Rebase onto e4ad989506ec7d71f7302cc3067abd82730a4beb HEAD rootfs

Signed-off-by: Alyssa Ross <hi@alyssa.is>

19 files changed, 76 insertions, 171 deletions

diff --git a/pkgs/applications/science/math/R/default.nix b/pkgs/applications/science/math/R/default.nix
index d3ca419c48d..f4cc1f1fbfe 100644
--- a/pkgs/applications/science/math/R/default.nix
+++ b/pkgs/applications/science/math/R/default.nix
@@ -1,5 +1,5 @@
 { lib, stdenv, fetchurl, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng
-, libtiff, ncurses, pango, pcre2, perl, readline, tcl, texlive, texLive, tk, xz, zlib
+, libtiff, ncurses, pango, pcre2, perl, readline, tcl, texlive, texliveSmall, tk, xz, zlib
 , less, texinfo, graphviz, icu, pkg-config, bison, imake, which, jdk, blas, lapack
 , curl, Cocoa, Foundation, libobjc, libcxx, tzdata
 , withRecommendedPackages ? true
@@ -15,13 +15,13 @@ assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "R";
-  version = "4.3.1";
+  version = "4.3.2";
 
   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-jdC/JPECPG9hjDsxc4PSkbSklPQNc7mDrCL/6pnkupk=";
+    sha256 = "sha256-s/V2CsLu6AJqPw7vyyW0dyPZeAOO7o6ER2IJTIYMRSo=";
   };
 
   outputs = [ "out" "tex" ];
@@ -31,7 +31,7 @@ stdenv.mkDerivation (finalAttrs: {
   nativeBuildInputs = [ pkg-config ];
   buildInputs = [
     bzip2 gfortran libX11 libXmu libXt libXt libjpeg libpng libtiff ncurses
-    pango pcre2 perl readline texLive xz zlib less texinfo graphviz icu
+    pango pcre2 perl readline (texliveSmall.withPackages (ps: with ps; [ inconsolata helvetic ps.texinfo fancyvrb cm-super rsfs ])) xz zlib less texinfo graphviz icu
     bison imake which blas lapack curl tcl tk jdk tzdata
   ] ++ lib.optionals stdenv.isDarwin [ Cocoa Foundation libobjc libcxx ];
 
diff --git a/pkgs/applications/science/math/caffe/default.nix b/pkgs/applications/science/math/caffe/default.nix
index 5af927294d6..42c16039359 100644
--- a/pkgs/applications/science/math/caffe/default.nix
+++ b/pkgs/applications/science/math/caffe/default.nix
@@ -1,12 +1,13 @@
 { config, stdenv, lib
 , fetchFromGitHub
 , fetchurl
+, fetchpatch
 , cmake
 , boost
 , gflags
 , glog
 , hdf5-cpp
-, opencv3
+, opencv4
 , protobuf
 , doxygen
 , blas
@@ -71,7 +72,7 @@ stdenv.mkDerivation rec {
       ++ ["-DUSE_LEVELDB=${toggle leveldbSupport}"]
       ++ ["-DUSE_LMDB=${toggle lmdbSupport}"];
 
-  buildInputs = [ boost gflags glog protobuf hdf5-cpp opencv3 blas ]
+  buildInputs = [ boost gflags glog protobuf hdf5-cpp opencv4 blas ]
                 ++ lib.optional cudaSupport cudatoolkit
                 ++ lib.optional cudnnSupport cudnn
                 ++ lib.optional lmdbSupport lmdb
@@ -96,6 +97,11 @@ stdenv.mkDerivation rec {
 
   patches = [
     ./darwin.patch
+    (fetchpatch {
+       name = "support-opencv4";
+       url = "https://github.com/BVLC/caffe/pull/6638/commits/0a04cc2ccd37ba36843c18fea2d5cbae6e7dd2b5.patch";
+       hash = "sha256-ZegTvp0tTHlopQv+UzHDigs6XLkP2VfqLCWXl6aKJSI=";
+     })
   ] ++ lib.optional pythonSupport (substituteAll {
     src = ./python.patch;
     inherit (python.sourceVersion) major minor;  # Should be changed in case of PyPy
@@ -148,7 +154,7 @@ stdenv.mkDerivation rec {
     '';
     homepage = "http://caffe.berkeleyvision.org/";
     maintainers = with maintainers; [ ];
-    broken = pythonSupport && (python.isPy310);
+    broken = (pythonSupport && (python.isPy310)) || cudaSupport;
     license = licenses.bsd2;
     platforms = platforms.linux ++ platforms.darwin;
   };
diff --git a/pkgs/applications/science/math/calc/default.nix b/pkgs/applications/science/math/calc/default.nix
index 0c70a6e03b2..86ec445d9b3 100644
--- a/pkgs/applications/science/math/calc/default.nix
+++ b/pkgs/applications/science/math/calc/default.nix
@@ -10,18 +10,18 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "calc";
-  version = "2.14.3.5";
+  version = "2.15.0.1";
 
   src = fetchurl {
     urls = [
       "https://github.com/lcn2/calc/releases/download/v${finalAttrs.version}/calc-${finalAttrs.version}.tar.bz2"
       "http://www.isthe.com/chongo/src/calc/calc-${finalAttrs.version}.tar.bz2"
     ];
-    hash = "sha256-4eXs6NDfsJO5Vr9Mo2jC16hTRAyt++1s+Z/JrWDKwUk=";
+    hash = "sha256-u/mt9y4805IWYDdEHz94dPb4V+d4YVrrhzz8v3B+q24=";
   };
 
   postPatch = ''
-    substituteInPlace Makefile \
+    substituteInPlace Makefile.target \
       --replace '-install_name ''${LIBDIR}/libcalc''${LIB_EXT_VERSION}' '-install_name ''${T}''${LIBDIR}/libcalc''${LIB_EXT_VERSION}' \
       --replace '-install_name ''${LIBDIR}/libcustcalc''${LIB_EXT_VERSION}' '-install_name ''${T}''${LIBDIR}/libcustcalc''${LIB_EXT_VERSION}'
   '';
diff --git a/pkgs/applications/science/math/clp/default.nix b/pkgs/applications/science/math/clp/default.nix
index c7d19f044d6..52a74ff3979 100644
--- a/pkgs/applications/science/math/clp/default.nix
+++ b/pkgs/applications/science/math/clp/default.nix
@@ -1,13 +1,13 @@
 { lib, stdenv, fetchFromGitHub, pkg-config, coin-utils, zlib, osi }:
 
 stdenv.mkDerivation rec {
-  version = "1.17.8";
+  version = "1.17.9";
   pname = "clp";
   src = fetchFromGitHub {
     owner = "coin-or";
     repo = "Clp";
     rev = "releases/${version}";
-    hash = "sha256-3Z6ysoCcDVB8UePiwbZNqvO/o/jgPcv6XFkpJZBK+Os=";
+    hash = "sha256-kHCDji+yIf5mCoxKB2b/HaATGmwwIAPEV74tthIMeMY=";
   };
 
   nativeBuildInputs = [ pkg-config ];
diff --git a/pkgs/applications/science/math/cntk/default.nix b/pkgs/applications/science/math/cntk/default.nix
deleted file mode 100644
index 91d208a56ed..00000000000
--- a/pkgs/applications/science/math/cntk/default.nix
+++ /dev/null
@@ -1,134 +0,0 @@
-{ lib, stdenv, fetchFromGitHub, cmake
-, fetchpatch
-, openblas, blas, lapack, opencv3, libzip, boost, protobuf, mpi
-, onebitSGDSupport ? false
-, config
-, cudaSupport ? config.cudaSupport, cudaPackages ? { }, addOpenGLRunpath, cudatoolkit, nvidia_x11
-, cudnnSupport ? cudaSupport
-}:
-
-let
-  inherit (cudaPackages) cudatoolkit cudnn;
-in
-
-assert cudnnSupport -> cudaSupport;
-assert blas.implementation == "openblas" && lapack.implementation == "openblas";
-
-let
-  # Old specific version required for CNTK.
-  cub = fetchFromGitHub {
-    owner = "NVlabs";
-    repo = "cub";
-    rev = "1.7.4";
-    sha256 = "0ksd5n1lxqhm5l5cd2lps4cszhjkf6gmzahaycs7nxb06qci8c66";
-  };
-
-in stdenv.mkDerivation rec {
-  pname = "CNTK";
-  version = "2.7";
-
-  src = fetchFromGitHub {
-    owner = "Microsoft";
-    repo = "CNTK";
-    rev = "v${version}";
-    sha256 = "sha256-2rIrPJyvZhnM5EO6tNhF6ARTocfUHce4N0IZk/SZiaI=";
-    fetchSubmodules = true;
-  };
-
-  patches = [
-    # Fix build with protobuf 3.18+
-    # Remove with onnx submodule bump to 1.9+
-    (fetchpatch {
-      url = "https://github.com/onnx/onnx/commit/d3bc82770474761571f950347560d62a35d519d7.patch";
-      extraPrefix = "Source/CNTKv2LibraryDll/proto/onnx/onnx_repo/";
-      stripLen = 1;
-      sha256 = "00raqj8wx30b06ky6cdp5vvc1mrzs7hglyi6h58hchw5lhrwkzxp";
-    })
-  ];
-
-  postPatch = ''
-    # Fix build with protobuf 3.18+
-    substituteInPlace Source/CNTKv2LibraryDll/Serialization.cpp \
-      --replace 'SetTotalBytesLimit(INT_MAX, INT_MAX)' \
-                'SetTotalBytesLimit(INT_MAX)' \
-      --replace 'SetTotalBytesLimit(limit, limit)' \
-                'SetTotalBytesLimit(limit)'
-  '';
-
-  nativeBuildInputs = [ cmake ] ++ lib.optional cudaSupport addOpenGLRunpath;
-
-  # Force OpenMPI to use g++ in PATH.
-  OMPI_CXX = "g++";
-
-  # Uses some deprecated tensorflow functions
-  env.NIX_CFLAGS_COMPILE = "-Wno-error=deprecated-declarations";
-
-  buildInputs = [ openblas opencv3 libzip boost protobuf mpi ]
-             ++ lib.optional cudaSupport cudatoolkit
-             ++ lib.optional cudnnSupport cudnn;
-
-  configureFlags = [
-    "--with-opencv=${opencv3}"
-    "--with-libzip=${libzip.dev}"
-    "--with-openblas=${openblas.dev}"
-    "--with-boost=${boost.dev}"
-    "--with-protobuf=${protobuf}"
-    "--with-mpi=${mpi}"
-    "--cuda=${if cudaSupport then "yes" else "no"}"
-    # FIXME
-    "--asgd=no"
-  ] ++ lib.optionals cudaSupport [
-    "--with-cuda=${cudatoolkit}"
-    "--with-gdk-include=${cudatoolkit}/include"
-    "--with-gdk-nvml-lib=${nvidia_x11}/lib"
-    "--with-cub=${cub}"
-  ] ++ lib.optional onebitSGDSupport "--1bitsgd=yes";
-
-  configurePhase = ''
-    sed -i \
-      -e 's,^GIT_STATUS=.*,GIT_STATUS=,' \
-      -e 's,^GIT_COMMIT=.*,GIT_COMMIT=v${version},' \
-      -e 's,^GIT_BRANCH=.*,GIT_BRANCH=v${version},' \
-      -e 's,^BUILDER=.*,BUILDER=nixbld,' \
-      -e 's,^BUILDMACHINE=.*,BUILDMACHINE=machine,' \
-      -e 's,^BUILDPATH=.*,BUILDPATH=/homeless-shelter,' \
-      -e '/git does not exist/d' \
-      Tools/generate_build_info
-
-    patchShebangs .
-    mkdir build
-    cd build
-    ${lib.optionalString cudnnSupport ''
-      mkdir cuda
-      ln -s ${cudnn}/include cuda
-      export configureFlags="$configureFlags --with-cudnn=$PWD"
-    ''}
-
-    ../configure $configureFlags
-  '';
-
-  installPhase = ''
-    mkdir -p $out/bin
-    # Moving to make patchelf remove references later.
-    mv lib $out
-    cp bin/cntk $out/bin
-  '';
-
-  postFixup = lib.optionalString cudaSupport ''
-    for lib in $out/lib/*; do
-      addOpenGLRunpath "$lib"
-    done
-  '';
-
-  meta = with lib; {
-    homepage = "https://github.com/Microsoft/CNTK";
-    description = "An open source deep-learning toolkit";
-    license = if onebitSGDSupport then licenses.unfreeRedistributable else licenses.mit;
-    platforms = [ "x86_64-linux" ];
-    maintainers = with maintainers; [ abbradar ];
-    # Newer cub is included with cudatoolkit now and it breaks the build.
-    # https://github.com/Microsoft/CNTK/issues/3191
-    # broken = cudaSupport;
-    broken = true; # at 2022-11-23
-  };
-}
diff --git a/pkgs/applications/science/math/colpack/default.nix b/pkgs/applications/science/math/colpack/default.nix
index 3cc9290a762..d5ab38ff751 100644
--- a/pkgs/applications/science/math/colpack/default.nix
+++ b/pkgs/applications/science/math/colpack/default.nix
@@ -35,7 +35,7 @@ stdenv.mkDerivation rec {
   meta = with lib; {
     description = "A package comprising of implementations of algorithms for
     vertex coloring and derivative computation";
-    homepage = "http://cscapes.cs.purdue.edu/coloringpage/software.htm#functionalities";
+    homepage = "https://cscapes.cs.purdue.edu/coloringpage/software.htm#functionalities";
     license = licenses.lgpl3Plus;
     platforms = platforms.unix;
     maintainers = with maintainers; [ edwtjo ];
diff --git a/pkgs/applications/science/math/eigenmath/default.nix b/pkgs/applications/science/math/eigenmath/default.nix
index 8abcd96f08d..1e80d9a06eb 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-2023-08-03";
+  version = "unstable-2023-11-17";
 
   src = fetchFromGitHub {
     owner = "georgeweigt";
     repo = pname;
-    rev = "f202cf0c342e54e994c4d416daecc1b1dc8b9c98";
-    hash = "sha256-kp4zWTPYt2DiuPgTK+ib8NbKg2BJVxJDDCvIlWNuwgs=";
+    rev = "b0d822f10243ad5b1c88efb5a82b43a0bbf1bfbc";
+    hash = "sha256-eJ/EmzV5UZGxwZNIna/XXkYY+vkLc610KcywBFPRfyM=";
   };
 
   checkPhase = let emulator = stdenv.hostPlatform.emulator buildPackages; in ''
diff --git a/pkgs/applications/science/math/giac/default.nix b/pkgs/applications/science/math/giac/default.nix
index 752b05fe4fe..0dc12b6dcb0 100644
--- a/pkgs/applications/science/math/giac/default.nix
+++ b/pkgs/applications/science/math/giac/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, lib, fetchurl, fetchpatch, texlive, bison, flex, lapack, blas
+{ stdenv, lib, fetchurl, fetchpatch, texliveSmall, bison, flex, lapack, blas
 , autoreconfHook, gmp, mpfr, pari, ntl, gsl, mpfi, ecm, glpk, nauty
 , buildPackages, readline, gettext, libpng, libao, gfortran, perl
 , enableGUI ? false, libGL, libGLU, xorg, fltk
@@ -60,7 +60,7 @@ stdenv.mkDerivation rec {
   '';
 
   nativeBuildInputs = [
-    autoreconfHook texlive.combined.scheme-small bison flex
+    autoreconfHook texliveSmall bison flex
   ];
 
   # perl is only needed for patchShebangs fixup.
diff --git a/pkgs/applications/science/math/ginac/default.nix b/pkgs/applications/science/math/ginac/default.nix
index 057b242e609..d9d12cbf388 100644
--- a/pkgs/applications/science/math/ginac/default.nix
+++ b/pkgs/applications/science/math/ginac/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "ginac";
-  version = "1.8.6";
+  version = "1.8.7";
 
   src = fetchurl {
     url = "https://www.ginac.de/ginac-${version}.tar.bz2";
-    sha256 = "sha256-ALMgsRFsrlt7QzZNv/t5EkcdFx9ITYJ2RgXXFYWNl1s=";
+    sha256 = "sha256-cf9PLYoA5vB86P7mm3bcweu7cnvmdgtYfB+7XM97Yeo=";
   };
 
   propagatedBuildInputs = [ cln ];
diff --git a/pkgs/applications/science/math/mxnet/default.nix b/pkgs/applications/science/math/mxnet/default.nix
index d65de87d8eb..993da2b8989 100644
--- a/pkgs/applications/science/math/mxnet/default.nix
+++ b/pkgs/applications/science/math/mxnet/default.nix
@@ -1,5 +1,5 @@
 { config, stdenv, lib, fetchurl, fetchpatch, bash, cmake
-, opencv3, gtest, blas, gomp, llvmPackages, perl
+, opencv4, gtest, blas, gomp, llvmPackages, perl
 , cudaSupport ? config.cudaSupport, cudaPackages ? { }, nvidia_x11
 , cudnnSupport ? cudaSupport
 }:
@@ -37,7 +37,7 @@ stdenv.mkDerivation rec {
 
   nativeBuildInputs = [ cmake perl ];
 
-  buildInputs = [ opencv3 gtest blas.provider ]
+  buildInputs = [ opencv4 gtest blas.provider ]
     ++ lib.optional stdenv.cc.isGNU gomp
     ++ lib.optional stdenv.cc.isClang llvmPackages.openmp
     # FIXME: when cuda build is fixed, remove nvidia_x11, and use /run/opengl-driver/lib
diff --git a/pkgs/applications/science/math/pari/default.nix b/pkgs/applications/science/math/pari/default.nix
index 44647ce8139..2480ff3eba8 100644
--- a/pkgs/applications/science/math/pari/default.nix
+++ b/pkgs/applications/science/math/pari/default.nix
@@ -7,7 +7,7 @@
 , libpthreadstubs
 , perl
 , readline
-, tex
+, texliveBasic
 , withThread ? true
 }:
 
@@ -31,7 +31,7 @@ stdenv.mkDerivation rec {
     libX11
     perl
     readline
-    tex
+    texliveBasic
   ] ++ lib.optionals withThread [
     libpthreadstubs
   ];
diff --git a/pkgs/applications/science/math/polymake/default.nix b/pkgs/applications/science/math/polymake/default.nix
index 2e79ca03635..fe9210641d2 100644
--- a/pkgs/applications/science/math/polymake/default.nix
+++ b/pkgs/applications/science/math/polymake/default.nix
@@ -28,13 +28,13 @@ in
 
 stdenv.mkDerivation rec {
   pname = "polymake";
-  version = "4.10";
+  version = "4.11";
 
   src = fetchurl {
     # "The minimal version is a packager friendly version which omits
     # the bundled sources of cdd, lrs, libnormaliz, nauty and jReality."
     url = "https://polymake.org/lib/exe/fetch.php/download/polymake-${version}-minimal.tar.bz2";
-    sha256 = "sha256-YDiyZtbUC76ZVe3oRtzPRBfkEU+qh+d1ZWFhzUyi+Pg=";
+    sha256 = "sha256-XfbwrNcAEZvQxLV2Z2KFL/vYV3ZbXcyIgC/10hCK3SM=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/applications/science/math/qalculate-gtk/default.nix b/pkgs/applications/science/math/qalculate-gtk/default.nix
index 191ee7a00fd..ade614c89b0 100644
--- a/pkgs/applications/science/math/qalculate-gtk/default.nix
+++ b/pkgs/applications/science/math/qalculate-gtk/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, intltool, autoreconfHook, pkg-config, libqalculate, gtk3, curl, wrapGAppsHook }:
+{ lib, stdenv, fetchFromGitHub, intltool, autoreconfHook, pkg-config, libqalculate, gtk3, curl, wrapGAppsHook, desktopToDarwinBundle }:
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "qalculate-gtk";
@@ -13,7 +13,8 @@ stdenv.mkDerivation (finalAttrs: {
 
   hardeningDisable = [ "format" ];
 
-  nativeBuildInputs = [ intltool pkg-config autoreconfHook wrapGAppsHook ];
+  nativeBuildInputs = [ intltool pkg-config autoreconfHook wrapGAppsHook ]
+    ++ lib.optionals stdenv.isDarwin [ desktopToDarwinBundle ];
   buildInputs = [ libqalculate gtk3 curl ];
   enableParallelBuilding = true;
 
diff --git a/pkgs/applications/science/math/readstat/default.nix b/pkgs/applications/science/math/readstat/default.nix
index efbf80ba16e..08555d12640 100644
--- a/pkgs/applications/science/math/readstat/default.nix
+++ b/pkgs/applications/science/math/readstat/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, autoreconfHook, pkg-config, libiconv }:
+{ lib, stdenv, fetchFromGitHub, fetchpatch, autoreconfHook, pkg-config, libiconv }:
 
 stdenv.mkDerivation rec {
   pname = "readstat";
@@ -11,6 +11,13 @@ stdenv.mkDerivation rec {
     sha256 = "sha256-4lRJgZPB2gfaQ9fQKvDDpGhy1eDNT/nT1QmeZlCmCis=";
   };
 
+  patches = [
+    (fetchpatch {
+      url = "https://github.com/WizardMac/ReadStat/commit/211c342a1cfe46fb7fb984730dd7a29ff4752f35.patch";
+      hash = "sha256-nkaEgusylVu7NtzSzBklBuOnqO9qJPovf0qn9tTE6ls=";
+    })
+  ];
+
   nativeBuildInputs = [ pkg-config autoreconfHook ];
 
   buildInputs = [ libiconv ];
@@ -22,5 +29,6 @@ stdenv.mkDerivation rec {
     description = "Command-line tool (+ C library) for converting SAS, Stata, and SPSS files";
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ swflint ];
+    platforms = lib.platforms.all;
   };
 }
diff --git a/pkgs/applications/science/math/sage/README.md b/pkgs/applications/science/math/sage/README.md
index c4de5da45db..35e8d0deeff 100644
--- a/pkgs/applications/science/math/sage/README.md
+++ b/pkgs/applications/science/math/sage/README.md
@@ -2,7 +2,7 @@
 
 Sage is a pretty complex package that depends on many other complex packages and patches some of those. As a result, the sage nix package is also quite complex.
 
-Don't feel discouraged to fix, simplify or improve things though. The individual files have comments explaining their purpose. The most importent ones are `default.nix` linking everything together, `sage-src.nix` adding patches and `sagelib.nix` building the actual sage package.
+Don't feel discouraged to fix, simplify or improve things though. The individual files have comments explaining their purpose. The most important ones are `default.nix` linking everything together, `sage-src.nix` adding patches and `sagelib.nix` building the actual sage package.
 
 ## The sage build is broken
 
diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix
index 9fe07603fe7..97754c04d95 100644
--- a/pkgs/applications/science/math/sage/sage-src.nix
+++ b/pkgs/applications/science/math/sage/sage-src.nix
@@ -104,11 +104,32 @@ stdenv.mkDerivation rec {
       sha256 = "sha256-GqMgoi0tsP7zcCcPumhdsbvhPB6fgw1ufx6gHlc6iSc=";
     })
 
-    # https://github.com/sagemath/sage/pull/36006, positively reviewed
+    # https://github.com/sagemath/sage/pull/36006, landed in 10.2.beta2
     (fetchpatch {
       name = "gmp-6.3-upgrade.patch";
-      url = "https://github.com/sagemath/sage/commit/d88bc3815c0901bfdeaa3e4a31107c084199f614.diff";
-      sha256 = "sha256-dXaEwk2wXxmx02sCw4Vu9mF0ZrydhFD4LRwNAiQsPgM=";
+      url = "https://github.com/sagemath/sage/commit/5e841de46c3baa99cd1145b36ff9163e9340a55c.diff";
+      sha256 = "sha256-fJPDryLtGBQz9qHDiCkBwjiW2lN6v7HiHgxY7CTeHcs=";
+    })
+
+    # https://github.com/sagemath/sage/pull/36279, landed in 10.2.beta4
+    (fetchpatch {
+       name = "matplotlib-3.8-upgrade.patch";
+       url = "https://github.com/sagemath/sage/commit/0fcf88935908440930c5f79202155aca4ad57518.diff";
+       sha256 = "sha256-mvqAHaTCXsxPv901L8HSTnrfghfXYdq0wfLoP/cYQZI=";
+    })
+
+    # https://github.com/sagemath/sage/pull/35658, landed in 10.1.beta2
+    (fetchpatch {
+      name = "sphinx-7-upgrade.patch";
+      url = "https://github.com/sagemath/sage/commit/cacd9a89b5c4fdcf84a8dd2b7d5bdc10cc78109a.diff";
+      sha256 = "sha256-qJvliTJjR3XBc5pH6Q0jtm8c4bhtZcTcF3O04Ro1uaU=";
+    })
+
+    # https://github.com/sagemath/sage/pull/36296, landed in 10.2.beta4
+    (fetchpatch {
+      name = "duplicate-args-region_plot.patch";
+      url = "https://github.com/sagemath/sage/commit/461727b453712550a2c5dc0ae11933523255aaed.diff";
+      sha256 = "sha256-mC8084VQoUBk4hocALF+Y9Cwb38Zt360eldi/SSjna8=";
     })
   ];
 
diff --git a/pkgs/applications/science/math/sage/sagelib.nix b/pkgs/applications/science/math/sage/sagelib.nix
index d8d5586e219..f8beabaac1f 100644
--- a/pkgs/applications/science/math/sage/sagelib.nix
+++ b/pkgs/applications/science/math/sage/sagelib.nix
@@ -78,6 +78,7 @@
 , sphinx
 , sympy
 , typing-extensions
+, nbclassic
 }:
 
 assert (!blas.isILP64) && (!lapack.isILP64);
@@ -181,6 +182,8 @@ buildPythonPackage rec {
     sphinx
     sympy
     typing-extensions
+
+    nbclassic
   ];
 
   preBuild = ''
diff --git a/pkgs/applications/science/math/singular/default.nix b/pkgs/applications/science/math/singular/default.nix
index 1f06f0d1aef..f77bd5a9224 100644
--- a/pkgs/applications/science/math/singular/default.nix
+++ b/pkgs/applications/science/math/singular/default.nix
@@ -17,7 +17,7 @@
 # use letters instead of numbers for post-appendix chapters, and we
 # want it to match the upstream format because sage depends on it.
 , texinfo4
-, texlive
+, texliveSmall
 , enableDocs ? !stdenv.isDarwin
 , enableGfanlib ? true
 }:
@@ -86,7 +86,7 @@ stdenv.mkDerivation rec {
     graphviz
     latex2html
     texinfo4
-    texlive.combined.scheme-small
+    texliveSmall
   ] ++ lib.optionals stdenv.isDarwin [ getconf ];
   depsBuildBuild = [ buildPackages.stdenv.cc ];
 
diff --git a/pkgs/applications/science/math/wxmaxima/default.nix b/pkgs/applications/science/math/wxmaxima/default.nix
index c475dbd5ef2..d30d560f47f 100644
--- a/pkgs/applications/science/math/wxmaxima/default.nix
+++ b/pkgs/applications/science/math/wxmaxima/default.nix
@@ -12,13 +12,13 @@
 
 stdenv.mkDerivation (finalAttrs:{
   pname = "wxmaxima";
-  version = "23.02.1";
+  version = "23.10.0";
 
   src = fetchFromGitHub {
     owner = "wxMaxima-developers";
     repo = "wxmaxima";
     rev = "Version-${finalAttrs.version}";
-    sha256 = "sha256-Lrj/oJNmKlCkNbnCGY2TewCospwajKdWgmKkreHzEIU=";
+    sha256 = "sha256-3zQzpw0KWNAAvML55O2FMlid9j0GtP8OWy1eqifzVwI=";
   };
 
   buildInputs = [