diff options
Diffstat (limited to 'pkgs/applications/science/math')
40 files changed, 78 insertions, 54 deletions
diff --git a/pkgs/applications/science/math/LiE/default.nix b/pkgs/applications/science/math/LiE/default.nix index d05cc90ca44c..7eb9edbb3b19 100644 --- a/pkgs/applications/science/math/LiE/default.nix +++ b/pkgs/applications/science/math/LiE/default.nix @@ -9,6 +9,7 @@ stdenv.mkDerivation { meta = { description = "A Computer algebra package for Lie group computations"; + mainProgram = "lie"; homepage = "http://wwwmathlabo.univ-poitiers.fr/~maavl/LiE/"; license = lib.licenses.lgpl3; # see the website diff --git a/pkgs/applications/science/math/R/default.nix b/pkgs/applications/science/math/R/default.nix index f4cc1f1fbfea..acfc38686ea4 100644 --- a/pkgs/applications/science/math/R/default.nix +++ b/pkgs/applications/science/math/R/default.nix @@ -15,13 +15,13 @@ assert (!blas.isILP64) && (!lapack.isILP64); stdenv.mkDerivation (finalAttrs: { pname = "R"; - version = "4.3.2"; + version = "4.3.3"; src = let inherit (finalAttrs) pname version; in fetchurl { url = "https://cran.r-project.org/src/base/R-${lib.versions.major version}/${pname}-${version}.tar.gz"; - sha256 = "sha256-s/V2CsLu6AJqPw7vyyW0dyPZeAOO7o6ER2IJTIYMRSo="; + sha256 = "sha256-gIUSMTk7hb84d+6eObKC51Dthkxexgy9aObhOfBSAzA="; }; outputs = [ "out" "tex" ]; diff --git a/pkgs/applications/science/math/almonds/default.nix b/pkgs/applications/science/math/almonds/default.nix index ec3891667c58..2b05b552253d 100644 --- a/pkgs/applications/science/math/almonds/default.nix +++ b/pkgs/applications/science/math/almonds/default.nix @@ -19,6 +19,7 @@ with python3.pkgs; buildPythonApplication rec { meta = with lib; { description = "Terminal Mandelbrot fractal viewer"; + mainProgram = "almonds"; homepage = "https://github.com/Tenchi2xh/Almonds"; license = licenses.mit; maintainers = with maintainers; [ infinisil ]; diff --git a/pkgs/applications/science/math/bcal/default.nix b/pkgs/applications/science/math/bcal/default.nix index fdf07a2a3299..9ba028d1cb65 100644 --- a/pkgs/applications/science/math/bcal/default.nix +++ b/pkgs/applications/science/math/bcal/default.nix @@ -29,6 +29,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Storage conversion and expression calculator"; + mainProgram = "bcal"; homepage = "https://github.com/jarun/bcal"; license = licenses.gpl3Only; platforms = platforms.unix; diff --git a/pkgs/applications/science/math/bliss/default.nix b/pkgs/applications/science/math/bliss/default.nix index 4fccc3a46403..33969c705d05 100644 --- a/pkgs/applications/science/math/bliss/default.nix +++ b/pkgs/applications/science/math/bliss/default.nix @@ -30,6 +30,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "An open source tool for computing automorphism groups and canonical forms of graphs. It has both a command line user interface as well as C++ and C programming language APIs"; + mainProgram = "bliss"; homepage = "http://www.tcs.hut.fi/Software/bliss/"; license = licenses.lgpl3; platforms = [ "i686-linux" "x86_64-linux" "aarch64-linux" ]; diff --git a/pkgs/applications/science/math/calc/default.nix b/pkgs/applications/science/math/calc/default.nix index 0f8982eac5b9..699f3d25caf7 100644 --- a/pkgs/applications/science/math/calc/default.nix +++ b/pkgs/applications/science/math/calc/default.nix @@ -56,6 +56,7 @@ stdenv.mkDerivation (finalAttrs: { meta = { homepage = "http://www.isthe.com/chongo/tech/comp/calc/"; description = "C-style arbitrary precision calculator"; + mainProgram = "calc"; changelog = "https://github.com/lcn2/calc/blob/v${finalAttrs.version}/CHANGES"; # The licensing situation depends on readline (see section 3 of the LGPL) # If linked against readline then GPLv2 otherwise LGPLv2.1 diff --git a/pkgs/applications/science/math/calculix/default.nix b/pkgs/applications/science/math/calculix/default.nix index 7a89fdd73c84..8af2ea9f4bce 100644 --- a/pkgs/applications/science/math/calculix/default.nix +++ b/pkgs/applications/science/math/calculix/default.nix @@ -37,6 +37,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "http://www.calculix.de/"; description = "Three-dimensional structural finite element program"; + mainProgram = "ccx"; license = licenses.gpl2Plus; maintainers = with maintainers; [ gebner ]; platforms = platforms.unix; diff --git a/pkgs/applications/science/math/cemu-ti/default.nix b/pkgs/applications/science/math/cemu-ti/default.nix index 2f2440eacfed..c8d5bea6f602 100644 --- a/pkgs/applications/science/math/cemu-ti/default.nix +++ b/pkgs/applications/science/math/cemu-ti/default.nix @@ -36,6 +36,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Third-party TI-84 Plus CE / TI-83 Premium CE emulator, focused on developer features"; + mainProgram = "CEmu"; homepage = "https://ce-programming.github.io/CEmu"; license = licenses.gpl3Plus; maintainers = with maintainers; [ luc65r ]; diff --git a/pkgs/applications/science/math/clp/default.nix b/pkgs/applications/science/math/clp/default.nix index 4cfff4702e69..06032b4a3182 100644 --- a/pkgs/applications/science/math/clp/default.nix +++ b/pkgs/applications/science/math/clp/default.nix @@ -20,6 +20,7 @@ stdenv.mkDerivation rec { license = licenses.epl20; homepage = "https://github.com/coin-or/Clp"; description = "An open-source linear programming solver written in C++"; + mainProgram = "clp"; platforms = platforms.darwin ++ platforms.linux; maintainers = [ maintainers.vbgl ]; }; diff --git a/pkgs/applications/science/math/ecm/default.nix b/pkgs/applications/science/math/ecm/default.nix index c59b1a8729a2..222db0e98e6a 100644 --- a/pkgs/applications/science/math/ecm/default.nix +++ b/pkgs/applications/science/math/ecm/default.nix @@ -23,6 +23,7 @@ stdenv.mkDerivation { meta = { description = "Elliptic Curve Method for Integer Factorization"; + mainProgram = "ecm"; license = lib.licenses.gpl2Plus; homepage = "http://ecm.gforge.inria.fr/"; maintainers = [ lib.maintainers.roconnor ]; diff --git a/pkgs/applications/science/math/eigenmath/default.nix b/pkgs/applications/science/math/eigenmath/default.nix index 674a5ea0d973..358e491b2f4a 100644 --- a/pkgs/applications/science/math/eigenmath/default.nix +++ b/pkgs/applications/science/math/eigenmath/default.nix @@ -7,13 +7,13 @@ stdenv.mkDerivation rec { pname = "eigenmath"; - version = "unstable-2024-03-11"; + version = "unstable-2024-03-20"; src = fetchFromGitHub { owner = "georgeweigt"; repo = pname; - rev = "dfa24af6c747e1c90d79a462c2a5a0716b3a1dc0"; - hash = "sha256-kgC+E/ecgl27Hs+qCyqg8CjbEyB91AgN397DST/dPMI="; + rev = "262a6525225be7bcef52c3072b1061db3c238055"; + hash = "sha256-QH8mLlcCOuq77vLer8RsSnD9VeJu9kAVv2qWAH3ky6I="; }; checkPhase = let emulator = stdenv.hostPlatform.emulator buildPackages; in '' @@ -40,6 +40,7 @@ stdenv.mkDerivation rec { meta = with lib;{ description = "Computer algebra system written in C"; + mainProgram = "eigenmath"; homepage = "https://georgeweigt.github.io"; license = licenses.bsd2; maintainers = with maintainers; [ nickcao ]; diff --git a/pkgs/applications/science/math/engauge-digitizer/default.nix b/pkgs/applications/science/math/engauge-digitizer/default.nix index 4c26dc2887c8..95306a0820fa 100644 --- a/pkgs/applications/science/math/engauge-digitizer/default.nix +++ b/pkgs/applications/science/math/engauge-digitizer/default.nix @@ -52,6 +52,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Engauge Digitizer is a tool for recovering graph data from an image file"; + mainProgram = "engauge"; homepage = "https://markummitchell.github.io/engauge-digitizer"; license = with licenses; [ gpl2Only ]; platforms = platforms.linux; diff --git a/pkgs/applications/science/math/getdp/default.nix b/pkgs/applications/science/math/getdp/default.nix index b5f4263c793d..d28f59e4be2f 100644 --- a/pkgs/applications/science/math/getdp/default.nix +++ b/pkgs/applications/science/math/getdp/default.nix @@ -2,10 +2,10 @@ stdenv.mkDerivation rec { pname = "getdp"; - version = "3.5.0"; + version = "3.6.0"; src = fetchurl { url = "http://getdp.info/src/getdp-${version}-source.tgz"; - sha256 = "sha256-C/dsSe+puIQBpFfBL3qr2XWXrUnvYy0/uTCKqOpDe9w="; + sha256 = "sha256-N1cb72W77Dr+TzeHpLgv5FuFb+SJqyGcfn+kOfEvZgA="; }; inherit (petsc) mpiSupport; @@ -17,6 +17,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "A General Environment for the Treatment of Discrete Problems"; + mainProgram = "getdp"; longDescription = '' GetDP is a free finite element solver using mixed elements to discretize de Rham-type complexes in one, two and three dimensions. The main diff --git a/pkgs/applications/science/math/glsurf/default.nix b/pkgs/applications/science/math/glsurf/default.nix index b4e8c6fb23db..d2ebba75638b 100644 --- a/pkgs/applications/science/math/glsurf/default.nix +++ b/pkgs/applications/science/math/glsurf/default.nix @@ -66,6 +66,7 @@ stdenv.mkDerivation rec { meta = { homepage = "https://raffalli.eu/~christophe/glsurf/"; description = "A program to draw implicit surfaces and curves"; + mainProgram = "glsurf"; license = lib.licenses.gpl2Plus; platforms = lib.platforms.all; }; diff --git a/pkgs/applications/science/math/gmsh/default.nix b/pkgs/applications/science/math/gmsh/default.nix index 62a0c3c405df..669d3a3ab8f1 100644 --- a/pkgs/applications/science/math/gmsh/default.nix +++ b/pkgs/applications/science/math/gmsh/default.nix @@ -64,6 +64,7 @@ stdenv.mkDerivation rec { meta = { description = "A three-dimensional finite element mesh generator"; + mainProgram = "gmsh"; homepage = "https://gmsh.info/"; license = lib.licenses.gpl2Plus; }; diff --git a/pkgs/applications/science/math/jags/default.nix b/pkgs/applications/science/math/jags/default.nix index 087807013694..50d7df24417a 100644 --- a/pkgs/applications/science/math/jags/default.nix +++ b/pkgs/applications/science/math/jags/default.nix @@ -17,6 +17,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Just Another Gibbs Sampler"; + mainProgram = "jags"; license = licenses.gpl2; homepage = "http://mcmc-jags.sourceforge.net"; maintainers = [ maintainers.andres ]; diff --git a/pkgs/applications/science/math/lp_solve/default.nix b/pkgs/applications/science/math/lp_solve/default.nix index ee54def6eb97..fdabc8896a58 100644 --- a/pkgs/applications/science/math/lp_solve/default.nix +++ b/pkgs/applications/science/math/lp_solve/default.nix @@ -59,6 +59,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "A Mixed Integer Linear Programming (MILP) solver"; + mainProgram = "lp_solve"; homepage = "https://lpsolve.sourceforge.net"; license = licenses.gpl2Plus; maintainers = with maintainers; [ smironov ]; diff --git a/pkgs/applications/science/math/msieve/default.nix b/pkgs/applications/science/math/msieve/default.nix index 6456608e7dbc..1de6d416a0e6 100644 --- a/pkgs/applications/science/math/msieve/default.nix +++ b/pkgs/applications/science/math/msieve/default.nix @@ -1,12 +1,13 @@ -{ lib, stdenv, fetchurl, zlib, gmp, ecm }: +{ lib, stdenv, fetchsvn, zlib, gmp, ecm }: stdenv.mkDerivation rec { pname = "msieve"; - version = "1.53"; + version = "r1050"; - src = fetchurl { - url = "mirror://sourceforge/msieve/msieve/Msieve%20v${version}/msieve${lib.replaceStrings ["."] [""] version}_src.tar.gz"; - sha256 = "1d1vv7j4rh3nnxsmvafi73qy7lw7n3akjlm5pjl3m936yapvmz65"; + src = fetchsvn { + url = "svn://svn.code.sf.net/p/msieve/code/trunk"; + rev = "1050"; + hash = "sha256-cn6OhE4zhrpB7BFrRdOnucjATbfo5mLkK7O0Usx1quE="; }; buildInputs = [ zlib gmp ecm ]; @@ -23,6 +24,7 @@ stdenv.mkDerivation rec { meta = { description = "A C library implementing a suite of algorithms to factor large integers"; + mainProgram = "msieve"; license = lib.licenses.publicDomain; homepage = "http://msieve.sourceforge.net/"; maintainers = [ lib.maintainers.roconnor ]; diff --git a/pkgs/applications/science/math/nauty/default.nix b/pkgs/applications/science/math/nauty/default.nix index ef8c041039b1..c1feeffdcb6d 100644 --- a/pkgs/applications/science/math/nauty/default.nix +++ b/pkgs/applications/science/math/nauty/default.nix @@ -4,11 +4,11 @@ }: stdenv.mkDerivation rec { pname = "nauty"; - version = "2.7r4"; + version = "2.8.8"; src = fetchurl { - url = "https://pallini.di.uniroma1.it/nauty${builtins.replaceStrings ["."] [""] version}.tar.gz"; - sha256 = "sha256-uBDIWm/imfO0yfJKr5KcrH+VRsLzXCDh3Qrbx0CISKY="; + url = "https://pallini.di.uniroma1.it/nauty${builtins.replaceStrings ["."] ["_"] version}.tar.gz"; + sha256 = "sha256-FZ0hVoEKa7JAQQzWHrZBrdhQiNnxXIiM2qN7hoH5Kc4="; }; outputs = [ "out" "dev" ]; @@ -44,7 +44,7 @@ stdenv.mkDerivation rec { # I'm not sure if the filename will remain the same for future changelog or # if it will track changes to minor releases. Lets see. Better than nothing # in any case. - changelog = "https://pallini.di.uniroma1.it/changes24-27.txt"; + changelog = "https://pallini.di.uniroma1.it/changes24-28.txt"; homepage = "https://pallini.di.uniroma1.it/"; }; } diff --git a/pkgs/applications/science/math/nota/default.nix b/pkgs/applications/science/math/nota/default.nix index 897785ef6e8b..810d7d6d72bc 100644 --- a/pkgs/applications/science/math/nota/default.nix +++ b/pkgs/applications/science/math/nota/default.nix @@ -37,4 +37,5 @@ mkDerivation rec { homepage = "https://kary.us/nota"; license = lib.licenses.mpl20; maintainers = with lib.maintainers; [ dtzWill ]; + mainProgram = "nota"; } diff --git a/pkgs/applications/science/math/palp/default.nix b/pkgs/applications/science/math/palp/default.nix index ffe17bc3dec2..2fe77aa14a65 100644 --- a/pkgs/applications/science/math/palp/default.nix +++ b/pkgs/applications/science/math/palp/default.nix @@ -10,11 +10,11 @@ let in stdenv.mkDerivation rec { pname = "palp"; - version = "2.20"; + version = "2.21"; src = fetchurl { url = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/palp/${pname}-${version}.tar.gz"; - sha256 = "1q1cl3vpdir16szy0jcadysydcrjp48hqxyx42kr8g9digkqjgkj"; + sha256 = "sha256-fkp78hmZioRMC8zgoXbknQdDy0tQWg4ZUym/LsGW3dc="; }; hardeningDisable = [ diff --git a/pkgs/applications/science/math/pcalc/default.nix b/pkgs/applications/science/math/pcalc/default.nix index 97888b712eb1..64ab5acebed2 100644 --- a/pkgs/applications/science/math/pcalc/default.nix +++ b/pkgs/applications/science/math/pcalc/default.nix @@ -19,6 +19,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://vapier.github.io/pcalc/"; description = "Programmer's calculator"; + mainProgram = "pcalc"; license = licenses.gpl2Plus; maintainers = with maintainers; [ ftrvxmtrx ]; platforms = platforms.unix; diff --git a/pkgs/applications/science/math/perseus/default.nix b/pkgs/applications/science/math/perseus/default.nix index bbfc8aed4428..9a37eeac66da 100644 --- a/pkgs/applications/science/math/perseus/default.nix +++ b/pkgs/applications/science/math/perseus/default.nix @@ -25,6 +25,7 @@ stdenv.mkDerivation { meta = { description = "The Persistent Homology Software"; + mainProgram = "perseus"; longDescription = '' Persistent homology - or simply, persistence - is an algebraic topological invariant of a filtered cell complex. Perseus diff --git a/pkgs/applications/science/math/programmer-calculator/default.nix b/pkgs/applications/science/math/programmer-calculator/default.nix index ee48a1d0f1a3..9cb220ceca6a 100644 --- a/pkgs/applications/science/math/programmer-calculator/default.nix +++ b/pkgs/applications/science/math/programmer-calculator/default.nix @@ -21,6 +21,7 @@ gccStdenv.mkDerivation rec { meta = with lib; { description = "A terminal calculator for programmers"; + mainProgram = "pcalc"; longDescription = '' Terminal calculator made for programmers working with multiple number representations, sizes, and overall close to the bits diff --git a/pkgs/applications/science/math/ratpoints/default.nix b/pkgs/applications/science/math/ratpoints/default.nix index 42e6b7d00a5e..69b972fe9790 100644 --- a/pkgs/applications/science/math/ratpoints/default.nix +++ b/pkgs/applications/science/math/ratpoints/default.nix @@ -27,6 +27,7 @@ stdenv.mkDerivation rec { meta = { description = "A program to find rational points on hyperelliptic curves"; + mainProgram = "ratpoints"; license = lib.licenses.gpl2Plus; maintainers = [lib.maintainers.raskin]; platforms = lib.platforms.unix; diff --git a/pkgs/applications/science/math/ries/default.nix b/pkgs/applications/science/math/ries/default.nix index eb759723256d..5c0626913e3c 100644 --- a/pkgs/applications/science/math/ries/default.nix +++ b/pkgs/applications/science/math/ries/default.nix @@ -14,6 +14,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://mrob.com/pub/ries/"; description = "Tool to produce a list of equations that approximately solve to a given number"; + mainProgram = "ries"; platforms = platforms.all; maintainers = with maintainers; [ symphorien ]; license = licenses.gpl3Plus; diff --git a/pkgs/applications/science/math/ripser/default.nix b/pkgs/applications/science/math/ripser/default.nix index 50ccee58f503..83cf6bc51aa4 100644 --- a/pkgs/applications/science/math/ripser/default.nix +++ b/pkgs/applications/science/math/ripser/default.nix @@ -50,6 +50,7 @@ stdenv.mkDerivation { meta = { description = "A lean C++ code for the computation of Vietoris–Rips persistence barcodes"; + mainProgram = "ripser"; homepage = "https://github.com/Ripser/ripser"; license = lib.licenses.lgpl3; maintainers = with lib.maintainers; [erikryb]; diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix index 765c691c9555..6624dcc36528 100644 --- a/pkgs/applications/science/math/sage/default.nix +++ b/pkgs/applications/science/math/sage/default.nix @@ -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. diff --git a/pkgs/applications/science/math/sage/env-locations.nix b/pkgs/applications/science/math/sage/env-locations.nix index 39d358a1f9a8..1ca0f471a7ee 100644 --- a/pkgs/applications/science/math/sage/env-locations.nix +++ b/pkgs/applications/science/math/sage/env-locations.nix @@ -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" diff --git a/pkgs/applications/science/math/sage/python-modules/sage-docbuild.nix b/pkgs/applications/science/math/sage/python-modules/sage-docbuild.nix index fb8c3ec8a204..b45998bbcb86 100644 --- a/pkgs/applications/science/math/sage/python-modules/sage-docbuild.nix +++ b/pkgs/applications/science/math/sage/python-modules/sage-docbuild.nix @@ -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 = '' diff --git a/pkgs/applications/science/math/sage/sage-env.nix b/pkgs/applications/science/math/sage/sage-env.nix index 4c22470de910..4f179ea3a42b 100644 --- a/pkgs/applications/science/math/sage/sage-env.nix +++ b/pkgs/applications/science/math/sage/sage-env.nix @@ -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 ]) diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix index a77565e4072a..11bcc9ee3d5a 100644 --- a/pkgs/applications/science/math/sage/sage-src.nix +++ b/pkgs/applications/science/math/sage/sage-src.nix @@ -10,14 +10,14 @@ # all get the same sources with the same patches applied. stdenv.mkDerivation rec { - version = "10.2"; + version = "10.3"; pname = "sage-src"; src = fetchFromGitHub { owner = "sagemath"; repo = "sage"; rev = version; - sha256 = "sha256-VXnPdJhtw5Y/anecrVpevJDCyBVfnjksyuuZslNipm4="; + hash = "sha256-OHtMv8t0RrP6R8XIREU+C1vpazeQLWa75wx9Mv6BN1U="; }; # contains essential files (e.g., setup.cfg) generated by the bootstrap script. @@ -25,8 +25,8 @@ stdenv.mkDerivation rec { configure-src = fetchurl { # the hash below is the tagged commit's _parent_. it can also be found by looking for # the "configure" asset at https://github.com/sagemath/sage/releases/tag/${version} - url = "mirror://sageupstream/configure/configure-b2813506039143e6f0abe859ab67a343abf72c2e.tar.gz"; - sha256 = "sha256-a1v0XyoKI+zO6Sjm8DzEwItRHbIgRDbpj4UfwVH+/hw="; + url = "mirror://sageupstream/configure/configure-ab1a517b64b02bf15bbcb8d7c2d4d643bd5eff9b.tar.gz"; + hash = "sha256-pe9AxTM+gFSR4/eVfUzay+4bwjoubbYeDPc+avKjlaw="; }; # Patches needed because of particularities of nix or the way this is packaged. @@ -62,11 +62,11 @@ stdenv.mkDerivation rec { # should come from or be proposed to upstream. This list will probably never # be empty since dependencies update all the time. packageUpgradePatches = [ - # https://github.com/sagemath/sage/pull/37123, to land in 10.3.beta7 + # https://github.com/sagemath/sage/pull/37492 (fetchpatch { - name = "scipy-1.12-upgrade.patch"; - url = "https://github.com/sagemath/sage/commit/54eec464e9fdf18b411d9148aecb918178e95909.diff"; - sha256 = "sha256-9wyNrcSfF6mYFTIV4ev2OdD7igb0AeyZZYWSc/+JrIU="; + name = "singular-4.3.2p14-upgrade.patch"; + url = "https://github.com/sagemath/sage/commit/a0c56816b051e97da44ac0a4e4d4f6915cf7fa0f.diff"; + sha256 = "sha256-WGMmPeBoj2LUC+2qxWuaJL89QUuGt6axGvxWkpM9LYg="; }) ]; diff --git a/pkgs/applications/science/math/sage/sage.nix b/pkgs/applications/science/math/sage/sage.nix index 227e4bbdbfdb..81b55e841d24 100644 --- a/pkgs/applications/science/math/sage/sage.nix +++ b/pkgs/applications/science/math/sage/sage.nix @@ -56,6 +56,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab"; + mainProgram = "sage"; homepage = "https://www.sagemath.org"; license = licenses.gpl2Plus; maintainers = teams.sage.members; diff --git a/pkgs/applications/science/math/sage/sagelib.nix b/pkgs/applications/science/math/sage/sagelib.nix index 5a1f4ee473c9..b67b74e3a0f2 100644 --- a/pkgs/applications/science/math/sage/sagelib.nix +++ b/pkgs/applications/science/math/sage/sagelib.nix @@ -10,7 +10,6 @@ , iml , libpng , readline -, arb , blas , boost , brial @@ -18,7 +17,7 @@ , eclib , ecm , fflas-ffpack -, flint +, flint3 , gap , giac , givaro @@ -45,6 +44,7 @@ , singular , sqlite , symmetrica +, conway-polynomials , cvxopt , cypari2 , cysignals @@ -92,6 +92,7 @@ buildPythonPackage rec { version = src.version; pname = "sagelib"; src = sage-src; + pyproject = true; nativeBuildInputs = [ iml @@ -112,7 +113,6 @@ buildPythonPackage rec { propagatedBuildInputs = [ # native dependencies (TODO: determine which ones need to be propagated) - arb blas boost brial @@ -120,7 +120,7 @@ buildPythonPackage rec { eclib ecm fflas-ffpack - flint + flint3 gap giac givaro @@ -149,6 +149,7 @@ buildPythonPackage rec { symmetrica # from src/sage/setup.cfg and requirements.txt + conway-polynomials cvxopt cypari2 cysignals @@ -202,11 +203,7 @@ buildPythonPackage rec { mkdir -p "$SAGE_SHARE/sage/ext/notebook-ipython" mkdir -p "var/lib/sage/installed" - # version lower bounds are useful, but upper bounds are a hassle because - # Sage tests already catch any relevant API breakage. - # according to the discussion at https://trac.sagemath.org/ticket/33520, - # upper bounds will be less noisy starting from Sage 9.6. - sed -i 's/, <[^, ]*//' build/pkgs/*/install-requires.txt + sed -i "/sage-conf/d" src/{setup.cfg,pyproject.toml,requirements.txt} cd build/pkgs/sagelib/src ''; diff --git a/pkgs/applications/science/math/scalp/default.nix b/pkgs/applications/science/math/scalp/default.nix index 4145407d7aaa..fc230a11966f 100644 --- a/pkgs/applications/science/math/scalp/default.nix +++ b/pkgs/applications/science/math/scalp/default.nix @@ -50,6 +50,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Scalable Linear Programming Library"; + mainProgram = "scalp"; homepage = "https://digidev.digi.e-technik.uni-kassel.de/scalp/"; license = licenses.lgpl3; platforms = platforms.unix; diff --git a/pkgs/applications/science/math/singular/default.nix b/pkgs/applications/science/math/singular/default.nix index f77bd5a92243..a6c64066d88e 100644 --- a/pkgs/applications/science/math/singular/default.nix +++ b/pkgs/applications/science/math/singular/default.nix @@ -5,7 +5,7 @@ , sharutils , file , getconf -, flint +, flint3 , ntl , cddlib , gfan @@ -18,13 +18,13 @@ # want it to match the upstream format because sage depends on it. , texinfo4 , texliveSmall -, enableDocs ? !stdenv.isDarwin +, enableDocs ? true , enableGfanlib ? true }: stdenv.mkDerivation rec { pname = "singular"; - version = "4.3.2p2"; + version = "4.3.2p16"; # since the tarball does not contain tests, we fetch from GitHub. src = fetchFromGitHub { @@ -34,7 +34,7 @@ stdenv.mkDerivation rec { # if a release is tagged (which sometimes does not happen), it will # be in the format below. rev = "Release-${lib.replaceStrings ["."] ["-"] version}"; - sha256 = "sha256-dtZmN8xUCZ9eSgmtBxqfJeWsM4W5Baq7xWXuNAxNLjA="; + sha256 = "sha256-5JZgI5lnfX4JlBSEAL7Wv6uao/57GBaMqwgslJt9Bjk="; # the repository's .gitattributes file contains the lines "/Tst/ # export-ignore" and "/doc/ export-ignore" so some directories are @@ -68,7 +68,7 @@ stdenv.mkDerivation rec { ncurses readline ntl - flint + flint3 lrcalc gfan ] ++ lib.optionals enableGfanlib [ diff --git a/pkgs/applications/science/math/speedcrunch/default.nix b/pkgs/applications/science/math/speedcrunch/default.nix index 98bc6b031f19..a77474b86ffa 100644 --- a/pkgs/applications/science/math/speedcrunch/default.nix +++ b/pkgs/applications/science/math/speedcrunch/default.nix @@ -23,6 +23,7 @@ mkDerivation rec { homepage = "http://speedcrunch.org"; license = licenses.gpl2Plus; description = "A fast power user calculator"; + mainProgram = "speedcrunch"; longDescription = '' SpeedCrunch is a fast, high precision and powerful desktop calculator. Among its distinctive features are a scrollable display, up to 50 decimal diff --git a/pkgs/applications/science/math/weka/default.nix b/pkgs/applications/science/math/weka/default.nix index 004060f832c2..6f907ba9c0c3 100644 --- a/pkgs/applications/science/math/weka/default.nix +++ b/pkgs/applications/science/math/weka/default.nix @@ -24,6 +24,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://www.cs.waikato.ac.nz/ml/weka/"; description = "Collection of machine learning algorithms for data mining tasks"; + mainProgram = "weka"; sourceProvenance = with sourceTypes; [ binaryBytecode ]; license = licenses.gpl2Plus; maintainers = [ maintainers.mimame ]; diff --git a/pkgs/applications/science/math/wxmaxima/default.nix b/pkgs/applications/science/math/wxmaxima/default.nix index 057a11fa3cdd..4d2815d12997 100644 --- a/pkgs/applications/science/math/wxmaxima/default.nix +++ b/pkgs/applications/science/math/wxmaxima/default.nix @@ -46,6 +46,7 @@ stdenv.mkDerivation (finalAttrs:{ meta = with lib; { description = "Cross platform GUI for the computer algebra system Maxima"; + mainProgram = "wxmaxima"; license = licenses.gpl2; homepage = "https://wxmaxima-developers.github.io/wxmaxima/"; maintainers = with maintainers; [ doronbehar ]; diff --git a/pkgs/applications/science/math/zegrapher/default.nix b/pkgs/applications/science/math/zegrapher/default.nix index 32633eb8015d..2beaf5757a55 100644 --- a/pkgs/applications/science/math/zegrapher/default.nix +++ b/pkgs/applications/science/math/zegrapher/default.nix @@ -26,6 +26,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://zegrapher.com/"; description = "An open source math plotter"; + mainProgram = "ZeGrapher"; longDescription = '' An open source, free and easy to use math plotter. It can plot functions, sequences, parametric equations and data on the plane. |