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|
{ nixpkgs
, withDoc ? false
}:
let
inherit (nixpkgs) fetchpatch fetchurl symlinkJoin callPackage nodePackages_8_x;
# https://trac.sagemath.org/ticket/15980 for tracking of python3 support
python = nixpkgs.python2.override {
packageOverrides = self: super: {
cypari2 = super.cypari2.override { inherit pari; };
cysignals = super.cysignals.override { inherit pari; };
cvxopt = super.cvxopt.override { inherit glpk; };
# python packages that appear unmaintained and were not accepted into the nixpkgs
# tree because of that. These packages are only dependencies of the more-or-less
# deprecated sagenb. However sagenb is still a default dependency and the doctests
# depend on it.
# See https://github.com/NixOS/nixpkgs/pull/38787 for a discussion.
flask-oldsessions = self.callPackage ./flask-oldsessions.nix {};
flask-openid = self.callPackage ./flask-openid.nix {};
python-openid = self.callPackage ./python-openid.nix {};
pybrial = self.callPackage ./pybrial.nix {};
sagelib = self.callPackage ./sagelib.nix {
inherit flint ecl pari glpk eclib ntl arb;
inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular;
linbox = nixpkgs.linbox.override { withSage = true; };
};
sagenb = self.callPackage ./sagenb.nix {
mathjax = nodePackages_8_x.mathjax;
};
sagedoc = self.callPackage ./sagedoc.nix {
inherit sage-src;
};
env-locations = self.callPackage ./env-locations.nix {
inherit pari_data ecl pari;
inherit singular;
three = nodePackages_8_x.three;
mathjax = nodePackages_8_x.mathjax;
};
sage-env = self.callPackage ./sage-env.nix {
inherit sage-src python rWrapper openblas-cblas-pc glpk ecl singular eclib pari palp flint pynac pythonEnv giac ntl;
pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
};
sage-with-env = self.callPackage ./sage-with-env.nix {
inherit pari eclib pythonEnv ntl;
inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular giac;
pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
three = nodePackages_8_x.three;
};
sage = self.callPackage ./sage.nix { };
sage-wrapper = self.callPackage ./sage-wrapper.nix {
inherit sage-src withDoc;
};
};
};
openblas-blas-pc = callPackage ./openblas-pc.nix { name = "blas"; };
openblas-cblas-pc = callPackage ./openblas-pc.nix { name = "cblas"; };
openblas-lapack-pc = callPackage ./openblas-pc.nix { name = "lapack"; };
sage-src = callPackage ./sage-src.nix {};
pythonRuntimeDeps = with python.pkgs; [
sagelib
pybrial
sagenb
cvxopt
networkx
service-identity
psutil
sympy
fpylll
matplotlib
scipy
ipywidgets
rpy2
sphinx
typing
pillow
];
pythonEnv = python.buildEnv.override {
extraLibs = pythonRuntimeDeps;
ignoreCollisions = true;
} // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible
# needs to be rWrapper, standard "R" doesn't include default packages
rWrapper = nixpkgs.rWrapper.override {
# https://trac.sagemath.org/ticket/25674
R = nixpkgs.R.overrideAttrs (attrs: rec {
name = "R-3.4.4";
src = fetchurl {
url = "http://cran.r-project.org/src/base/R-3/${name}.tar.gz";
sha256 = "0dq3jsnwsb5j3fhl0wi3p5ycv8avf8s5j1y4ap3d2mkjmcppvsdk";
};
});
};
# https://trac.sagemath.org/ticket/25532
ntl = nixpkgs.ntl.overrideAttrs (oldAttrs: rec {
name = "ntl-10.5.0";
sourceRoot = "${name}/src";
src = fetchurl {
url = "http://www.shoup.net/ntl/${name}.tar.gz";
sha256 = "1lmldaldgfr2b2a6585m3np5ds8bq1bis2s1ajycjm49vp4kc2xr";
};
});
giac = nixpkgs.giac.override { inherit ntl; };
arb = nixpkgs.arb.override { inherit flint; };
# update causes issues
# https://groups.google.com/forum/#!topic/sage-packaging/cS3v05Q0zso
# https://trac.sagemath.org/ticket/24735
singular = (nixpkgs.singular.override { inherit ntl flint; }).overrideAttrs (oldAttrs: {
name = "singular-4.1.0p3";
src = fetchurl {
url = "http://www.mathematik.uni-kl.de/ftp/pub/Math/Singular/SOURCES/4-1-0/singular-4.1.0p3.tar.gz";
sha256 = "105zs3zk46b1cps403ap9423rl48824ap5gyrdgmg8fma34680a4";
};
});
# *not* to confuse with the python package "pynac"
# https://trac.sagemath.org/ticket/24838 (depends on arb update)
pynac = nixpkgs.pynac.override { inherit singular flint; };
eclib = nixpkgs.eclib.override { inherit pari ntl; };
# With openblas (64 bit), the tests fail the same way as when sage is build with
# openblas instead of openblasCompat. Apparently other packages somehow use flints
# blas when it is available. Alternative would be to override flint to use
# openblasCompat.
flint = nixpkgs.flint.override { withBlas = false; inherit ntl; };
# Multiple palp dimensions need to be available and sage expects them all to be
# in the same folder.
palp = symlinkJoin {
name = "palp-${nixpkgs.palp.version}";
paths = [
(nixpkgs.palp.override { dimensions = 4; doSymlink = false; })
(nixpkgs.palp.override { dimensions = 5; doSymlink = false; })
(nixpkgs.palp.override { dimensions = 6; doSymlink = true; })
(nixpkgs.palp.override { dimensions = 11; doSymlink = false; })
];
};
# Sage expects those in the same directory.
pari_data = symlinkJoin {
name = "pari_data";
paths = with nixpkgs; [
pari-galdata
pari-seadata-small
];
};
# https://trac.sagemath.org/ticket/22191
ecl = nixpkgs.ecl_16_1_2;
# sage currently uses an unreleased version of pari
pari = (nixpkgs.pari.override { withThread = false; }).overrideAttrs (attrs: rec {
version = "2.10-1280-g88fb5b3"; # on update remove pari-stackwarn patch from `sage-src.nix`
src = fetchurl {
url = "mirror://sageupstream/pari/pari-${version}.tar.gz";
sha256 = "19gbsm8jqq3hraanbmsvzkbh88iwlqbckzbnga3y76r7k42akn7m";
};
});
# https://trac.sagemath.org/ticket/24824
glpk = nixpkgs.glpk.overrideAttrs (attrs: rec {
version = "4.63";
name = "glpk-${version}";
src = fetchurl {
url = "mirror://gnu/glpk/${name}.tar.gz";
sha256 = "1xp7nclmp8inp20968bvvfcwmz3mz03sbm0v3yjz8aqwlpqjfkci";
};
patches = (attrs.patches or []) ++ [
# Alternatively patch sage with debians
# https://sources.debian.org/data/main/s/sagemath/8.1-7/debian/patches/t-version-glpk-4.60-extra-hack-fixes.patch
# The header of that debian patch contains a good description of the issue. The gist of it:
# > If GLPK in Sage causes one error, and this is caught by Sage and recovered from, then
# > later (because upstream GLPK does not clear the "error" flag) Sage will append
# > all subsequent terminal output of GLPK into the error_message string but not
# > actually forward it to the user's terminal. This breaks some doctests.
(fetchpatch {
name = "error_recovery.patch";
url = "https://git.sagemath.org/sage.git/plain/build/pkgs/glpk/patches/error_recovery.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
sha256 = "0z99z9gd31apb6x5n5n26411qzx0ma3s6dnznc4x61x86bhq31qf";
})
# Allow setting a exact verbosity level (OFF|ERR|ON|ALL|DBG)
(fetchpatch {
name = "exact_verbosity.patch";
url = "https://git.sagemath.org/sage.git/plain/build/pkgs/glpk/patches/glp_exact_verbosity.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
sha256 = "15gm5i2alqla3m463i1qq6jx6c0ns6lip7njvbhp37pgxg4s9hx8";
})
];
});
in
python.pkgs.sage-wrapper // {
doc = python.pkgs.sagedoc;
lib = python.pkgs.sagelib;
}
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