Merge branch 'master' into issue997-incompatible_with_Python_3_12

.github/workflows/nix.yml

@@ -1,5 +1,5 @@
 ---
-name: nix
+name: Test Nix
 on: [push, pull_request]
 jobs:
   test:
@@ -11,12 +11,22 @@ 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: ${{ runner.os }}-http_cache.sqlite
+      - run: nix develop --command bash -c "python setup.py test"
+      - run: nix develop --command bash -c "py.test --nbval --nbval-sanitize-with examples/sanitize.cfg examples/index.ipynb"
+      - uses: actions/cache/save@v3
+        if: always()
+        with:
+          path: /run/user/${{ env.UID }}/http_cache.sqlite
+          key: ${{ runner.os }}-http_cache.sqlite

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

examples/diffusion/mesh1D.py

@@ -720,24 +720,30 @@
 
 and solve the steady-state problem
 
->>> DiffusionTerm(coeff=D).solve(var=phi) #doctest: +PYSPARSE_SOLVER
+>>> try:
+...     DiffusionTerm(coeff=D).solve(var=phi)
+... except:
+...     pass
 >>> if __name__ == '__main__':
 ...     viewer.plot()
 >>> from fipy import input
 >>> if __name__ == '__main__':
-...     input("No-flux - stead-state failure. \
+...     input("No-flux - steady-state failure. \
 ... Press <return> to proceed...")
 
->>> print(numerix.allclose(phi, 0.0)) #doctest: +PYSPARSE_SOLVER
-True
+>>> print(numerix.allclose(phi, 0.2, atol=1e-5)) # doctest: +NOT_TRILINOS_SOLVER
+False
 
 .. image:: /figures/examples/diffusion/mesh1D-noflux_steady_fail.*
    :width: 90%
    :align: center
    :alt: (failed) steady-state solution for no-flux boundary conditions
 
-we find that the value is uniformly zero! What happened to our no-flux boundary
-conditions?
+Depending on the solver, we find that the value may be uniformly zero,
+infinity, or NaN, or the solver may just fail!
+What happened to our no-flux boundary conditions?
+Trilinos actually manages to get the correct solution, but this should not
+be relied on; this problem has an infinite number of solutions.
 
 The problem is that in the implicit discretization of :math:`\nabla\cdot(D\nabla\phi) = 0`,
 

examples/sanitize.cfg

@@ -1,3 +1,7 @@
-[regex]
+[regex1]
 regex: <Figure size [0-9]{3,4}x[0-9]{3,4}(?:.[0-9])? with [0-9]{1,3} Axes>
 replace: <Figure size>
+
+[regex2]
+regex: <fipy.viewers.matplotlibViewer.matplotlib2DGridViewer.Matplotlib2DGridViewer at .{1,}>
+replace: <fipy.viewers.matplotlibViewer.matplotlib2DGridViewer.Matplotlib2DGridViewer>

fipy/__init__.py

@@ -76,12 +76,17 @@ def _excepthook(*args):
 
 if _log.isEnabledFor(logging.DEBUG):
     try:
-        _fipy_environment["conda"] = environment.conda_info()
+        _fipy_environment.update(environment.conda_info())
     except:
         pass
 
     try:
-        _fipy_environment["pip"] = environment.pip_info()
+        _fipy_environment.update(environment.pip_info())
+    except:
+        pass
+
+    try:
+        _fipy_environment.update(environment.nix_info())
     except:
         pass
 

fipy/solvers/__init__.py

@@ -190,6 +190,12 @@ def _import_mesh_matrices(suite):
                  test=lambda: solver_suite != 'pyamgx',
                  why="the PyAMGX solver is being used.",
                  skipWarning=True)
+
+register_skipper(flag='NOT_TRILINOS_SOLVER',
+                 test=lambda: solver_suite not in ['trilinos', 'no-pysparse'],
+                 why="the Trilinos solvers are being used.",
+                 skipWarning=True)
+
 del register_skipper
 
 _log.info("Solver suite is %s", solver_suite)

fipy/tools/logging/environment.py

@@ -3,7 +3,7 @@
 import subprocess
 import sys
 
-__all__ = ["conda_info", "pip_info", "package_info", "platform_info"]
+__all__ = ["conda_info", "pip_info", "package_info", "platform_info", "nix_info"]
 
 def conda_info(conda="conda"):
     """Collect information about conda environment.
@@ -25,6 +25,7 @@ def conda_info(conda="conda"):
     stdout = stdout.decode('ascii')
 
     info["conda_info"] = json.loads(stdout)
+
     p = subprocess.Popen([conda, "env", "export",
                           "--name", info["conda_info"]["active_prefix_name"],
                           "--json"],
@@ -53,7 +54,41 @@ def pip_info(python="python"):
     stdout, _ = p.communicate()
     stdout = stdout.decode('ascii')
 
-    return json.loads(stdout)
+    info["pip"] = json.loads(stdout)
+
+    return info
+
+def nix_info():
+    """Collect information about nix environment.
+
+    Returns
+    -------
+    dict
+        Result of `nix derivation show .#fipy `.
+    """
+    info = {}
+
+    # Better output would be from
+    #
+    #     $ nix-store -q --tree $(nix-store --realize $(nix eval --raw .#fipy.drvPath))
+    #
+    # However, this is difficult to execute and can require another build.
+    # Also doesn't return json.
+
+    p = subprocess.Popen(
+        [
+         "nix",
+         "derivation",
+         "show",
+         ".#fipy"
+        ], stdout=subprocess.PIPE)
+
+    stdout, _ = p.communicate()
+    stdout = stdout.decode('ascii')
+
+    info["nix"] = json.loads(stdout)
+
+    return info
 
 def package_info():
     """Collect information about installed packages FiPy uses.

fipy/variables/operatorVariable.py

@@ -208,7 +208,7 @@ def _py3kInstructions(self, op, style, argDict, id, freshen):
                     # Removed in Python 3
                     stack.append("`" + stack.pop() + "`")
                 elif ins.opname == 'BINARY_SUBSCR':
-                    stack.append(stack.pop(-2) + "[" + stack.pop() + "]")
+                    stack.append(stack.pop(-2) + "[" + str(stack.pop()) + "]")
                 elif ins.opname == 'RETURN_VALUE':
                     s = stack.pop()
                     if style == 'C':
@@ -371,6 +371,11 @@ def _testBinOp(self):
         >>> ttns((v1 / v2 - v3 * v4 + v1 * v4)._getRepresentation(style='C', id=""))
         '(((var000[i] / var001[i]) - (var010[i] * var011[i])) + (var10[i] * var11[i]))'
 
+    Test that the representation of indexing works correctly
+
+        >>> ttns(v1[1]._getRepresentation()) # doctest: +ELLIPSIS
+        'Variable(value=array([1, 2, 3, 4]))[...]'
+
     Check that unit works for a `binOp`
 
         >>> (Variable(value="1 m") * Variable(value="1 s")).unit == Variable(value="1 s*m").unit

flake.nix

@@ -0,0 +1,49 @@
+{
+  description = "Python environment for fipy";
+
+  inputs = {
+    nixpkgs.url = "github:NixOS/nixpkgs/nixos-23.11";
+    utils.url = "github:numtide/flake-utils";
+  };
+
+  outputs = { self, nixpkgs, utils}: (utils.lib.eachSystem ["x86_64-linux" "x86_64-darwin" ] (system:
+    let
+      pkgs = nixpkgs.legacyPackages.${system};
+      pypkgs = pkgs.python310Packages;
+
+      env = (pypkgs.fipy.overridePythonAttrs (old: rec {
+
+        src = pkgs.lib.cleanSource ./.;
+
+        nativeBuildInputs = with pypkgs; [
+          pip
+          pkgs.openssh
+          nbval
+          ipython
+          ipykernel
+          jupyterlab
+          traitlets
+          notebook
+        ] ++ propagatedBuildInputs;
+
+        propagatedBuildInputs = old.propagatedBuildInputs;
+
+        postShellHook = ''
+          SOURCE_DATE_EPOCH=$(date +%s)
+          export PYTHONUSERBASE=$PWD/.local
+          export USER_SITE=`python -c "import site; print(site.USER_SITE)"`
+          export PYTHONPATH=$PYTHONPATH:$USER_SITE:$(pwd)
+          export PATH=$PATH:$PYTHONUSERBASE/bin
+
+          export OMPI_MCA_plm_rsh_agent=${pkgs.openssh}/bin/ssh
+
+        '';
+      }));
+   in
+     rec {
+       packages.fipy = env;
+       packages.default = self.packages.${system}.fipy;
+       devShells.default = env;
+     }
+  ));
+}