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|
{ 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 // {
pkgs = pkgs.python3.pkgs.overrideScope (self: super: {
# `sagelib`, i.e. all of sage except some wrappers and runtime dependencies
sagelib = self.callPackage ./sagelib.nix {
inherit flint3;
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;
};
});
};
# matches src/sage/repl/ipython_kernel/install.py:kernel_spec
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 = "sage";
# 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 flint3 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 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
notebook # for "sage -n"
rpy2
sphinx
pillow
] ++ extraPythonPackages python3.pkgs;
pythonEnv = python3.buildEnv.override {
extraLibs = pythonRuntimeDeps;
ignoreCollisions = true;
} // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible
singular = pkgs.singular.override { inherit flint3; };
maxima = pkgs.maxima-ecl.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.
flint3 = pkgs.flint3.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-definition jupyter-kernel-specs;
inherit withDoc requireSageTests;
}
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