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sage: refactor

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This commit is contained in:
Timo Kaufmann
2018-11-24 23:14:33 +01:00
parent 9b4a518465
commit 3832ddedb9
13 changed files with 216 additions and 195 deletions
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pkgs/applications/science/math/sage/default.nix
+77 -54
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@@ -1,65 +1,87 @@
{ nixpkgs
{ pkgs
, withDoc ? false
}:
# 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 (nixpkgs) fetchpatch fetchurl symlinkJoin callPackage nodePackages;
inherit (pkgs) fetchurl symlinkJoin callPackage nodePackages_8_x;
# https://trac.sagemath.org/ticket/15980 for tracking of python3 support
python = nixpkgs.python2.override {
python = pkgs.python2.override {
packageOverrides = 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.
# The dependency on the sage notebook (and therefore these packages) will be
# removed in the future:
# https://trac.sagemath.org/ticket/25837
flask-oldsessions = self.callPackage ./flask-oldsessions.nix {};
flask-openid = self.callPackage ./flask-openid.nix {};
python-openid = self.callPackage ./python-openid.nix {};
sagenb = self.callPackage ./sagenb.nix {
mathjax = nodePackages_8_x.mathjax;
};
# Package with a cyclic dependency with sage
pybrial = self.callPackage ./pybrial.nix {};
# `sagelib`, i.e. all of sage except some wrappers and runtime dependencies
sagelib = self.callPackage ./sagelib.nix {
inherit flint ecl 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.mathjax;
};
sagedoc = self.callPackage ./sagedoc.nix {
inherit sage-src;
};
env-locations = self.callPackage ./env-locations.nix {
inherit pari_data ecl;
inherit singular;
three = nodePackages.three;
mathjax = nodePackages.mathjax;
};
sage-env = self.callPackage ./sage-env.nix {
inherit sage-src python rWrapper openblas-cblas-pc ecl singular palp flint pynac pythonEnv;
pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
};
sage-with-env = self.callPackage ./sage-with-env.nix {
inherit 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.three;
};
sage = self.callPackage ./sage.nix { };
sage-wrapper = self.callPackage ./sage-wrapper.nix {
inherit sage-src withDoc;
linbox = pkgs.linbox.override { withSage = true; };
};
};
};
# 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 ecl;
inherit singular;
cysignals = python.pkgs.cysignals;
three = nodePackages_8_x.three;
mathjax = nodePackages_8_x.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 = python.pkgs.sagelib;
inherit env-locations;
inherit python rWrapper openblas-cblas-pc ecl singular palp flint pynac pythonEnv;
pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
};
# The documentation for sage, building it takes a lot of ram.
sagedoc = callPackage ./sagedoc.nix {
inherit sage-with-env;
inherit python;
};
# 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 pythonEnv;
inherit sage-env;
inherit openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular;
pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
three = nodePackages_8_x.three;
};
# 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;
};
# FIXME
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"; };
@@ -91,9 +113,9 @@ let
} // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible
# needs to be rWrapper, standard "R" doesn't include default packages
rWrapper = nixpkgs.rWrapper.override {
rWrapper = pkgs.rWrapper.override {
# https://trac.sagemath.org/ticket/25674
R = nixpkgs.R.overrideAttrs (attrs: rec {
R = pkgs.R.overrideAttrs (attrs: rec {
name = "R-3.4.4";
src = fetchurl {
url = "http://cran.r-project.org/src/base/R-3/${name}.tar.gz";
@@ -102,44 +124,45 @@ let
});
};
arb = nixpkgs.arb.override { inherit flint; };
arb = pkgs.arb.override { inherit flint; };
singular = nixpkgs.singular.override { inherit flint; };
singular = pkgs.singular.override { inherit flint; };
# *not* to confuse with the python package "pynac"
pynac = nixpkgs.pynac.override { inherit singular flint; };
pynac = pkgs.pynac.override { inherit singular flint; };
# With openblas (64 bit), the tests fail the same way as when sage is build with
# openblas instead of openblasCompat. Apparently other packages somehow use flints
# blas when it is available. Alternative would be to override flint to use
# openblasCompat.
flint = nixpkgs.flint.override { withBlas = false; };
flint = pkgs.flint.override { withBlas = false; };
# Multiple palp dimensions need to be available and sage expects them all to be
# in the same folder.
palp = symlinkJoin {
name = "palp-${nixpkgs.palp.version}";
name = "palp-${pkgs.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; })
(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 nixpkgs; [
paths = with pkgs; [
pari-galdata
pari-seadata-small
];
};
# https://trac.sagemath.org/ticket/22191
ecl = nixpkgs.ecl_16_1_2;
ecl = pkgs.ecl_16_1_2;
in
python.pkgs.sage-wrapper // {
doc = python.pkgs.sagedoc;
lib = python.pkgs.sagelib;
}
# 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;
inherit withDoc;
}