Merge branch 'master' into Refactor_matrices

.circleci/config.yml

@@ -69,6 +69,11 @@ commands:
       - attach_workspace:
           at: ~/project
 
+      - run:
+          name: Output Environment
+          command: |
+            conda env export --prefix ~/project/<< parameters.condaenv >>
+
       - run:
           name: Run Tests
           no_output_timeout: 30m
@@ -80,11 +85,6 @@ commands:
             fi
             << parameters.mpirun >> python setup.py test --deprecation-errors
 
-      - run:
-          name: Output Environment
-          command: |
-            conda env export --prefix ~/project/<< parameters.condaenv >>
-
       - store_artifacts:
           path: test-reports
           destination: test-reports
@@ -229,7 +229,7 @@ jobs:
 
     steps:
       - install_conda_packages:
-          packages: "python=2.7 fipy"
+          packages: "python=2.7 fipy \"traitsui<7.0.0\""
           condaenv: "test-environment-27"
 
   conda3_env:
@@ -612,16 +612,16 @@ workflows:
       - build-binaries:
           requires:
             - conda3_env
-            - build-36-docs
-            - pylint
-            - flake8
-            - black
-            - pyspelling
-            - test-27-pysparse
-            - test-27-trilinos-serial
-            - test-27-trilinos-parallel
-            - test-27-petsc-serial
-            - test-27-petsc-parallel
-            - test-36-scipy
-            - test-36-petsc-serial
-            - test-36-petsc-parallel
+#             - build-36-docs
+#             - pylint
+#             - flake8
+#             - black
+#             - pyspelling
+#             - test-27-pysparse
+#             - test-27-trilinos-serial
+#             - test-27-trilinos-parallel
+#             - test-27-petsc-serial
+#             - test-27-petsc-parallel
+#             - test-36-scipy
+#             - test-36-petsc-serial
+#             - test-36-petsc-parallel

.travis.yml

@@ -48,6 +48,9 @@ before_install:
   - conda create --quiet --name test-environment --show-channel-urls --channel conda-forge python=$TRAVIS_PYTHON_VERSION fipy "gmsh<4.0";
   - source activate test-environment
   - conda remove --quiet --channel conda-forge --force fipy
+  - if [[ $PY3K -eq 0 ]]; then
+      conda install --channel conda-forge "traitsui<7.0.0";
+    fi
   # Useful for debugging any issues with conda
   - conda info -a
   - pip install scikit-fmm

CHANGELOG.rst

@@ -11,6 +11,48 @@ Change Log
 Version |release|
 -----------------
 
+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`
+
+--------------------------
+Version 3.4.1 - 2020-02-14
+--------------------------
+
 This release is primarily for compatibility with :ref:`NumPy` 1.18.
 
 Pulls

INSTALLATION.rst

@@ -28,7 +28,7 @@ for details on how to use :term:`FiPy`.
       endorse the views expressed, or concur with the facts presented on
       these sites. Further, NIST does not endorse any commercial products
       that may be mentioned on these sites. Please address comments about
-      this page to fipy@nist.gov.
+      this page to fipy@list.nist.gov.
 
 -----------------------
 Pre-Installed on Binder
@@ -92,8 +92,21 @@ Recommended Method
       activate <MYFIPYENV>
       pip install fipy
 
+  .. attention::
+
+     Bit rot has started to set in for Python 2.7.  One consequence is that
+     :class:`~fipy.viewers.vtkViewer.VTKViewer`\s can raise errors
+     (probably other uses of :term:`Mayavi`, too).  You can remedy this by
+     creating your environment with::
+
+     $ conda create --name <MYFIPYENV> --channel conda-forge python=2.7 fipy "traitsui<7.0.0"
+
 * enable this new environment with::
 
+    $ conda activate <MYFIPYENV>
+
+  or
+
     $ source activate <MYFIPYENV>
 
   .. note::

README.rst

@@ -161,7 +161,7 @@ or a
 .. |CircleCI|      image:: https://img.shields.io/circleci/project/github/usnistgov/fipy/master.svg?label=Linux
 .. _CircleCI:      https://circleci.com/gh/usnistgov/fipy
 .. |TravisCI|      image:: https://img.shields.io/travis/usnistgov/fipy/master.svg?label=macOS
-.. _TravisCI:      https://travis-ci.org/usnistgov/fipy
+.. _TravisCI:      https://travis-ci.com/github/usnistgov/fipy
 .. |AppVeyor|      image:: https://ci.appveyor.com/api/projects/status/github/usnistgov/fipy?branch=master&svg=true&failingText=Windows%20-%20failing&passingText=Windows%20-%20passing&pendingText=Windows%20-%20pending
 .. _AppVeyor:      https://ci.appveyor.com/project/usnistgov/fipy
 .. |OpenHub|       image:: https://www.openhub.net/p/fipy/widgets/project_thin_badge.gif

documentation/ADMINISTRATA.rst

@@ -272,7 +272,7 @@ request to update the fipy-feedstock_ with:
 Announce
 --------
 
-Make an announcement to `fipy@nist.gov`_
+Make an announcement to `fipy@list.nist.gov`_
 
 .. _GitHub: https://github.com/
 .. _fipy repository: https://github.com/usnistgov/fipy
@@ -285,5 +285,5 @@ Make an announcement to `fipy@nist.gov`_
 .. _Squash and merge: https://help.github.com/en/articles/about-pull-request-merges/#squash-and-merge-your-pull-request-commits
 .. _twine: https://pypi.org/project/twine
 .. _fipy-feedstock: https://github.com/conda-forge/fipy-feedstock
-.. _fipy@nist.gov: mailto:fipy@nist.gov
+.. _fipy@list.nist.gov: mailto:fipy@list.nist.gov
 .. _feedstock maintainers: https://github.com/conda-forge/fipy-feedstock#feedstock-maintainers

documentation/MAIL.rst

@@ -3,35 +3,33 @@ Mailing List
 ------------
 
 In order to discuss :term:`FiPy` with other users and with the developers,
-we encourage you to sign up for the mailing list by sending a
-`subscription email <mailto:fipy-request@nist.gov?&body=subscribe>`__:
-
-    To:
-	``fipy-request@nist.gov``
-
-    Subject:
-	*(optional)*
-
-    Body:
-	``subscribe``
+we encourage you to sign up for the mailing list by sending a `subscription
+email <mailto:fipy+subscribe@list.nist.gov>`__ to
+<mailto:fipy+subscribe@list.nist.gov>.
 
 Once you are subscribed, you can post messages to the list simply by
-addressing email to <mailto:fipy@nist.gov>. If you are new to mailing
+addressing email to <mailto:fipy@list.nist.gov>. If you are new to mailing
 lists, you may want to read the following resource about asking
 effective questions:  http://www.catb.org/~esr/faqs/smart-questions.html
 
-To get off the list follow the instructions above, but place
-``unsubscribe`` in the text body.
+To get off the list, send a message to
+<mailto:fipy+unsubscribe@list.nist.gov>.
 
-Send ``help`` in the text body to learn other mailing list configurations
-you can change.
+Send a message to <mailto:fipy+help@list.nist.gov> to learn other mailing
+list configurations you can change.
+
+The list is hosted as a Google group.  If you are subscribed with a Google
+account, you can interact with the list, configure your subscription, and
+see the archives at https://list.nist.gov/fipy.
 
 List Archive
 ------------
 
-https://www.mail-archive.com/fipy@nist.gov/
+https://www.mail-archive.com/fipy@list.nist.gov/
+
+Copies of messages sent to fipy@list.nist.gov are stored at `The Mail Archive`_.
 
-Copies of messages sent to fipy@nist.gov are stored at `The Mail Archive`_.
+Older messages are archived at https://www.mail-archive.com/fipy@nist.gov/.
 
 (note: we have also historically sent copies to
 http://dir.gmane.org/gmane.comp.python.fipy, but the GMANE_ site now

documentation/_templates/index.html

@@ -96,9 +96,11 @@ <h1>FiPy: A Finite Volume PDE Solver Using Python</h1>
   <a href="/cgi-bin/redirect.py?url=https://github.com/usnistgov/fipy/issues">issue tracker</a>,
   or ask a question on 
   <a href="/cgi-bin/redirect.py?url=https://stackoverflow.com/questions/tagged/fipy">StackOverflow</a>.</p>
-  <p>We encourage you to review the 
-  <a href="https://www.mail-archive.com/fipy@nist.gov/">mailing list archive</a> 
-  before posting a question.</p>
+  <p>We encourage you to review the
+  <a href="https://www.mail-archive.com/fipy@list.nist.gov/">mailing list
+  archive</a> (or the <a
+  href="https://www.mail-archive.com/fipy@nist.gov/">older mailing list
+  archive</a>) before posting a question.</p>
   </div>
  {% block tables %}
    <h2>Documentation</h2>

examples/README.rst

@@ -72,4 +72,4 @@ please `contact us`_.
 
 .. _Python:         http://www.python.org/
 .. _doctest:        http://www.python.org/doc/current/lib/module-doctest.html
-.. _contact us:     mailto:fipy@nist.gov
+.. _contact us:     mailto:fipy@list.nist.gov

examples/elphf/diffusion/mesh1D.py

@@ -115,9 +115,15 @@
 Since there is nothing to maintain the concentration separation in this problem,
 we verify that the concentrations have become uniform
 
->>> print(substitutionals[0].allclose(0.45, rtol = 1e-7, atol = 2e-7))
+.. note::
+
+   Between `petsc=3.13.2=h82b89f7_0` and `petsc=3.13.4=h82b89f7_0`, PETSc
+   ceased achieving 1e-7 tolerance when solving on 2 processors on Linux.
+   Solving on macOS is OK. Solving on 1, 3, or 4 processors is OK.
+
+>>> print(substitutionals[0].allclose(0.45, rtol = 2e-7, atol = 2e-7))
 True
->>> print(substitutionals[1].allclose(0.45, rtol = 1e-7, atol = 1e-7))
+>>> print(substitutionals[1].allclose(0.45, rtol = 2e-7, atol = 2e-7))
 True
 """
 from __future__ import unicode_literals