nomicon/pkgs/applications/science/math/sage/default.nix

{ pkgs
, withDoc ? false
, requireSageTests ? true
, extraPythonPackages ? ps: []
}:

# Here sage and its dependencies are put together. Some dependencies may be pinned
# as a last resort. Patching sage for compatibility with newer dependency versions
# is always preferred, see `sage-src.nix` for that.

let
  inherit (pkgs) symlinkJoin callPackage nodePackages;

  python3 = pkgs.python3.override {
    packageOverrides = self: super: {
      # `sagelib`, i.e. all of sage except some wrappers and runtime dependencies
      sagelib = self.callPackage ./sagelib.nix {
        inherit flint arb;
        inherit sage-src env-locations singular;
        inherit (maxima) lisp-compiler;
        linbox = pkgs.linbox.override { withSage = true; };
        pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config
      };

      sage-docbuild = self.callPackage ./python-modules/sage-docbuild.nix {
        inherit sage-src;
      };

      sage-setup = self.callPackage ./python-modules/sage-setup.nix {
        inherit sage-src;
      };
    };
  };

  jupyter-kernel-definition = {
    displayName = "SageMath ${sage-src.version}";
    argv = [
      "${sage-with-env}/bin/sage" # FIXME which sage
      "--python"
      "-m"
      "sage.repl.ipython_kernel"
      "-f"
      "{connection_file}"
    ];
    language = "sagemath";
    # just one 16x16 logo is available
    logo32 = "${sage-src}/src/doc/common/themes/sage/static/sageicon.png";
    logo64 = "${sage-src}/src/doc/common/themes/sage/static/sageicon.png";
  };

  jupyter-kernel-specs = pkgs.jupyter-kernel.create {
    definitions = pkgs.jupyter-kernel.default // {
      sagemath = jupyter-kernel-definition;
    };
  };

  three = callPackage ./threejs-sage.nix { };

  # A bash script setting various environment variables to tell sage where
  # the files its looking fore are located. Also see `sage-env`.
  env-locations = callPackage ./env-locations.nix {
    inherit pari_data;
    inherit singular maxima;
    inherit three;
    cysignals = python3.pkgs.cysignals;
    mathjax = nodePackages.mathjax;
  };

  # The shell file that gets sourced on every sage start. Will also source
  # the env-locations file.
  sage-env = callPackage ./sage-env.nix {
    sagelib = python3.pkgs.sagelib;
    sage-docbuild = python3.pkgs.sage-docbuild;
    inherit env-locations;
    inherit python3 singular palp flint pythonEnv maxima;
    pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config
  };

  # The documentation for sage, building it takes a lot of ram.
  sagedoc = callPackage ./sagedoc.nix {
    inherit sage-with-env;
    inherit python3 maxima jupyter-kernel-specs;
  };

  # sagelib with added wrappers and a dependency on sage-tests to make sure thet tests were run.
  sage-with-env = callPackage ./sage-with-env.nix {
    inherit python3 pythonEnv;
    inherit sage-env;
    inherit singular maxima;
    inherit three;
    pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config
  };

  # Doesn't actually build anything, just runs sages testsuite. This is a
  # separate derivation to make it possible to re-run the tests without
  # rebuilding sagelib (which takes ~30 minutes).
  # Running the tests should take something in the order of 1h.
  sage-tests = callPackage ./sage-tests.nix {
    inherit sage-with-env;
  };

  sage-src = callPackage ./sage-src.nix {};

  pythonRuntimeDeps = with python3.pkgs; [
    sagelib
    sage-docbuild
    cvxopt
    networkx
    service-identity
    psutil
    sympy
    fpylll
    matplotlib
    tkinter # optional, as a matplotlib backend (use with `%matplotlib tk`)
    scipy
    ipywidgets
    rpy2
    sphinx
    pillow
  ] ++ extraPythonPackages python3.pkgs;

  pythonEnv = python3.buildEnv.override {
    extraLibs = pythonRuntimeDeps;
    ignoreCollisions = true;
  } // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible

  arb = pkgs.arb.override { inherit flint; };

  singular = pkgs.singular.override { inherit flint; };

  maxima = pkgs.maxima.override {
    lisp-compiler = pkgs.ecl.override {
      # "echo syntax error | ecl > /dev/full 2>&1" segfaults in
      # ECL. We apply a patch to fix it (write_error.patch), but it
      # only works if threads are disabled.  sage 9.2 tests this
      # (src/sage/interfaces/tests.py) and ships ecl like so.
      # https://gitlab.com/embeddable-common-lisp/ecl/-/merge_requests/1#note_1657275
      threadSupport = false;

      # if we don't use the system boehmgc, sending a SIGINT to ecl
      # can segfault if we it happens during memory allocation.
      # src/sage/libs/ecl.pyx would intermittently fail in this case.
      useBoehmgc = true;
    };
  };

  # With openblas (64 bit), the tests fail the same way as when sage is build with
  # openblas instead of openblasCompat. Apparently other packages somehow use flints
  # blas when it is available. Alternative would be to override flint to use
  # openblasCompat.
  flint = pkgs.flint.override { withBlas = false; };

  # Multiple palp dimensions need to be available and sage expects them all to be
  # in the same folder.
  palp = symlinkJoin {
    name = "palp-${pkgs.palp.version}";
    paths = [
      (pkgs.palp.override { dimensions = 4; doSymlink = false; })
      (pkgs.palp.override { dimensions = 5; doSymlink = false; })
      (pkgs.palp.override { dimensions = 6; doSymlink = true; })
      (pkgs.palp.override { dimensions = 11; doSymlink = false; })
    ];
  };

  # Sage expects those in the same directory.
  pari_data = symlinkJoin {
    name = "pari_data";
    paths = with pkgs; [
      pari-galdata
      pari-seadata-small
    ];
  };
in
# A wrapper around sage that makes sure sage finds its docs (if they were build).
callPackage ./sage.nix {
  inherit sage-tests sage-with-env sagedoc jupyter-kernel-specs;
  inherit withDoc requireSageTests;
}