3.4.4: Maintenance Release

This maintenance release adds Logging and resolves compatibility issues with recent builds of PETSc and NumPy.

What's Changed

• Discourage StackOverflow by @guyer in #876
• Add Logging by @guyer in #875
• Add tests for the Nix build by @wd15 in #791
• Manually clean up PETSc objects by @guyer in #899
• Get CI working again by @guyer in #925
• Fix numpy 1.25 issues by @guyer in #930

Curated Changelog: https://github.com/usnistgov/fipy/blob/3.4.4/CHANGELOG.rst

Full Changelog: 3.4.3...3.4.4

3.4.3: Maintenance release

This maintenance release adds a new example contributed by @Jon83Carvalho, clarifies many points in the documentation, migrates all CI to Azure, updates to using wheels for distribution, and substantially refactors matrices to work more consistently across solvers.

What's Changed

• Debug CI failures by @guyer in #749
• Stokes Cavity - non-newtonian by @Jon83Carvalho in #748
• Disable TVTK tests if its prerequisites aren't met by @guyer in #764
• Tabulate versions of FiPy dependencies when tests are run by @guyer in #763
• Refactor matrices by @guyer in #721
• Raise ImportError before trying to unpack solvers by @guyer in #768
• Introduce SharedTemporaryFile (bis) by @guyer in #769
• Get website documentation to display math by @guyer in #773
• Add future package to Binder environment by @guyer in #779
• Document parallel gmsh by @guyer in #793
• Remove future from setup.py and _setup commands by @guyer in #785
• Fix broken circleSquare with newer Gmsh by @guyer in #794
• Move trilinos tests to Py3k by @guyer in #797
• Replace deprecated numpy types by @guyer in #798
• Fix Python 2.7 conda environment by @wd15 in #795
• Speed up conda environment creation by @guyer in #804
• Fix python 3.9 represenation of abs by @guyer in #812
• Set up CI with Azure Pipelines by @guyer in #822
• fix: stop divide by zero warning in LU solvers by @wd15 in #790
• Change colorbar argument to valid value by @guyer in #829
• Get gmsh version from stderr or stdout by @guyer in #846
• Collect contact information on single page by @guyer in #847
• Debug CIs by @guyer in #848
• Refine azure runs by @guyer in #851
• Issue858 pysparse ci failure by @guyer in #859
• Fix missing Qt on headless CI by @guyer in #864
• Update CI documentation to refer only to Azure by @guyer in #863
• Shift CI from eggs to wheels by @guyer in #860
• Document the things by @guyer in #866
• Document viewer attributes by @guyer in #867
• Define _localNonOverlappingFaceIDs for Gmsh by @guyer in #857
• Update changelog by @guyer in #871

New Contributors

• @Jon83Carvalho made their first contribution in #748

Curated Changelog: https://github.com/usnistgov/fipy/blob/3.4.3/CHANGELOG.rst

Full Changelog: 3.4.2.1...3.4.3

Moved mailing list

This release fixes assorted viewer issues, fixes a problem with convection
boundary conditions, and introduces spherical meshes.

Support numpy 1.18

Make compatible with numpy 1.18

Deprecated `order="FORTRAN"` has now been removed.

Other changes found during release of FiPy 3.4

Support PETSc

This release adds support for the PETSc solvers for solving in parallel.

Pulls

• Add support for PETSc solvers (#701)
• Assorted fixes while supporting PETSc (#700)
  • Fix print statements for Py3k
  • Resolve Gmsh issues
  • Dump only on processor 0
  • Only write timetests on processor 0
  • Fix conda-forge link
  • Upload PDF
  • Document print option of FIPY_DISPLAY_MATRIX
  • Use legacy numpy formatting when testing individual modules
  • Switch to matplotlib's built-in symlog scaling
  • Clean up tests
• Assorted fixes for benchmark 8 (#699)
  • Stipulate --force option for conda remove fipy
  • Update Miniconda installation url
  • Replace _CellVolumeAverageVariable class with Variable expression
  • Fix output for bad call stack
• Make CircleCI build docs on Py3k (#698)
• Fix link to Nick Croft's thesis (#681)
• Fix NIST header footer (#680)
• Use Nixpkgs version of FiPy expression (#661)
• Update the Nix recipe (#658)

Fixes

• #692: Can't copy example scripts with the command line
• #669: input() deadlock on parallel runs
• #643: Automate release process

Py3k

This release brings support for Python 2 and Python 3 from the same source,
without any translation. Thanks to @pya and @woodscn for getting things started.

Pulls

• Automate spell check (#657)
• Fix gmsh on windows (#648)
• Fix sphinx documentation (#647)
• Migrate to Py3k (#645)
• gmshMesh.py compatibility with Gmsh > 3.0.6 (#644)
  Thanks to @xfong.

Fixes

• #655: When Python 2 and 3 are installed, Mayavi wont work.
  Thanks to @Hendrik410.
• #646: Deprecate develop branch
• #643: Automate release process
• #601: contents.rst and manual.rst are a recursive mess
• #597: Use GitHub link for the compressed archive in documentation
• #557: faceGradAverage is stupid
• #552: documentation integration
• #458: Documentation wrong for precedence of Lx and dx for
  NonUniformGrids
• #457: Special methods are not included in Sphinx documentation
• #432: Python 3 issues
• #340: Don't upload packages to PyPi, just add the master url

3.2

DevOps release
conda-forge and CIs

version-3_1_3

• [closed] gmane is defunct #502
• [documentation][enhancement] Move the mail archive link to a more prominent place on web page. #253

version-3_1_2

• [closed] nonlinear source term #498
• [bug][solvers] scipy.LinearBicgstabSolver doesn't take arguments #496
• [closed] Gmsh call errors #494
• [closed] Reviewable.io has read-only access, can't leave comments #493
• [bug][parallel] globalValue raises error from mpi4py #491
• [closed] PySparse tests fail #484
• [installation][tests] FiPy development version string not compliant with PEP 440 #482
• [bug][installation][tests] setuptools 18.4 breaks test suite #476
• [bug][meshes][numerix] Grid3D broken by numpy 1.10 #475
• [closed] Mesh3D cellToCellIDs is broken #470
• [closed] Out-of-sequence Viewer imports #467

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](https://github.com/usnistgov/fipy/issu...