Unverified Commit e21968aa authored by Mauricio Collares's avatar Mauricio Collares Committed by GitHub
Browse files

Merge pull request #294062 from collares/sage-10.3 

sage: 10.2 -> 10.3
parents 83b32add d403e1be

pkgs/applications/science/math/nauty/default.nix

+4 −4
Original line number Diff line number Diff line
@@ -4,11 +4,11 @@ 
}:

stdenv.mkDerivation rec {

  pname = "nauty";

  version = "2.7r4";

  version = "2.8.8";



  src = fetchurl {

    url = "https://pallini.di.uniroma1.it/nauty${builtins.replaceStrings ["."] [""] version}.tar.gz";

    sha256 = "sha256-uBDIWm/imfO0yfJKr5KcrH+VRsLzXCDh3Qrbx0CISKY=";

    url = "https://pallini.di.uniroma1.it/nauty${builtins.replaceStrings ["."] ["_"] version}.tar.gz";

    sha256 = "sha256-FZ0hVoEKa7JAQQzWHrZBrdhQiNnxXIiM2qN7hoH5Kc4=";

  };



  outputs = [ "out" "dev" ];
@@ -44,7 +44,7 @@ stdenv.mkDerivation rec { 
    # I'm not sure if the filename will remain the same for future changelog or

    # if it will track changes to minor releases. Lets see. Better than nothing

    # in any case.

    changelog = "https://pallini.di.uniroma1.it/changes24-27.txt";

    changelog = "https://pallini.di.uniroma1.it/changes24-28.txt";

    homepage = "https://pallini.di.uniroma1.it/";

  };

}

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

+4 −6
Original line number Diff line number Diff line
@@ -15,7 +15,7 @@ let 
    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 flint arb;

        inherit flint3;

        inherit sage-src env-locations singular;

        inherit (maxima) lisp-compiler;

        linbox = pkgs.linbox.override { withSage = true; };
@@ -73,7 +73,7 @@ let 
    sagelib = python3.pkgs.sagelib;

    sage-docbuild = python3.pkgs.sage-docbuild;

    inherit env-locations;

    inherit python3 singular palp flint pythonEnv maxima;

    inherit python3 singular palp flint3 pythonEnv maxima;

    pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config

  };
@@ -125,9 +125,7 @@ let 
    ignoreCollisions = true;

  } // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible



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



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

  singular = pkgs.singular.override { inherit flint3; };



  maxima = pkgs.maxima-ecl.override {

    lisp-compiler = pkgs.ecl.override {
@@ -149,7 +147,7 @@ let 
  # 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; };

  flint3 = pkgs.flint3.override { withBlas = false; };



  # Multiple palp dimensions need to be available and sage expects them all to be

  # in the same folder.

pkgs/applications/science/math/sage/env-locations.nix

+1 −5
Original line number Diff line number Diff line
@@ -3,7 +3,6 @@ 
, pari

, singular

, maxima

, conway_polynomials

, graphs

, elliptic_curves

, polytopes_db
@@ -27,16 +26,13 @@ writeTextFile rec { 
    export GPDOCDIR="${pari}/share/pari/doc"

    export SINGULARPATH='${singular}/share/singular'

    export SINGULAR_SO='${singular}/lib/libSingular.so'

    export GAP_SO='${gap}/lib/libgap.so'

    export SINGULAR_EXECUTABLE='${singular}/bin/Singular'

    export MAXIMA_FAS='${maxima}/lib/maxima/${maxima.version}/binary-ecl/maxima.fas'

    export MAXIMA_PREFIX="${maxima}"

    export CONWAY_POLYNOMIALS_DATA_DIR='${conway_polynomials}/share/conway_polynomials'

    export GRAPHS_DATA_DIR='${graphs}/share/graphs'

    export ELLCURVE_DATA_DIR='${elliptic_curves}/share/ellcurves'

    export POLYTOPE_DATA_DIR='${polytopes_db}/share/reflexive_polytopes'

    export GAP_LIB_DIR='${gap}/lib/gap'

    export GAP_SHARE_DIR='${gap}/share/gap'

    export GAP_ROOT_PATHS='${gap}/lib/gap;${gap}/share/gap'

    export ECLDIR='${maxima.lisp-compiler}/lib/${maxima.lisp-compiler.pname}-${maxima.lisp-compiler.version}/'

    export COMBINATORIAL_DESIGN_DATA_DIR="${combinatorial_designs}/share/combinatorial_designs"

    export CREMONA_MINI_DATA_DIR="${elliptic_curves}/share/cremona"

pkgs/applications/science/math/sage/python-modules/sage-docbuild.nix

+2 −0
Original line number Diff line number Diff line
@@ -4,6 +4,7 @@ 
, jupyter-sphinx

, sphinx

, sphinx-copybutton

, sphinx-inline-tabs

}:



buildPythonPackage rec {
@@ -15,6 +16,7 @@ buildPythonPackage rec { 
    jupyter-sphinx

    sphinx

    sphinx-copybutton

    sphinx-inline-tabs

  ];



  preBuild = ''

pkgs/applications/science/math/sage/sage-env.nix

+3 −3
Original line number Diff line number Diff line
@@ -42,7 +42,7 @@ 
, flintqs

, blas

, lapack

, flint

, flint3

, gmp

, mpfr

, zlib
@@ -155,7 +155,7 @@ writeTextFile rec { 
    # cython needs to find these libraries, otherwise will fail with `ld: cannot find -lflint` or similar

    export LDFLAGS='${

      lib.concatStringsSep " " (map (pkg: "-L${pkg}/lib") [

        flint

        flint3

        gap

        glpk

        gmp
@@ -174,7 +174,7 @@ writeTextFile rec { 
        singular

        gmp.dev

        glpk

        flint

        flint3

        gap

        mpfr.dev

      ])