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[WIP] sage: use proper overlays #43755

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[WIP] sage: use proper overlays #43755

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370 changes: 178 additions & 192 deletions pkgs/applications/science/math/sage/default.nix
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Expand Up @@ -3,199 +3,185 @@
}:

let
inherit (nixpkgs) fetchpatch fetchurl symlinkJoin fetchFromGitHub 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;
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;
pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
};

sage-with-env = self.callPackage ./sage-with-env.nix {
inherit pari eclib pythonEnv;
inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular;
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";
};
});
};

# update causes issues
# https://groups.google.com/forum/#!topic/sage-packaging/cS3v05Q0zso
# https://trac.sagemath.org/ticket/24735
singular = nixpkgs.singular.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; };

eclib = nixpkgs.eclib.override { inherit pari; };

# 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; };

# 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";
inherit (sagepkgs) fetchpatch fetchurl symlinkJoin fetchFromGitHub callPackage nodePackages_8_x;

sagepkgs = import nixpkgs.path {
overlays = [
(self: super: {
# https://trac.sagemath.org/ticket/15980 for tracking of python3 support
python2 = super.python2.override {
packageOverrides = pSelf: pSuper: { # distinguish from nixpkgs self/super
# 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 = pSelf.callPackage ./flask-oldsessions.nix {};
flask-openid = pSelf.callPackage ./flask-openid.nix {};
python-openid = pSelf.callPackage ./python-openid.nix {};

pybrial = pSelf.callPackage ./pybrial.nix {};

sagelib = pSelf.callPackage ./sagelib.nix {
pynac = self.pynac;
linbox = self.linbox.override { withSage = true; };
};

sagenb = pSelf.callPackage ./sagenb.nix {
mathjax = nodePackages_8_x.mathjax;
};

sagedoc = pSelf.callPackage ./sagedoc.nix { };

env-locations = pSelf.callPackage ./env-locations.nix {
# Sage expects those in the same directory.
pari_data = symlinkJoin {
name = "pari_data";
paths = with self; [
pari-galdata
pari-seadata-small
];
};
three = nodePackages_8_x.three;
mathjax = nodePackages_8_x.mathjax;
};

sagePython2Env = let
pythonRuntimeDeps = with self.python2.pkgs; [
sagelib
pybrial
sagenb
cvxopt
networkx
service-identity
psutil
sympy
fpylll
matplotlib
scipy
ipywidgets
rpy2
sphinx
typing
pillow
];
in
self.python2.buildEnv.override {
extraLibs = pythonRuntimeDeps;
ignoreCollisions = true;
} // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible

sage-env = pSelf.callPackage ./sage-env.nix {
pynac = self.pynac;
pkg-config = self.pkgconfig; # not to confuse with pythonPackages.pkgconfig
};

sage-with-env = pSelf.callPackage ./sage-with-env.nix {
pynac = self.pynac;
pkg-config = self.pkgconfig; # not to confuse with pythonPackages.pkgconfig
three = nodePackages_8_x.three;
};

sage = pSelf.callPackage ./sage.nix { };

sage-wrapper = pSelf.callPackage ./sage-wrapper.nix {
inherit withDoc;
};
};
};

# update causes issues
# https://groups.google.com/forum/#!topic/sage-packaging/cS3v05Q0zso
# https://trac.sagemath.org/ticket/24735
singular = super.singular.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";
};
});

# sage currently uses an unreleased version of pari
pari = (super.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";
};
});

# 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 = super.flint.override { withBlas = false; };

# https://trac.sagemath.org/ticket/24824
glpk = super.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";
})
];
});

# https://trac.sagemath.org/ticket/22191
ecl = super.ecl_16_1_2;

# https://trac.sagemath.org/ticket/25674
R = super.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";
};
});

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 {};

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