Fipy

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

This maintenance release adds a new example contributed by
`Jon83Carvalho <https://github.com/Jon83Carvalho>`_,
clarifies many points in the documentation,
migrates all :ref:`CONTINUOUSINTEGRATION` to
`Azure <https://dev.azure.com>`_,
updates to using
`wheels <https://packaging.python.org/en/latest/specifications/binary-distribution-format/>`_
for distribution,
and substantially refactors matrices to work more consistently across
solvers.

Pulls
-----

- Update CI documentation to refer only to Azure
(`863 <https://github.com/usnistgov/fipy/pull/863>`_)
- Refine azure runs
(`851 <https://github.com/usnistgov/fipy/pull/851>`_)
- Debug CIs
(`848 <https://github.com/usnistgov/fipy/pull/848>`_)
- Collect contact information on single page
(`847 <https://github.com/usnistgov/fipy/pull/847>`_)
- Set up CI with Azure Pipelines
(`822 <https://github.com/usnistgov/fipy/pull/822>`_)
- Replace deprecated numpy types
(`798 <https://github.com/usnistgov/fipy/pull/798>`_)
- Move trilinos tests to Py3k
(`797 <https://github.com/usnistgov/fipy/pull/797>`_)
- Fix Python 2.7 conda environment
(`795 <https://github.com/usnistgov/fipy/pull/795>`_)
- fix: stop divide by zero warning in LU solvers
(`790 <https://github.com/usnistgov/fipy/pull/790>`_)
- Introduce `SharedTemporaryFile` (bis)
(`769 <https://github.com/usnistgov/fipy/pull/769>`_)
- Raise `ImportError` before trying to unpack solvers
(`768 <https://github.com/usnistgov/fipy/pull/768>`_)
- Disable TVTK tests if its prerequisites aren't met
(`764 <https://github.com/usnistgov/fipy/pull/764>`_)
- Tabulate versions of FiPy dependencies when tests are run
(`763 <https://github.com/usnistgov/fipy/pull/763>`_)
- Debug CI failures
(`749 <https://github.com/usnistgov/fipy/pull/749>`_)
- Stokes Cavity - non-Newtonian
(`748 <https://github.com/usnistgov/fipy/pull/748>`_)
Thanks to `Jon83Carvalho <https://github.com/Jon83Carvalho>`_.
- Refactor matrices
(`721 <https://github.com/usnistgov/fipy/pull/721>`_)

Fixes
-----

- `862 <https://github.com/usnistgov/fipy/issues/862>`_:
Could not load the Qt platform plugin "`xcb`"
- `858 <https://github.com/usnistgov/fipy/issues/858>`_:
CI issues
- `856 <https://github.com/usnistgov/fipy/issues/856>`_:
`FaceVariable` does not accumulate properly in parallel
- `850 <https://github.com/usnistgov/fipy/issues/850>`_:
Switch to wheels
- `849 <https://github.com/usnistgov/fipy/issues/849>`_:
`linux-py27-pysparse` fails
- `841 <https://github.com/usnistgov/fipy/issues/841>`_:
`Matplotlib2DViewer` should accept color map as string
- `836 <https://github.com/usnistgov/fipy/issues/836>`_:
Document that coupled and high-order diffusion terms are
incompatible
- `833 <https://github.com/usnistgov/fipy/issues/833>`_:
`fipy.tools.dump` undocumented that it always gzips
- `828 <https://github.com/usnistgov/fipy/issues/828>`_:
`colorbar=True` no longer works Stokes flow example
- `826 <https://github.com/usnistgov/fipy/issues/826>`_:
Gmsh load issue
- `818 <https://github.com/usnistgov/fipy/issues/818>`_:
Document that `GridND` meshes are always Cartesian
- `811 <https://github.com/usnistgov/fipy/issues/811>`_:
In python 3.9 __repr__ throws an exception with abs
- `801 <https://github.com/usnistgov/fipy/issues/801>`_:
CircleCI test-36-trilinos-serial extremely slow
- `800 <https://github.com/usnistgov/fipy/issues/800>`_:
CircleCI conda2_env is really slow and ends up installing FiPy 3.3
- `796 <https://github.com/usnistgov/fipy/issues/796>`_:
`examples.phase.polyxtal` freezes on CircleCI with Py3k and scipy
solvers
- `792 <https://github.com/usnistgov/fipy/issues/792>`_:
`circleQuad` example fails with Gmsh > 4.4
- `781 <https://github.com/usnistgov/fipy/issues/781>`_:
`MatplolibViewer.axes` property is not documented
- `778 <https://github.com/usnistgov/fipy/issues/778>`_:
Binder failed build
- `762 <https://github.com/usnistgov/fipy/issues/762>`_:
Equations on Website don't show right
- `742 <https://github.com/usnistgov/fipy/issues/742>`_:
No documentation for `Variable.mag`
- `735 <https://github.com/usnistgov/fipy/issues/735>`_:
`pip install fipy` fails
- `734 <https://github.com/usnistgov/fipy/issues/734>`_:
Document the residual
- `688 <https://github.com/usnistgov/fipy/issues/688>`_:
try-except not needed for circle Viewer
- `676 <https://github.com/usnistgov/fipy/issues/676>`_:
Default no-flux condition is not explicitly stated
- `609 <https://github.com/usnistgov/fipy/issues/609>`_:
Parallelizing of Gmsh meshes not clearly documented
- `400 <https://github.com/usnistgov/fipy/issues/400>`_:
Fix `FaceVariable.globalValue` method

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

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

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

.. attention::

There are
`known <https://travis-ci.com/github/usnistgov/fipy/builds/177879719>`_
`failures <https://app.circleci.com/pipelines/github/usnistgov/fipy/248/workflows/4babcd98-aafc-4931-a353-64bbb3c93cb6>`_
with the VTK viewers (bitrot has started to set
in since the `demise of Python 2.7`_). There's also a new parallel
failure in `NonUniformGrid1D` that we need to figure out.

.. _demise of Python 2.7: https://www.python.org/dev/peps/pep-0373/#update

Pulls
-----

- Move mailing list
(`747 <https://github.com/usnistgov/fipy/pull/747>`_)
- `Spherical1D` (`Uniform` and `NonUniform`) meshes
(`732 <https://github.com/usnistgov/fipy/pull/732>`_)
Thanks to `klkuhlm <https://github.com/klkuhlm>`_.
- fix Neumann BCs using constraints with convection terms
(`719 <https://github.com/usnistgov/fipy/pull/719>`_)
Thanks to `atismer <https://github.com/atismer>`_.
- Add vertex index inversions
(`716 <https://github.com/usnistgov/fipy/pull/716>`_)

Fixes
-----

- `726 <https://github.com/usnistgov/fipy/issues/726>`_:
`MayaviClient` not compatible with Python 3
- `663 <https://github.com/usnistgov/fipy/issues/663>`_:
`datamin`/`datamax` argument ignored by viewer
- `662 <https://github.com/usnistgov/fipy/issues/662>`_:
Issues Scaling `Colorbar` with `Datamin` and `Datamax` `Args`

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

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

This release is primarily for compatibility with :ref:`NumPy` 1.18.

Pulls
-----

- Fix documentation
(`711 <https://github.com/usnistgov/fipy/pull/711>`_)
- build(nix): fix broken plm_rsh_agent error
(`710 <https://github.com/usnistgov/fipy/pull/710>`_)
- CIs error on deprecation warning
(`708 <https://github.com/usnistgov/fipy/pull/708>`_)

Fixes
-----

- `703 <https://github.com/usnistgov/fipy/issues/703>`_:
FORTRAN array ordering is deprecated

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

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

This release adds support for the :term:`PETSc` solvers for
:ref:`PARALLEL`.

Pulls
-----

- Add support for PETSc solvers
(`701 <https://github.com/usnistgov/fipy/pull/701>`_)
- Assorted fixes while supporting PETSc
(`700 <https://github.com/usnistgov/fipy/pull/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 <https://github.com/usnistgov/fipy/pull/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 <https://github.com/usnistgov/fipy/pull/698>`_)
- Fix link to Nick Croft's thesis
(`681 <https://github.com/usnistgov/fipy/pull/681>`_)
- Fix NIST header footer
(`680 <https://github.com/usnistgov/fipy/pull/680>`_)
- Use Nixpkgs version of FiPy expression
(`661 <https://github.com/usnistgov/fipy/pull/661>`_)
- Update the Nix recipe
(`658 <https://github.com/usnistgov/fipy/pull/658>`_)

Fixes
-----

- `692 <https://github.com/usnistgov/fipy/issues/692>`_:
Can't copy example scripts with the command line
- `669 <https://github.com/usnistgov/fipy/issues/669>`_:
input() deadlock on parallel runs
- `643 <https://github.com/usnistgov/fipy/issues/643>`_:
Automate release process

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

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

This release brings support for Python 2 and Python 3 from the same source,
without any translation. Thanks to `pya <https://github.com/pya>`_ and
`woodscn <https://github.com/woodscn>`_ for getting things started.

Pulls
-----

- Automate spell check
(`657 <https://github.com/usnistgov/fipy/pull/657>`_)
- Fix gmsh on windows
(`648 <https://github.com/usnistgov/fipy/pull/648>`_)
- Fix sphinx documentation
(`647 <https://github.com/usnistgov/fipy/pull/647>`_)
- Migrate to Py3k
(`645 <https://github.com/usnistgov/fipy/pull/645>`_)
- `gmshMesh.py` compatibility with Gmsh > 3.0.6
(`644 <https://github.com/usnistgov/fipy/pull/644>`_)
Thanks to `xfong <https://github.com/xfong>`_.

Fixes
-----

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

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

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

This is predominantly a `DevOps`_ release. The focus has been on making
FiPy easier to install with :term:`conda`. It's also possible to install a
minimal set of prerequisites with :term:`pip`. Further, :term:`FiPy` is
automatically tested on all major platforms using cloud-based
:ref:`CONTINUOUSINTEGRATION` (:term:`linux` with :term:`CircleCI`,
:term:`macOS` with :term:`TravisCI`, and :term:`Windows` with
:term:`AppVeyor`).

Pulls
-----

- Make badges work in GitHub and pdf
(`636 <https://github.com/usnistgov/fipy/pull/636>`_)
- Fix Robin errors
(`615 <https://github.com/usnistgov/fipy/pull/615>`_)
- Issue555 inclusive license
(`613 <https://github.com/usnistgov/fipy/pull/613>`_)
- Update CIs
(`607 <https://github.com/usnistgov/fipy/pull/607>`_)
- Add CHANGELOG and tool to generate from issues and pull requests
(`600 <https://github.com/usnistgov/fipy/pull/600>`_)
- Explain where to get examples
(`596 <https://github.com/usnistgov/fipy/pull/596>`_)
- spelling corrections using en_US dictionary
(`594 <https://github.com/usnistgov/fipy/pull/594>`_)
- Remove `SmoothedAggregationSolver`
(`593 <https://github.com/usnistgov/fipy/pull/593>`_)
- Nix recipe for FiPy
(`585 <https://github.com/usnistgov/fipy/pull/585>`_)
- Point PyPI to github master tarball
(`582 <https://github.com/usnistgov/fipy/pull/582>`_)
- Revise Navier-Stokes expression in the viscous limit
(`580 <https://github.com/usnistgov/fipy/pull/580>`_)
- Update `stokesCavity.py`
(`579 <https://github.com/usnistgov/fipy/pull/579>`_)
Thanks to `Rowin <https://github.com/Rowin>`_.
- Add `--inline` to TravisCI tests
(`578 <https://github.com/usnistgov/fipy/pull/578>`_)
- Add support for binder
(`577 <https://github.com/usnistgov/fipy/pull/577>`_)
- Fix `epetra vector not numarray`
(`574 <https://github.com/usnistgov/fipy/pull/574>`_)
- add Codacy badge
(`572 <https://github.com/usnistgov/fipy/pull/572>`_)
- Fix output when PyTrilinos or PyTrilinos version is unavailable
(`570 <https://github.com/usnistgov/fipy/pull/570>`_)
Thanks to `shwina <https://github.com/shwina>`_.
- Fix check for PyTrilinos
(`569 <https://github.com/usnistgov/fipy/pull/569>`_)
Thanks to `shwina <https://github.com/shwina>`_.
- Adding support for GPU solvers via pyamgx
(`567 <https://github.com/usnistgov/fipy/pull/567>`_)
Thanks to `shwina <https://github.com/shwina>`_.
- revise dedication to the public domain
(`556 <https://github.com/usnistgov/fipy/pull/556>`_)
- Fix tests that don't work in parallel
(`550 <https://github.com/usnistgov/fipy/pull/550>`_)
- add badges to index and readme
(`546 <https://github.com/usnistgov/fipy/pull/546>`_)
- Ensure vector is `dtype` float before matrix multiply
(`544 <https://github.com/usnistgov/fipy/pull/544>`_)
- Revert "Issue534 physical field mishandles compound units"
(`536 <https://github.com/usnistgov/fipy/pull/536>`_)
- Document boundary conditions
(`532 <https://github.com/usnistgov/fipy/pull/532>`_)
- Deadlocks and races
(`524 <https://github.com/usnistgov/fipy/pull/524>`_)
- Make max/min global
(`520 <https://github.com/usnistgov/fipy/pull/520>`_)
- Add a Gitter chat badge to :file:`README.rst`
(`516 <https://github.com/usnistgov/fipy/pull/516>`_)
Thanks to `gitter-badger <https://github.com/gitter-badger>`_.
- Add TravisCI build recipe
(`489 <https://github.com/usnistgov/fipy/pull/489>`_)

Fixes
-----

- `631 <https://github.com/usnistgov/fipy/issues/631>`_:
Clean up :file:`INSTALLATION.rst`
- `628 <https://github.com/usnistgov/fipy/issues/628>`_:
Problems with the viewer
- `627 <https://github.com/usnistgov/fipy/issues/627>`_:
Document OMP_NUM_THREADS
- `625 <https://github.com/usnistgov/fipy/issues/625>`_:
`setup.py` should not import fipy
- `623 <https://github.com/usnistgov/fipy/issues/623>`_:
Start using `versioneer`
- `621 <https://github.com/usnistgov/fipy/issues/621>`_:
Plot `FaceVariable` with matplotlib
- `617 <https://github.com/usnistgov/fipy/issues/617>`_:
Pick 1st Value and last Value of 1D `CellVariable` while running in
parallel
- `611 <https://github.com/usnistgov/fipy/issues/611>`_:
The coefficient cannot be a `FaceVariable` ??
- `610 <https://github.com/usnistgov/fipy/issues/610>`_:
Anisotropy example: Contour plot displaying in legend of figure !?
- `608 <https://github.com/usnistgov/fipy/issues/608>`_:
`var.mesh`: `Property` object not callable...?
- `603 <https://github.com/usnistgov/fipy/issues/603>`_:
Can't run basic test or examples
- `602 <https://github.com/usnistgov/fipy/issues/602>`_:
Revise build and release documentation
- `592 <https://github.com/usnistgov/fipy/issues/592>`_:
is :file:`resources.rst` useful?
- `590 <https://github.com/usnistgov/fipy/issues/590>`_:
No module named `pyAMGSolver`
- `584 <https://github.com/usnistgov/fipy/issues/584>`_:
Viewers don't animate in jupyter notebook
- `566 <https://github.com/usnistgov/fipy/issues/566>`_:
Support for GPU solvers using pyamgx
- `565 <https://github.com/usnistgov/fipy/issues/565>`_:
pip install does not work on empty env
- `564 <https://github.com/usnistgov/fipy/issues/564>`_:
Get green boxes across the board
- `561 <https://github.com/usnistgov/fipy/issues/561>`_:
Cannot cast array data from `dtype('int64')` to `dtype('int32')`
according to the rule `safe`
- `555 <https://github.com/usnistgov/fipy/issues/555>`_:
inclusive license
- `551 <https://github.com/usnistgov/fipy/issues/551>`_:
Sphinx spews many warnings:
- `545 <https://github.com/usnistgov/fipy/issues/545>`_:
Many Py3k failures
- `543 <https://github.com/usnistgov/fipy/issues/543>`_:
Epetra Vector can't be integer
- `539 <https://github.com/usnistgov/fipy/issues/539>`_:
`examples/diffusion/explicit/mixedElement.py` is a mess
- `538 <https://github.com/usnistgov/fipy/issues/538>`_:
badges
- `534 <https://github.com/usnistgov/fipy/issues/534>`_:
`PhysicalField` mishandles compound units
- `533 <https://github.com/usnistgov/fipy/issues/533>`_:
pip or conda installation don't make clear where to get examples
- `531 <https://github.com/usnistgov/fipy/issues/531>`_:
`drop_tol` argument to `scipy.sparse.linalg.splu` is gone
- `530 <https://github.com/usnistgov/fipy/issues/530>`_:
conda installation instructions not explicit about python version
- `528 <https://github.com/usnistgov/fipy/issues/528>`_:
scipy 1.0.0 incompatibilities
- `525 <https://github.com/usnistgov/fipy/issues/525>`_:
conda `guyer/pysparse` doesn't run on osx
- `513 <https://github.com/usnistgov/fipy/issues/513>`_:
Stokes example gives wrong equation
- `510 <https://github.com/usnistgov/fipy/issues/510>`_:
Weave, Scipy and `--inline`
- `509 <https://github.com/usnistgov/fipy/issues/509>`_:
Unable to use conda for installing FiPy in Windows
- `506 <https://github.com/usnistgov/fipy/issues/506>`_:
Error using spatially varying anisotropic diffusion coefficient
- `488 <https://github.com/usnistgov/fipy/issues/488>`_:
Gmsh 2.11 breaks `GmshGrids`
- `435 <https://github.com/usnistgov/fipy/issues/435>`_:
`pip install pysparse` fails with
"`fatal error: 'spmatrix.h' file not found`"
- `434 <https://github.com/usnistgov/fipy/issues/434>`_:
`pip install fipy` fails with
"`ImportError: No module named ez_setup`"

.. _DevOps: https://en.wikipedia.org/wiki/DevOps

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