switch nix recipe to flake (#992)

* switch nix recipe to flake

* fix notebook output to be consistent

Changes required as running the notebook live and running notebook
with nbval resulted in different outputs.

* update github ci to use flake

* update nix installation instructions

* add nix environment logging

---------

Co-authored-by: Jonathan Guyer <[email protected]>
Co-authored-by: Trevor Keller <[email protected]>

Author: 3 people

.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/index.ipynb

@@ -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>

examples/sanitize.cfg

@@ -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/__init__.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/tools/logging/environment.py

@@ -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;
+     }
+  ));
+}