
• [deprecations][enhancement] remove deprecated fipy.meshes.numMesh submodule #279
• [deprecations][enhancement] remove deprecated forms of Gmsh meshes #278
• [deprecations][enhancement] remove deprecated steps= from Solver #277
• [bug][duplicate] mpirun -np 2 python setup.py test --no-pysparse hangs on bunter #275
• [bug] Epetra Norm2 failure in parallel #274
• [bug][terms] Make DiffusionTermNoCorrection the default #273
• [bug][meshes] Error adding meshes #272
• [bug][wontfix] examples/diffusion/anisotropy.py fails from base fipy directory #271
• [bug][tests] tests take too long!!! #270
• [bug] Rename GridXD #269
• [task] Set up Zizou as a working slave #268
• [enhancement] Reduce the run times for chemotaxis tests #267
• [bug][parallel][wontfix] Exception on one process prevents tests from finishing #265
• [bug][duplicate][parallel] HANG in parallel test of examples/chemotaxis/input2D.py on some configurations #264
• [bug][invalid] Example mesh1D.py not working on ubuntu 11.04 #263
• [bug] issue with solvers #262
• [bug][meshes] GmshImport should read element colors #261
• [bug][meshes] GmshImport should support all element types #260
• [enhancement][meshes] Introduce mesh.x as shorthand for mesh.cellCenters[0] etc #259
• [bug][meshes] GmshExport is not tested and does not work #258
• [bug] Grid1D(dx=(1,2,3)) failure #256
• [enhancement] Include Benny's improved interpolation patch #252
• [bug] parallel is broken #251
• [bug][documentation] TeX is wrong in examples.phase.quaternary #250
• [bug] diffusionTerm(var=var1).solver(var=var0) should fail sensibly #247
• [bug] Fix fipy.terms._BinaryTerm test failure in parallel #245
• [bug][invalid] Remove self.var is self.var or self.var is None. #244
• [bug] close out reconstrain branch #243
• [bug] update documentation #242
• [bug] Set Sandbox up as a working slave #241
• [bug] Profile and merge reconstrain branch #240
• [bug][tests] _BinaryTerm.var is not predictable #238
• [bug][solvers] --Trilinos --no-pysparse uses PySparse?!? #237
• [boundaryConditions][bug] anisotropic diffusion and constraints don't mix #236
• [boundaryConditions][bug] changed constraints don't propagate #235
• [bug] coupled convection-diffusion always treated as Upwind #233
• [bug][viewers] Mayavi broken on windows becase it has no SIGHUP. #232
• [bug] factoryMeshes.py not up to date with respect to keyword arguments #231
• [bug][duplicate] factoryMeshes.py not up to date with respect to keyword arguments #230
• [bug][invalid] review the inclusion of mpi4py in the stdeb #229
• [bug] --pysparse configuration should never attempt MPI imports #228
• [bug][viewers] MatplotlibViewer fails if backend doesn't support flush_events() #226
• [bug] Windows interactive plotting mostly broken #225
• [bug] 'matrices are not aligned' errors in example test suite #224
• [bug] mesh in FiPy name space #223
• [bug][meshes] Non-uniform Grid3D fails to add #222
• [bug][meshes] Problem with fipy and gmsh #221
• [bug][variables][wontfix] _FixedBCFaceGradVariable mangles FaceGrad, even with no boundary conditions #220
• [bug] matforge css is hammer-headed #219
• [bug][tests] Absence of enthought.tvtk causes test failures #218
• [bug][meshes] Gmsh CellVariables can't be unpickled #217
• [bug][viewers] Fresh FiPy gives "ImportError: No viewers found" #216
• [enhancement][invalid][tests] parallel tests on bitten #214
• [bug][installation] pypi is failing #213
• [bug] add rhie chow correction term in stokes cavity example #209
• [bug][viewers] gnuplot1d gives error on plot of facevariable #206
• [bug][meshes] wrong cell to cell normal in periodic meshes #205
• [bug][invalid][solvers] error with diffusion for periodic mesh and steady state #204
• [bug][meshes] Give helpfull error on - or / of meshes #203
• [bug][meshes] mesh manipulation of periodic meshes leads to errors #202
• [bug][documentation] Use physical velocity in the manual/FAQ #201
• [bug][documentation] FAQ gives bad guidance for anisotropic diffusion #200
• [bug] dummy viewer results in "NotImplementedError: can't instantiate abstract base class" #199
• [bug][meshes] bug problem with CylindricalGrid1D #198
• [bug][installation] How to tell if parallel is configured properly? #197
• [bug][solvers] PySparse won't import in Python 2.6.5 on Windows #196
• [bug][terms] term multiplication changes result #195
• [bug][viewers] FIPY_DISPLAY_MATRIX on empty matrix with large b-vector throws ValueError #194
• [bug][viewers] FIPY_DISPLAY_MATRIX raises ImportError in FiPy 2.1 and trunk #193
• [bug][viewers] FIPY_DISPLAY_MATRIX=terms raises TypeError in FiPy 2.1 and trunk #192
• [bug][viewers] sphereDaemon.py missing in FiPy 2.1 and from trunk #191
• [bug][viewers] 'matplotlib: list index out of range' when no title given, but only sometimes #190
• [bug] SMTPSenderRefused: (553, '5.1.8 trac@matdl-osi.org... Domain of sender address trac@matdl-osi.org does not exist', u'"FiPy" trac@matdl-osi.org') #188
• [bug][meshes] Concatenated Mesh garbled by dump.write/read #187
• [enhancement][invalid] Testing spam filter... #186
• [enhancement][invalid] Test ticket #185
• [bug][meshes] gmshExport.exportAsMesh() doesn't work #184
• [bug][solvers] FiPy2.0.2 LinearJORSolver.init calls Solver rather than PysparseSolver #183
• [bug][variables] ~binOp doesn't work on branches/version-2_0 #182
• [bug][duplicate][examples] navier stokes again #181
• [bug] broken arithmetic face to cell distance calculations #180
• [bug][installation] easy_install instructions for MacOSX are broken #179
• [bug][duplicate] broken setuptools url with python 2.6 #178
• [bug] broken setuptools url with python 2.6 #177
• [bug][installation] Win32 distribution test error #176
• [bug][meshes] Grid3D getFaceCenters incorrect when mesh is offset #175
• [bug][variables] Variable doesn't implement __invert__ #170
• [bug][documentation] The FiPy webpage seems to be broken on Internet Explorer #169
• [bug][documentation][wontfix] PDF TOC doesn't go as deep when built on dogbert vs. benson #168
• [documentation][duplicate][enhancement] example showing how to go from 1.2 to 2.0 #167
• [documentation][task] Still references to VectorCell and VectorFace Variable in manual #166
• [documentation][task] Edit the what's new section of the manual #165
• [bug][terms] Default time steps should be infinite #163
• [bug][numerix] remove ones and zeros from numerix.py #162
• [bug][installation] get pysparse working with python 2.4 #161
• [duplicate][enhancement][meshes] Grid class #160
• [enhancement][invalid][tests] bitten build should show more detailed configuration info #158
• [bug][tests] temp files on widows #157
• [enhancement][viewers] update the mayavi viewer to use mayavi 2 #156
• [enhancement][tests] fix some of the deprecation warnings appearing in the tests #155
• [documentation][task] Update manuals #154
• [documentation][task] Switch documentation to use :math: directive #153
• [solvers][task] (Re)Implement SciPy solvers #152
• [duplicate][enhancement][viewers] update mayavi viewer to use mayavi2 #151
• [installation][task] PythonXY installation? #150
• [task][viewers] Test viewers #149
• [bug][solvers] SciPy 0.7.0 solver failures on Macs #148
• [solvers][task] Disable CGS solver in pysparse #147
• [bug][viewers] Viewer factory fails for rank-1 CellVariable #145
• [--inline][bug] intermittent failure on examples/diffusion/explicit/mixedelement.py --inline #144
• [documentation][task] Document syntax changes #143
• [task][viewers] merge Viewers branch #142
• [installation][task] enthought toolset? #141
• [installation][task] easy_install fipy #140
• [task][tests] Get a Windows Bitten build slave #139
• [documentation][task] FAQ on boundary conditions #138
• [documentation][task] Backport examples from manuscript #137
• [documentation][task] Document anisotropic diffusion #136
• [documentation][task] Trilinos documentation #135
• [boundaryConditions][bug][invalid] Problem with coefficients and FixedFlux boundary condition #134
• [bug][viewers] MatplotlibViewer doesn't properly report the supported file extensions #131
• [enhancement][tests] tests should be run with fipy.tests() #130
• [bug][variables] Trying to "solve" an integer CellVariable should raise an error #128
• [bug][tests] Examples can be very fragile with respect to floating point #127
• [bug][variables] Variable, float, integer #126
• [bug][examples] Pickled test data embeds obsolete packages #125
• [bug][variables] Can't pickle a binOp #124
• [bug][numerix] numerix.dot doesn't support tensors #123
• [bug] check argument types for meshes #122
• [bug][examples] simpleTrenchSystem.py #121
• [bug][duplicate][viewers] mayavi display problems #120
• [bug] max is broken for Variables #119
• [duplicate][task][variables] Automatically handle casting of Variable from int to float when necessary. #118
• [documentation][enhancement] getFacesBottom, getFacesTop etc. lack clear description in the reference #117
• [bug] Linux: failed test, TypeError: No array interface... in solve() #116
• [bug][viewers] viewing 3D Cahn-Hilliard is broken #115
• [bug][viewers][wontfix] memory leak in Gist2DViewer #114
• [bug][installation] OS X (MacBook Pro; Intel) FiPy installation problems #113
• [bug][duplicate][viewers] stokesCavity.py doesn't display properly with matplotlib #112
• [bug][viewers] Can't display Grid2D variables with matplotlib on Linux #111
• [bug][examples] "Numeric array value must be dimensionless" in ElPhF examples #110
• [bug][variables] doctest of fipy.variables.variable.Variable.array #109
• [bug][variables] numerix.array * FaceVariable is broken #108
• [bug][viewers] Can't move matplotlib windows on Mac #107
• [bug][meshes] Concatenation of Grid1D objects doesn't always work #106
• [duplicate][enhancement][tests] useless broken array tests should be removed #105
• [bug][viewers] Syntax error in MatplotlibVectorViewer._plot() #104
• [bug][variables] subscriber()._markStale() AttributeError #103
• [enhancement][viewers] viewer limits should just be set as arguments, rather than as a dict #102
• [bug] matplotlib 1D viewer autoscales when a limit is set to 0 #101
• [enhancement][tests] testing from the Windows dist using the ipython command line #100
• [bug][viewers] Matplotlib2DGridViewer cannot update multiple views #99
• [bug] Windows patch for some broken test cases #98
• [bug][numerix] Windows does not seem to handle NaN correctly. #97
• [bug][meshes] broken tests with version 2.0 of gmsh #96
• [--inline][bug] attached code breaks with --inline #95
• [bug][duplicate] --inline error for attached code #94
• [bug][duplicate][examples] Broken examples #93
• [task][viewers] Pygist is dead (it's official) #92
• [examples][task] update the examples to use "from fipy import *" #91
• [bug] bug in matplotlib 0.87.7: TypeError: only length-1 arrays can be converted to Python scalars. #90
• [bug][viewers][wontfix] MayaviSurfactantViewer has empty regions on the interface #89
• [enhancement][meshes][wontfix] Create wrapped Grid class for Grid1D, Grid2D and Grid3D. #87
• [enhancement][meshes] Grids should take Lx, Ly, Lz arguments #86
• [bug][models][wontfix] bug in surfactant and expandingCircle.py needs improvements #85
• [bug][duplicate][tests] Test failures on Intel Mac #84
• [bug][terms] ZeroDivisionError for CellTerm when calling getOld() on its coefficient #83
• [bug][invalid] purged #82
• [bug][invalid] purged #81
• [task][tests] Windows - testing - idle -ipython #80
• [enhancement][viewers] viewers.make() to viewers.Viewer() #79
• [boundaryConditions][enhancement][invalid] boundary conditions should reshape the value argument if it is a cell or face variable #78
• [enhancement][variables] CellVariable hasOld() should set self.old #77
• [bug] solve() and sweep() accept dt=CellVariable #76
• [bug] installation of fipy shoould auto include REAMDE as a docstring #75
• [bug][terms] Some combinations of DiffusionTerm and ConvectionTerm do not work #74
• [bug] needless rebuilding of variables #72
• [[general]][invalid] purged #71
• [[general]][invalid] purged #70
• [bug][invalid] purged #69
• [bug][invalid] purged #68
• [enhancement][viewers] Mesh viewing and unstructured data. #67
• [bug] PDF rendering issues for the guide on various palforms #66
• [--inline][bug][invalid] purged #65
• [--inline][bug][invalid] purged #64
• [enhancement][wontfix] Incorporate Spherical Coordinates in FiPy #63
• [bug] fipy guide pdf bug: "an unrecognised token 13c was found" #62
• [examples][task] Move 'ImplicitDiffusionTerm().solve(var) == 0' "failure" from examples.phase.simple to examples.diffusion.mesh1D? #61
• [bug][wontfix] Update Mayavi viewers to use TVTK #60
• [bug][wontfix] --cache failure in examples.phase.binary #59
• [bug][wontfix] superfill mayavi viewer leaves gaps on the interface #58
• [bug][documentation][wontfix] hacked epdoc-generated api.tex doesn't compile #57
• [bug][wontfix] allclose() broken in various ways for variables #56
• [bug] Error for internal BCs #55
• [bug][tests] python setup.py test fails #54
• [bug][wontfix] Gist2DViewer broken on x86_64 architectues #53
• [closed] FaceVariable * FaceVectorVariable memory #52
• [bug] pos doesn't work for terms #51
• [bug][examples] Broken examples #50
• [closed] Documentation for many ConvectionTerms is wrong #49
• [closed] Documentation is not inherited from &hidden& classes #48
• [closed] Terms should throw an error on bad coeff type #47
• [boundaryConditions][bug] Variable needs to consider boundary conditions #46
• [enhancement][variables] Slicing a vector Variable should produce a scalar Variable #45
• [enhancement][examples] Navier Stokes #44
• [bug][viewers] TSVViewer doesn't always get the right shape for the var #43
• [bug] fipy.models.phase.phase.addOverFacesVariable is gross #42
• [enhancement] EFFICIENCY.txt example fails to make viewer #41
• [tests] broken levelset test case #40
• [bug] matplotlib broken on mac with version 0.72.1 #39
• [closed] multiple BCs on one face broken? #38
• [closed] Better support for periodic boundary conditions #37
• [closed] Gnuplot doesn't display the electroChem problem on windows. #36
• [closed] gmsh write problemon windows #35
• [bug][numerix] float(&infinity&) issue on windows #34
• [closed] DiffusionTerm(coeff = CellVariable) functionality #33
• [tests] conflict_handler = 'ignore' not valid in Python 2.4 #32
• [closed] Support simple import notation #31
• [closed] periodic boundary condition support #30
• [closed] periodic boundary conditions are broken #29
• [closed] invoke the == for terms #28
• [bug][wontfix] Combine implicit and explicit diffusion terms #27
• [closed] doctest extraction with python2.4 #26
• [bug] make phase field examples more explicit #25
• [closed] PySparse windows binaries #24
• [bug] sweep control, iterator object, error norms #23
• [closed] automated efficiency_test problems #22
• [bug] Update FiPy to use numpy #21
• [closed] Test with Python version 2.4 #20
• [enhancement][terms] Peclet number #19
• [closed] Memory leak for the leveling problem #18
• [closed] distanceVariable is broken #17
• [bug][duplicate] Dimensions #16
• [bug][duplicate] Boundary conditions and Terms #15
• [closed] Testing mailing list interface #14
• [enhancement][meshes] Mesh refactor #13
• [closed] Refactor viewers #12
• [closed] Reconcile versions of pysparse #11
• [closed] check phase field crystal growth #10
• [closed] implement levelling surfactant equation #9
• [closed] merge depositionRateVar and extensionVelocity #8
• [closed] Automate FiPy efficiency test #7
• [closed] FiPy breaks on windows with Numeric 23.6 #6
• [closed] axisymmetric 2D mesh #5
• [closed] Windows installation wizard #4
• [closed] Windows installation instructions #3
• [tests] Some tests fail on windows XP #2
• [viewers] Gnuplot doesn't display on windows #1