Mauricio Collares
GitHub
commit
e21968aa89
16 changed files with 66 additions and 87 deletions
|
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@ -4,11 +4,11 @@
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}:
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stdenv.mkDerivation rec {
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pname = "nauty";
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version = "2.7r4";
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version = "2.8.8";
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src = fetchurl {
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url = "https://pallini.di.uniroma1.it/nauty${builtins.replaceStrings ["."] [""] version}.tar.gz";
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sha256 = "sha256-uBDIWm/imfO0yfJKr5KcrH+VRsLzXCDh3Qrbx0CISKY=";
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url = "https://pallini.di.uniroma1.it/nauty${builtins.replaceStrings ["."] ["_"] version}.tar.gz";
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sha256 = "sha256-FZ0hVoEKa7JAQQzWHrZBrdhQiNnxXIiM2qN7hoH5Kc4=";
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};
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outputs = [ "out" "dev" ];
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@ -44,7 +44,7 @@ stdenv.mkDerivation rec {
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# I'm not sure if the filename will remain the same for future changelog or
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# if it will track changes to minor releases. Lets see. Better than nothing
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# in any case.
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changelog = "https://pallini.di.uniroma1.it/changes24-27.txt";
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changelog = "https://pallini.di.uniroma1.it/changes24-28.txt";
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homepage = "https://pallini.di.uniroma1.it/";
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};
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}
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@ -15,7 +15,7 @@ let
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pkgs = pkgs.python3.pkgs.overrideScope (self: super: {
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# `sagelib`, i.e. all of sage except some wrappers and runtime dependencies
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sagelib = self.callPackage ./sagelib.nix {
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inherit flint arb;
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inherit flint3;
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inherit sage-src env-locations singular;
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inherit (maxima) lisp-compiler;
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linbox = pkgs.linbox.override { withSage = true; };
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@ -73,7 +73,7 @@ let
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sagelib = python3.pkgs.sagelib;
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sage-docbuild = python3.pkgs.sage-docbuild;
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inherit env-locations;
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inherit python3 singular palp flint pythonEnv maxima;
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inherit python3 singular palp flint3 pythonEnv maxima;
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pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config
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};
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@ -125,9 +125,7 @@ let
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ignoreCollisions = true;
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} // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible
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arb = pkgs.arb.override { inherit flint; };
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singular = pkgs.singular.override { inherit flint; };
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singular = pkgs.singular.override { inherit flint3; };
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maxima = pkgs.maxima-ecl.override {
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lisp-compiler = pkgs.ecl.override {
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@ -149,7 +147,7 @@ let
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# openblas instead of openblasCompat. Apparently other packages somehow use flints
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# blas when it is available. Alternative would be to override flint to use
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# openblasCompat.
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flint = pkgs.flint.override { withBlas = false; };
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flint3 = pkgs.flint3.override { withBlas = false; };
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# Multiple palp dimensions need to be available and sage expects them all to be
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# in the same folder.
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@ -3,7 +3,6 @@
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, pari
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, singular
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, maxima
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, conway_polynomials
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, graphs
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, elliptic_curves
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, polytopes_db
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@ -27,16 +26,13 @@ writeTextFile rec {
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export GPDOCDIR="${pari}/share/pari/doc"
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export SINGULARPATH='${singular}/share/singular'
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export SINGULAR_SO='${singular}/lib/libSingular.so'
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export GAP_SO='${gap}/lib/libgap.so'
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export SINGULAR_EXECUTABLE='${singular}/bin/Singular'
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export MAXIMA_FAS='${maxima}/lib/maxima/${maxima.version}/binary-ecl/maxima.fas'
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export MAXIMA_PREFIX="${maxima}"
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export CONWAY_POLYNOMIALS_DATA_DIR='${conway_polynomials}/share/conway_polynomials'
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export GRAPHS_DATA_DIR='${graphs}/share/graphs'
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export ELLCURVE_DATA_DIR='${elliptic_curves}/share/ellcurves'
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export POLYTOPE_DATA_DIR='${polytopes_db}/share/reflexive_polytopes'
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export GAP_LIB_DIR='${gap}/lib/gap'
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export GAP_SHARE_DIR='${gap}/share/gap'
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export GAP_ROOT_PATHS='${gap}/lib/gap;${gap}/share/gap'
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export ECLDIR='${maxima.lisp-compiler}/lib/${maxima.lisp-compiler.pname}-${maxima.lisp-compiler.version}/'
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export COMBINATORIAL_DESIGN_DATA_DIR="${combinatorial_designs}/share/combinatorial_designs"
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export CREMONA_MINI_DATA_DIR="${elliptic_curves}/share/cremona"
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@ -4,6 +4,7 @@
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, jupyter-sphinx
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, sphinx
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, sphinx-copybutton
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, sphinx-inline-tabs
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}:
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buildPythonPackage rec {
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@ -15,6 +16,7 @@ buildPythonPackage rec {
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jupyter-sphinx
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sphinx
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sphinx-copybutton
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sphinx-inline-tabs
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];
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preBuild = ''
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@ -42,7 +42,7 @@
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, flintqs
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, blas
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, lapack
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, flint
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, flint3
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, gmp
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, mpfr
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, zlib
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@ -155,7 +155,7 @@ writeTextFile rec {
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# cython needs to find these libraries, otherwise will fail with `ld: cannot find -lflint` or similar
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export LDFLAGS='${
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lib.concatStringsSep " " (map (pkg: "-L${pkg}/lib") [
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flint
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flint3
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gap
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glpk
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gmp
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@ -174,7 +174,7 @@ writeTextFile rec {
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singular
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gmp.dev
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glpk
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flint
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flint3
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gap
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mpfr.dev
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])
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@ -10,14 +10,14 @@
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# all get the same sources with the same patches applied.
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stdenv.mkDerivation rec {
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version = "10.2";
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version = "10.3";
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pname = "sage-src";
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src = fetchFromGitHub {
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owner = "sagemath";
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repo = "sage";
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rev = version;
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sha256 = "sha256-VXnPdJhtw5Y/anecrVpevJDCyBVfnjksyuuZslNipm4=";
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hash = "sha256-OHtMv8t0RrP6R8XIREU+C1vpazeQLWa75wx9Mv6BN1U=";
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};
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# contains essential files (e.g., setup.cfg) generated by the bootstrap script.
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@ -25,8 +25,8 @@ stdenv.mkDerivation rec {
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configure-src = fetchurl {
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# the hash below is the tagged commit's _parent_. it can also be found by looking for
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# the "configure" asset at https://github.com/sagemath/sage/releases/tag/${version}
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url = "mirror://sageupstream/configure/configure-b2813506039143e6f0abe859ab67a343abf72c2e.tar.gz";
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sha256 = "sha256-a1v0XyoKI+zO6Sjm8DzEwItRHbIgRDbpj4UfwVH+/hw=";
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url = "mirror://sageupstream/configure/configure-ab1a517b64b02bf15bbcb8d7c2d4d643bd5eff9b.tar.gz";
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hash = "sha256-pe9AxTM+gFSR4/eVfUzay+4bwjoubbYeDPc+avKjlaw=";
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};
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# Patches needed because of particularities of nix or the way this is packaged.
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@ -62,11 +62,11 @@ stdenv.mkDerivation rec {
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# should come from or be proposed to upstream. This list will probably never
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# be empty since dependencies update all the time.
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packageUpgradePatches = [
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# https://github.com/sagemath/sage/pull/37123, to land in 10.3.beta7
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# https://github.com/sagemath/sage/pull/37492
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(fetchpatch {
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name = "scipy-1.12-upgrade.patch";
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url = "https://github.com/sagemath/sage/commit/54eec464e9fdf18b411d9148aecb918178e95909.diff";
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sha256 = "sha256-9wyNrcSfF6mYFTIV4ev2OdD7igb0AeyZZYWSc/+JrIU=";
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name = "singular-4.3.2p14-upgrade.patch";
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url = "https://github.com/sagemath/sage/commit/a0c56816b051e97da44ac0a4e4d4f6915cf7fa0f.diff";
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sha256 = "sha256-WGMmPeBoj2LUC+2qxWuaJL89QUuGt6axGvxWkpM9LYg=";
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})
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];
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@ -10,7 +10,6 @@
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, iml
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, libpng
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, readline
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, arb
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, blas
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, boost
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, brial
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@ -18,7 +17,7 @@
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, eclib
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, ecm
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, fflas-ffpack
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, flint
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, flint3
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, gap
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, giac
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, givaro
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@ -45,6 +44,7 @@
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, singular
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, sqlite
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, symmetrica
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, conway-polynomials
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, cvxopt
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, cypari2
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, cysignals
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@ -92,6 +92,7 @@ buildPythonPackage rec {
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version = src.version;
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pname = "sagelib";
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src = sage-src;
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pyproject = true;
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nativeBuildInputs = [
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iml
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@ -112,7 +113,6 @@ buildPythonPackage rec {
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propagatedBuildInputs = [
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# native dependencies (TODO: determine which ones need to be propagated)
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arb
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blas
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boost
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brial
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@ -120,7 +120,7 @@ buildPythonPackage rec {
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eclib
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ecm
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fflas-ffpack
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flint
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flint3
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gap
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giac
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givaro
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@ -149,6 +149,7 @@ buildPythonPackage rec {
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symmetrica
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# from src/sage/setup.cfg and requirements.txt
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conway-polynomials
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cvxopt
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cypari2
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cysignals
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@ -202,11 +203,7 @@ buildPythonPackage rec {
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mkdir -p "$SAGE_SHARE/sage/ext/notebook-ipython"
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mkdir -p "var/lib/sage/installed"
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# version lower bounds are useful, but upper bounds are a hassle because
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# Sage tests already catch any relevant API breakage.
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# according to the discussion at https://trac.sagemath.org/ticket/33520,
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# upper bounds will be less noisy starting from Sage 9.6.
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sed -i 's/, <[^, ]*//' build/pkgs/*/install-requires.txt
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sed -i "/sage-conf/d" src/{setup.cfg,pyproject.toml,requirements.txt}
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cd build/pkgs/sagelib/src
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'';
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|
|
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@ -5,7 +5,7 @@
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, sharutils
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, file
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, getconf
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, flint
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, flint3
|
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, ntl
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, cddlib
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, gfan
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@ -18,13 +18,13 @@
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# want it to match the upstream format because sage depends on it.
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, texinfo4
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, texliveSmall
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, enableDocs ? !stdenv.isDarwin
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, enableDocs ? true
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, enableGfanlib ? true
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}:
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stdenv.mkDerivation rec {
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pname = "singular";
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version = "4.3.2p2";
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version = "4.3.2p16";
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|
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# since the tarball does not contain tests, we fetch from GitHub.
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src = fetchFromGitHub {
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|
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@ -34,7 +34,7 @@ stdenv.mkDerivation rec {
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# if a release is tagged (which sometimes does not happen), it will
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# be in the format below.
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rev = "Release-${lib.replaceStrings ["."] ["-"] version}";
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sha256 = "sha256-dtZmN8xUCZ9eSgmtBxqfJeWsM4W5Baq7xWXuNAxNLjA=";
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||||
sha256 = "sha256-5JZgI5lnfX4JlBSEAL7Wv6uao/57GBaMqwgslJt9Bjk=";
|
||||
|
||||
# the repository's .gitattributes file contains the lines "/Tst/
|
||||
# export-ignore" and "/doc/ export-ignore" so some directories are
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||||
|
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@ -68,7 +68,7 @@ stdenv.mkDerivation rec {
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|||
ncurses
|
||||
readline
|
||||
ntl
|
||||
flint
|
||||
flint3
|
||||
lrcalc
|
||||
gfan
|
||||
] ++ lib.optionals enableGfanlib [
|
||||
|
|
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|||
|
|
@ -1,41 +0,0 @@
|
|||
{ lib, stdenv
|
||||
, fetchurl
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||||
, python3
|
||||
}:
|
||||
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||||
stdenv.mkDerivation rec {
|
||||
pname = "conway_polynomials";
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||||
version = "0.5";
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||||
|
||||
src = fetchurl {
|
||||
url = "mirror://sageupstream/conway_polynomials/conway_polynomials-${version}.tar.bz2";
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||||
sha256 = "05zb1ly9x2bbscqv0jgc45g48xx77mfs7qdbqhn4ihmihn57iwnq";
|
||||
};
|
||||
|
||||
# Script that creates the "database" (nested python array) and pickles it
|
||||
spkg-install = fetchurl {
|
||||
url = "https://raw.githubusercontent.com/sagemath/sage/9.2/build/pkgs/conway_polynomials/spkg-install.py";
|
||||
sha256 = "1bwnqasnyv793hxg29viing4dnliz29grkhldsirq19d509yk1fs";
|
||||
};
|
||||
|
||||
installPhase = ''
|
||||
# directory layout as spkg-install.py expects
|
||||
dir="$PWD"
|
||||
cd ..
|
||||
ln -s "$dir" "src"
|
||||
|
||||
# environment spkg-install.py expects
|
||||
mkdir -p "$out/share"
|
||||
export SAGE_SHARE="$out/share"
|
||||
export PYTHONPATH=$PWD
|
||||
|
||||
${python3.interpreter} ${spkg-install}
|
||||
'';
|
||||
|
||||
meta = with lib; {
|
||||
description = "Contains a small database of Conway polynomials";
|
||||
license = licenses.gpl2;
|
||||
platforms = platforms.all;
|
||||
maintainers = teams.sage.members;
|
||||
};
|
||||
}
|
||||
|
|
@ -31,6 +31,7 @@ stdenv.mkDerivation rec {
|
|||
configureFlags = [
|
||||
"--with-blas-libs=-lcblas"
|
||||
"--with-lapack-libs=-llapacke"
|
||||
"--without-archnative"
|
||||
] ++ lib.optionals stdenv.isx86_64 [
|
||||
# disable SIMD instructions (which are enabled *when available* by default)
|
||||
# for now we need to be careful to disable *all* relevant versions of an instruction set explicitly (https://github.com/linbox-team/fflas-ffpack/issues/284)
|
||||
|
|
|
|||
|
|
@ -24,16 +24,19 @@ stdenv.mkDerivation rec {
|
|||
sha256 = "sha256-ezEaAFA6hjiB64F32+uEMi8pOZ89fXLzsaTJuh1XlLQ=";
|
||||
};
|
||||
|
||||
propagatedBuildInputs = [
|
||||
nativeBuildInputs = [
|
||||
autoconf
|
||||
automake
|
||||
gettext
|
||||
libtool
|
||||
];
|
||||
|
||||
propagatedBuildInputs = [
|
||||
mpfr
|
||||
];
|
||||
|
||||
buildInputs = [
|
||||
gmp
|
||||
mpfr
|
||||
] ++ lib.optionals withBlas [
|
||||
openblas
|
||||
] ++ lib.optionals withNtl [
|
||||
|
|
|
|||
|
|
@ -34,7 +34,7 @@ stdenv.mkDerivation rec {
|
|||
propagatedBuildInputs = [ gmpxx ];
|
||||
|
||||
configureFlags = [
|
||||
"--disable-optimization"
|
||||
"--without-archnative"
|
||||
] ++ lib.optionals stdenv.isx86_64 [
|
||||
# disable SIMD instructions (which are enabled *when available* by default)
|
||||
"--${if stdenv.hostPlatform.sse3Support then "enable" else "disable"}-sse3"
|
||||
|
|
|
|||
|
|
@ -37,7 +37,7 @@ stdenv.mkDerivation rec {
|
|||
|
||||
configureFlags = [
|
||||
"--with-blas-libs=-lblas"
|
||||
"--disable-optimization"
|
||||
"--without-archnative"
|
||||
] ++ lib.optionals stdenv.isx86_64 [
|
||||
# disable SIMD instructions (which are enabled *when available* by default)
|
||||
"--${if stdenv.hostPlatform.sse3Support then "enable" else "disable"}-sse3"
|
||||
|
|
|
|||
|
|
@ -0,0 +1,23 @@
|
|||
{ lib
|
||||
, fetchPypi
|
||||
, buildPythonPackage
|
||||
}:
|
||||
|
||||
buildPythonPackage rec {
|
||||
pname = "conway-polynomials";
|
||||
version = "0.9";
|
||||
|
||||
src = fetchPypi {
|
||||
inherit pname version;
|
||||
hash = "sha256-btIwBgm8558BddW4VGhY7sAoVPi+MjfbjRRJzMzBxYE=";
|
||||
};
|
||||
|
||||
pythonImportsCheck = [ "conway_polynomials" ];
|
||||
|
||||
meta = with lib; {
|
||||
description = "Python interface to Frank Lübeck's Conway polynomial database";
|
||||
homepage = "https://github.com/sagemath/conway-polynomials";
|
||||
maintainers = teams.sage.members;
|
||||
license = licenses.gpl3Plus;
|
||||
};
|
||||
}
|
||||
|
|
@ -28821,8 +28821,6 @@ with pkgs;
|
|||
|
||||
commit-mono = callPackage ../data/fonts/commit-mono { };
|
||||
|
||||
conway_polynomials = callPackage ../data/misc/conway_polynomials { };
|
||||
|
||||
cooper-hewitt = callPackage ../data/fonts/cooper-hewitt { };
|
||||
|
||||
d2coding = callPackage ../data/fonts/d2coding { };
|
||||
|
|
|
|||
|
|
@ -1955,6 +1955,8 @@ self: super: with self; {
|
|||
|
||||
connio = callPackage ../development/python-modules/connio { };
|
||||
|
||||
conway-polynomials = callPackage ../development/python-modules/conway-polynomials {};
|
||||
|
||||
correctionlib = callPackage ../development/python-modules/correctionlib { };
|
||||
|
||||
coqpit = callPackage ../development/python-modules/coqpit { };
|
||||
|
|
|
|||
Loading…
Reference in a new issue