Merge branch 'master' into harmonize_solvers

.azure/pipelines.yml

@@ -220,7 +220,7 @@ stages:
       - bash: |
           conda create --quiet --name wheelEnvironment --channel conda-forge python=3.10
           source activate wheelEnvironment
-          mkdir tmp
+          mkdir -p tmp
           cd tmp
           python -m pip install ../dist/*.whl
           FIPY_SOLVERS=scipy python -c "import fipy; fipy.test()"
@@ -232,11 +232,11 @@ stages:
       - bash: |
           source activate myEnvironment
           FIPY_VERSION=`python setup.py --version`
-          mkdir tmp
+          mkdir -p tmp
           cd tmp
-          cp ../dist/FiPy-${FIPY_VERSION}.tar.gz .
-          tar zxvf FiPy-${FIPY_VERSION}.tar.gz
-          cd FiPy-${FIPY_VERSION}
+          cp ../dist/fipy-${FIPY_VERSION}.tar.gz .
+          tar zxvf fipy-${FIPY_VERSION}.tar.gz
+          cd fipy-${FIPY_VERSION}
           python setup.py install
           cd ..
           python -c "import fipy; fipy.test()"
@@ -248,7 +248,7 @@ stages:
       - bash: |
           source activate myEnvironment
           FIPY_VERSION=`python setup.py --version`
-          mkdir tmp
+          mkdir -p tmp
           cd tmp
           cp ../dist/FiPy-${FIPY_VERSION}.zip .
           unzip FiPy-${FIPY_VERSION}.zip

.github/workflows/nix.yml

@@ -1,5 +1,5 @@
 ---
-name: nix
+name: Test Nix
 on: [push, pull_request]
 jobs:
   test:
@@ -11,12 +11,23 @@ jobs:
       run:
         working-directory: ./
     steps:
-      - uses: actions/checkout@v2.3.4
-      - uses: cachix/install-nix-action@v14.1
+      - uses: actions/checkout@v3
+      - uses: cachix/install-nix-action@v20
         with:
           nix_path: nixpkgs=channel:nixos-unstable
           name: fipy
           authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
           extraPullNames: nix-community
-      - run: nix-shell --pure --command "python setup.py test"
-      - run: nix-shell --pure --command "py.test --nbval --sanitize-with examples/sanitize.cfg examples/index.ipynb"
+      - run: echo "UID=${UID}" >> $GITHUB_ENV
+      - uses: actions/cache/restore@v3
+        with:
+          path: /run/user/${{ env.UID }}/http_cache.sqlite
+          key: ${{ runner.os }}-http_cache.sqlite
+      - run: nix develop --command bash -c "python setup.py egg_info"
+      - run: nix develop --command bash -c "python setup.py test"
+      - run: nix develop --command bash -c "py.test --nbval --nbval-sanitize-with examples/sanitize.cfg examples/index.ipynb"
+      - uses: actions/cache/save@v3
+        if: always()
+        with:
+          path: /run/user/${{ env.UID }}/http_cache.sqlite
+          key: ${{ runner.os }}-http_cache.sqlite

CHANGELOG.rst

@@ -11,6 +11,76 @@ Change Log
 Version |release|
 -----------------
 
+This maintenance release:
+
+- Addresses compatibility with recent releases of
+  Python 3.12, NumPy 2.0, SciPy 1.14, and PETSc 3.20.
+- Adds `conda-lock <https://github.com/conda/conda-lock>`_ environment
+  lock files with specified compatible versions of FiPy prerequisites.
+- Fixes numerous documentation errors.
+
+.. attention::
+
+   SciPy 1.13.0 generates one test suite error for
+   ``fipy.matrices.scipyMatrix._ScipyMatrix.CSR``.  Either ignore the test
+   failure or upgrade to SciPy >= 1.13.1
+
+.. attention::
+
+   PETSc 3.21 crashes our test suite when running in parallel (`#1054
+   <https://github.com/usnistgov/fipy/issues/1054>`_).  PETSc <= 3.20 is
+   recommended, although `petsc 3.20.2_*_102 is broken on macOS
+   <https://github.com/conda-forge/petsc-feedstock/issues/180>`_.
+
+Pulls
+-----
+
+- Introduce Timer context manager
+  (`#995 <https://github.com/usnistgov/fipy/pull/995>`_)
+- switch nix recipe to flake
+  (`#992 <https://github.com/usnistgov/fipy/pull/992>`_)
+- Tweak documentation
+  (`#991 <https://github.com/usnistgov/fipy/pull/991>`_)
+- Log much more information about FiPy environment
+  (`#990 <https://github.com/usnistgov/fipy/pull/990>`_)
+- Fix inclusion of `environments/README.rst`
+  (`#988 <https://github.com/usnistgov/fipy/pull/988>`_)
+- Environment pinning
+  (`#985 <https://github.com/usnistgov/fipy/pull/985>`_)
+
+Fixes
+-----
+
+- `#1049 <https://github.com/usnistgov/fipy/issues/1049>`_:
+  Numpy 2.0.0 breaks things
+- `#1010 <https://github.com/usnistgov/fipy/issues/1010>`_:
+  `examples.diffusion.mesh1D` No-flux - steady-state doesn't always give
+  zero
+- `#1000 <https://github.com/usnistgov/fipy/issues/1000>`_:
+  `examples.diffusion.mesh1D` constrains a gradient but calls it a flux
+- `#997 <https://github.com/usnistgov/fipy/issues/997>`_:
+  `future.standard_library` breaking python 3.12 compatibility
+- `#967 <https://github.com/usnistgov/fipy/issues/967>`_:
+  Sign error in Robin condition
+- `#963 <https://github.com/usnistgov/fipy/issues/963>`_:
+  PETSc 3.20.0 broke the world
+- `#961 <https://github.com/usnistgov/fipy/issues/961>`_:
+  Representation of index variables is broken
+- `#952 <https://github.com/usnistgov/fipy/issues/952>`_:
+  Uncaught Exception from the no-flux steady-state diffusion example
+- `#944 <https://github.com/usnistgov/fipy/issues/944>`_:
+  Having problem with Viewer
+- `#865 <https://github.com/usnistgov/fipy/issues/865>`_:
+  Sphinx search is broken on website
+- `#673 <https://github.com/usnistgov/fipy/issues/673>`_:
+  Deprecations don't properly format properties
+- `#512 <https://github.com/usnistgov/fipy/issues/512>`_:
+  Default coefficient of `ImplicitSourceTerm` is 0
+
+--------------------------
+Version 3.4.4 - 2023-06-27
+--------------------------
+
 This maintenance release adds :ref:`LOGGING` and resolves compatibility issues
 with recent builds of :term:`PETSc` and :term:`NumPy`.
 

_setup/changelog.py

@@ -194,7 +194,9 @@ def run(self):
         wontfix = issues.labels.apply(lambda x: 'wontfix' in x)
         invalid = issues.labels.apply(lambda x: 'invalid' in x)
         question = issues.labels.apply(lambda x: 'question' in x)
-        issues = issues[~wontfix & ~invalid & ~question]
+        worksforme = issues.labels.apply(lambda x: 'worksforme' in x)
+        duplicate = issues.labels.apply(lambda x: 'duplicate' in x)
+        issues = issues[~wontfix & ~invalid & ~question & ~worksforme & ~duplicate]
 
         # fix the dates to reflect dates from original Trac issue tracker
         trac = (r" _Imported from trac ticket .*,  "

docs/source/NIX-README.rst

@@ -4,64 +4,27 @@ Nix Installation
 :term:`FiPy` now has a `Nix`_ expression for installing :term:`FiPy`
 using `Nix`_. `Nix`_ is a powerful package manager for Linux and other
 Unix systems that makes package management reliable and
-reproducible. The recipe works on both Linux and Mac OS X.
-
-Getting Started with Nix
-------------------------
-
-There are a number of tutorials on getting started with `Nix`_. The
-page that I used when getting started is on the Blog of the HPC team
-of GRICAD,
-
-https://gricad.github.io/calcul/nix/tuto/2017/07/04/nix-tutorial.html
-
-I also made my own notes,
-
-https://github.com/wd15/nixes/blob/master/NIX-NOTES.md
-
-which are a succinct steps that I use when setting up a new system with
-Nix.
+reproducible. The recipe works on both Linux and Mac OS X. Go to
+`nix.dev`_ to get started with Nix.
 
 Installing
 ----------
 
 Once you have a working Nix installation use::
 
-    $ nix-shell --pure
+    $ nix develop
 
 in the base :term:`FiPy` directory to install :term:`FiPy` with Python
-3 by default. Modify the `shell.nix` file to use another version of
-Python. ``nix-shell`` drops the user into a shell with a working
+3 by default. ``nix develop`` drops the user into a shell with a working
 version of :term:`FiPy`. To test your installation use::
 
-    $ nix-shell --pure --command "python setup.py test"
+    $ nix develop --command bash -c "python setup.py test"
 
 .. note::
 
-   :term:`Trilinos` is currently not available as part of the Nix
-   :term:`FiPy` installation.
-
-
-Additional Packages
--------------------
-
-To install additional packages available from Nixpkgs_ include them in
-the `nativeBuildInputs` list in `shell.nix`.
-
-
-Using Pip
----------
-
-Packages unavailable from Nix can be installed using :term:`Pip`. In
-this case, the installation has been set up so that the Nix shell
-knows about a ``.local`` directory in the base :term:`FiPy` directory
-used by :term:`Pip` for installation.  So, for example, to install the
-``toolz`` package from within the Nix shell use::
-
-    $ python -m pip install --user toolz
+   The SciPy solvers are the only available solvers currently.
 
-The ``.local`` directory will persist after the Nix shell has been
-closed.
 
 .. _Nix: https://nixos.org/nix/
 .. _Nixpkgs:  https://nixos.org/nixpkgs/
+.. _nix.dev: https://nix.dev

docs/source/sphinxext/redirecting_html.py

@@ -1,9 +1,9 @@
 from __future__ import unicode_literals
-from future import standard_library
-standard_library.install_aliases()
 from docutils import nodes
-import urllib.parse
-
+try:
+    from urllib.parse import urlparse
+except ImportError:
+    from urlparse import urlparse
 from sphinx.builders.html import StandaloneHTMLBuilder
 
 class RedirectingHTMLBuilder(StandaloneHTMLBuilder):
@@ -17,7 +17,7 @@ def write_doc(self, docname, doctree):
         for node in doctree.traverse(nodes.reference):
             try:
                 uri = node['refuri']
-                uri = urllib.parse.urlparse(uri)
+                uri = urlparse(uri)
                 if uri.scheme in ["http", "https"]:
                     if not uri.netloc.endswith("nist.gov"):
                         node['refuri'] = "/cgi-bin/redirect.py?url=" + uri.geturl()