uboot: (firmwareOdroidC2/C4) don't invoke patch tool, use patches = [] instead

https://github.com/NixOS/nixpkgs/blob/master/pkgs/stdenv/generic/setup.sh#L948 this can do it nicely. Signed-off-by: Anton Arapov <anton@deadbeef.mx>
2021-04-03 12:58:10 +02:00 · 2021-04-03 12:58:10 +02:00 · 56de2bcd43
commit 56de2bcd43
30691 changed files with 3076956 additions and 0 deletions
--- a/pkgs/applications/science/math/4ti2/default.nix
+++ b/pkgs/applications/science/math/4ti2/default.nix
@ -0,0 +1,38 @@
+{ lib
+, stdenv
+, fetchFromGitHub
+, autoreconfHook
+, glpk
+, gmp
+}:
+
+stdenv.mkDerivation rec{
+  pname = "4ti2";
+  version = "1.6.9";
+
+  src = fetchFromGitHub {
+    owner = pname;
+    repo = pname;
+    rev = "Release_${builtins.replaceStrings ["."] ["_"] version}";
+    hash = "sha256-cywneIM0sHt1iQsNfjyQDoDfdRjxpz4l3rfysi9YN20=";
+  };
+
+  nativeBuildInputs = [
+    autoreconfHook
+  ];
+
+  buildInputs = [
+    glpk
+    gmp
+  ];
+
+  installFlags = [ "install-exec" ];
+
+  meta = with lib;{
+    homepage = "https://4ti2.github.io/";
+    description = "A software package for algebraic, geometric and combinatorial problems on linear spaces";
+    license = with licenses; [ gpl2Plus ];
+    maintainers = with maintainers; [ AndersonTorres ];
+    platforms = platforms.all;
+  };
+}
--- a/pkgs/applications/science/math/LiE/default.nix
+++ b/pkgs/applications/science/math/LiE/default.nix
@ -0,0 +1,47 @@
+{ lib, stdenv, fetchurl
+, bison, readline }:
+
+stdenv.mkDerivation {
+  version = "2.2.2";
+     # The current version of LiE is 2.2.2, which is more or less unchanged
+     # since about the year 2000. Minor bugfixes do get applied now and then.
+  pname = "lie";
+
+  meta = {
+    description = "A Computer algebra package for Lie group computations";
+    homepage = "http://wwwmathlabo.univ-poitiers.fr/~maavl/LiE/";
+    license = lib.licenses.lgpl3; # see the website
+
+    longDescription = ''
+      LiE is a computer algebra system that is specialised in computations
+      involving (reductive) Lie groups and their representations. It is
+      publically available for free in source code. For a description of its
+      characteristics, we refer to the following sources of information.
+    ''; # take from the website
+
+    platforms = lib.platforms.linux;
+    maintainers = [ ]; # this package is probably not going to change anyway
+  };
+
+  src = fetchurl {
+    url = "http://wwwmathlabo.univ-poitiers.fr/~maavl/LiE/conLiE.tar.gz";
+    sha256 = "07lbj75qqr4pq1j1qz8fyfnmrz1gnk92lnsshxycfavxl5zzdmn4";
+  };
+
+  buildInputs = [ bison readline ];
+
+  patchPhase = ''
+    substituteInPlace make_lie \
+      --replace \`/bin/pwd\` $out
+  '';
+
+  installPhase = ''
+    mkdir -vp $out/bin
+
+    cp -v Lie.exe $out
+    cp -v lie $out/bin
+
+    cp -v LEARN* $out
+    cp -v INFO* $out
+  '';
+}
--- a/pkgs/applications/science/math/R/default.nix
+++ b/pkgs/applications/science/math/R/default.nix
@ -0,0 +1,133 @@
+{ lib, stdenv, fetchurl, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng
+, libtiff, ncurses, pango, pcre2, perl, readline, tcl, texLive, tk, xz, zlib
+, less, texinfo, graphviz, icu, pkg-config, bison, imake, which, jdk, blas, lapack
+, curl, Cocoa, Foundation, libobjc, libcxx, tzdata
+, withRecommendedPackages ? true
+, enableStrictBarrier ? false
+, enableMemoryProfiling ? false
+# R as of writing does not support outputting both .so and .a files; it outputs:
+#     --enable-R-static-lib conflicts with --enable-R-shlib and will be ignored
+, static ? false
+}:
+
+assert (!blas.isILP64) && (!lapack.isILP64);
+
+stdenv.mkDerivation rec {
+  pname = "R";
+  version = "4.2.0";
+
+  src = fetchurl {
+    url = "https://cran.r-project.org/src/base/R-${lib.versions.major version}/${pname}-${version}.tar.gz";
+    sha256 = "sha256-OOq3cZt60JU4jwaqCQxaKyAnkZRd5g0+K7DqsfUJdIg=";
+  };
+
+  dontUseImakeConfigure = true;
+
+  buildInputs = [
+    bzip2 gfortran libX11 libXmu libXt libXt libjpeg libpng libtiff ncurses
+    pango pcre2 perl readline texLive xz zlib less texinfo graphviz icu
+    pkg-config bison imake which blas lapack curl tcl tk jdk
+  ] ++ lib.optionals stdenv.isDarwin [ Cocoa Foundation libobjc libcxx ];
+
+  patches = [
+    ./no-usr-local-search-paths.patch
+    ./test-reg-packages.patch
+  ];
+
+  # Test of the examples for package 'tcltk' fails in Darwin sandbox. See:
+  # https://github.com/NixOS/nixpkgs/issues/146131
+  postPatch = lib.optionalString stdenv.isDarwin ''
+    substituteInPlace configure \
+      --replace "-install_name libRblas.dylib" "-install_name $out/lib/R/lib/libRblas.dylib" \
+      --replace "-install_name libRlapack.dylib" "-install_name $out/lib/R/lib/libRlapack.dylib" \
+      --replace "-install_name libR.dylib" "-install_name $out/lib/R/lib/libR.dylib"
+    substituteInPlace tests/Examples/Makefile.in \
+      --replace "test-Examples: test-Examples-Base" "test-Examples:" # do not test the examples
+  '';
+
+  dontDisableStatic = static;
+
+  preConfigure = ''
+    configureFlagsArray=(
+      --disable-lto
+      --with${lib.optionalString (!withRecommendedPackages) "out"}-recommended-packages
+      --with-blas="-L${blas}/lib -lblas"
+      --with-lapack="-L${lapack}/lib -llapack"
+      --with-readline
+      --with-tcltk --with-tcl-config="${tcl}/lib/tclConfig.sh" --with-tk-config="${tk}/lib/tkConfig.sh"
+      --with-cairo
+      --with-libpng
+      --with-jpeglib
+      --with-libtiff
+      --with-ICU
+      ${lib.optionalString enableStrictBarrier "--enable-strict-barrier"}
+      ${lib.optionalString enableMemoryProfiling "--enable-memory-profiling"}
+      ${if static then "--enable-R-static-lib" else "--enable-R-shlib"}
+      AR=$(type -p ar)
+      AWK=$(type -p gawk)
+      CC=$(type -p cc)
+      CXX=$(type -p c++)
+      FC="${gfortran}/bin/gfortran" F77="${gfortran}/bin/gfortran"
+      JAVA_HOME="${jdk}"
+      RANLIB=$(type -p ranlib)
+      R_SHELL="${stdenv.shell}"
+  '' + lib.optionalString stdenv.isDarwin ''
+      --disable-R-framework
+      --without-x
+      OBJC="clang"
+      CPPFLAGS="-isystem ${lib.getDev libcxx}/include/c++/v1"
+      LDFLAGS="-L${lib.getLib libcxx}/lib"
+  '' + ''
+    )
+    echo >>etc/Renviron.in "TCLLIBPATH=${tk}/lib"
+    echo >>etc/Renviron.in "TZDIR=${tzdata}/share/zoneinfo"
+  '';
+
+  installTargets = [ "install" "install-info" "install-pdf" ];
+
+  # The store path to "which" is baked into src/library/base/R/unix/system.unix.R,
+  # but Nix cannot detect it as a run-time dependency because the installed file
+  # is compiled and compressed, which hides the store path.
+  postFixup = "echo ${which} > $out/nix-support/undetected-runtime-dependencies";
+
+  doCheck = true;
+  preCheck = "export HOME=$TMPDIR; export TZ=CET; bin/Rscript -e 'sessionInfo()'";
+
+  enableParallelBuilding = true;
+
+  # disable stackprotector on aarch64-darwin for now
+  # https://github.com/NixOS/nixpkgs/issues/158730
+  # see https://github.com/NixOS/nixpkgs/issues/127608 for a similar issue
+  hardeningDisable = lib.optionals (stdenv.isAarch64 && stdenv.isDarwin) [ "stackprotector" ];
+
+  setupHook = ./setup-hook.sh;
+
+  meta = with lib; {
+    homepage = "http://www.r-project.org/";
+    description = "Free software environment for statistical computing and graphics";
+    license = licenses.gpl2Plus;
+
+    longDescription = ''
+      GNU R is a language and environment for statistical computing and
+      graphics that provides a wide variety of statistical (linear and
+      nonlinear modelling, classical statistical tests, time-series
+      analysis, classification, clustering, ...) and graphical
+      techniques, and is highly extensible. One of R's strengths is the
+      ease with which well-designed publication-quality plots can be
+      produced, including mathematical symbols and formulae where
+      needed. R is an integrated suite of software facilities for data
+      manipulation, calculation and graphical display. It includes an
+      effective data handling and storage facility, a suite of operators
+      for calculations on arrays, in particular matrices, a large,
+      coherent, integrated collection of intermediate tools for data
+      analysis, graphical facilities for data analysis and display
+      either on-screen or on hardcopy, and a well-developed, simple and
+      effective programming language which includes conditionals, loops,
+      user-defined recursive functions and input and output facilities.
+    '';
+
+    platforms = platforms.all;
+
+    maintainers = with maintainers; [ jbedo ] ++ teams.sage.members;
+  };
+}
--- a/pkgs/applications/science/math/R/no-usr-local-search-paths.patch
+++ b/pkgs/applications/science/math/R/no-usr-local-search-paths.patch
@ -0,0 +1,24 @@
+diff -ubr R-3.0.1-orig/configure R-3.0.1/configure
+--- R-3.0.1-orig/configure	2013-07-04 10:46:42.336133947 +0200
+++ R-3.0.1/configure	2013-07-04 10:46:17.181919960 +0200
+@@ -3800,13 +3800,13 @@
+ : ${LIBnn=$libnn}
+ ## We provide these defaults so that headers and libraries in
+ ## '/usr/local' are found (by the native tools, mostly).
+-if test -f "/sw/etc/fink.conf"; then
+-  : ${CPPFLAGS="-I/sw/include -I/usr/local/include"}
+-  : ${LDFLAGS="-L/sw/lib -L/usr/local/lib"}
+-else
+-  : ${CPPFLAGS="-I/usr/local/include"}
+-  : ${LDFLAGS="-L/usr/local/${LIBnn}"}
+-fi
+# if test -f "/sw/etc/fink.conf"; then
+#   : ${CPPFLAGS="-I/sw/include -I/usr/local/include"}
+#   : ${LDFLAGS="-L/sw/lib -L/usr/local/lib"}
+# else
+#   : ${CPPFLAGS="-I/usr/local/include"}
+#   : ${LDFLAGS="-L/usr/local/${LIBnn}"}
+# fi
+ 
+ ## take care not to  override the command-line setting
+ if test "${libdir}" = '${exec_prefix}/lib'; then
--- a/pkgs/applications/science/math/R/setup-hook.sh
+++ b/pkgs/applications/science/math/R/setup-hook.sh
@ -0,0 +1,7 @@
+addRLibPath () {
+    if [[ -d "$1/library" ]]; then
+        addToSearchPath R_LIBS_SITE "$1/library"
+    fi
+}
+
+addEnvHooks "$targetOffset" addRLibPath
--- a/pkgs/applications/science/math/R/test-reg-packages.patch
+++ b/pkgs/applications/science/math/R/test-reg-packages.patch
@ -0,0 +1,15 @@
+Upper bounds shifts due to extra warnings re. internet connectivity.
+
+diff --git a/tests/reg-packages.R b/tests/reg-packages.R
+index c9962ce..a40b0fa 100644
+--- a/tests/reg-packages.R
+++ b/tests/reg-packages.R
+@@ -260,7 +260,7 @@ stopifnot(exprs = {
+     (lenN <- length(print(iN <- grep("^[1-9][0-9]:", tlines)))) >= 2
+     iN - iw == seq_len(lenN) # these (3) lines come immediately after 'Warning',
+     ## and "related" to the some 'missing .. paren' above:
+-    8 <= print(iw - i) & iw - i <= 20 # see ~14
+    8 <= print(iw - i) & iw - i <= 22 # see ~14
+ }) ## failed in R <= 4.1.1
+
+
--- a/pkgs/applications/science/math/adolc/default.nix
+++ b/pkgs/applications/science/math/adolc/default.nix
@ -0,0 +1,23 @@
+{ lib, stdenv, fetchFromGitHub }:
+
+stdenv.mkDerivation rec {
+  pname = "adolc";
+  version = "2.7.2";
+
+  src = fetchFromGitHub {
+    owner = "coin-or";
+    repo = "ADOL-C";
+    sha256 = "1w0x0p32r1amfmh2lyx33j4cb5bpkwjr5z0ll43zi5wf5gsvckd1";
+    rev = "releases/${version}";
+  };
+
+  configureFlags = [ "--with-openmp-flag=-fopenmp" ];
+
+  meta = with lib; {
+    description = "Automatic Differentiation of C/C++";
+    homepage = "https://github.com/coin-or/ADOL-C";
+    maintainers = [ maintainers.bzizou ];
+    license = licenses.gpl2Plus;
+  };
+}
+
--- a/pkgs/applications/science/math/almonds/default.nix
+++ b/pkgs/applications/science/math/almonds/default.nix
@ -0,0 +1,26 @@
+{ lib, python3, fetchFromGitHub, ncurses }:
+
+with python3.pkgs; buildPythonApplication rec {
+  pname = "almonds";
+  version = "1.25b";
+
+  src = fetchFromGitHub {
+    owner = "Tenchi2xh";
+    repo = "Almonds";
+    rev = version;
+    sha256 = "0j8d8jizivnfx8lpc4w6sbqj5hq35nfz0vdg7ld80sc5cs7jr3ws";
+  };
+
+  nativeBuildInputs = [ pytest ];
+  buildInputs = [ ncurses ];
+  propagatedBuildInputs = [ pillow ];
+
+  checkPhase = "py.test";
+
+  meta = with lib; {
+    description = "Terminal Mandelbrot fractal viewer";
+    homepage = "https://github.com/Tenchi2xh/Almonds";
+    license = licenses.mit;
+    maintainers = with maintainers; [ infinisil ];
+  };
+}
--- a/pkgs/applications/science/math/bcal/default.nix
+++ b/pkgs/applications/science/math/bcal/default.nix
@ -0,0 +1,37 @@
+{ lib
+, stdenv
+, fetchFromGitHub
+, readline
+, bc
+, python3Packages
+}:
+
+stdenv.mkDerivation rec {
+  pname = "bcal";
+  version = "2.4";
+
+  src = fetchFromGitHub {
+    owner = "jarun";
+    repo = "bcal";
+    rev = "v${version}";
+    sha256 = "sha256-PleWU2yyJzkUAZEvEYoCGdpEXqOgRvZK9zXTYrxRtQU=";
+  };
+
+  buildInputs = [ readline ];
+
+  installFlags = [ "PREFIX=$(out)" ];
+
+  doCheck = true;
+
+  checkInputs = [ bc python3Packages.pytestCheckHook ];
+
+  pytestFlagsArray = [ "test.py" ];
+
+  meta = with lib; {
+    description = "Storage conversion and expression calculator";
+    homepage = "https://github.com/jarun/bcal";
+    license = licenses.gpl3Only;
+    platforms = platforms.unix;
+    maintainers = with maintainers; [ jfrankenau ];
+  };
+}
--- a/pkgs/applications/science/math/bliss/default.nix
+++ b/pkgs/applications/science/math/bliss/default.nix
@ -0,0 +1,37 @@
+{ lib, stdenv, fetchurl, unzip, doxygen }:
+
+stdenv.mkDerivation rec {
+  pname = "bliss";
+  version = "0.73";
+
+  src = fetchurl {
+    url = "http://www.tcs.hut.fi/Software/bliss/${pname}-${version}.zip";
+    sha256 = "f57bf32804140cad58b1240b804e0dbd68f7e6bf67eba8e0c0fa3a62fd7f0f84";
+  };
+
+  patches = fetchurl {
+    url = "http://scip.zib.de/download/bugfixes/scip-5.0.1/bliss-0.73.patch";
+    sha256 = "815868d6586bcd49ff3c28e14ccb536d38b2661151088fe08187c13909c5dab0";
+  };
+
+  nativeBuildInputs = [ unzip doxygen ];
+
+  preBuild = ''
+    doxygen Doxyfile
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin $out/share/doc/bliss $out/lib $out/include/bliss
+    mv bliss $out/bin
+    mv html/* COPYING* $out/share/doc/bliss
+    mv *.a $out/lib
+    mv *.h *.hh $out/include/bliss
+  '';
+
+  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";
+    homepage = "http://www.tcs.hut.fi/Software/bliss/";
+    license = licenses.lgpl3;
+    platforms = [ "i686-linux" "x86_64-linux" ];
+  };
+}
--- a/pkgs/applications/science/math/caffe/darwin.patch
+++ b/pkgs/applications/science/math/caffe/darwin.patch
@ -0,0 +1,47 @@
+diff --git a/Makefile b/Makefile
+index c823f66e..65b90c5e 100644
+--- a/Makefile
+++ b/Makefile
+@@ -32,9 +32,9 @@ SRC_DIRS := $(shell find * -type d -exec bash -c "find {} -maxdepth 1 \
+ LIBRARY_NAME := $(PROJECT)
+ LIB_BUILD_DIR := $(BUILD_DIR)/lib
+ STATIC_NAME := $(LIB_BUILD_DIR)/lib$(LIBRARY_NAME).a
+-DYNAMIC_VERSION_MAJOR 		:= 1
+-DYNAMIC_VERSION_MINOR 		:= 0
+-DYNAMIC_VERSION_REVISION 	:= 0
+DYNAMIC_VERSION_MAJOR		:= 1
+DYNAMIC_VERSION_MINOR		:= 0
+DYNAMIC_VERSION_REVISION	:= 0
+ DYNAMIC_NAME_SHORT := lib$(LIBRARY_NAME).so
+ #DYNAMIC_SONAME_SHORT := $(DYNAMIC_NAME_SHORT).$(DYNAMIC_VERSION_MAJOR)
+ DYNAMIC_VERSIONED_NAME_SHORT := $(DYNAMIC_NAME_SHORT).$(DYNAMIC_VERSION_MAJOR).$(DYNAMIC_VERSION_MINOR).$(DYNAMIC_VERSION_REVISION)
+diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake
+index c48255c8..cf4c580e 100644
+--- a/cmake/Dependencies.cmake
+++ b/cmake/Dependencies.cmake
+@@ -105,7 +105,6 @@ if(USE_OPENCV)
+ endif()
+ 
+ # ---[ BLAS
+-if(NOT APPLE)
+   set(BLAS "Atlas" CACHE STRING "Selected BLAS library")
+   set_property(CACHE BLAS PROPERTY STRINGS "Atlas;Open;MKL")
+ 
+@@ -123,17 +122,6 @@ if(NOT APPLE)
+     list(APPEND Caffe_LINKER_LIBS PUBLIC ${MKL_LIBRARIES})
+     list(APPEND Caffe_DEFINITIONS PUBLIC -DUSE_MKL)
+   endif()
+-elseif(APPLE)
+-  find_package(vecLib REQUIRED)
+-  list(APPEND Caffe_INCLUDE_DIRS PUBLIC ${vecLib_INCLUDE_DIR})
+-  list(APPEND Caffe_LINKER_LIBS PUBLIC ${vecLib_LINKER_LIBS})
+-
+-  if(VECLIB_FOUND)
+-    if(NOT vecLib_INCLUDE_DIR MATCHES "^/System/Library/Frameworks/vecLib.framework.*")
+-      list(APPEND Caffe_DEFINITIONS PUBLIC -DUSE_ACCELERATE)
+-    endif()
+-  endif()
+-endif()
+ 
+ # ---[ Python
+ if(BUILD_python)
--- a/pkgs/applications/science/math/caffe/default.nix
+++ b/pkgs/applications/science/math/caffe/default.nix
@ -0,0 +1,149 @@
+{ config, stdenv, lib
+, fetchFromGitHub
+, fetchurl
+, cmake
+, boost
+, gflags
+, glog
+, hdf5-cpp
+, opencv3
+, protobuf
+, doxygen
+, blas
+, Accelerate, CoreGraphics, CoreVideo
+, lmdbSupport ? true, lmdb
+, leveldbSupport ? true, leveldb, snappy
+, cudaSupport ? config.cudaSupport or false, cudaPackages ? {}
+, cudnnSupport ? cudaSupport
+, ncclSupport ? false
+, pythonSupport ? false, python ? null, numpy ? null
+, substituteAll
+}:
+
+let
+  inherit (cudaPackages) cudatoolkit cudnn nccl;
+in
+
+assert leveldbSupport -> (leveldb != null && snappy != null);
+assert cudnnSupport -> cudaSupport;
+assert ncclSupport -> cudaSupport;
+assert pythonSupport -> (python != null && numpy != null);
+
+let
+  toggle = bool: if bool then "ON" else "OFF";
+
+  test_model_weights = fetchurl {
+    url = "http://dl.caffe.berkeleyvision.org/bvlc_reference_caffenet.caffemodel";
+    sha256 = "472d4a06035497b180636d8a82667129960371375bd10fcb6df5c6c7631f25e0";
+  };
+
+in
+
+stdenv.mkDerivation rec {
+  pname = "caffe";
+  version = "1.0";
+
+  src = fetchFromGitHub {
+    owner = "BVLC";
+    repo = "caffe";
+    rev = version;
+    sha256 = "104jp3cm823i3cdph7hgsnj6l77ygbwsy35mdmzhmsi4jxprd9j3";
+  };
+
+  nativeBuildInputs = [ cmake doxygen ];
+
+  cmakeFlags =
+    # It's important that caffe is passed the major and minor version only because that's what
+    # boost_python expects
+    [ (if pythonSupport then "-Dpython_version=${python.pythonVersion}" else "-DBUILD_python=OFF")
+      "-DBLAS=open"
+    ] ++ (if cudaSupport then [
+           "-DCUDA_ARCH_NAME=All"
+           "-DCUDA_HOST_COMPILER=${cudatoolkit.cc}/bin/cc"
+         ] else [ "-DCPU_ONLY=ON" ])
+      ++ ["-DUSE_NCCL=${toggle ncclSupport}"]
+      ++ ["-DUSE_LEVELDB=${toggle leveldbSupport}"]
+      ++ ["-DUSE_LMDB=${toggle lmdbSupport}"];
+
+  buildInputs = [ boost gflags glog protobuf hdf5-cpp opencv3 blas ]
+                ++ lib.optional cudaSupport cudatoolkit
+                ++ lib.optional cudnnSupport cudnn
+                ++ lib.optional lmdbSupport lmdb
+                ++ lib.optional ncclSupport nccl
+                ++ lib.optionals leveldbSupport [ leveldb snappy ]
+                ++ lib.optionals pythonSupport [ python numpy ]
+                ++ lib.optionals stdenv.isDarwin [ Accelerate CoreGraphics CoreVideo ]
+                ;
+
+  propagatedBuildInputs = lib.optionals pythonSupport (
+    # requirements.txt
+    let pp = python.pkgs; in ([
+      pp.numpy pp.scipy pp.scikitimage pp.h5py
+      pp.matplotlib pp.ipython pp.networkx pp.nose
+      pp.pandas pp.python-dateutil pp.protobuf pp.gflags
+      pp.pyyaml pp.pillow pp.six
+    ] ++ lib.optional leveldbSupport pp.leveldb)
+  );
+
+  outputs = [ "bin" "out" ];
+  propagatedBuildOutputs = []; # otherwise propagates out -> bin cycle
+
+  patches = [
+    ./darwin.patch
+  ] ++ lib.optional pythonSupport (substituteAll {
+    src = ./python.patch;
+    inherit (python.sourceVersion) major minor;  # Should be changed in case of PyPy
+  });
+
+  postPatch = ''
+    substituteInPlace src/caffe/util/io.cpp --replace \
+      'SetTotalBytesLimit(kProtoReadBytesLimit, 536870912)' \
+      'SetTotalBytesLimit(kProtoReadBytesLimit)'
+  '' + lib.optionalString (cudaSupport && lib.versionAtLeast cudatoolkit.version "9.0") ''
+    # CUDA 9.0 doesn't support sm_20
+    sed -i 's,20 21(20) ,,' cmake/Cuda.cmake
+  '';
+
+  preConfigure = lib.optionalString pythonSupport ''
+    # We need this when building with Python bindings
+    export BOOST_LIBRARYDIR="${boost.out}/lib";
+  '';
+
+  postInstall = ''
+    # Internal static library.
+    rm $out/lib/libproto.a
+
+    # Install models
+    cp -a ../models $out/share/Caffe/models
+
+    moveToOutput "bin" "$bin"
+  '' + lib.optionalString pythonSupport ''
+    mkdir -p $out/${python.sitePackages}
+    mv $out/python/caffe $out/${python.sitePackages}
+    rm -rf $out/python
+  '';
+
+  doInstallCheck = false; # build takes more than 30 min otherwise
+  installCheckPhase = ''
+    model=bvlc_reference_caffenet
+    m_path="$out/share/Caffe/models/$model"
+    $bin/bin/caffe test \
+      -model "$m_path/deploy.prototxt" \
+      -solver "$m_path/solver.prototxt" \
+      -weights "${test_model_weights}"
+  '';
+
+  meta = with lib; {
+    description = "Deep learning framework";
+    longDescription = ''
+      Caffe is a deep learning framework made with expression, speed, and
+      modularity in mind. It is developed by the Berkeley Vision and Learning
+      Center (BVLC) and by community contributors.
+    '';
+    homepage = "http://caffe.berkeleyvision.org/";
+    maintainers = with maintainers; [ ];
+    broken = pythonSupport && (python.isPy310);
+    license = licenses.bsd2;
+    platforms = platforms.linux ++ platforms.darwin;
+  };
+}
--- a/pkgs/applications/science/math/caffe/python.patch
+++ b/pkgs/applications/science/math/caffe/python.patch
@ -0,0 +1,70 @@
+commit b14ca23651d390fcae4a929dedc7c33a83453a66
+Author: Frederik Rietdijk <fridh@fridh.nl>
+Date:   Sun Feb 17 08:41:27 2019 +0100
+
+    Find boost_pythonXX
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 08f56a33..0a04592a 100644
+--- a/CMakeLists.txt
+++ b/CMakeLists.txt
+@@ -99,10 +99,10 @@ add_subdirectory(docs)
+ add_custom_target(lint COMMAND ${CMAKE_COMMAND} -P ${PROJECT_SOURCE_DIR}/cmake/lint.cmake)
+ 
+ # ---[ pytest target
+-if(BUILD_python)
+-  add_custom_target(pytest COMMAND python${python_version} -m unittest discover -s caffe/test WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/python )
+-  add_dependencies(pytest pycaffe)
+-endif()
+# if(BUILD_python)
+#   add_custom_target(pytest COMMAND python${python_version} -m unittest discover -s caffe/test WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/python )
+#   add_dependencies(pytest pycaffe)
+# endif()
+ 
+ # ---[ uninstall target
+ configure_file(
+diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake
+index 4a5bac47..be026d43 100644
+--- a/cmake/Dependencies.cmake
+++ b/cmake/Dependencies.cmake
+@@ -141,37 +141,14 @@ if(BUILD_python)
+     # use python3
+     find_package(PythonInterp 3.0)
+     find_package(PythonLibs 3.0)
+-    find_package(NumPy 1.7.1)
+-    # Find the matching boost python implementation
+-    set(version ${PYTHONLIBS_VERSION_STRING})
+-
+-    STRING( REGEX REPLACE "[^0-9]" "" boost_py_version ${version} )
+-    find_package(Boost 1.46 COMPONENTS "python-py${boost_py_version}")
+-    set(Boost_PYTHON_FOUND ${Boost_PYTHON-PY${boost_py_version}_FOUND})
+-
+-    while(NOT "${version}" STREQUAL "" AND NOT Boost_PYTHON_FOUND)
+-      STRING( REGEX REPLACE "([0-9.]+).[0-9]+" "\\1" version ${version} )
+-
+-      STRING( REGEX REPLACE "[^0-9]" "" boost_py_version ${version} )
+-      find_package(Boost 1.46 COMPONENTS "python-py${boost_py_version}")
+-      set(Boost_PYTHON_FOUND ${Boost_PYTHON-PY${boost_py_version}_FOUND})
+-
+-      STRING( REGEX MATCHALL "([0-9.]+).[0-9]+" has_more_version ${version} )
+-      if("${has_more_version}" STREQUAL "")
+-        break()
+-      endif()
+-    endwhile()
+-    if(NOT Boost_PYTHON_FOUND)
+-      find_package(Boost 1.46 COMPONENTS python)
+-    endif()
+   else()
+     # disable Python 3 search
+     find_package(PythonInterp 2.7)
+     find_package(PythonLibs 2.7)
+-    find_package(NumPy 1.7.1)
+-    find_package(Boost 1.46 COMPONENTS python)
+   endif()
+-  if(PYTHONLIBS_FOUND AND NUMPY_FOUND AND Boost_PYTHON_FOUND)
+  find_package(NumPy 1.7.1)
+  find_package(Boost 1.46 REQUIRED COMPONENTS python@major@@minor@)
+  if(PYTHONLIBS_FOUND AND NUMPY_FOUND AND Boost_PYTHON@major@@minor@_FOUND)
+     set(HAVE_PYTHON TRUE)
+     if(BUILD_python_layer)
+       list(APPEND Caffe_DEFINITIONS PRIVATE -DWITH_PYTHON_LAYER)
--- a/pkgs/applications/science/math/calc/default.nix
+++ b/pkgs/applications/science/math/calc/default.nix
@ -0,0 +1,51 @@
+{ stdenv, lib, fetchurl, util-linux, makeWrapper
+, enableReadline ? true, readline, ncurses }:
+
+stdenv.mkDerivation rec {
+  pname = "calc";
+  version = "2.14.1.0";
+
+  src = fetchurl {
+    urls = [
+      "https://github.com/lcn2/calc/releases/download/${version}/${pname}-${version}.tar.bz2"
+      "http://www.isthe.com/chongo/src/calc/${pname}-${version}.tar.bz2"
+    ];
+    sha256 = "sha256-C1YWZS4x7htUWF3MhRLQIYChL4rdwJxASdPQjttUr0A=";
+  };
+
+  postPatch = ''
+    substituteInPlace Makefile \
+      --replace '-install_name ''${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''${LIB_EXT_VERSION}'
+  '';
+
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ util-linux ]
+             ++ lib.optionals enableReadline [ readline ncurses ];
+
+  makeFlags = [
+    "T=$(out)"
+    "INCDIR="
+    "BINDIR=/bin"
+    "LIBDIR=/lib"
+    "CALC_SHAREDIR=/share/calc"
+    "CALC_INCDIR=/include"
+    "MANDIR=/share/man/man1"
+
+    # Handle LDFLAGS defaults in calc
+    "DEFAULT_LIB_INSTALL_PATH=$(out)/lib"
+  ] ++ lib.optionals enableReadline [
+    "READLINE_LIB=-lreadline"
+    "USE_READLINE=-DUSE_READLINE"
+  ];
+
+  meta = with lib; {
+    description = "C-style arbitrary precision calculator";
+    homepage = "http://www.isthe.com/chongo/tech/comp/calc/";
+    # The licensing situation depends on readline (see section 3 of the LGPL)
+    # If linked against readline then GPLv2 otherwise LGPLv2.1
+    license = with licenses; if enableReadline then gpl2Only else lgpl21Only;
+    maintainers = with maintainers; [ matthewbauer ];
+    platforms = platforms.all;
+  };
+}
--- a/pkgs/applications/science/math/calculix/calculix.patch
+++ b/pkgs/applications/science/math/calculix/calculix.patch
@ -0,0 +1,23 @@
+diff --git a/ccx_2.19/src/Makefile b/ccx_2.19/src/Makefile
+index c503513..8a69a0c 100755
+--- a/ccx_2.19/src/Makefile
+++ b/ccx_2.19/src/Makefile
+@@ -18,15 +18,10 @@ OCCXF = $(SCCXF:.f=.o)
+ OCCXC = $(SCCXC:.c=.o)
+ OCCXMAIN = $(SCCXMAIN:.c=.o)
+ 
+-DIR=../../../SPOOLES.2.2
+LIBS = -lpthread -lm -lc -lspooles -larpack -lblas -llapack
+ 
+-LIBS = \
+-       $(DIR)/spooles.a \
+-	../../../ARPACK/libarpack_INTEL.a \
+-       -lpthread -lm -lc
+-
+-ccx_2.19: $(OCCXMAIN) ccx_2.19.a  $(LIBS)
+-	./date.pl; $(CC) $(CFLAGS) -c ccx_2.19.c; $(FC)  -Wall -O2 -o $@ $(OCCXMAIN) ccx_2.19.a $(LIBS) -fopenmp
+ccx_2.19: $(OCCXMAIN) ccx_2.19.a
+	$(CC) $(CFLAGS) -c ccx_2.19.c; $(FC)  -Wall -O2 -o $@ $(OCCXMAIN) ccx_2.19.a $(LIBS) -fopenmp
+ 
+ ccx_2.19.a: $(OCCXF) $(OCCXC)
+ 	ar vr $@ $?
--- a/pkgs/applications/science/math/calculix/default.nix
+++ b/pkgs/applications/science/math/calculix/default.nix
@ -0,0 +1,40 @@
+{ lib, stdenv, fetchurl, gfortran, arpack, spooles, blas, lapack }:
+
+stdenv.mkDerivation rec {
+  pname = "calculix";
+  version = "2.19";
+
+  src = fetchurl {
+    url = "http://www.dhondt.de/ccx_${version}.src.tar.bz2";
+    sha256 = "01vdy9sns58hkm39z6d0r5y7gzqf5z493d18jin9krqib1l6jnn7";
+  };
+
+  nativeBuildInputs = [ gfortran ];
+
+  buildInputs = [ arpack spooles blas lapack ];
+
+  NIX_CFLAGS_COMPILE = [
+    "-I${spooles}/include/spooles"
+    "-std=legacy"
+  ];
+
+  patches = [
+    ./calculix.patch
+  ];
+
+  postPatch = ''
+    cd ccx*/src
+  '';
+
+  installPhase = ''
+    install -Dm0755 ccx_${version} $out/bin/ccx
+  '';
+
+  meta = with lib; {
+    homepage = "http://www.calculix.de/";
+    description = "Three-dimensional structural finite element program";
+    license = licenses.gpl2Plus;
+    maintainers = with maintainers; [ gebner ];
+    platforms = platforms.unix;
+  };
+}
--- a/pkgs/applications/science/math/cbc/default.nix
+++ b/pkgs/applications/science/math/cbc/default.nix
@ -0,0 +1,33 @@
+{ lib, stdenv, fetchurl, zlib, bzip2 }:
+
+stdenv.mkDerivation rec {
+  pname = "cbc";
+  version = "2.10.4";
+
+  # Note: Cbc 2.10.5 contains Clp 1.17.5 which hits this bug
+  # that breaks or-tools https://github.com/coin-or/Clp/issues/130
+
+  src = fetchurl {
+    url = "https://www.coin-or.org/download/source/Cbc/Cbc-${version}.tgz";
+    sha256 = "0zq66j1vvpslswhzi9yfgkv6vmg7yry4pdmfgqaqw2vhyqxnsy39";
+  };
+
+  # or-tools has a hard dependency on Cbc static libraries, so we build both
+  configureFlags = [ "-C" "--enable-static" ];
+
+  enableParallelBuilding = true;
+
+  hardeningDisable = [ "format" ];
+
+  buildInputs = [ zlib bzip2 ];
+
+  # FIXME: move share/coin/Data to a separate output?
+
+  meta = {
+    homepage = "https://projects.coin-or.org/Cbc";
+    license = lib.licenses.epl10;
+    maintainers = [ lib.maintainers.eelco ];
+    platforms = lib.platforms.linux ++ lib.platforms.darwin;
+    description = "A mixed integer programming solver";
+  };
+}
--- a/pkgs/applications/science/math/cemu/default.nix
+++ b/pkgs/applications/science/math/cemu/default.nix
@ -0,0 +1,57 @@
+{ fetchFromGitHub
+, lib
+, SDL2
+, libGL
+, libarchive
+, libusb-compat-0_1
+, qtbase
+, qmake
+, git
+, libpng
+, pkg-config
+, wrapQtAppsHook
+, stdenv
+}:
+
+stdenv.mkDerivation rec {
+  pname = "CEmu";
+  version = "1.3";
+  src = fetchFromGitHub {
+    owner = "CE-Programming";
+    repo = "CEmu";
+    rev = "v${version}";
+    sha256 = "1wcdnzcqscawj6jfdj5wwmw9g9vsd6a1rx0rrramakxzf8b7g47r";
+    fetchSubmodules = true;
+  };
+
+  nativeBuildInputs = [
+    qmake
+    git
+    wrapQtAppsHook
+    pkg-config
+  ];
+
+  buildInputs = [
+    SDL2
+    libGL
+    libarchive
+    libusb-compat-0_1
+    qtbase
+    libpng
+  ];
+
+  qmakeFlags = [
+    "gui/qt"
+    "CONFIG+=ltcg"
+  ];
+
+  meta = with lib; {
+    changelog = "https://github.com/CE-Programming/CEmu/releases/tag/v${version}";
+    description = "Third-party TI-84 Plus CE / TI-83 Premium CE emulator, focused on developer features";
+    homepage = "https://ce-programming.github.io/CEmu";
+    license = licenses.gpl3;
+    maintainers = with maintainers; [ luc65r ];
+    platforms = [ "x86_64-linux" "x86_64-darwin" ];
+    broken = stdenv.isDarwin;
+  };
+}
--- a/pkgs/applications/science/math/clp/default.nix
+++ b/pkgs/applications/science/math/clp/default.nix
@ -0,0 +1,22 @@
+{ lib, stdenv, fetchurl, zlib }:
+
+stdenv.mkDerivation rec {
+  version = "1.17.6";
+  pname = "clp";
+  src = fetchurl {
+    url = "https://www.coin-or.org/download/source/Clp/Clp-${version}.tgz";
+    sha256 = "0ap1f0lxppa6pnbc4bg7ih7a96avwaki482nig8w5fr3vg9wvkzr";
+  };
+
+  propagatedBuildInputs = [ zlib ];
+
+  doCheck = true;
+
+  meta = with lib; {
+    license = licenses.epl10;
+    homepage = "https://github.com/coin-or/Clp";
+    description = "An open-source linear programming solver written in C++";
+    platforms = platforms.darwin ++ [ "x86_64-linux" ];
+    maintainers = [ maintainers.vbgl ];
+  };
+}
--- a/pkgs/applications/science/math/cntk/default.nix
+++ b/pkgs/applications/science/math/cntk/default.nix
@ -0,0 +1,132 @@
+{ lib, stdenv, fetchFromGitHub, cmake
+, fetchpatch
+, openblas, blas, lapack, opencv3, libzip, boost, protobuf, mpi
+, onebitSGDSupport ? false
+, cudaSupport ? false, cudaPackages ? {}, addOpenGLRunpath, cudatoolkit, nvidia_x11
+, cudnnSupport ? cudaSupport
+}:
+
+let
+  inherit (cudaPackages) cudatoolkit cudnn;
+in
+
+assert cudnnSupport -> cudaSupport;
+assert blas.implementation == "openblas" && lapack.implementation == "openblas";
+
+let
+  # Old specific version required for CNTK.
+  cub = fetchFromGitHub {
+    owner = "NVlabs";
+    repo = "cub";
+    rev = "1.7.4";
+    sha256 = "0ksd5n1lxqhm5l5cd2lps4cszhjkf6gmzahaycs7nxb06qci8c66";
+  };
+
+in stdenv.mkDerivation rec {
+  pname = "CNTK";
+  version = "2.7";
+
+  src = fetchFromGitHub {
+    owner = "Microsoft";
+    repo = "CNTK";
+    rev = "v${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
+  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; {
+    # Newer cub is included with cudatoolkit now and it breaks the build.
+    # https://github.com/Microsoft/CNTK/issues/3191
+    broken = cudaSupport;
+    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 ];
+  };
+}
--- a/pkgs/applications/science/math/colpack/default.nix
+++ b/pkgs/applications/science/math/colpack/default.nix
@ -0,0 +1,43 @@
+{ lib, stdenv, fetchFromGitHub, autoreconfHook }:
+
+stdenv.mkDerivation rec {
+
+  pname = "ColPack";
+  version = "1.0.10";
+
+  src = fetchFromGitHub {
+    owner = "CSCsw";
+    repo = pname;
+    rev = "v" + version;
+    sha256 = "1p05vry940mrjp6236c0z83yizmw9pk6ly2lb7d8rpb7j9h03glr";
+  };
+
+  nativeBuildInputs = [ autoreconfHook ];
+
+  configureFlags = [
+    "--enable-openmp=${if stdenv.isLinux then "yes" else "no"}"
+    "--enable-examples=no"
+  ];
+
+  postInstall = ''
+    # Remove libtool archive
+    rm $out/lib/*.la
+
+    # Remove compiled examples (Basic examples get compiled anyway)
+    rm -r $out/examples
+
+    # Copy the example sources (Basic tree contains scripts and object files)
+    mkdir -p $out/share/ColPack/examples/Basic
+    cp SampleDrivers/Basic/*.cpp $out/share/ColPack/examples/Basic
+    cp -r SampleDrivers/Matrix* $out/share/ColPack/examples
+  '';
+
+  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";
+    license = licenses.lgpl3Plus;
+    platforms = platforms.unix;
+    maintainers = with maintainers; [ edwtjo ];
+  };
+}
--- a/pkgs/applications/science/math/cplex/default.nix
+++ b/pkgs/applications/science/math/cplex/default.nix
@ -0,0 +1,87 @@
+{ lib, stdenv, makeWrapper, openjdk, gtk2, xorg, glibcLocales, releasePath ? null }:
+
+# To use this package, you need to download your own cplex installer from IBM
+# and override the releasePath attribute to point to the location of the file.
+#
+# Note: cplex creates an individual build for each license which screws
+# somewhat with the use of functions like requireFile as the hash will be
+# different for every user.
+
+stdenv.mkDerivation rec {
+  pname = "cplex";
+  version = "128";
+
+  src =
+    if releasePath == null then
+      throw ''
+        This nix expression requires that the cplex installer is already
+        downloaded to your machine. Get it from IBM:
+        https://developer.ibm.com/docloud/blog/2017/12/20/cplex-optimization-studio-12-8-now-available/
+
+        Set `cplex.releasePath = /path/to/download;` in your
+        ~/.config/nixpkgs/config.nix for `nix-*` commands, or
+        `config.cplex.releasePath = /path/to/download;` in your
+        `configuration.nix` for NixOS.
+      ''
+    else
+      releasePath;
+
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ openjdk gtk2 xorg.libXtst glibcLocales ];
+
+  unpackPhase = "cp $src $name";
+
+  patchPhase = ''
+    sed -i -e 's|/usr/bin/tr"|tr"         |' $name
+  '';
+
+  buildPhase = ''
+    sh $name -i silent -DLICENSE_ACCEPTED=TRUE -DUSER_INSTALL_DIR=$out
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin
+    ln -s $out/opl/bin/x86-64_linux/oplrun\
+      $out/opl/bin/x86-64_linux/oplrunjava\
+      $out/opl/oplide/oplide\
+      $out/cplex/bin/x86-64_linux/cplex\
+      $out/cpoptimizer/bin/x86-64_linux/cpoptimizer\
+      $out/bin
+  '';
+
+  fixupPhase =
+  let
+    libraryPath = lib.makeLibraryPath [ stdenv.cc.cc gtk2 xorg.libXtst ];
+  in ''
+    interpreter=${stdenv.cc.libc}/lib/ld-linux-x86-64.so.2
+
+    for pgm in $out/opl/bin/x86-64_linux/oplrun $out/opl/bin/x86-64_linux/oplrunjava $out/opl/oplide/oplide;
+    do
+      patchelf --set-interpreter "$interpreter" $pgm;
+      wrapProgram $pgm \
+        --prefix LD_LIBRARY_PATH : $out/opl/bin/x86-64_linux:${libraryPath} \
+        --set LOCALE_ARCHIVE ${glibcLocales}/lib/locale/locale-archive;
+    done
+
+    for pgm in $out/cplex/bin/x86-64_linux/cplex $out/cpoptimizer/bin/x86-64_linux/cpoptimizer $out/opl/oplide/jre/bin/*;
+    do
+      if grep ELF $pgm > /dev/null;
+      then
+        patchelf --set-interpreter "$interpreter" $pgm;
+      fi
+    done
+  '';
+
+  passthru = {
+    libArch = "x86-64_linux";
+    libSuffix = "${version}0";
+  };
+
+  meta = with lib; {
+    description = "Optimization solver for mathematical programming";
+    homepage = "https://www.ibm.com/be-en/marketplace/ibm-ilog-cplex";
+    license = licenses.unfree;
+    platforms = [ "x86_64-linux" ];
+    maintainers = with maintainers; [ bfortz ];
+  };
+}
--- a/pkgs/applications/science/math/csdp/default.nix
+++ b/pkgs/applications/science/math/csdp/default.nix
@ -0,0 +1,30 @@
+{ lib, stdenv, fetchurl, blas, gfortran, lapack }:
+
+stdenv.mkDerivation rec {
+  pname = "csdp";
+  version = "6.1.1";
+
+  src = fetchurl {
+    url = "https://www.coin-or.org/download/source/Csdp/Csdp-${version}.tgz";
+    sha256 = "1f9ql6cjy2gwiyc51ylfan24v1ca9sjajxkbhszlds1lqmma8n05";
+  };
+
+  buildInputs = [ blas gfortran.cc.lib lapack ];
+
+  postPatch = ''
+    substituteInPlace Makefile --replace /usr/local/bin $out/bin
+  '';
+
+  preInstall = ''
+    rm -f INSTALL
+    mkdir -p $out/bin
+  '';
+
+  meta = {
+    homepage = "https://projects.coin-or.org/Csdp";
+    license = lib.licenses.cpl10;
+    maintainers = [ lib.maintainers.roconnor ];
+    description = "A C Library for Semidefinite Programming";
+    platforms = lib.platforms.unix;
+  };
+}
--- a/pkgs/applications/science/math/dap/default.nix
+++ b/pkgs/applications/science/math/dap/default.nix
@ -0,0 +1,37 @@
+{ lib
+, stdenv
+, fetchurl
+}:
+
+stdenv.mkDerivation rec {
+  pname = "dap";
+  version = "3.10";
+
+  src = fetchurl {
+    url = "mirror://gnu/${pname}/${pname}-${version}.tar.gz";
+    sha256 = "Bk5sty/438jLb1PpurMQ5OqMbr6JqUuuQjcg2bejh2Y=";
+  };
+
+  hardeningDisable = [ "format" ];
+
+  meta = with lib; {
+    homepage = "https://www.gnu.org/software/dap";
+    description = "A small statistics and graphics package based on C";
+    longDescription = ''
+      Dap is a small statistics and graphics package based on C. Version 3.0 and
+      later of Dap can read SBS programs (based on the utterly famous, industry
+      standard statistics system with similar initials - you know the one I
+      mean)! The user wishing to perform basic statistical analyses is now freed
+      from learning and using C syntax for straightforward tasks, while
+      retaining access to the C-style graphics and statistics features provided
+      by the original implementation. Dap provides core methods of data
+      management, analysis, and graphics that are commonly used in statistical
+      consulting practice (univariate statistics, correlations and regression,
+      ANOVA, categorical data analysis, logistic regression, and nonparametric
+      analyses).
+    '';
+    license = licenses.gpl3Plus;
+    maintainers = with maintainers; [ AndersonTorres ];
+    platforms = platforms.unix;
+  };
+}
--- a/pkgs/applications/science/math/ecm/default.nix
+++ b/pkgs/applications/science/math/ecm/default.nix
@ -0,0 +1,31 @@
+{ lib, stdenv, fetchurl, gmp, m4 }:
+
+let
+  pname = "ecm";
+  version = "7.0.4";
+  name = "${pname}-${version}";
+in
+
+stdenv.mkDerivation {
+  inherit name;
+
+  src = fetchurl {
+    url = "http://gforge.inria.fr/frs/download.php/file/36224/ecm-${version}.tar.gz";
+    sha256 = "0hxs24c2m3mh0nq1zz63z3sb7dhy1rilg2s1igwwcb26x3pb7xqc";
+  };
+
+  # See https://trac.sagemath.org/ticket/19233
+  configureFlags = lib.optional stdenv.isDarwin "--disable-asm-redc";
+
+  buildInputs = [ m4 gmp ];
+
+  doCheck = true;
+
+  meta = {
+    description = "Elliptic Curve Method for Integer Factorization";
+    license = lib.licenses.gpl2Plus;
+    homepage = "http://ecm.gforge.inria.fr/";
+    maintainers = [ lib.maintainers.roconnor ];
+    platforms = with lib.platforms; linux ++ darwin;
+  };
+}
--- a/pkgs/applications/science/math/engauge-digitizer/default.nix
+++ b/pkgs/applications/science/math/engauge-digitizer/default.nix
@ -0,0 +1,60 @@
+{ lib, stdenv, fetchFromGitHub, fftw, libjpeg, log4cpp, openjpeg
+, libpng12, poppler, qtbase, qt5, qmake, wrapQtAppsHook
+}:
+
+stdenv.mkDerivation rec {
+  pname = "engauge-digitizer";
+  version = "12.2.2";
+
+  src = fetchFromGitHub {
+    owner = "markummitchell";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "sha256-Wj9o3wWbtHsEi6LFH4xDpwVR9BwcWc472jJ/QFDQZvY=";
+  };
+
+  nativeBuildInputs = [ qmake wrapQtAppsHook ];
+
+  buildInputs = [
+    qtbase
+    qt5.qttools
+    poppler
+    libpng12
+    openjpeg
+    openjpeg.dev
+    log4cpp
+    libjpeg
+    fftw
+  ];
+
+  qmakeFlags = [
+    "CONFIG+=jpeg2000"
+    "CONFIG+=pdf"
+    "CONFIG+=log4cpp_null"
+  ];
+
+  POPPLER_INCLUDE = "${poppler.dev}/include/poppler/qt5";
+
+  POPPLER_LIB = "${poppler}/lib";
+
+  OPENJPEG_INCLUDE = "${openjpeg.dev}/include/${openjpeg.pname}-${lib.versions.majorMinor openjpeg.version}";
+
+  OPENJPEG_LIB = "${openjpeg}/lib";
+
+  installPhase = ''
+    runHook preInstall
+
+    mkdir -p $out/bin
+    cp bin/engauge $out/bin/
+
+    runHook postInstall
+  '';
+
+  meta = with lib; {
+    description = "Engauge Digitizer is a tool for recovering graph data from an image file";
+    homepage = "https://markummitchell.github.io/engauge-digitizer";
+    license = with licenses; [ gpl2Only ];
+    platforms = platforms.linux;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}
--- a/pkgs/applications/science/math/eukleides/default.nix
+++ b/pkgs/applications/science/math/eukleides/default.nix
@ -0,0 +1,73 @@
+{ lib, stdenv, fetchurl, bison, flex, makeWrapper, texinfo4, getopt, readline, texlive }:
+
+lib.fix (eukleides: stdenv.mkDerivation rec {
+  pname = "eukleides";
+  version = "1.5.4";
+
+  src = fetchurl {
+    url = "http://www.eukleides.org/files/${pname}-${version}.tar.bz2";
+    sha256 = "0s8cyh75hdj89v6kpm3z24i48yzpkr8qf0cwxbs9ijxj1i38ki0q";
+  };
+
+  patches = [
+    # use $CC instead of hardcoded gcc
+    ./use-CC.patch
+    # allow PostScript transparency in epstopdf call
+    ./gs-allowpstransparency.patch
+  ];
+
+  nativeBuildInputs = [ bison flex texinfo4 makeWrapper ];
+
+  buildInputs = [ getopt readline ];
+
+  preConfigure = ''
+    substituteInPlace Makefile \
+      --replace mktexlsr true
+
+    substituteInPlace doc/Makefile \
+      --replace ginstall-info install-info
+
+    substituteInPlace Config \
+      --replace '/usr/local' "$out" \
+      --replace '$(SHARE_DIR)/texmf' "$tex"
+  '';
+
+  # Workaround build failure on -fno-common toolchains like upstream
+  # gcc-10. Otherwise build fails as:
+  #   ld: eukleides_build/triangle.o:(.bss+0x28): multiple definition of `A';
+  #     eukleides_build/quadrilateral.o:(.bss+0x18): first defined here
+  NIX_CFLAGS_COMPILE = "-fcommon";
+
+  preInstall = ''
+    mkdir -p $out/bin
+  '';
+
+  postInstall = ''
+    wrapProgram $out/bin/euktoeps \
+      --prefix PATH : ${lib.makeBinPath [ getopt ]}
+  '';
+
+  outputs = [ "out" "doc" "tex" ];
+
+  passthru.tlType = "run";
+  passthru.pkgs = [ eukleides.tex ]
+    # packages needed by euktoeps, euktopdf and eukleides.sty
+    ++ (with texlive; collection-pstricks.pkgs ++ epstopdf.pkgs ++ iftex.pkgs ++ moreverb.pkgs);
+
+  meta = {
+    description = "Geometry Drawing Language";
+    homepage = "http://www.eukleides.org/";
+    license = lib.licenses.gpl3Plus;
+
+    longDescription = ''
+      Eukleides is a computer language devoted to elementary plane
+      geometry. It aims to be a fairly comprehensive system to create
+      geometric figures, either static or dynamic. Eukleides allows to
+      handle basic types of data: numbers and strings, as well as
+      geometric types of data: points, vectors, sets (of points), lines,
+      circles and conics.
+    '';
+
+    platforms = lib.platforms.unix;
+  };
+})
--- a/pkgs/applications/science/math/eukleides/gs-allowpstransparency.patch
+++ b/pkgs/applications/science/math/eukleides/gs-allowpstransparency.patch
@ -0,0 +1,10 @@
+--- a/bash/euktopdf
+++ b/bash/euktopdf
+@@ -55,6 +55,6 @@ do
+     exit 1
+   fi
+   dvips -q -E -o $base.eps $base.dvi &&
+-  epstopdf $base.eps &&
+  epstopdf --gsopt=-dALLOWPSTRANSPARENCY $base.eps &&
+   rm -f $base.{tex,log,dvi,eps}
+ done
--- a/pkgs/applications/science/math/eukleides/use-CC.patch
+++ b/pkgs/applications/science/math/eukleides/use-CC.patch
@ -0,0 +1,11 @@
+--- a/build/Makefile
+++ b/build/Makefile
+@@ -11,7 +11,7 @@ LEX = flex
+ LFLAGS = -8
+ YACC = bison
+ YFLAGS = -d
+-CC = gcc
+CC ?= gcc
+ IFLAGS = -I$(COMMON_DIR) -I$(MAIN_DIR) -I$(BUILD_DIR) 
+ ifneq ($(strip $(LOCALES)),)
+ MOFLAGS = -DMO_DIR=\"$(MO_DIR)\" 
--- a/pkgs/applications/science/math/form/default.nix
+++ b/pkgs/applications/science/math/form/default.nix
@ -0,0 +1,22 @@
+{ lib, stdenv, fetchurl, gmp, zlib }:
+
+stdenv.mkDerivation {
+  version = "4.2.1";
+  pname = "form";
+
+  # This tarball is released by author, it is not downloaded from tag, so can't use fetchFromGitHub
+  src = fetchurl {
+    url = "https://github.com/vermaseren/form/releases/download/v4.2.1/form-4.2.1.tar.gz";
+    sha256 = "0a0smc10gm85vxd85942n5azy88w5qs5avbqrw0lw0yb9injswpj";
+  };
+
+  buildInputs = [ gmp zlib ];
+
+  meta = with lib; {
+    description = "The FORM project for symbolic manipulation of very big expressions";
+    homepage = "https://www.nikhef.nl/~form/";
+    license = licenses.gpl3;
+    maintainers = [ maintainers.veprbl ];
+    platforms = platforms.unix;
+  };
+}
--- a/pkgs/applications/science/math/fricas/default.nix
+++ b/pkgs/applications/science/math/fricas/default.nix
@ -0,0 +1,24 @@
+{ lib, stdenv, fetchurl, sbcl, libX11, libXpm, libICE, libSM, libXt, libXau, libXdmcp }:
+
+stdenv.mkDerivation rec {
+  pname = "fricas";
+  version = "1.3.7";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/fricas/fricas/${version}/fricas-${version}-full.tar.bz2";
+    sha256 = "sha256-cOqMvSe3ef/ZeVy5cj/VU/aTRtxgfxZfRbE4lWE5TU4=";
+  };
+
+  buildInputs = [ sbcl libX11 libXpm libICE libSM libXt libXau libXdmcp ];
+
+  dontStrip = true;
+
+  meta = {
+    homepage = "http://fricas.sourceforge.net/";
+    description = "An advanced computer algebra system";
+    license = lib.licenses.bsd3;
+
+    platforms = lib.platforms.linux;
+    maintainers = [ lib.maintainers.sprock ];
+  };
+}
--- a/pkgs/applications/science/math/gap/default.nix
+++ b/pkgs/applications/science/math/gap/default.nix
@ -0,0 +1,159 @@
+{ stdenv
+, lib
+, fetchurl
+, makeWrapper
+, readline
+, gmp
+, zlib
+# one of
+# - "minimal" (~400M):
+#     Install the bare minimum of packages required by gap to start.
+#     This is likely to break a lot of stuff. Do not expect upstream support with
+#     this configuration.
+# - "standard" (~700M):
+#     Install the "standard packages" which gap autoloads by default. These
+#     packages are effectively considered a part of gap.
+# - "full" (~1.7G):
+#     Install all available packages. This takes a lot of space.
+, packageSet ? "standard"
+# Kept for backwards compatibility. Overrides packageSet to "full".
+, keepAllPackages ? false
+}:
+let
+  # packages absolutely required for gap to start
+  # `*` represents the version where applicable
+  requiredPackages = [
+    "GAPDoc-*"
+    "primgrp-*"
+    "SmallGrp-*"
+    "transgrp"
+  ];
+  # packages autoloaded by default if available
+  autoloadedPackages = [
+    "atlasrep"
+    "autpgrp-*"
+    "alnuth-*"
+    "crisp-*"
+    "ctbllib-*"
+    "FactInt-*"
+    "fga"
+    "irredsol-*"
+    "laguna-*"
+    "polenta-*"
+    "polycyclic-*"
+    "resclasses-*"
+    "sophus-*"
+    "tomlib-*"
+  ];
+  keepAll = keepAllPackages || (packageSet == "full");
+  packagesToKeep = requiredPackages ++ lib.optionals (packageSet == "standard") autoloadedPackages;
+
+  # Generate bash script that removes all packages from the `pkg` subdirectory
+  # that are not on the whitelist. The whitelist consists of strings expected by
+  # `find`'s `-name`.
+  removeNonWhitelistedPkgs = whitelist: ''
+    find pkg -type d -maxdepth 1 -mindepth 1 \
+  '' + (lib.concatStringsSep "\n" (map (str: "-not -name '${str}' \\") whitelist)) + ''
+    -exec echo "Removing package {}" \; \
+    -exec rm -r '{}' \;
+  '';
+in
+stdenv.mkDerivation rec {
+  pname = "gap";
+  # https://www.gap-system.org/Releases/
+  version = "4.11.1";
+
+  src = fetchurl {
+    url = "https://github.com/gap-system/gap/releases/download/v${version}/gap-${version}.tar.gz";
+    sha256 = "sha256-ZjXF2n2CdV+DOUhrnKwzdm9YcS8pfoI0+6QIGJAuowQ=";
+  };
+
+  # remove all non-essential packages (which take up a lot of space)
+  preConfigure = lib.optionalString (!keepAll) (removeNonWhitelistedPkgs packagesToKeep) + ''
+    patchShebangs .
+  '';
+
+  buildInputs = [
+    readline
+    gmp
+    zlib
+  ];
+
+  nativeBuildInputs = [
+    makeWrapper
+  ];
+
+  # "teststandard" is a superset of testinstall. It takes ~1h instead of ~1min.
+  # tests are run twice, once with all packages loaded and once without
+  # checkTarget = "teststandard";
+
+  doInstallCheck = true;
+  installCheckTarget = "check";
+
+  preInstallCheck = ''
+    # gap tests check that the home directory exists
+    export HOME="$TMP/gap-home"
+    mkdir -p "$HOME"
+
+    # make sure gap is in PATH
+    export PATH="$out/bin:$PATH"
+
+    # make sure we don't accidentally use the wrong gap binary
+    rm -r bin
+
+    # like the defaults the Makefile, but use gap from PATH instead of the
+    # one from builddir
+    installCheckFlagsArray+=(
+      "TESTGAP=gap --quitonbreak -b -m 100m -o 1g -q -x 80 -r -A"
+      "TESTGAPauto=gap --quitonbreak -b -m 100m -o 1g -q -x 80 -r"
+    )
+  '';
+
+  postBuild = ''
+    pushd pkg
+    bash ../bin/BuildPackages.sh
+    popd
+  '';
+
+  installTargets = [
+    "install-libgap"
+    "install-headers"
+  ];
+
+  # full `make install` is not yet implemented, just for libgap and headers
+  postInstall = ''
+    # Install config.h, which is not currently handled by `make install-headers`
+    cp gen/config.h "$out/include/gap"
+
+    mkdir -p "$out/bin" "$out/share/gap/"
+
+    echo "Copying files to target directory"
+    cp -ar . "$out/share/gap/build-dir"
+
+    makeWrapper "$out/share/gap/build-dir/bin/gap.sh" "$out/bin/gap" \
+      --set GAP_DIR $out/share/gap/build-dir
+  '';
+
+  preFixup = ''
+    # patchelf won't strip references to the build dir if it still exists
+    rm -rf pkg
+  '';
+
+  meta = with lib; {
+    description = "Computational discrete algebra system";
+    maintainers = with maintainers;
+    [
+      raskin
+      chrisjefferson
+      timokau
+    ];
+    platforms = platforms.all;
+    broken = stdenv.isDarwin;
+    # keeping all packages increases the package size considerably, which is
+    # why a local build is preferable in that situation. The timeframe is
+    # reasonable and that way the binary cache doesn't get overloaded.
+    hydraPlatforms = lib.optionals (!keepAllPackages) meta.platforms;
+    license = licenses.gpl2;
+    homepage = "https://www.gap-system.org";
+  };
+}
--- a/pkgs/applications/science/math/geogebra/default.nix
+++ b/pkgs/applications/science/math/geogebra/default.nix
@ -0,0 +1,92 @@
+{ lib, stdenv, fetchurl, jre, makeDesktopItem, makeWrapper, unzip, language ? "en_US" }:
+let
+  pname = "geogebra";
+  version = "5-0-706-0";
+
+  srcIcon = fetchurl {
+    url = "http://static.geogebra.org/images/geogebra-logo.svg";
+    sha256 = "01sy7ggfvck350hwv0cla9ynrvghvssqm3c59x4q5lwsxjsxdpjm";
+  };
+
+  desktopItem = makeDesktopItem {
+    name = "geogebra";
+    exec = "geogebra";
+    icon = "geogebra";
+    desktopName = "Geogebra";
+    genericName = "Geogebra";
+    comment = meta.description;
+    categories = [ "Education" "Science" "Math" ];
+    mimeTypes = [ "application/vnd.geogebra.file" "application/vnd.geogebra.tool" ];
+  };
+
+  meta = with lib; {
+    description = "Dynamic mathematics software with graphics, algebra and spreadsheets";
+    longDescription = ''
+      Dynamic mathematics software for all levels of education that brings
+      together geometry, algebra, spreadsheets, graphing, statistics and
+      calculus in one easy-to-use package.
+    '';
+    homepage = "https://www.geogebra.org/";
+    maintainers = with maintainers; [ sikmir imsofi ];
+    license = with licenses; [ gpl3 cc-by-nc-sa-30 geogebra ];
+    platforms = with platforms; linux ++ darwin;
+    hydraPlatforms = [];
+  };
+
+  linuxPkg = stdenv.mkDerivation {
+    inherit pname version meta srcIcon desktopItem;
+
+    preferLocalBuild = true;
+
+    src = fetchurl {
+      urls = [
+        "https://download.geogebra.org/installers/5.0/GeoGebra-Linux-Portable-${version}.tar.bz2"
+        "https://web.archive.org/web/20220516130744/https://download.geogebra.org/installers/5.0/GeoGebra-Linux-Portable-${version}.tar.bz2"
+      ];
+      sha256 = "d18f3d20baff693606331f035fa4bf73e7418d28090f038054da98444b06f69b";
+    };
+
+    nativeBuildInputs = [ makeWrapper ];
+
+    installPhase = ''
+      install -D geogebra/* -t "$out/libexec/geogebra/"
+
+      makeWrapper "$out/libexec/geogebra/geogebra" "$out/bin/geogebra" \
+        --set JAVACMD "${jre}/bin/java" \
+        --set GG_PATH "$out/libexec/geogebra" \
+        --add-flags "--language=${language}"
+
+      install -Dm644 "${desktopItem}/share/applications/"* \
+        -t $out/share/applications/
+
+      install -Dm644 "${srcIcon}" \
+        "$out/share/icons/hicolor/scalable/apps/geogebra.svg"
+    '';
+  };
+
+  darwinPkg = stdenv.mkDerivation {
+    inherit pname version meta;
+
+    preferLocalBuild = true;
+
+    src = fetchurl {
+      urls = [
+        "https://download.geogebra.org/installers/5.0/GeoGebra-MacOS-Installer-withJava-${version}.zip"
+        "https://web.archive.org/web/20220516132502/https://download.geogebra.org/installers/5.0/GeoGebra-MacOS-Installer-withJava-${version}.zip"
+      ];
+      sha256 = "0070ec8d8d5f79c921b5d7433048c2c114ec4b812d839bb04e67848fce24ee0a";
+    };
+
+    dontUnpack = true;
+
+    nativeBuildInputs = [ unzip ];
+
+    installPhase = ''
+      install -dm755 $out/Applications
+      unzip $src -d $out/Applications
+    '';
+  };
+in
+if stdenv.isDarwin
+then darwinPkg
+else linuxPkg
--- a/pkgs/applications/science/math/geogebra/geogebra6.nix
+++ b/pkgs/applications/science/math/geogebra/geogebra6.nix
@ -0,0 +1,73 @@
+{ lib, stdenv, unzip, fetchurl, electron, makeWrapper, geogebra }:
+let
+  pname = "geogebra";
+  version = "6-0-676-0";
+
+  srcIcon = geogebra.srcIcon;
+  desktopItem = geogebra.desktopItem;
+
+  meta = with lib; geogebra.meta // {
+    license = licenses.geogebra;
+    maintainers = with maintainers; [ voidless sikmir ];
+    platforms = with platforms; linux ++ darwin;
+  };
+
+  linuxPkg = stdenv.mkDerivation {
+    inherit pname version meta;
+
+    src = fetchurl {
+      urls = [
+        "https://download.geogebra.org/installers/6.0/GeoGebra-Linux64-Portable-${version}.zip"
+        "https://web.archive.org/web/20211123222708/https://download.geogebra.org/installers/6.0/GeoGebra-Linux64-Portable-${version}.zip"
+      ];
+      sha256 = "0wn90n2nd476rkf83gk9vvcpbjflkrvyri50pnmv52j76n023hmm";
+    };
+
+    dontConfigure = true;
+    dontBuild = true;
+
+    nativeBuildInputs = [
+      unzip
+      makeWrapper
+    ];
+
+    unpackPhase = ''
+      unzip $src
+    '';
+
+    installPhase = ''
+      mkdir -p $out/libexec/geogebra/ $out/bin
+      cp -r GeoGebra-linux-x64/{resources,locales} "$out/"
+      makeWrapper ${lib.getBin electron}/bin/electron $out/bin/geogebra --add-flags "$out/resources/app"
+      install -Dm644 "${desktopItem}/share/applications/"* \
+        -t $out/share/applications/
+
+      install -Dm644 "${srcIcon}" \
+        "$out/share/icons/hicolor/scalable/apps/geogebra.svg"
+    '';
+  };
+
+  darwinPkg = stdenv.mkDerivation {
+    inherit pname version meta;
+
+    src = fetchurl {
+      urls = [
+        "https://download.geogebra.org/installers/6.0/GeoGebra-Classic-6-MacOS-Portable-${version}.zip"
+        "https://web.archive.org/web/20211124143625/https://download.geogebra.org/installers/6.0/GeoGebra-Classic-6-MacOS-Portable-${version}.zip"
+      ];
+      sha256 = "1dwv2f94a1c2y10lmy0i66cafynalp7dkqgnpk4f0mk6pir2fdgj";
+    };
+
+    dontUnpack = true;
+
+    nativeBuildInputs = [ unzip ];
+
+    installPhase = ''
+      install -dm755 $out/Applications
+      unzip $src -d $out/Applications
+    '';
+  };
+in
+if stdenv.isDarwin
+then darwinPkg
+else linuxPkg
--- a/pkgs/applications/science/math/getdp/default.nix
+++ b/pkgs/applications/science/math/getdp/default.nix
@ -0,0 +1,32 @@
+{ lib, stdenv, fetchurl, cmake, gfortran, blas, lapack, mpi, petsc, python3 }:
+
+stdenv.mkDerivation rec {
+  pname = "getdp";
+  version = "3.4.0";
+  src = fetchurl {
+    url = "http://getdp.info/src/getdp-${version}-source.tgz";
+    sha256 = "sha256-d5YxJgtMf94PD6EHvIXpPBFPKC+skI/2v1K5Sad51hA=";
+  };
+
+  inherit (petsc) mpiSupport;
+  nativeBuildInputs = [ cmake python3 ];
+  buildInputs = [ gfortran blas lapack petsc ]
+    ++ lib.optional mpiSupport mpi
+  ;
+  cmakeFlags = lib.optional mpiSupport "-DENABLE_MPI=1";
+
+  meta = with lib; {
+    description = "A General Environment for the Treatment of Discrete Problems";
+    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
+      feature of GetDP is the closeness between the input data defining
+      discrete problems (written by the user in ASCII data files) and the
+      symbolic mathematical expressions of these problems.
+    '';
+    homepage = "http://getdp.info/";
+    license = licenses.gpl2Plus;
+    maintainers = with maintainers; [ ];
+    platforms = platforms.linux;
+  };
+}
--- a/pkgs/applications/science/math/gfan/default.nix
+++ b/pkgs/applications/science/math/gfan/default.nix
@ -0,0 +1,30 @@
+{lib, stdenv, fetchurl, gmp, mpir, cddlib}:
+stdenv.mkDerivation rec {
+  pname = "gfan";
+  version = "0.6.2";
+
+  src = fetchurl {
+    url = "http://home.math.au.dk/jensen/software/gfan/gfan${version}.tar.gz";
+    sha256 = "02pihqb1lb76a0xbfwjzs1cd6ay3ldfxsm8dvsbl6qs3vkjxax56";
+  };
+
+  patches = [
+    ./gfan-0.6.2-cddlib-prefix.patch
+  ];
+
+  postPatch = lib.optionalString stdenv.cc.isClang ''
+    substituteInPlace Makefile --replace "-fno-guess-branch-probability" ""
+  '';
+
+  buildFlags = [ "CC=${stdenv.cc.targetPrefix}cc" "CXX=${stdenv.cc.targetPrefix}c++" ];
+  installFlags = [ "PREFIX=$(out)" ];
+  buildInputs = [ gmp mpir cddlib ];
+
+  meta = {
+    description = "A software package for computing Gröbner fans and tropical varieties";
+    license = lib.licenses.gpl2 ;
+    maintainers = [lib.maintainers.raskin];
+    platforms = lib.platforms.unix;
+    homepage = "http://home.math.au.dk/jensen/software/gfan/gfan.html";
+  };
+}
--- a/pkgs/applications/science/math/gfan/gfan-0.6.2-cddlib-prefix.patch
+++ b/pkgs/applications/science/math/gfan/gfan-0.6.2-cddlib-prefix.patch
@ -0,0 +1,55 @@
+diff -ru gfan0.6.2.orig/src/app_librarytest.cpp gfan0.6.2/src/app_librarytest.cpp
+--- gfan0.6.2.orig/src/app_librarytest.cpp	2020-10-19 08:41:27.981863500 +0900
+++ gfan0.6.2/src/app_librarytest.cpp	2020-10-19 08:42:44.551863500 +0900
+@@ -12,8 +12,8 @@
+ #include "setoper.h"
+ #include "cdd.h"
+ #else
+-#include "cdd/setoper.h"
+-#include "cdd/cdd.h"
+#include "cddlib/setoper.h"
+#include "cddlib/cdd.h"
+ #endif
+ #include <iostream>
+ #include <fstream>
+diff -ru gfan0.6.2.orig/src/gfanlib_zcone.cpp gfan0.6.2/src/gfanlib_zcone.cpp
+--- gfan0.6.2.orig/src/gfanlib_zcone.cpp	2020-10-19 08:41:27.981863500 +0900
+++ gfan0.6.2/src/gfanlib_zcone.cpp	2020-10-19 08:42:44.571863500 +0900
+@@ -16,8 +16,8 @@
+ #include "setoper.h"
+ #include "cdd.h"
+ #else
+-#include "cdd/setoper.h"
+-#include "cdd/cdd.h"
+#include "cddlib/setoper.h"
+#include "cddlib/cdd.h"
+ #endif
+ //}
+ 
+@@ -52,8 +52,8 @@
+ 				  "dd_free_global_constants()\n"
+ 				  "in your deinitialisation code (only available for cddlib version>=094d).\n"
+ 				  "This requires the header includes:\n"
+-				  "#include \"cdd/setoper.h\"\n"
+-				  "#include \"cdd/cdd.h\"\n"
+				  "#include \"cddlib/setoper.h\"\n"
+				  "#include \"cddlib/cdd.h\"\n"
+ 				  "\n"
+ 				  "Alternatively, you may call gfan:initializeCddlibIfRequired() and deinitializeCddlibIfRequired()\n"
+ 				  "if gfanlib is the only code using cddlib. If at some point cddlib is no longer required by gfanlib\n"
+diff -ru gfan0.6.2.orig/src/lp_cdd.cpp gfan0.6.2/src/lp_cdd.cpp
+--- gfan0.6.2.orig/src/lp_cdd.cpp	2020-10-19 08:41:27.991863500 +0900
+++ gfan0.6.2/src/lp_cdd.cpp	2020-10-19 08:42:44.571863500 +0900
+@@ -5,9 +5,9 @@
+ #include "cdd.h"
+ #include "cdd_f.h"
+ #else
+-#include "cdd/setoper.h"
+-#include "cdd/cdd.h"
+-#include "cdd/cdd_f.h"
+#include "cddlib/setoper.h"
+#include "cddlib/cdd.h"
+#include "cddlib/cdd_f.h"
+ #endif
+ //}
+ #include "termorder.h"
--- a/pkgs/applications/science/math/giac/default.nix
+++ b/pkgs/applications/science/math/giac/default.nix
@ -0,0 +1,116 @@
+{ stdenv, lib, fetchurl, fetchpatch, texlive, 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
+, enableMicroPy ? false, python3
+}:
+
+assert (!blas.isILP64) && (!lapack.isILP64);
+
+stdenv.mkDerivation rec {
+  pname = "giac${lib.optionalString enableGUI "-with-xcas"}";
+  version = "1.9.0-5"; # TODO try to remove preCheck phase on upgrade
+
+  src = fetchurl {
+    url = "https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/giac_${version}.tar.gz";
+    sha256 = "sha256-EP8wRi8QZPrr1lfKN6da87s1FCy8AuDYbzcvsJCWyLE=";
+  };
+
+  patches = [
+    (fetchpatch {
+      name = "pari_2_11.patch";
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/giac/patches/pari_2_11.patch?id=21ba7540d385a9864b44850d6987893dfa16bfc0";
+      sha256 = "sha256-vEo/5MNzMdYRPWgLFPsDcMT1W80Qzj4EPBjx/B8j68k=";
+    })
+  ] ++ lib.optionals (!enableGUI) [
+    # when enableGui is false, giac is compiled without fltk. That
+    # means some outputs differ in the make check. Patch around this:
+    (fetchpatch {
+      name = "nofltk-check.patch";
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/giac/patches/nofltk-check.patch?id=7553a3c8dfa7bcec07241a07e6a4e7dcf5bb4f26";
+      sha256 = "0xkmfc028vg5w6va04gp2x2iv31n8v4shd6vbyvk4blzgfmpj2cw";
+    })
+  ];
+
+  # 1.9.0-5's tarball contains a binary (src/mkjs) which is executed
+  # at build time. we will delete and rebuild it.
+  depsBuildBuild = [ buildPackages.stdenv.cc ];
+
+  postPatch = ''
+    for i in doc/*/Makefile* micropython*/xcas/Makefile*; do
+      substituteInPlace "$i" --replace "/bin/cp" "cp";
+    done;
+    rm src/mkjs
+    substituteInPlace src/Makefile.am --replace "g++ mkjs.cc" \
+      "${buildPackages.stdenv.cc.targetPrefix}c++ mkjs.cc"
+  '';
+
+  nativeBuildInputs = [
+    autoreconfHook texlive.combined.scheme-small bison flex
+  ];
+
+  # perl is only needed for patchShebangs fixup.
+  buildInputs = [
+    gmp mpfr pari ntl gsl blas mpfi glpk nauty
+    readline gettext libpng libao perl ecm
+    # gfortran.cc default output contains static libraries compiled without -fPIC
+    # we want libgfortran.so.3 instead
+    (lib.getLib gfortran.cc)
+    lapack blas
+  ] ++ lib.optionals enableGUI [
+    libGL libGLU fltk xorg.libX11
+  ] ++ lib.optional enableMicroPy python3;
+
+  # xcas Phys and Turtle menus are broken with split outputs
+  # and interactive use is likely to need docs
+  outputs = [ "out" ] ++ lib.optional (!enableGUI) "doc";
+
+  doCheck = true;
+  preCheck = lib.optionalString (!enableGUI) ''
+    # even with the nofltk patch, some changes in src/misc.cc (grep
+    # for HAVE_LIBFLTK) made it so that giac behaves differently
+    # when fltk is disabled. disable these tests for now.
+    echo > check/chk_fhan2
+    echo > check/chk_fhan9
+  '';
+
+  enableParallelBuilding = true;
+
+  configureFlags = [
+    "--enable-gc" "--enable-png" "--enable-gsl" "--enable-lapack"
+    "--enable-pari" "--enable-ntl" "--enable-gmpxx" # "--enable-cocoa"
+    "--enable-ao" "--enable-ecm" "--enable-glpk"
+  ] ++ lib.optionals enableGUI [
+    "--enable-gui" "--with-x"
+  ] ++ lib.optional (!enableMicroPy) "--disable-micropy";
+
+  postInstall = ''
+    # example Makefiles contain the full path to some commands
+    # notably texlive, and we don't want texlive to become a runtime
+    # dependency
+    for file in $(find $out -name Makefile) ; do
+      sed -i "s@/nix/store/[^/]*/bin/@@" "$file" ;
+    done;
+
+    # reference cycle
+    rm "$out/share/giac/doc/el/"{casinter,tutoriel}/Makefile
+
+    if [ -n "$doc" ]; then
+      mkdir -p "$doc/share/giac"
+      mv "$out/share/giac/doc" "$doc/share/giac"
+      mv "$out/share/giac/examples" "$doc/share/giac"
+    fi
+  '' + lib.optionalString (!enableGUI) ''
+    for i in pixmaps application-registry applications icons; do
+      rm -r "$out/share/$i";
+    done;
+  '';
+
+  meta = with lib; {
+    description = "A free computer algebra system (CAS)";
+    homepage = "https://www-fourier.ujf-grenoble.fr/~parisse/giac.html";
+    license = licenses.gpl3Plus;
+    platforms = platforms.linux ++ (optionals (!enableGUI) platforms.darwin);
+    maintainers = [ maintainers.symphorien ];
+  };
+}
--- a/pkgs/applications/science/math/ginac/default.nix
+++ b/pkgs/applications/science/math/ginac/default.nix
@ -0,0 +1,35 @@
+{ lib, stdenv, fetchurl, cln, pkg-config, readline, gmp, python3 }:
+
+stdenv.mkDerivation rec {
+  pname = "ginac";
+  version = "1.8.2";
+
+  src = fetchurl {
+    url = "https://www.ginac.de/ginac-${version}.tar.bz2";
+    sha256 = "sha256-v811Gryviv3bg5WMKtInY6deokAyVT5QPumzjj6jtsM=";
+  };
+
+  propagatedBuildInputs = [ cln ];
+
+  buildInputs = [ readline ]
+    ++ lib.optional stdenv.isDarwin gmp;
+
+  nativeBuildInputs = [ pkg-config python3 ];
+
+  strictDeps = true;
+
+  preConfigure = ''
+    patchShebangs ginsh
+  '';
+
+  configureFlags = [ "--disable-rpath" ];
+
+  meta = with lib; {
+    broken = stdenv.isDarwin;
+    description = "GiNaC is Not a CAS";
+    homepage = "https://www.ginac.de/";
+    maintainers = with maintainers; [ lovek323 ];
+    license = licenses.gpl2;
+    platforms = platforms.all;
+  };
+}
--- a/pkgs/applications/science/math/glsurf/default.nix
+++ b/pkgs/applications/science/math/glsurf/default.nix
@ -0,0 +1,67 @@
+{ lib
+, stdenv
+, fetchurl
+, ocamlPackages
+, makeWrapper
+, libGLU
+, libGL
+, freeglut
+, mpfr
+, gmp
+, pkgsHostTarget
+}:
+
+let
+  inherit (pkgsHostTarget.targetPackages.stdenv) cc;
+in
+
+stdenv.mkDerivation rec {
+  pname = "glsurf";
+  version = "3.3.1";
+
+  src = fetchurl {
+    url = "https://raffalli.eu/~christophe/glsurf/glsurf-${version}.tar.gz";
+    sha256 = "0w8xxfnw2snflz8wdr2ca9f5g91w5vbyp1hwlx1v7vg83d4bwqs7";
+  };
+
+  nativeBuildInputs = [
+    makeWrapper
+  ] ++ (with ocamlPackages; [
+    ocaml
+    findlib
+  ]);
+
+  buildInputs = [
+    freeglut
+    libGL
+    libGLU
+    mpfr
+    gmp
+  ] ++ (with ocamlPackages; [
+    camlp4
+    lablgl
+    camlimages_4_2_4
+  ]);
+
+  postPatch = ''
+    for f in callbacks*/Makefile src/Makefile; do
+      substituteInPlace "$f" --replace "+camlp4" \
+        "${ocamlPackages.camlp4}/lib/ocaml/${ocamlPackages.ocaml.version}/site-lib/camlp4"
+    done
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin $out/share/doc/glsurf
+    cp ./src/glsurf.opt $out/bin/glsurf
+    cp ./doc/doc.pdf $out/share/doc/glsurf
+    cp -r ./examples $out/share/doc/glsurf
+
+    wrapProgram "$out/bin/glsurf" --set CC "${cc}/bin/${cc.targetPrefix}cc"
+  '';
+
+  meta = {
+    homepage = "https://raffalli.eu/~christophe/glsurf/";
+    description = "A program to draw implicit surfaces and curves";
+    license = lib.licenses.gpl2Plus;
+  };
+}
--- a/pkgs/applications/science/math/gmsh/default.nix
+++ b/pkgs/applications/science/math/gmsh/default.nix
@ -0,0 +1,32 @@
+{ lib, stdenv, fetchurl, cmake, blas, lapack, gfortran, gmm, fltk, libjpeg
+, zlib, libGL, libGLU, xorg, opencascade-occt }:
+
+assert (!blas.isILP64) && (!lapack.isILP64);
+
+stdenv.mkDerivation rec {
+  pname = "gmsh";
+  version = "4.10.2";
+
+  src = fetchurl {
+    url = "https://gmsh.info/src/gmsh-${version}-source.tgz";
+    sha256 = "sha256-2SEQnmxBn2jVUH2WEu6BXUC1I5pdsXXygoXgzQ2/JRc=";
+  };
+
+  buildInputs = [
+    blas lapack gmm fltk libjpeg zlib opencascade-occt
+  ] ++ lib.optionals (!stdenv.isDarwin) [
+    libGL libGLU xorg.libXrender xorg.libXcursor xorg.libXfixes
+    xorg.libXext xorg.libXft xorg.libXinerama xorg.libX11 xorg.libSM
+    xorg.libICE
+  ];
+
+  nativeBuildInputs = [ cmake gfortran ];
+
+  doCheck = true;
+
+  meta = {
+    description = "A three-dimensional finite element mesh generator";
+    homepage = "https://gmsh.info/";
+    license = lib.licenses.gpl2Plus;
+  };
+}
--- a/pkgs/applications/science/math/gretl/default.nix
+++ b/pkgs/applications/science/math/gretl/default.nix
@ -0,0 +1,43 @@
+{ lib, stdenv, fetchurl, curl, fftw, gmp, gnuplot, gtk3, gtksourceview3, json-glib
+, lapack, libxml2, mpfr, openblas, pkg-config, readline }:
+
+stdenv.mkDerivation rec {
+  pname = "gretl";
+  version = "2022a";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/gretl/${pname}-${version}.tar.xz";
+    sha256 = "sha256-J+JcuCda2xYJ5aVz6UXR+nWiid6QxpDtt4DXlb6L4UA=";
+  };
+
+  buildInputs = [
+    curl
+    fftw
+    gmp
+    gnuplot
+    gtk3
+    gtksourceview3
+    json-glib
+    lapack
+    libxml2
+    mpfr
+    openblas
+    readline
+  ];
+
+  nativeBuildInputs = [ pkg-config ];
+
+  enableParallelBuilding = true;
+
+  meta = with lib; {
+    description = "A software package for econometric analysis";
+    longDescription = ''
+      gretl is a cross-platform software package for econometric analysis,
+      written in the C programming language.
+    '';
+    homepage = "http://gretl.sourceforge.net";
+    license = licenses.gpl3;
+    maintainers = with maintainers; [ dmrauh ];
+    platforms = with platforms; all;
+  };
+}
--- a/pkgs/applications/science/math/gurobi/default.nix
+++ b/pkgs/applications/science/math/gurobi/default.nix
@ -0,0 +1,54 @@
+{ stdenv, lib, fetchurl, autoPatchelfHook, python3 }:
+
+stdenv.mkDerivation rec {
+  pname = "gurobi";
+  version = "9.5.1";
+
+  src = fetchurl {
+    url = "https://packages.gurobi.com/${lib.versions.majorMinor version}/gurobi${version}_linux64.tar.gz";
+    sha256 = "sha256-+oKFnTPwj7iuudpmsPvZFxjtVzxTT1capSNyyd64kdo=";
+  };
+
+  sourceRoot = "gurobi${builtins.replaceStrings ["."] [""] version}/linux64";
+
+  nativeBuildInputs = [ autoPatchelfHook ];
+  buildInputs = [ (python3.withPackages (ps: [ ps.gurobipy ])) ];
+
+  strictDeps = true;
+
+  makeFlags = [ "--directory=src/build" ];
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp bin/* $out/bin/
+    rm $out/bin/gurobi.sh
+    rm $out/bin/python*
+
+    cp lib/gurobi.py $out/bin/gurobi.sh
+
+    mkdir -p $out/include
+    cp include/gurobi*.h $out/include/
+
+    mkdir -p $out/lib
+    cp lib/*.jar $out/lib/
+    cp lib/libGurobiJni*.so $out/lib/
+    cp lib/libgurobi*.so* $out/lib/
+    cp lib/libgurobi*.a $out/lib/
+    cp src/build/*.a $out/lib/
+
+    mkdir -p $out/share/java
+    ln -s $out/lib/gurobi.jar $out/share/java/
+    ln -s $out/lib/gurobi-javadoc.jar $out/share/java/
+  '';
+
+  passthru.libSuffix = lib.replaceStrings [ "." ] [ "" ] (lib.versions.majorMinor version);
+
+  meta = with lib; {
+    description = "Optimization solver for mathematical programming";
+    homepage = "https://www.gurobi.com";
+    sourceProvenance = with sourceTypes; [ binaryBytecode ];
+    license = licenses.unfree;
+    platforms = [ "x86_64-linux" ];
+    maintainers = with maintainers; [ jfrankenau ];
+  };
+}
--- a/pkgs/applications/science/math/hmetis/default.nix
+++ b/pkgs/applications/science/math/hmetis/default.nix
@ -0,0 +1,42 @@
+{ lib, stdenv, fetchurl, ghostscript }:
+
+stdenv.mkDerivation rec {
+  pname = "hmetis";
+  version = "1.5";
+
+  src = fetchurl {
+    url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/hmetis/hmetis-${version}-linux.tar.gz";
+    sha256 = "e835a098c046e9c26cecb8addfea4d18ff25214e49585ffd87038e72819be7e1";
+  };
+
+  nativeBuildInputs = [ ghostscript ];
+
+  binaryFiles = "hmetis khmetis shmetis";
+
+  patchPhase = ''
+    for binaryfile in $binaryFiles; do
+      patchelf \
+        --set-interpreter ${stdenv.cc.libc}/lib/ld-linux.so.2 \
+        --set-rpath ${stdenv.cc.libc}/lib \
+        $binaryfile
+    done
+  '';
+
+  buildPhase = ''
+    gs -sOutputFile=manual.pdf -sDEVICE=pdfwrite -SNOPAUSE -dBATCH manual.ps
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin $out/share/doc/hmetis $out/lib
+    mv $binaryFiles $out/bin
+    mv manual.pdf $out/share/doc/hmetis
+    mv libhmetis.a $out/lib
+  '';
+
+  meta = with lib; {
+    description = "hMETIS is a set of programs for partitioning hypergraphs";
+    homepage = "http://glaros.dtc.umn.edu/gkhome/metis/hmetis/overview";
+    license = licenses.unfree;
+    platforms = [ "i686-linux" "x86_64-linux" ];
+  };
+}
--- a/pkgs/applications/science/math/jags/default.nix
+++ b/pkgs/applications/science/math/jags/default.nix
@ -0,0 +1,25 @@
+{ lib, stdenv, fetchurl, gfortran, blas, lapack }:
+
+stdenv.mkDerivation rec {
+  pname = "JAGS";
+  version = "4.3.0";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/mcmc-jags/JAGS-${version}.tar.gz";
+    sha256 = "1z3icccg2ic56vmhyrpinlsvpq7kcaflk1731rgpvz9bk1bxvica";
+  };
+
+  nativeBuildInputs = [ gfortran ];
+
+  buildInputs = [ blas lapack ];
+
+  configureFlags = [ "--with-blas=-lblas" "--with-lapack=-llapack" ];
+
+  meta = with lib; {
+    description = "Just Another Gibbs Sampler";
+    license = licenses.gpl2;
+    homepage = "http://mcmc-jags.sourceforge.net";
+    maintainers = [ maintainers.andres ];
+    platforms = platforms.unix;
+  };
+}
--- a/pkgs/applications/science/math/lp_solve/default.nix
+++ b/pkgs/applications/science/math/lp_solve/default.nix
@ -0,0 +1,52 @@
+{ lib, stdenv, fetchurl, cctools, fixDarwinDylibNames }:
+
+stdenv.mkDerivation rec {
+
+  pname = "lp_solve";
+  version = "5.5.2.11";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/project/lpsolve/lpsolve/${version}/lp_solve_${version}_source.tar.gz";
+    sha256 = "sha256-bUq/9cxqqpM66ObBeiJt8PwLZxxDj2lxXUHQn+gfkC8=";
+  };
+
+  nativeBuildInputs = lib.optionals stdenv.isDarwin [
+    cctools
+    fixDarwinDylibNames
+  ];
+
+  dontConfigure = true;
+
+  buildPhase = let
+    ccc = if stdenv.isDarwin then "ccc.osx" else "ccc";
+  in ''
+    runHook preBuild
+
+    (cd lpsolve55 && bash -x -e ${ccc})
+    (cd lp_solve  && bash -x -e ${ccc})
+
+    runHook postBuild
+  '';
+
+  installPhase = ''
+    runHook preInstall
+
+    install -d -m755 $out/bin $out/lib $out/include/lpsolve
+    install -m755 lp_solve/bin/*/lp_solve -t $out/bin
+    install -m644 lpsolve55/bin/*/liblpsolve* -t $out/lib
+    install -m644 lp_*.h -t $out/include/lpsolve
+
+    rm $out/lib/liblpsolve*.a
+    rm $out/include/lpsolve/lp_solveDLL.h  # A Windows header
+
+    runHook postInstall
+  '';
+
+  meta = with lib; {
+    description = "A Mixed Integer Linear Programming (MILP) solver";
+    homepage    = "http://lpsolve.sourceforge.net";
+    license     = licenses.gpl2Plus;
+    maintainers = with maintainers; [ smironov ];
+    platforms   = platforms.unix;
+  };
+}
--- a/pkgs/applications/science/math/lrcalc/default.nix
+++ b/pkgs/applications/science/math/lrcalc/default.nix
@ -0,0 +1,30 @@
+{ lib, stdenv
+, fetchFromBitbucket
+, autoreconfHook
+}:
+
+stdenv.mkDerivation rec {
+  version = "2.1";
+  pname = "lrcalc";
+
+  src = fetchFromBitbucket {
+    owner = "asbuch";
+    repo = "lrcalc";
+    rev = "lrcalc-${version}";
+    sha256 = "0s3amf3z75hnrjyszdndrvk4wp5p630dcgyj341i6l57h43d1p4k";
+  };
+
+  doCheck = true;
+
+  nativeBuildInputs = [
+    autoreconfHook
+  ];
+
+  meta = with lib; {
+    description = "Littlewood-Richardson calculator";
+    homepage = "http://math.rutgers.edu/~asbuch/lrcalc/";
+    license = licenses.gpl2Plus;
+    maintainers = teams.sage.members;
+    platforms = platforms.unix;
+  };
+}
--- a/pkgs/applications/science/math/mathematica/10.nix
+++ b/pkgs/applications/science/math/mathematica/10.nix
@ -0,0 +1,131 @@
+{ lib
+, patchelf
+, requireFile
+, stdenv
+# arguments from default.nix
+, lang
+, meta
+, name
+, src
+, version
+# dependencies
+, alsa-lib
+, coreutils
+, cudaPackages
+, fontconfig
+, freetype
+, gcc
+, glib
+, libuuid
+, libxml2
+, ncurses
+, opencv2
+, openssl
+, unixODBC
+, xorg
+# options
+, cudaSupport
+}:
+
+let
+  platform =
+    if stdenv.hostPlatform.system == "i686-linux" || stdenv.hostPlatform.system == "x86_64-linux" then
+      "Linux"
+    else
+      throw "Mathematica requires i686-linux or x86_64 linux";
+in
+stdenv.mkDerivation rec {
+  inherit meta src version;
+
+  pname = "mathematica";
+
+  buildInputs = [
+    coreutils
+    patchelf
+    alsa-lib
+    coreutils
+    fontconfig
+    freetype
+    gcc.cc
+    gcc.libc
+    glib
+    ncurses
+    opencv2
+    openssl
+    unixODBC
+    libxml2
+    libuuid
+  ] ++ (with xorg; [
+    libX11
+    libXext
+    libXtst
+    libXi
+    libXmu
+    libXrender
+    libxcb
+    libXcursor
+    libXfixes
+    libXrandr
+    libICE
+    libSM
+  ]);
+
+  ldpath = lib.makeLibraryPath buildInputs
+    + lib.optionalString (stdenv.hostPlatform.system == "x86_64-linux")
+      (":" + lib.makeSearchPathOutput "lib" "lib64" buildInputs);
+
+  phases = "unpackPhase installPhase fixupPhase";
+
+  unpackPhase = ''
+    echo "=== Extracting makeself archive ==="
+    # find offset from file
+    offset=$(${stdenv.shell} -c "$(grep -axm1 -e 'offset=.*' $src); echo \$offset" $src)
+    dd if="$src" ibs=$offset skip=1 | tar -xf -
+    cd Unix
+  '';
+
+  installPhase = ''
+    cd Installer
+    # don't restrict PATH, that has already been done
+    sed -i -e 's/^PATH=/# PATH=/' MathInstaller
+
+    echo "=== Running MathInstaller ==="
+    ./MathInstaller -auto -createdir=y -execdir=$out/bin -targetdir=$out/libexec/Mathematica -platforms=${platform} -silent
+  '';
+
+  preFixup = ''
+    echo "=== PatchElfing away ==="
+    # This code should be a bit forgiving of errors, unfortunately
+    set +e
+    find $out/libexec/Mathematica/SystemFiles -type f -perm -0100 | while read f; do
+      type=$(readelf -h "$f" 2>/dev/null | grep 'Type:' | sed -e 's/ *Type: *\([A-Z]*\) (.*/\1/')
+      if [ -z "$type" ]; then
+        :
+      elif [ "$type" == "EXEC" ]; then
+        echo "patching $f executable <<"
+        patchelf --shrink-rpath "$f"
+        patchelf \
+    --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \
+          --set-rpath "$(patchelf --print-rpath "$f"):${ldpath}" \
+          "$f" \
+          && patchelf --shrink-rpath "$f" \
+          || echo unable to patch ... ignoring 1>&2
+      elif [ "$type" == "DYN" ]; then
+        echo "patching $f library <<"
+        patchelf \
+          --set-rpath "$(patchelf --print-rpath "$f"):${ldpath}" \
+          "$f" \
+          && patchelf --shrink-rpath "$f" \
+          || echo unable to patch ... ignoring 1>&2
+      else
+        echo "not patching $f <<: unknown elf type"
+      fi
+    done
+  '';
+
+  # all binaries are already stripped
+  dontStrip = true;
+
+  # we did this in prefixup already
+  dontPatchELF = true;
+}
--- a/pkgs/applications/science/math/mathematica/11.nix
+++ b/pkgs/applications/science/math/mathematica/11.nix
@ -0,0 +1,145 @@
+{ lib
+, patchelf
+, requireFile
+, stdenv
+# arguments from default.nix
+, lang
+, meta
+, name
+, src
+, version
+# dependencies
+, alsa-lib
+, coreutils
+, cudaPackages
+, dbus
+, fontconfig
+, freetype
+, gcc
+, glib
+, libGL
+, libGLU
+, libuuid
+, libxml2
+, ncurses
+, opencv2
+, openssl
+, unixODBC
+, xkeyboard_config
+, xorg
+, zlib
+# options
+, cudaSupport
+}:
+
+stdenv.mkDerivation rec {
+  inherit meta name src version;
+
+  buildInputs = [
+    coreutils
+    patchelf
+    alsa-lib
+    coreutils
+    dbus
+    fontconfig
+    freetype
+    gcc.cc
+    gcc.libc
+    glib
+    ncurses
+    opencv2
+    openssl
+    unixODBC
+    xkeyboard_config
+    libxml2
+    libuuid
+    zlib
+    libGL
+    libGLU
+  ] ++ (with xorg; [
+    libX11
+    libXext
+    libXtst
+    libXi
+    libXmu
+    libXrender
+    libxcb
+    libXcursor
+    libXfixes
+    libXrandr
+    libICE
+    libSM
+  ]);
+
+  ldpath = lib.makeLibraryPath buildInputs
+    + lib.optionalString (stdenv.hostPlatform.system == "x86_64-linux")
+      (":" + lib.makeSearchPathOutput "lib" "lib64" buildInputs);
+
+  phases = "unpackPhase installPhase fixupPhase";
+
+  unpackPhase = ''
+    echo "=== Extracting makeself archive ==="
+    # find offset from file
+    offset=$(${stdenv.shell} -c "$(grep -axm1 -e 'offset=.*' $src); echo \$offset" $src)
+    dd if="$src" ibs=$offset skip=1 | tar -xf -
+    cd Unix
+  '';
+
+  installPhase = ''
+    cd Installer
+    # don't restrict PATH, that has already been done
+    sed -i -e 's/^PATH=/# PATH=/' MathInstaller
+    sed -i -e 's/\/bin\/bash/\/bin\/sh/' MathInstaller
+
+    echo "=== Running MathInstaller ==="
+    ./MathInstaller -auto -createdir=y -execdir=$out/bin -targetdir=$out/libexec/Mathematica -silent
+
+    # Fix library paths
+    cd $out/libexec/Mathematica/Executables
+    for path in mathematica MathKernel Mathematica WolframKernel wolfram math; do
+      sed -i -e 's#export LD_LIBRARY_PATH$#export LD_LIBRARY_PATH=${zlib}/lib:\''${LD_LIBRARY_PATH}#' $path
+    done
+
+    # Fix xkeyboard config path for Qt
+    for path in mathematica Mathematica; do
+      line=$(grep -n QT_PLUGIN_PATH $path | sed 's/:.*//')
+      sed -i -e "$line iexport QT_XKB_CONFIG_ROOT=\"${xkeyboard_config}/share/X11/xkb\"" $path
+    done
+  '';
+
+  preFixup = ''
+    echo "=== PatchElfing away ==="
+    # This code should be a bit forgiving of errors, unfortunately
+    set +e
+    find $out/libexec/Mathematica/SystemFiles -type f -perm -0100 | while read f; do
+      type=$(readelf -h "$f" 2>/dev/null | grep 'Type:' | sed -e 's/ *Type: *\([A-Z]*\) (.*/\1/')
+      if [ -z "$type" ]; then
+        :
+      elif [ "$type" == "EXEC" ]; then
+        echo "patching $f executable <<"
+        patchelf --shrink-rpath "$f"
+        patchelf \
+    --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \
+          --set-rpath "$(patchelf --print-rpath "$f"):${ldpath}" \
+          "$f" \
+          && patchelf --shrink-rpath "$f" \
+          || echo unable to patch ... ignoring 1>&2
+      elif [ "$type" == "DYN" ]; then
+        echo "patching $f library <<"
+        patchelf \
+          --set-rpath "$(patchelf --print-rpath "$f"):${ldpath}" \
+          "$f" \
+          && patchelf --shrink-rpath "$f" \
+          || echo unable to patch ... ignoring 1>&2
+      else
+        echo "not patching $f <<: unknown elf type"
+      fi
+    done
+  '';
+
+  # all binaries are already stripped
+  dontStrip = true;
+
+  # we did this in prefixup already
+  dontPatchELF = true;
+}
--- a/pkgs/applications/science/math/mathematica/9.nix
+++ b/pkgs/applications/science/math/mathematica/9.nix
@ -0,0 +1,117 @@
+{ lib
+, patchelf
+, requireFile
+, stdenv
+# arguments from default.nix
+, lang
+, meta
+, name
+, src
+, version
+# dependencies
+, alsa-lib
+, coreutils
+, cudaPackages
+, fontconfig
+, freetype
+, gcc
+, glib
+, ncurses
+, opencv2
+, openssl
+, unixODBC
+, xorg
+# options
+, cudaSupport
+}:
+
+let
+  platform =
+    if stdenv.hostPlatform.system == "i686-linux" || stdenv.hostPlatform.system == "x86_64-linux" then
+      "Linux"
+    else
+      throw "Mathematica requires i686-linux or x86_64 linux";
+in
+stdenv.mkDerivation rec {
+  inherit meta src version;
+  pname = "mathematica";
+
+  buildInputs = [
+    coreutils
+    patchelf
+    alsa-lib
+    coreutils
+    fontconfig
+    freetype
+    gcc.cc
+    gcc.libc
+    glib
+    ncurses
+    opencv2
+    openssl
+    unixODBC
+  ] ++ (with xorg; [
+    libX11
+    libXext
+    libXtst
+    libXi
+    libXmu
+    libXrender
+    libxcb
+  ]);
+
+  ldpath = lib.makeLibraryPath buildInputs
+    + lib.optionalString (stdenv.hostPlatform.system == "x86_64-linux")
+    (":" + lib.makeSearchPathOutput "lib" "lib64" buildInputs);
+
+  phases = "unpackPhase installPhase fixupPhase";
+
+  unpackPhase = ''
+    echo "=== Extracting makeself archive ==="
+    # find offset from file
+    offset=$(${stdenv.shell} -c "$(grep -axm1 -e 'offset=.*' $src); echo \$offset" $src)
+    dd if="$src" ibs=$offset skip=1 | tar -xf -
+    cd Unix
+  '';
+
+  installPhase = ''
+    cd Installer
+    # don't restrict PATH, that has already been done
+    sed -i -e 's/^PATH=/# PATH=/' MathInstaller
+
+    echo "=== Running MathInstaller ==="
+    ./MathInstaller -auto -createdir=y -execdir=$out/bin -targetdir=$out/libexec/Mathematica -platforms=${platform} -silent
+  '';
+
+  preFixup = ''
+    echo "=== PatchElfing away ==="
+    find $out/libexec/Mathematica/SystemFiles -type f -perm -0100 | while read f; do
+      type=$(readelf -h "$f" 2>/dev/null | grep 'Type:' | sed -e 's/ *Type: *\([A-Z]*\) (.*/\1/')
+      if [ -z "$type" ]; then
+        :
+      elif [ "$type" == "EXEC" ]; then
+        echo "patching $f executable <<"
+        patchelf \
+            --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \
+            --set-rpath "${ldpath}" \
+            "$f"
+        patchelf --shrink-rpath "$f"
+      elif [ "$type" == "DYN" ]; then
+        echo "patching $f library <<"
+        patchelf \
+          --set-rpath "$(patchelf --print-rpath "$f"):${ldpath}" \
+          "$f" \
+          && patchelf --shrink-rpath "$f" \
+          || echo unable to patch ... ignoring 1>&2
+      else
+        echo "not patching $f <<: unknown elf type"
+      fi
+    done
+  '';
+
+  # all binaries are already stripped
+  dontStrip = true;
+
+  # we did this in prefixup already
+  dontPatchELF = true;
+}
--- a/pkgs/applications/science/math/mathematica/default.nix
+++ b/pkgs/applications/science/math/mathematica/default.nix
@ -0,0 +1,53 @@
+{ callPackage
+, config
+, lib
+, cudaPackages
+, cudaSupport ? config.cudaSupport or false
+, lang ? "en"
+, version ? null
+}:
+
+let versions = callPackage ./versions.nix { };
+
+    matching-versions =
+      lib.sort (v1: v2: lib.versionAtLeast v1.version v2.version) (lib.filter
+        (v: v.lang == lang
+            && (if version == null then true else isMatching v.version version))
+        versions);
+
+    found-version =
+      if matching-versions == []
+      then throw ("No registered Mathematica version found to match"
+                  + " version=${version} and language=${lang}")
+      else lib.head matching-versions;
+
+    specific-drv = ./. + "/(lib.versions.major found-version.version).nix";
+
+    real-drv = if lib.pathExists specific-drv
+               then specific-drv
+               else ./generic.nix;
+
+    isMatching = v1: v2:
+      let as      = lib.splitVersion v1;
+          bs      = lib.splitVersion v2;
+          n       = lib.min (lib.length as) (lib.length bs);
+          sublist = l: lib.sublist 0 n l;
+      in lib.compareLists lib.compare (sublist as) (sublist bs) == 0;
+
+in
+
+callPackage real-drv {
+  inherit cudaSupport cudaPackages;
+  inherit (found-version) version lang src;
+  name = ("mathematica"
+          + lib.optionalString cudaSupport "-cuda"
+          + "-${found-version.version}"
+          + lib.optionalString (lang != "en") "-${lang}");
+  meta = with lib; {
+    description = "Wolfram Mathematica computational software system";
+    homepage = "http://www.wolfram.com/mathematica/";
+    license = licenses.unfree;
+    maintainers = with maintainers; [ herberteuler ];
+    platforms = [ "x86_64-linux" ];
+  };
+}
--- a/pkgs/applications/science/math/mathematica/generic.nix
+++ b/pkgs/applications/science/math/mathematica/generic.nix
@ -0,0 +1,192 @@
+{ addOpenGLRunpath
+, autoPatchelfHook
+, lib
+, makeWrapper
+, requireFile
+, runCommand
+, stdenv
+, symlinkJoin
+# arguments from default.nix
+, lang
+, meta
+, name
+, src
+, version
+# dependencies
+, alsa-lib
+, cudaPackages
+, cups
+, dbus
+, flite
+, fontconfig
+, freetype
+, gcc-unwrapped
+, glib
+, gmpxx
+, keyutils
+, libGL
+, libGLU
+, libpcap
+, libtins
+, libuuid
+, libxkbcommon
+, libxml2
+, llvmPackages_12
+, matio
+, mpfr
+, ncurses
+, opencv4
+, openjdk11
+, openssl
+, pciutils
+, tre
+, unixODBC
+, xkeyboard_config
+, xorg
+, zlib
+# options
+, cudaSupport
+}:
+
+let cudaEnv = symlinkJoin {
+      name = "mathematica-cuda-env";
+      paths = with cudaPackages; [
+        cuda_cudart cuda_nvcc libcublas libcufft libcurand libcusparse
+      ];
+      postBuild = ''
+        ln -s ${addOpenGLRunpath.driverLink}/lib/libcuda.so $out/lib
+        ln -s lib $out/lib64
+      '';
+    };
+
+in stdenv.mkDerivation {
+  inherit meta name src version;
+
+  nativeBuildInputs = [
+    autoPatchelfHook
+    makeWrapper
+  ] ++ lib.optional cudaSupport addOpenGLRunpath;
+
+  buildInputs = [
+    alsa-lib
+    cups.lib
+    dbus
+    flite
+    fontconfig
+    freetype
+    glib
+    gmpxx
+    keyutils.lib
+    libGL
+    libGLU
+    libpcap
+    libtins
+    libuuid
+    libxkbcommon
+    libxml2
+    llvmPackages_12.libllvm.lib
+    matio
+    mpfr
+    ncurses
+    opencv4
+    openjdk11
+    openssl
+    pciutils
+    tre
+    unixODBC
+    xkeyboard_config
+  ] ++ (with xorg; [
+    libICE
+    libSM
+    libX11
+    libXScrnSaver
+    libXcomposite
+    libXcursor
+    libXdamage
+    libXext
+    libXfixes
+    libXi
+    libXinerama
+    libXmu
+    libXrandr
+    libXrender
+    libXtst
+    libxcb
+  ]) ++ lib.optional cudaSupport cudaEnv;
+
+  wrapProgramFlags = [
+    "--prefix LD_LIBRARY_PATH : ${lib.makeLibraryPath [ gcc-unwrapped.lib zlib ]}"
+    "--prefix PATH : ${lib.makeBinPath [ stdenv.cc ]}"
+    # Fix libQt errors - #96490
+    "--set USE_WOLFRAM_LD_LIBRARY_PATH 1"
+    # Fix xkeyboard config path for Qt
+    "--set QT_XKB_CONFIG_ROOT ${xkeyboard_config}/share/X11/xkb"
+  ] ++ lib.optionals cudaSupport [
+    "--set CUDA_PATH ${cudaEnv}"
+    "--set NVIDIA_DRIVER_LIBRARY_PATH ${addOpenGLRunpath.driverLink}/lib/libnvidia-tls.so"
+    "--set CUDA_LIBRARY_PATH ${addOpenGLRunpath.driverLink}/lib/libcuda.so"
+  ];
+
+  unpackPhase = ''
+    runHook preUnpack
+
+    # Find offset from file
+    offset=$(${stdenv.shell} -c "$(grep -axm1 -e 'offset=.*' $src); echo \$offset" $src)
+    tail -c +$(($offset + 1)) $src | tar -xf -
+
+    runHook postUnpack
+  '';
+
+  installPhase = ''
+    runHook preInstall
+
+    cd "$TMPDIR/Unix/Installer"
+
+    mkdir -p "$out/lib/udev/rules.d"
+
+    # Patch MathInstaller's shebangs and udev rules dir
+    patchShebangs MathInstaller
+    substituteInPlace MathInstaller \
+      --replace /etc/udev/rules.d $out/lib/udev/rules.d
+
+    # Remove PATH restriction, root and avahi daemon checks, and hostname call
+    sed -i '
+      s/^PATH=/# &/
+      s/isRoot="false"/# &/
+      s/^checkAvahiDaemon$/# &/
+      s/`hostname`/""/
+    ' MathInstaller
+
+    # NOTE: some files placed under HOME may be useful
+    XDG_DATA_HOME="$out/share" HOME="$TMPDIR/home" vernierLink=y \
+      ./MathInstaller -execdir="$out/bin" -targetdir="$out/libexec/Mathematica" -auto -verbose -createdir=y
+
+    # Check if MathInstaller produced any errors
+    errLog="$out/libexec/Mathematica/InstallErrors"
+    if [ -f "$errLog" ]; then
+      echo "Installation errors:"
+      cat "$errLog"
+      return 1
+    fi
+
+    runHook postInstall
+  '';
+
+  preFixup = ''
+    for bin in $out/libexec/Mathematica/Executables/*; do
+      wrapProgram "$bin" ''${wrapProgramFlags[@]}
+    done
+  '';
+
+  dontConfigure = true;
+  dontBuild = true;
+
+  # This is primarily an IO bound build; there's little benefit to building remotely
+  preferLocalBuild = true;
+
+  # All binaries are already stripped
+  dontStrip = true;
+
+  # NOTE: Some deps are still not found; ignore for now
+  autoPatchelfIgnoreMissingDeps = true;
+}
--- a/pkgs/applications/science/math/mathematica/versions.nix
+++ b/pkgs/applications/science/math/mathematica/versions.nix
@ -0,0 +1,103 @@
+{ lib, requireFile }:
+
+let versions = [
+  {
+    version = "13.0.1";
+    lang = "en";
+    language = "English";
+    sha256 = "sha256-NnKpIMG0rxr9SAcz9tZ2Zbr4JYdX3+WabtbXRAzybbo=";
+    installer = "Mathematica_13.0.1_BNDL_LINUX.sh";
+  }
+  {
+    version = "13.0.0";
+    lang = "en";
+    language = "English";
+    sha256 = "sha256-FbutOaWZUDEyXR0Xj2OwDnFwbT7JAB66bRaB+8mR0+E=";
+    installer = "Mathematica_13.0.0_BNDL_LINUX.sh";
+  }
+  {
+    version = "12.3.1";
+    lang = "en";
+    language = "English";
+    sha256 = "sha256-UbnKsS/ZGwCep61JaKLIpZ6U3FXS5swdcSrNW6LE1Qk=";
+    installer = "Mathematica_12.3.1_LINUX.sh";
+  }
+  {
+    version = "12.3.0";
+    lang = "en";
+    language = "English";
+    sha256 = "sha256-BF3wRfbnlt7Vn2TrLg8ZSayI3LodW24F+1PqCkrtchU=";
+    installer = "Mathematica_12.3.0_LINUX.sh";
+  }
+  {
+    version = "12.2.0";
+    lang = "en";
+    language = "English";
+    sha256 = "sha256-O2Z2ogPGrbfpxBilSEsDeXQoe1vgnGTn3+p03cDkANc=";
+    installer = "Mathematica_12.2.0_LINUX.sh";
+  }
+  {
+    version = "12.1.1";
+    lang = "en";
+    language = "English";
+    sha256 = "sha256-rUe4hr5KmGTXD1I/eSYVoFHU68mH2aD2VLZFtOtDswo=";
+    installer = "Mathematica_12.1.1_LINUX.sh";
+  }
+  {
+    version = "12.1.0";
+    lang = "en";
+    language = "English";
+    sha256 = "sha256-56P1KKOTJkQj+K9wppAsnYpej/YB3VUNL7DPLYGgqZY=";
+    installer = "Mathematica_12.1.0_LINUX.sh";
+  }
+  {
+    version = "12.0.0";
+    lang = "en";
+    language = "English";
+    sha256 = "sha256-uftx4a/MHXLCABlv+kNFEtII+ikg4geHhDP1BOWK6dc=";
+    installer = "Mathematica_12.0.0_LINUX.sh";
+  }
+  {
+    version = "11.3.0";
+    lang = "en";
+    language = "English";
+    sha256 = "sha256-D8/iCMHqyESOe+OvC9uENwsXvZxdBmwBOSjI7pWu0Q4=";
+    installer = "Mathematica_11.3.0_LINUX.sh";
+  }
+  {
+    version = "11.2.0";
+    lang = "ja";
+    language = "Japanese";
+    sha256 = "sha256-kWOS7dMr7YYiI430Nd2OhkJrsEMDijM28w3xDYGbSbE=";
+    installer = "Mathematica_11.2.0_ja_LINUX.sh";
+  }
+  {
+    version = "9.0.0";
+    lang = "en";
+    language = "English";
+    sha256 = "sha256-mKgxdd7dLWa5EOuR5C37SeU+UC9Cv5YTbY5xSK9y34A=";
+    installer = "Mathematica_9.0.0_LINUX.sh";
+  }
+  {
+    version = "10.0.2";
+    lang = "en";
+    language = "English";
+    sha256 = "sha256-NHUg1jzLos1EsIr8TdYdNaA5+3jEcFqVZIr9GVVUXrQ=";
+    installer = "Mathematica_10.0.2_LINUX.sh";
+  }
+];
+
+in
+
+lib.flip map versions ({ version, lang, language, sha256, installer }: {
+  inherit version lang;
+  src = requireFile {
+    name = installer;
+    message = ''
+      This nix expression requires that ${installer} is
+      already part of the store. Find the file on your Mathematica CD
+      and add it to the nix store with nix-store --add-fixed sha256 <FILE>.
+    '';
+    inherit sha256;
+  };
+})
--- a/pkgs/applications/science/math/maxima/default.nix
+++ b/pkgs/applications/science/math/maxima/default.nix
@ -0,0 +1,124 @@
+{ lib
+, stdenv
+, fetchurl
+, fetchpatch
+, texinfo
+, perl
+, python3
+, makeWrapper
+, autoreconfHook
+, rlwrap ? null
+, tk ? null
+, gnuplot ? null
+, lisp-compiler
+}:
+
+let
+  # Allow to remove some executables from the $PATH of the wrapped binary
+  searchPath = lib.makeBinPath
+    (lib.filter (x: x != null) [ lisp-compiler rlwrap tk gnuplot ]);
+in
+stdenv.mkDerivation rec {
+  pname = "maxima";
+  version = "5.45.1";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/${pname}/${pname}-${version}.tar.gz";
+    sha256 = "sha256-/pAWJ2lwvvIUoaJENIVYZEUU1/36pPyLnQ6Hr8u059w=";
+  };
+
+  nativeBuildInputs = [
+    autoreconfHook
+    lisp-compiler
+    makeWrapper
+    python3
+    texinfo
+  ];
+
+  strictDeps = true;
+
+  checkInputs = [
+    gnuplot
+  ];
+
+  postPatch = ''
+    substituteInPlace doc/info/Makefile.am --replace "/usr/bin/env perl" "${perl}/bin/perl"
+  '';
+
+  postInstall = ''
+    # Make sure that maxima can find its runtime dependencies.
+    for prog in "$out/bin/"*; do
+      wrapProgram "$prog" --prefix PATH ":" "$out/bin:${searchPath}"
+    done
+    # Move emacs modules and documentation into the right place.
+    mkdir -p $out/share/emacs $out/share/doc
+    ln -s ../maxima/${version}/emacs $out/share/emacs/site-lisp
+    ln -s ../maxima/${version}/doc $out/share/doc/maxima
+  ''
+   + (lib.optionalString (lisp-compiler.pname == "ecl") ''
+     cp src/binary-ecl/maxima.fas* "$out/lib/maxima/${version}/binary-ecl/"
+   '')
+  ;
+
+  patches = [
+    # fix path to info dir (see https://trac.sagemath.org/ticket/11348)
+    (fetchpatch {
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/maxima/patches/infodir.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
+      sha256 = "09v64n60f7i6frzryrj0zd056lvdpms3ajky4f9p6kankhbiv21x";
+    })
+
+    # fix https://sourceforge.net/p/maxima/bugs/2596/
+    (fetchpatch {
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/maxima/patches/matrixexp.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
+      sha256 = "06961hn66rhjijfvyym21h39wk98sfxhp051da6gz0n9byhwc6zg";
+    })
+
+    # undo https://sourceforge.net/p/maxima/code/ci/f5e9b0f7eb122c4e48ea9df144dd57221e5ea0ca
+    # see https://trac.sagemath.org/ticket/13364#comment:93
+    (fetchpatch {
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/maxima/patches/undoing_true_false_printing_patch.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
+      sha256 = "0fvi3rcjv6743sqsbgdzazy9jb6r1p1yq63zyj9fx42wd1hgf7yx";
+    })
+  ] ++ lib.optionals (lisp-compiler.pname == "ecl") [
+    # build fasl, needed for ECL support
+    (fetchpatch {
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/maxima/patches/maxima.system.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
+      sha256 = "18zafig8vflhkr80jq2ivk46k92dkszqlyq8cfmj0b2vcfjwwbar";
+    })
+  ];
+
+  # The test suite is disabled since 5.42.2 because of the following issues:
+  #
+  #   Error(s) found:
+  #   /build/maxima-5.44.0/share/linearalgebra/rtest_matrixexp.mac problems:
+  #   (20 21 22)
+  #   Tests that were expected to fail but passed:
+  #   /build/maxima-5.44.0/share/vector/rtest_vect.mac problem:
+  #   (19)
+  #   3 tests failed out of 16,184 total tests.
+  #
+  # These failures don't look serious. It would be nice to fix them, but I
+  # don't know how and probably won't have the time to find out.
+  doCheck = false;    # try to re-enable after next version update
+
+  enableParallelBuilding = true;
+
+  passthru = {
+    inherit lisp-compiler;
+  };
+
+  meta = with lib; {
+    description = "Computer algebra system";
+    homepage = "http://maxima.sourceforge.net";
+    license = licenses.gpl2Plus;
+
+    longDescription = ''
+      Maxima is a fairly complete computer algebra system written in
+      lisp with an emphasis on symbolic computation. It is based on
+      DOE-MACSYMA and licensed under the GPL. Its abilities include
+      symbolic integration, 3D plotting, and an ODE solver.
+    '';
+    maintainers = with maintainers; [ doronbehar ];
+    platforms = platforms.unix;
+  };
+}
--- a/pkgs/applications/science/math/msieve/default.nix
+++ b/pkgs/applications/science/math/msieve/default.nix
@ -0,0 +1,31 @@
+{ lib, stdenv, fetchurl, zlib, gmp, ecm }:
+
+stdenv.mkDerivation rec {
+  pname = "msieve";
+  version = "1.53";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/msieve/msieve/Msieve%20v${version}/msieve${lib.replaceStrings ["."] [""] version}_src.tar.gz";
+    sha256 = "1d1vv7j4rh3nnxsmvafi73qy7lw7n3akjlm5pjl3m936yapvmz65";
+  };
+
+  buildInputs = [ zlib gmp ecm ];
+
+  ECM = if ecm == null then "0" else "1";
+
+  # Doesn't hurt Linux but lets clang-based platforms like Darwin work fine too
+  makeFlags = [ "CC=${stdenv.cc.targetPrefix}cc" "all" ];
+
+  installPhase = ''
+    mkdir -p $out/bin/
+    cp msieve $out/bin/
+  '';
+
+  meta = {
+    description = "A C library implementing a suite of algorithms to factor large integers";
+    license = lib.licenses.publicDomain;
+    homepage = "http://msieve.sourceforge.net/";
+    maintainers = [ lib.maintainers.roconnor ];
+    platforms = [ "x86_64-linux" ] ++ lib.platforms.darwin;
+  };
+}
--- a/pkgs/applications/science/math/mxnet/default.nix
+++ b/pkgs/applications/science/math/mxnet/default.nix
@ -0,0 +1,85 @@
+{ config, stdenv, lib, fetchurl, fetchpatch, bash, cmake
+, opencv3, gtest, blas, gomp, llvmPackages, perl
+, cudaSupport ? config.cudaSupport or false, cudaPackages ? {}, nvidia_x11
+, cudnnSupport ? cudaSupport
+, cudaCapabilities ? [ "3.7" "5.0" "6.0" "7.0" "7.5" "8.0" "8.6" ]
+}:
+
+let
+  inherit (cudaPackages) cudatoolkit cudnn;
+in
+
+assert cudnnSupport -> cudaSupport;
+
+stdenv.mkDerivation rec {
+  pname = "mxnet";
+  version = "1.8.0";
+
+  src = fetchurl {
+    name = "apache-mxnet-src-${version}-incubating.tar.gz";
+    url = "https://dlcdn.apache.org/incubator/mxnet/${version}/apache-mxnet-src-${version}-incubating.tar.gz";
+    hash = "sha256-la/5hYlaukCcCNVRRRCuOLiEkM+2KBqzpf8PWCbI21Q=";
+  };
+
+  patches = [
+    # Fix build error https://github.com/apache/incubator-mxnet/issues/19405
+    (fetchpatch {
+      name = "mxnet-fix-gcc-linker-error-1.patch";
+      url = "https://github.com/apache/incubator-mxnet/commit/78e31d66d19e385ca4ef73245ce79a47e375d8d1.diff";
+      sha256 = "sha256-UfmGhh4RbvrEOXe6IJxHm1Aqpy1gS6gHxrX5KQBXjv4=";
+    })
+    (fetchpatch {
+      name = "mxnet-fix-gcc-linker-error-2.patch";
+      url = "https://github.com/apache/incubator-mxnet/commit/9bfe3116aabd01049fdbd90855cb245a30b795df.diff";
+      sha256 = "sha256-BL7Zf7Bgn0qpai9HbQ6LBxZNa3iLjVJSe5nxZgqI/fw=";
+    })
+  ];
+
+  nativeBuildInputs = [ cmake perl ];
+
+  buildInputs = [ opencv3 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
+    ++ lib.optionals cudaSupport [ cudatoolkit nvidia_x11 ]
+    ++ lib.optional cudnnSupport cudnn;
+
+  cmakeFlags =
+    [ "-DUSE_MKL_IF_AVAILABLE=OFF" ]
+    ++ (if cudaSupport then [
+      "-DUSE_OLDCMAKECUDA=ON"  # see https://github.com/apache/incubator-mxnet/issues/10743
+      "-DCUDA_ARCH_NAME=All"
+      "-DCUDA_HOST_COMPILER=${cudatoolkit.cc}/bin/cc"
+      "-DMXNET_CUDA_ARCH=${lib.concatStringsSep ";" cudaCapabilities}"
+    ] else [ "-DUSE_CUDA=OFF" ])
+    ++ lib.optional (!cudnnSupport) "-DUSE_CUDNN=OFF";
+
+  postPatch = ''
+    substituteInPlace 3rdparty/mkldnn/tests/CMakeLists.txt \
+      --replace "/bin/bash" "${bash}/bin/bash"
+
+    # Build against the system version of OpenMP.
+    # https://github.com/apache/incubator-mxnet/pull/12160
+    rm -rf 3rdparty/openmp
+  '';
+
+  postInstall = ''
+    rm "$out"/lib/*.a
+  '';
+
+  # used to mark cudaSupport in python310Packages.mxnet as broken;
+  # other attributes exposed for consistency
+  passthru = {
+    inherit cudaSupport cudnnSupport cudatoolkit cudnn;
+  };
+
+  meta = with lib; {
+    description = "Lightweight, Portable, Flexible Distributed/Mobile Deep Learning with Dynamic, Mutation-aware Dataflow Dep Scheduler";
+    homepage = "https://mxnet.incubator.apache.org/";
+    maintainers = with maintainers; [ abbradar ];
+    license = licenses.asl20;
+    platforms = platforms.unix;
+    # Build failures when linking mxnet_unit_tests: https://gist.github.com/6d17447ee3557967ec52c50d93b17a1d
+    broken = cudaSupport;
+  };
+}
--- a/pkgs/applications/science/math/nasc/default.nix
+++ b/pkgs/applications/science/math/nasc/default.nix
@ -0,0 +1,87 @@
+{ lib, stdenv
+, fetchFromGitHub
+, pkg-config
+, fetchpatch
+, python3
+, meson
+, ninja
+, vala
+, gtk3
+, glib
+, pantheon
+, gtksourceview
+, libgee
+, nix-update-script
+, webkitgtk
+, libqalculate
+, intltool
+, gnuplot
+, wrapGAppsHook
+}:
+
+stdenv.mkDerivation rec {
+  pname = "nasc";
+  version = "0.8.0";
+
+  src = fetchFromGitHub {
+    owner = "parnold-x";
+    repo = pname;
+    rev = version;
+    sha256 = "02b9a59a9fzsb6nn3ycwwbcbv04qfzm6x7csq2addpzx5wak6dd8";
+    fetchSubmodules = true;
+  };
+
+  nativeBuildInputs = [
+    glib # post_install.py
+    gtk3 # post_install.py
+    intltool # for libqalculate
+    meson
+    ninja
+    pkg-config
+    python3
+    vala
+    wrapGAppsHook
+  ];
+
+  buildInputs = [
+    glib
+    gtk3
+    gtksourceview
+    libgee
+    pantheon.granite
+    webkitgtk
+    # We add libqalculate's runtime dependencies because nasc has it as a modified subproject.
+  ] ++ libqalculate.buildInputs ++ libqalculate.propagatedBuildInputs;
+
+  postPatch = ''
+    chmod +x meson/post_install.py
+    patchShebangs meson/post_install.py
+
+    # patch subproject. same code in libqalculate expression
+    substituteInPlace subprojects/libqalculate/libqalculate/Calculator-plot.cc \
+      --replace 'commandline = "gnuplot"' 'commandline = "${gnuplot}/bin/gnuplot"' \
+      --replace '"gnuplot - ' '"${gnuplot}/bin/gnuplot - '
+  '';
+
+  passthru = {
+    updateScript = nix-update-script {
+      attrPath = pname;
+    };
+  };
+
+  meta = with lib; {
+    description = "Do maths like a normal person, designed for elementary OS";
+    longDescription = ''
+      It’s an app where you do maths like a normal person. It lets you
+      type whatever you want and smartly figures out what is math and
+      spits out an answer on the right pane. Then you can plug those
+      answers in to future equations and if that answer changes, so does
+      the equations it’s used in.
+    '';
+    homepage = "https://github.com/parnold-x/nasc";
+    maintainers = teams.pantheon.members;
+    platforms = platforms.linux;
+    license = licenses.gpl3Plus;
+    mainProgram = "com.github.parnold_x.nasc";
+  };
+}
--- a/pkgs/applications/science/math/nauty/default.nix
+++ b/pkgs/applications/science/math/nauty/default.nix
@ -0,0 +1,50 @@
+{ stdenv
+, lib
+, fetchurl
+}:
+stdenv.mkDerivation rec {
+  pname = "nauty";
+  version = "2.7r3";
+
+  src = fetchurl {
+    url = "https://pallini.di.uniroma1.it/nauty${builtins.replaceStrings ["."] [""] version}.tar.gz";
+    sha256 = "sha256-TwZltxalP3oU6irjAFnyPQZM4/5MEsATQE724e4LiMI=";
+  };
+
+  outputs = [ "out" "dev" ];
+
+  configureFlags = [
+    # Prevent nauty from sniffing some cpu features. While those are very
+    # widely available, it can lead to nasty bugs when they are not available:
+    # https://groups.google.com/forum/#!topic/sage-packaging/Pe4SRDNYlhA
+    "--enable-generic" # don't use -march=native
+    "--${if stdenv.hostPlatform.sse4_2Support then "enable" else "disable"}-popcnt"
+    "--${if stdenv.hostPlatform.sse4_aSupport then "enable" else "disable"}-clz"
+  ];
+
+  installPhase = ''
+    mkdir -p "$out"/{bin,share/doc/nauty} "$dev"/{lib,include/nauty}
+
+    find . -type f -perm -111 \! -name '*.*' \! -name configure -exec cp '{}' "$out/bin" \;
+    cp [Rr][Ee][Aa][Dd]* COPYRIGHT This* [Cc]hange* "$out/share/doc/nauty"
+
+    cp *.h "$dev/include/nauty"
+    for i in *.a; do
+      cp "$i" "$dev/lib/lib$i";
+    done
+  '';
+
+  checkTarget = "checks";
+
+  meta = with lib; {
+    description = "Programs for computing automorphism groups of graphs and digraphs";
+    license = licenses.asl20;
+    maintainers = teams.sage.members;
+    platforms = platforms.unix;
+    # I'm not sure if the filename will remain the same for future changelog or
+    # if it will track changes to minor releases. Lets see. Better than nothing
+    # in any case.
+    changelog = "https://pallini.di.uniroma1.it/changes24-27.txt";
+    homepage = "https://pallini.di.uniroma1.it/";
+  };
+}
--- a/pkgs/applications/science/math/nota/default.nix
+++ b/pkgs/applications/science/math/nota/default.nix
@ -0,0 +1,40 @@
+{ mkDerivation, haskellPackages, fetchurl, lib }:
+
+mkDerivation rec {
+  pname = "nota";
+  version = "1.0";
+
+  # Can't use fetchFromGitLab since codes.kary.us doesn't support https
+  src = fetchurl {
+    url = "http://codes.kary.us/nota/nota/-/archive/V${version}/nota-V${version}.tar.bz2";
+    sha256 = "0bbs6bm9p852hvqadmqs428ir7m65h2prwyma238iirv42pk04v8";
+  };
+
+  postUnpack = ''
+    export sourceRoot=$sourceRoot/source
+  '';
+
+  isLibrary = false;
+  isExecutable = true;
+
+  libraryHaskellDepends = with haskellPackages; [
+    base
+    bytestring
+    array
+    split
+    scientific
+    parsec
+    ansi-terminal
+    regex-compat
+    containers
+    terminal-size
+    numbers
+    text
+    time
+  ];
+
+  description = "The most beautiful command line calculator";
+  homepage = "https://kary.us/nota";
+  license = lib.licenses.mpl20;
+  maintainers = with lib.maintainers; [ dtzWill ];
+}
--- a/pkgs/applications/science/math/numworks-epsilon/0001-ion-linux-makerules.patch
+++ b/pkgs/applications/science/math/numworks-epsilon/0001-ion-linux-makerules.patch
@ -0,0 +1,12 @@
+diff --git a/ion/src/simulator/linux/Makefile b/ion/src/simulator/linux/Makefile
+index ca7da03fa..b05bba115 100644
+--- a/ion/src/simulator/linux/Makefile
+++ b/ion/src/simulator/linux/Makefile
+@@ -28,7 +28,6 @@ ion_src += $(addprefix ion/src/simulator/shared/, \
+   collect_registers.cpp \
+   haptics.cpp \
+   journal.cpp \
+-  platform_action_modifier_ctrl.cpp \
+   state_file.cpp \
+ )
+ 
--- a/pkgs/applications/science/math/numworks-epsilon/default.nix
+++ b/pkgs/applications/science/math/numworks-epsilon/default.nix
@ -0,0 +1,63 @@
+{ stdenv
+, lib
+, fetchFromGitHub
+, libpng
+, libjpeg
+, freetype
+, xorg
+, python3
+, imagemagick
+, gcc-arm-embedded
+, pkg-config
+}:
+
+stdenv.mkDerivation rec {
+  pname = "numworks-epsilon";
+  version = "15.5.0";
+
+  src = fetchFromGitHub {
+    owner = "numworks";
+    repo = "epsilon";
+    rev = version;
+    sha256 = "fPBO3FzZ4k5OxG+Ifc6R/au4Te974HNKAEdHz+aFdSg=";
+  };
+
+  nativeBuildInputs = [ pkg-config ];
+  buildInputs = [
+    libpng
+    libjpeg
+    freetype
+    xorg.libXext
+    python3
+    imagemagick
+    gcc-arm-embedded
+  ];
+
+  makeFlags = [
+    "PLATFORM=simulator"
+  ];
+
+  patches = [
+    # Remove make rule Introduced in cba596dde7
+    # which causes it to not build with nix
+    ./0001-ion-linux-makerules.patch
+  ];
+
+  installPhase = ''
+    runHook preInstall
+
+    mv ./output/release/simulator/linux/{epsilon.bin,epsilon}
+    mkdir -p $out/bin
+    cp -r ./output/release/simulator/linux/* $out/bin/
+
+    runHook postInstall
+  '';
+
+  meta = with lib; {
+    description = "Simulator for Epsilon, a High-performance graphing calculator operating system";
+    homepage = "https://numworks.com/";
+    license = licenses.cc-by-nc-sa-40;
+    maintainers = with maintainers; [ erikbackman ];
+    platforms = [ "x86_64-linux" ];
+  };
+}
--- a/pkgs/applications/science/math/palp/default.nix
+++ b/pkgs/applications/science/math/palp/default.nix
@ -0,0 +1,91 @@
+{ lib
+, stdenv
+, fetchurl
+, dimensions ? 6 # works for <= dimensions dimensions, but is only optimized for that exact value
+, doSymlink ? true # symlink the executables to the default location (without dimension postfix)
+}:
+
+let
+  dim = toString dimensions;
+in
+stdenv.mkDerivation rec {
+  pname = "palp";
+  version = "2.20";
+
+  src = fetchurl {
+    url = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/palp/${pname}-${version}.tar.gz";
+    sha256 = "1q1cl3vpdir16szy0jcadysydcrjp48hqxyx42kr8g9digkqjgkj";
+  };
+
+  hardeningDisable = [
+    "format"
+  ];
+
+  patchPhase = lib.optionalString stdenv.isDarwin ''
+    substituteInPlace GNUmakefile --replace gcc cc
+  '';
+
+  preBuild = ''
+    echo Building PALP optimized for ${dim} dimensions
+    sed -i "s/^#define[^a-zA-Z]*POLY_Dmax.*/#define POLY_Dmax ${dim}/" Global.h
+  '';
+
+  # palp has no tests of its own. This test is an adapted sage test that failed
+  # when #28029 was merged.
+  doCheck = true;
+  checkPhase = ''
+    ./nef.x -f -N << EOF | grep -q 'np='
+      3 6
+      1  0  0 -1  0  0
+      0  1  0  0 -1  0
+      0  0  1  0  0 -1
+    EOF
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin
+    for file in poly class cws nef mori; do
+      cp -p $file.x "$out/bin/$file-${dim}d.x"
+    done
+  '' + lib.optionalString doSymlink ''
+    cd $out/bin
+    for file in poly class cws nef mori; do
+      ln -sf $file-6d.x $file.x
+    done
+  '';
+
+  meta = with lib; {
+    description = "A Package for Analyzing Lattice Polytopes";
+    longDescription = ''
+      A Package for Analyzing Lattice Polytopes (PALP) is a set of C
+      programs for calculations with lattice polytopes and applications to
+      toric geometry.
+
+      It contains routines for vertex and facet enumeration, computation of
+      incidences and symmetries, as well as completion of the set of lattice
+      points in the convex hull of a given set of points. In addition, there
+      are procedures specialised to reflexive polytopes such as the
+      enumeration of reflexive subpolytopes, and applications to toric
+      geometry and string theory, like the computation of Hodge data and
+      fibration structures for toric Calabi-Yau varieties.  The package is
+      well tested and optimised in speed as it was used for time consuming
+      tasks such as the classification of reflexive polyhedra in 4
+      dimensions and the creation and manipulation of very large lists of
+      5-dimensional polyhedra.
+
+      While originally intended for low-dimensional applications, the
+      algorithms work in any dimension and our key routine for vertex and
+      facet enumeration compares well with existing packages.
+    '';
+    homepage = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/CYpalp.html";
+    # Not really a changelog, but a one-line summary of each update that should
+    # be reviewed on update.
+    changelog = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/CYpalp.html";
+    # Just a link on the website pointing to gpl -- now gplv3. When the last
+    # version was released that pointed to gplv2 however, so thats probably
+    # the right license.
+    license = licenses.gpl2;
+    maintainers = teams.sage.members;
+    platforms = platforms.unix;
+  };
+}
--- a/pkgs/applications/science/math/pari/default.nix
+++ b/pkgs/applications/science/math/pari/default.nix
@ -0,0 +1,88 @@
+{ lib
+, stdenv
+, fetchurl
+, gmp
+, libX11
+, perl
+, readline
+, tex
+, withThread ? true, libpthreadstubs
+}:
+
+assert withThread -> libpthreadstubs != null;
+
+stdenv.mkDerivation rec {
+  pname = "pari";
+  version = "2.13.4";
+
+  src = fetchurl {
+    urls = [
+      "https://pari.math.u-bordeaux.fr/pub/pari/unix/${pname}-${version}.tar.gz"
+      # old versions are at the url below
+      "https://pari.math.u-bordeaux.fr/pub/pari/OLD/${lib.versions.majorMinor version}/${pname}-${version}.tar.gz"
+    ];
+    hash = "sha256-vN6ezq4VkoFDgcFpfNtwY1Z7ZQQgGxvke7WJIPO84YU=";
+  };
+
+  buildInputs = [
+    gmp
+    libX11
+    perl
+    readline
+    tex
+  ] ++ lib.optionals withThread [
+    libpthreadstubs
+  ];
+
+  configureScript = "./Configure";
+  configureFlags = [
+    "--with-gmp=${lib.getDev gmp}"
+    "--with-readline=${lib.getDev readline}"
+  ]
+  ++ lib.optional stdenv.isDarwin "--host=x86_64-darwin"
+  ++ lib.optional withThread "--mt=pthread";
+
+  preConfigure = ''
+    export LD=$CC
+  '';
+
+  postConfigure = lib.optionalString stdenv.isDarwin ''
+    echo 'echo x86_64-darwin' > config/arch-osname
+  '';
+
+  makeFlags = [ "all" ];
+
+  meta = with lib; {
+    homepage = "http://pari.math.u-bordeaux.fr";
+    description = "Computer algebra system for high-performance number theory computations";
+    longDescription = ''
+       PARI/GP is a widely used computer algebra system designed for fast
+       computations in number theory (factorizations, algebraic number theory,
+       elliptic curves...), but also contains a large number of other useful
+       functions to compute with mathematical entities such as matrices,
+       polynomials, power series, algebraic numbers etc., and a lot of
+       transcendental functions. PARI is also available as a C library to allow
+       for faster computations.
+
+       Originally developed by Henri Cohen and his co-workers (Université
+       Bordeaux I, France), PARI is now under the GPL and maintained by Karim
+       Belabas with the help of many volunteer contributors.
+
+       - PARI is a C library, allowing fast computations.
+       - gp is an easy-to-use interactive shell giving access to the PARI
+         functions.
+       - GP is the name of gp's scripting language.
+       - gp2c, the GP-to-C compiler, combines the best of both worlds by
+         compiling GP scripts to the C language and transparently loading the
+         resulting functions into gp. (gp2c-compiled scripts will typically run
+         3 or 4 times faster.) gp2c currently only understands a subset of the
+         GP language.
+    '';
+    downloadPage = "http://pari.math.u-bordeaux.fr/download.html";
+    license = licenses.gpl2Plus;
+    maintainers = with maintainers; [ ertes AndersonTorres ] ++ teams.sage.members;
+    platforms = platforms.linux ++ platforms.darwin;
+    broken = stdenv.isDarwin && stdenv.isAarch64;
+    mainProgram = "gp";
+  };
+}
--- a/pkgs/applications/science/math/pari/gp2c.nix
+++ b/pkgs/applications/science/math/pari/gp2c.nix
@ -0,0 +1,34 @@
+{ lib
+, stdenv
+, fetchurl
+, pari
+, perl
+}:
+
+stdenv.mkDerivation rec {
+  pname = "gp2c";
+  version = "0.0.12";
+
+  src = fetchurl {
+    url = "https://pari.math.u-bordeaux.fr/pub/pari/GP2C/${pname}-${version}.tar.gz";
+    sha256 = "039ip7qkwwv46wrcdrz7y12m30kazzkjr44kqbc0h137g4wzd7zf";
+  };
+
+  buildInputs = [
+    pari
+    perl
+  ];
+
+  configureFlags = [
+    "--with-paricfg=${pari}/lib/pari/pari.cfg"
+    "--with-perl=${perl}/bin/perl"
+  ];
+
+  meta = with lib; {
+    description =  "A compiler to translate GP scripts to PARI programs";
+    homepage = "http://pari.math.u-bordeaux.fr/";
+    downloadPage = "http://pari.math.u-bordeaux.fr/download.html";
+    license = licenses.gpl2Plus;
+    maintainers = with maintainers; [ AndersonTorres ];
+  };
+}
--- a/pkgs/applications/science/math/pcalc/default.nix
+++ b/pkgs/applications/science/math/pcalc/default.nix
@ -0,0 +1,26 @@
+{ lib, stdenv, fetchFromGitHub, bison, flex }:
+
+stdenv.mkDerivation rec {
+  pname = "pcalc";
+  version = "20181202";
+
+  src = fetchFromGitHub {
+    owner = "vapier";
+    repo = "pcalc";
+    rev = "d93be9e19ecc0b2674cf00ec91cbb79d32ccb01d";
+    sha256 = "sha256-m4xdsEJGKxLgp/d5ipxQ+cKG3z7rlvpPL6hELnDu6Hk=";
+  };
+
+  makeFlags = [ "DESTDIR= BINDIR=$(out)/bin" ];
+  nativeBuildInputs = [ bison flex ];
+
+  enableParallelBuilding = true;
+
+  meta = with lib; {
+    homepage = "https://vapier.github.io/pcalc/";
+    description = "Programmer's calculator";
+    license = licenses.gpl2Plus;
+    maintainers = with maintainers; [ ftrvxmtrx ];
+    platforms = platforms.unix;
+  };
+}
--- a/pkgs/applications/science/math/perseus/default.nix
+++ b/pkgs/applications/science/math/perseus/default.nix
@ -0,0 +1,40 @@
+{ lib, stdenv, fetchurl, unzip }:
+
+stdenv.mkDerivation {
+  pname = "perseus";
+  version = "4-beta";
+  nativeBuildInputs = [ unzip ];
+
+  hardeningDisable = [ "stackprotector" ];
+
+  src = fetchurl {
+    url = "http://www.sas.upenn.edu/~vnanda/source/perseus_4_beta.zip";
+    sha256 = "09brijnqabhgfjlj5wny0bqm5dwqcfkp1x5wif6yzdmqh080jybj";
+  };
+
+  sourceRoot = ".";
+
+  buildPhase = ''
+    g++ Pers.cpp -O3 -fpermissive -o perseus
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp perseus $out/bin
+  '';
+
+  meta = {
+    description = "The Persistent Homology Software";
+    longDescription = ''
+      Persistent homology - or simply, persistence - is an algebraic
+      topological invariant of a filtered cell complex. Perseus
+      computes this invariant for a wide class of filtrations built
+      around datasets arising from point samples, images, distance
+      matrices and so forth.
+    '';
+    homepage = "http://www.sas.upenn.edu/~vnanda/perseus/index.html";
+    license = lib.licenses.gpl3;
+    maintainers = with lib.maintainers; [ erikryb ];
+    platforms = lib.platforms.linux;
+  };
+}
--- a/pkgs/applications/science/math/polymake/default.nix
+++ b/pkgs/applications/science/math/polymake/default.nix
@ -0,0 +1,51 @@
+{ lib, stdenv, fetchurl
+, perl, gmp, mpfr, flint, boost
+, bliss, ppl, singular, cddlib, lrs, nauty
+, ninja, ant, openjdk
+, perlPackages
+, makeWrapper
+}:
+
+# polymake compiles its own version of sympol and atint because we
+# don't have those packages. other missing optional dependencies:
+# javaview, libnormaliz, scip, soplex, jreality.
+
+stdenv.mkDerivation rec {
+  pname = "polymake";
+  version = "4.6";
+
+  src = fetchurl {
+    # "The minimal version is a packager friendly version which omits
+    # the bundled sources of cdd, lrs, libnormaliz, nauty and jReality."
+    url = "https://polymake.org/lib/exe/fetch.php/download/polymake-${version}-minimal.tar.bz2";
+    sha256 = "sha256-QjpE3e8R6uqEV6sV3V2G3beovMbJuxF3b54pWNfc+dA=";
+  };
+
+  buildInputs = [
+    perl gmp mpfr flint boost
+    bliss ppl singular cddlib lrs nauty
+    openjdk
+  ] ++ (with perlPackages; [
+    JSON TermReadLineGnu TermReadKey XMLSAX
+  ]);
+
+  nativeBuildInputs = [
+    makeWrapper ninja ant perl
+  ];
+
+  ninjaFlags = [ "-C" "build/Opt" ];
+
+  postInstall = ''
+    for i in "$out"/bin/*; do
+      wrapProgram "$i" --prefix PERL5LIB : "$PERL5LIB"
+    done
+  '';
+
+  meta = with lib; {
+    description = "Software for research in polyhedral geometry";
+    license = licenses.gpl2Plus;
+    maintainers = teams.sage.members;
+    platforms = platforms.linux;
+    homepage = "https://www.polymake.org/doku.php";
+  };
+}
--- a/pkgs/applications/science/math/primecount/default.nix
+++ b/pkgs/applications/science/math/primecount/default.nix
@ -0,0 +1,51 @@
+{ lib
+, stdenv
+, fetchFromGitHub
+, cmake
+, primesieve
+}:
+
+stdenv.mkDerivation rec {
+  pname = "primecount";
+  version = "7.3";
+
+  src = fetchFromGitHub {
+    owner = "kimwalisch";
+    repo = "primecount";
+    rev = "v${version}";
+    hash = "sha256-hxnn1uiGSB6XRC7yK+SXTwTsJfjhemWXsMNhhL7Ghek=";
+  };
+
+  nativeBuildInputs = [ cmake ];
+
+  buildInputs = [ primesieve ];
+
+  cmakeFlags = [
+    "-DBUILD_LIBPRIMESIEVE=ON"
+    "-DBUILD_PRIMECOUNT=ON"
+    "-DBUILD_SHARED_LIBS=ON"
+    "-DBUILD_STATIC_LIBS=OFF"
+    "-DBUILD_TESTS=ON"
+  ];
+
+  meta = with lib; {
+    homepage = "https://github.com/kimwalisch/primecount";
+    description = "Fast prime counting function implementations";
+    longDescription = ''
+      primecount is a command-line program and C/C++ library that counts the
+      primes below an integer x ≤ 10^31 using highly optimized implementations
+      of the combinatorial prime counting algorithms.
+
+      primecount includes implementations of all important combinatorial prime
+      counting algorithms known up to this date all of which have been
+      parallelized using OpenMP. primecount contains the first ever open source
+      implementations of the Deleglise-Rivat algorithm and Xavier Gourdon's
+      algorithm (that works). primecount also features a novel load balancer
+      that is shared amongst all implementations and that scales up to hundreds
+      of CPU cores. primecount has already been used to compute several prime
+      counting function world records.
+    '';
+    license = licenses.bsd2;
+    inherit (primesieve.meta) maintainers platforms;
+  };
+}
--- a/pkgs/applications/science/math/primesieve/default.nix
+++ b/pkgs/applications/science/math/primesieve/default.nix
@ -0,0 +1,36 @@
+{ lib
+, stdenv
+, fetchFromGitHub
+, cmake
+}:
+
+stdenv.mkDerivation rec {
+  pname = "primesieve";
+  version = "7.9";
+
+  src = fetchFromGitHub {
+    owner = "kimwalisch";
+    repo = "primesieve";
+    rev = "v${version}";
+    hash = "sha256-lwT+adKFoNI125y5FuJMovtMh8sFi9oqMLYGLabzrCI=";
+  };
+
+  nativeBuildInputs = [ cmake ];
+
+  meta = with lib; {
+    homepage = "https://primesieve.org/";
+    description = "Fast C/C++ prime number generator";
+    longDescription = ''
+      primesieve is a command-line program and C/C++ library for quickly
+      generating prime numbers. It is very cache efficient, it detects your
+      CPU's L1 & L2 cache sizes and allocates its main data structures
+      accordingly. It is also multi-threaded by default, it uses all available
+      CPU cores whenever possible i.e. if sequential ordering is not
+      required. primesieve can generate primes and prime k-tuplets up to 264.
+    '';
+    license = licenses.bsd2;
+    maintainers = teams.sage.members ++
+      (with maintainers; [ abbradar AndersonTorres ]);
+    platforms = platforms.unix;
+  };
+}
--- a/pkgs/applications/science/math/programmer-calculator/default.nix
+++ b/pkgs/applications/science/math/programmer-calculator/default.nix
@ -0,0 +1,34 @@
+{ lib, gccStdenv, fetchFromGitHub, ncurses }:
+
+gccStdenv.mkDerivation rec {
+  pname = "programmer-calculator";
+  version = "2.2";
+
+  src = fetchFromGitHub {
+    owner = "alt-romes";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "sha256-JQcYCYKdjdy8U2XMFzqTH9kAQ7CFv0r+sC1YfuAm7p8=";
+  };
+
+  buildInputs = [ ncurses ];
+
+  installPhase = ''
+    runHook preInstall
+    install -Dm 555 pcalc -t "$out/bin"
+    runHook postInstall
+  '';
+
+  meta = with lib; {
+    description = "A terminal calculator for programmers";
+    longDescription = ''
+      Terminal calculator made for programmers working with multiple number
+      representations, sizes, and overall close to the bits
+    '';
+    homepage = "https://alt-romes.github.io/programmer-calculator";
+    changelog = "https://github.com/alt-romes/programmer-calculator/releases/tag/v${version}";
+    license = licenses.gpl3Only;
+    maintainers = with lib.maintainers; [ cjab ];
+    platforms = platforms.all;
+  };
+}
--- a/pkgs/applications/science/math/pspp/default.nix
+++ b/pkgs/applications/science/math/pspp/default.nix
@ -0,0 +1,53 @@
+{ lib, stdenv, fetchurl, libxml2, readline, zlib, perl, cairo, gtk3, gsl
+, pkg-config, gtksourceview, pango, gettext, dconf
+, makeWrapper, gsettings-desktop-schemas, hicolor-icon-theme
+, texinfo, ssw, python3
+}:
+
+stdenv.mkDerivation rec {
+  pname = "pspp";
+  version = "1.4.1";
+
+  src = fetchurl {
+    url = "mirror://gnu/pspp/${pname}-${version}.tar.gz";
+    sha256 = "0lqrash677b09zxdlxp89z6k02y4i23mbqg83956dwl69wc53dan";
+  };
+
+  nativeBuildInputs = [ pkg-config texinfo python3 ];
+  buildInputs = [ libxml2 readline zlib perl cairo gtk3 gsl
+    gtksourceview pango gettext
+    makeWrapper gsettings-desktop-schemas hicolor-icon-theme ssw
+  ];
+
+  doCheck = false;
+
+  enableParallelBuilding = true;
+
+  preFixup = ''
+    wrapProgram "$out/bin/psppire" \
+     --prefix XDG_DATA_DIRS : "$out/share" \
+     --prefix XDG_DATA_DIRS : "$XDG_ICON_DIRS" \
+     --prefix XDG_DATA_DIRS : "$GSETTINGS_SCHEMAS_PATH" \
+     --prefix GIO_EXTRA_MODULES : "${lib.getLib dconf}/lib/gio/modules"
+  '';
+
+  meta = {
+    homepage = "https://www.gnu.org/software/pspp/";
+    description = "A free replacement for SPSS, a program for statistical analysis of sampled data";
+    license = lib.licenses.gpl3Plus;
+
+    longDescription = ''
+      PSPP is a program for statistical analysis of sampled data. It is
+      a Free replacement for the proprietary program SPSS.
+
+      PSPP can perform descriptive statistics, T-tests, anova, linear
+      and logistic regression, cluster analysis, factor analysis,
+      non-parametric tests and more. Its backend is designed to perform
+      its analyses as fast as possible, regardless of the size of the
+      input data. You can use PSPP with its graphical interface or the
+      more traditional syntax commands.
+    '';
+
+    platforms = lib.platforms.unix;
+  };
+}
--- a/pkgs/applications/science/math/pynac/default.nix
+++ b/pkgs/applications/science/math/pynac/default.nix
@ -0,0 +1,60 @@
+{ lib, stdenv
+, fetchpatch
+, fetchFromGitHub
+, autoreconfHook
+, pkg-config
+, flint
+, gmp
+, python3
+, singular
+, ncurses
+}:
+
+stdenv.mkDerivation rec {
+  version = "0.7.29";
+  pname = "pynac";
+
+  src = fetchFromGitHub {
+    owner = "pynac";
+    repo = "pynac";
+    rev = "pynac-${version}";
+    sha256 = "sha256-ocR7emXtKs+Xe2f6dh4xEDAacgiolY8mtlLnWnNBS8A=";
+  };
+
+  patches = [
+    # the patch below is included in sage 9.4 and should be included
+    # in a future pynac release. see https://trac.sagemath.org/ticket/28357
+    (fetchpatch {
+      name = "realpartloop.patch";
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/realpartloop.patch?h=9.4.beta5";
+      sha256 = "sha256-1nj0xtlFN5fZKEiRLD+tiW/ZtxMQre1ziEGA0OVUGE4=";
+    })
+  ];
+
+  buildInputs = [
+    flint
+    gmp
+    singular
+    python3
+    ncurses
+  ];
+
+  nativeBuildInputs = [
+    autoreconfHook
+    pkg-config
+  ];
+
+  meta = with lib; {
+    description = "Python is Not a CAS -- modified version of Ginac";
+    longDescription = ''
+      Pynac -- "Python is Not a CAS" is a modified version of Ginac that
+      replaces the depency of GiNaC on CLN by a dependency instead of Python.
+      It is a lite version of GiNaC as well, not implementing all the features
+      of the full GiNaC, and it is *only* meant to be used as a Python library.
+    '';
+    homepage    = "http://pynac.org";
+    license = licenses.gpl2Plus;
+    maintainers = teams.sage.members;
+    platforms   = platforms.unix;
+  };
+}
--- a/pkgs/applications/science/math/qalculate-gtk/default.nix
+++ b/pkgs/applications/science/math/qalculate-gtk/default.nix
@ -0,0 +1,27 @@
+{ lib, stdenv, fetchFromGitHub, intltool, autoreconfHook, pkg-config, libqalculate, gtk3, wrapGAppsHook }:
+
+stdenv.mkDerivation rec {
+  pname = "qalculate-gtk";
+  version = "4.2.0";
+
+  src = fetchFromGitHub {
+    owner = "qalculate";
+    repo = "qalculate-gtk";
+    rev = "v${version}";
+    sha256 = "sha256-SphruQ/b8z5S/wKb9yhbEy9/pwiY+frZltdIYj0CJBM=";
+  };
+
+  hardeningDisable = [ "format" ];
+
+  nativeBuildInputs = [ intltool pkg-config autoreconfHook wrapGAppsHook ];
+  buildInputs = [ libqalculate gtk3 ];
+  enableParallelBuilding = true;
+
+  meta = with lib; {
+    description = "The ultimate desktop calculator";
+    homepage = "http://qalculate.github.io";
+    maintainers = with maintainers; [ gebner doronbehar ];
+    license = licenses.gpl2Plus;
+    platforms = platforms.all;
+  };
+}
--- a/pkgs/applications/science/math/ratpoints/default.nix
+++ b/pkgs/applications/science/math/ratpoints/default.nix
@ -0,0 +1,35 @@
+{ lib, stdenv, fetchurl, fetchpatch, gmp }:
+stdenv.mkDerivation rec {
+  pname = "ratpoints";
+  version = "2.1.3.p4";
+
+  src = fetchurl {
+    url = "http://www.mathe2.uni-bayreuth.de/stoll/programs/ratpoints-${version}.tar.gz";
+    sha256 = "0zhad84sfds7izyksbqjmwpfw4rvyqk63yzdjd3ysd32zss5bgf4";
+  };
+
+  enableParallelBuilding = true;
+
+  patches = [
+    (fetchpatch {
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/ratpoints/patches/sturm_and_rp_private.patch?id=1615f58890e8f9881c4228c78a6b39b9aab1303a";
+      sha256 = "0q3wajncyfr3gahd8gwk9x7g56zw54lpywrl63lqk7drkf60mrcl";
+    })
+  ];
+
+  buildInputs = [ gmp ];
+
+  makeFlags = [ "CC=${stdenv.cc.targetPrefix}cc" ];
+  buildFlags = lib.optional stdenv.isDarwin ["CCFLAGS2=-lgmp -lc -lm" "CCFLAGS=-UUSE_SSE"];
+  installFlags = [ "INSTALL_DIR=$(out)" ];
+
+  preInstall = ''mkdir -p "$out"/{bin,share,lib,include}'';
+
+  meta = {
+    description = "A program to find rational points on hyperelliptic curves";
+    license = lib.licenses.gpl2Plus;
+    maintainers = [lib.maintainers.raskin];
+    platforms = lib.platforms.unix;
+    homepage = "http://www.mathe2.uni-bayreuth.de/stoll/programs/";
+  };
+}
--- a/pkgs/applications/science/math/ries/default.nix
+++ b/pkgs/applications/science/math/ries/default.nix
@ -0,0 +1,22 @@
+{ lib, stdenv, fetchzip }:
+stdenv.mkDerivation rec {
+  pname = "ries";
+  version = "2018.04.11-1";
+
+  # upstream does not provide a stable link
+  src = fetchzip {
+    url = "https://salsa.debian.org/debian/ries/-/archive/debian/${version}/ries-debian-${version}.zip";
+    sha256 = "1h2wvd4k7f0l0i1vm9niz453xdbcs3nxccmri50qyrzzzc1b0842";
+  };
+
+  makeFlags = [ "PREFIX=$(out)" ];
+
+  meta = with lib; {
+    homepage = "https://mrob.com/pub/ries/";
+    description = "Tool to produce a list of equations that approximately solve to a given number";
+    platforms = platforms.all;
+    maintainers = with maintainers; [ symphorien ];
+    license = licenses.gpl3Plus;
+  };
+}
+
--- a/pkgs/applications/science/math/ripser/default.nix
+++ b/pkgs/applications/science/math/ripser/default.nix
@ -0,0 +1,58 @@
+{ lib, stdenv, fetchFromGitHub
+, useCoefficients ? false
+, indicateProgress ? false
+, useGoogleHashmap ? false, sparsehash ? null
+, fileFormat ? "lowerTriangularCsv"
+}:
+
+with lib;
+
+assert assertOneOf "fileFormat" fileFormat
+  ["lowerTriangularCsv" "upperTriangularCsv" "dipha"];
+assert useGoogleHashmap -> sparsehash != null;
+
+let
+  inherit (lib) optional;
+  version = "1.2.1";
+in
+stdenv.mkDerivation {
+  pname = "ripser";
+  inherit version;
+
+  src = fetchFromGitHub {
+    owner = "Ripser";
+    repo = "ripser";
+    rev = "v${version}";
+    sha256 = "sha256-BxmkPQ/nl5cF+xwQMTjXnLgkLgdmT/39y7Kzl2wDfpE=";
+  };
+
+  buildInputs = optional useGoogleHashmap sparsehash;
+
+  buildFlags = [
+    "-std=c++11"
+    "-O3"
+    "-D NDEBUG"
+  ]
+  ++ optional useCoefficients "-D USE_COEFFICIENTS"
+  ++ optional indicateProgress "-D INDICATE_PROGRESS"
+  ++ optional useGoogleHashmap "-D USE_GOOGLE_HASHMAP"
+  ++ optional (fileFormat == "lowerTriangularCsv") "-D FILE_FORMAT_LOWER_TRIANGULAR_CSV"
+  ++ optional (fileFormat == "upperTriangularCsv") "-D FILE_FORMAT_UPPER_TRIANGULAR_CSV"
+  ++ optional (fileFormat == "dipha") "-D FILE_FORMAT_DIPHA"
+  ;
+
+  buildPhase = "c++ ripser.cpp -o ripser $buildFlags";
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp ripser $out/bin
+  '';
+
+  meta = {
+    description = "A lean C++ code for the computation of Vietoris–Rips persistence barcodes";
+    homepage = "https://github.com/Ripser/ripser";
+    license = lib.licenses.lgpl3;
+    maintainers = with lib.maintainers; [erikryb];
+    platforms = lib.platforms.linux;
+  };
+}
--- a/pkgs/applications/science/math/rofi-calc/0001-Patch-plugindir-to-output.patch
+++ b/pkgs/applications/science/math/rofi-calc/0001-Patch-plugindir-to-output.patch
@ -0,0 +1,25 @@
+From 0eaef67b683683fb423fcb2d5096b3cdf9a4a9cd Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Maciej=20Kr=C3=BCger?= <mkg20001@gmail.com>
+Date: Sun, 22 Mar 2020 12:26:10 +0100
+Subject: [PATCH] Patch plugindir to output
+
+---
+ configure.ac | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/configure.ac b/configure.ac
+index 50edb74..639ee86 100644
+--- a/configure.ac
+++ b/configure.ac
+@@ -50,7 +50,7 @@ PKG_CHECK_MODULES([glib],     [glib-2.0 >= 2.40 gio-unix-2.0 gmodule-2.0 ])
+ PKG_CHECK_MODULES([cairo],    [cairo])
+ PKG_CHECK_MODULES([rofi],     [rofi >= 1.5.4])
+ 
+-[rofi_PLUGIN_INSTALL_DIR]="`$PKG_CONFIG --variable=pluginsdir rofi`"
+[rofi_PLUGIN_INSTALL_DIR]="`echo $out/lib/rofi`"
+ AC_SUBST([rofi_PLUGIN_INSTALL_DIR])
+ 
+ LT_INIT([disable-static])
+-- 
+2.25.1
+
--- a/pkgs/applications/science/math/rofi-calc/default.nix
+++ b/pkgs/applications/science/math/rofi-calc/default.nix
@ -0,0 +1,54 @@
+{ lib, stdenv
+, fetchFromGitHub
+, autoreconfHook
+, pkg-config
+, rofi-unwrapped
+, libqalculate
+, glib
+, cairo
+, gobject-introspection
+, wrapGAppsHook
+}:
+
+stdenv.mkDerivation rec {
+  pname = "rofi-calc";
+  version = "2.1.0";
+
+  src = fetchFromGitHub {
+    owner = "svenstaro";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "sha256-sfUcBSUYf/+neBAhEd5LAtMOfIbdXM/ieUOztjk8Pwg=";
+  };
+
+  nativeBuildInputs = [
+    autoreconfHook
+    pkg-config
+    gobject-introspection
+    wrapGAppsHook
+  ];
+
+  buildInputs = [
+    rofi-unwrapped
+    libqalculate
+    glib
+    cairo
+  ];
+
+  patches = [
+    ./0001-Patch-plugindir-to-output.patch
+  ];
+
+  postPatch = ''
+    sed "s|qalc_binary = \"qalc\"|qalc_binary = \"${libqalculate}/bin/qalc\"|" -i src/calc.c
+  '';
+
+  meta = with lib; {
+    description = "Do live calculations in rofi!";
+    homepage = "https://github.com/svenstaro/rofi-calc";
+    license = licenses.mit;
+    maintainers = with maintainers; [ luc65r albakham ];
+    platforms = with platforms; linux;
+  };
+}
+
--- a/pkgs/applications/science/math/sage/README.md
+++ b/pkgs/applications/science/math/sage/README.md
@ -0,0 +1,78 @@
+# Sage on nixos
+
+Sage is a pretty complex package that depends on many other complex packages and patches some of those. As a result, the sage nix package is also quite complex.
+
+Don't feel discouraged to fix, simplify or improve things though. The individual files have comments explaining their purpose. The most importent ones are `default.nix` linking everything together, `sage-src.nix` adding patches and `sagelib.nix` building the actual sage package.
+
+## The sage build is broken
+
+First you should find out which change to nixpkgs is at fault (if you don't already know). You can use `git-bisect` for that (see the manpage).
+
+If the build broke as a result of a package update, try those solutions in order:
+
+- search the [sage trac](https://trac.sagemath.org/) for keywords like "Upgrade <package>". Maybe somebody has already proposed a patch that fixes the issue. You can then add a `fetchpatch` to `sage-src.nix`.
+
+- check if [gentoo](https://github.com/cschwan/sage-on-gentoo/tree/master/sci-mathematics/sage), [debian](https://salsa.debian.org/science-team/sagemath/tree/master/debian) or [arch linux](https://git.archlinux.org/svntogit/community.git/tree/trunk?h=packages/sagemath) already solved the problem. You can then again add a `fetchpatch` to `sage-src.nix`. If applicable you should also [propose the patch upstream](#proposing-a-sage-patch).
+
+- fix the problem yourself. First clone the sagemath source and then check out the sage version you want to patch:
+
+```
+[user@localhost ~]$ git clone https://github.com/sagemath/sage.git
+[user@localhost ~]$ cd sage
+[user@localhost sage]$ git checkout 8.2 # substitute the relevant version here
+```
+
+Then make the needed changes and generate a patch with `git diff`:
+
+```
+[user@localhost ~]$ <make changes>
+[user@localhost ~]$ git diff -u > /path/to/nixpkgs/pkgs/applications/science/math/sage/patches/name-of-patch.patch
+```
+
+Now just add the patch to `sage-src.nix` and test your changes. If they fix the problem, [propose them upstream](#proposing-a-sage-patch) and add a link to the trac ticket.
+
+- pin the package version in `default.nix` and add a note that explains why that is necessary.
+
+
+## Proposing a sage patch
+
+You can [login the sage trac using GitHub](https://trac.sagemath.org/login). Your username will then be `gh-<your-github-name>`. The only other way is to request a trac account via email. After that refer to [git the hard way](http://doc.sagemath.org/html/en/developer/manual_git.html#chapter-manual-git) in the sage documentation. The "easy way" requires a non-GitHub account (requested via email) and a special tool. The "hard way" is really not all that hard if you're a bit familiar with git.
+
+Here's the gist, assuming you want to use ssh key authentication. First, [add your public ssh key](https://trac.sagemath.org/prefs/sshkeys). Then:
+
+```
+[user@localhost ~]$ git clone https://github.com/sagemath/sage.git
+[user@localhost ~]$ cd sage
+[user@localhost sage]$ git remote add trac git@trac.sagemath.org:sage.git -t master
+[user@localhost sage]$ git checkout -b u/gh-<your-github-username>/<your-branch-name> develop
+[user@localhost sage]$ <make changes>
+[user@localhost sage]$ git add .
+[user@localhost sage]$ git commit
+[user@localhost sage]$ git show # review your changes
+[user@localhost sage]$ git push --set-upstream trac u/gh-<your-github-username>/<your-branch-name>
+```
+
+You now created a branch on the trac server (you *must* follow the naming scheme as you only have push access to branches with the `u/gh-<your-github-username>/` prefix).
+Now you can [create a new trac ticket](https://trac.sagemath.org/newticket).
+- Write a description of the change
+- set the type and component as appropriate
+- write your real name in the "Authors" field
+- write `u/gh-<your-github-username>/<your-branch-name>` in the "Branch" field
+- click "Create ticket"
+- click "Modify" on the top right of your ticket (for some reason you can only change the ticket status after you have created it)
+- set the ticket status from `new` to `needs_review`
+- click "Save changes"
+
+Refer to sages [Developer's Guide](http://doc.sagemath.org/html/en/developer/index.html) for further details.
+
+## I want to update sage
+
+You'll need to change the `version` field in `sage-src.nix`. Afterwards just try to build and let nix tell you which patches no longer apply (hopefully because they were adopted upstream). Remove those.
+
+Hopefully the build will succeed now. If it doesn't and the problem is obvious, fix it as described in [The sage build is broken](#the-sage-build-is-broken).
+If the problem is not obvious, you can try to first update sage to an intermediate version (remember that you can also set the `version` field to any git revision of sage) and locate the sage commit that introduced the issue. You can even use `git-bisect` for that (it will only be a bit tricky to keep track of which patches to apply). Hopefully after that the issue will be obvious.
+
+## Well, that didn't help!
+
+If you couldn't fix the problem, create a GitHub issue on the nixpkgs repo and ping @timokau (or whoever is listed in the `maintainers` list of the sage package).
+Describe what you did and why it didn't work. Afterwards it would be great if you help the next guy out and improve this documentation!
--- a/pkgs/applications/science/math/sage/default.nix
+++ b/pkgs/applications/science/math/sage/default.nix
@ -0,0 +1,177 @@
+{ pkgs
+, withDoc ? false
+, requireSageTests ? true
+, extraPythonPackages ? ps: []
+}:
+
+# 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 (pkgs) symlinkJoin callPackage nodePackages;
+
+  python3 = pkgs.python3.override {
+    packageOverrides = self: super: {
+      # `sagelib`, i.e. all of sage except some wrappers and runtime dependencies
+      sagelib = self.callPackage ./sagelib.nix {
+        inherit flint arb;
+        inherit sage-src env-locations singular;
+        inherit (maxima) lisp-compiler;
+        linbox = pkgs.linbox.override { withSage = true; };
+        pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config
+      };
+
+      sage-docbuild = self.callPackage ./python-modules/sage-docbuild.nix {
+        inherit sage-src;
+      };
+
+      sage-setup = self.callPackage ./python-modules/sage-setup.nix {
+        inherit sage-src;
+      };
+    };
+  };
+
+  jupyter-kernel-definition = {
+    displayName = "SageMath ${sage-src.version}";
+    argv = [
+      "${sage-with-env}/bin/sage" # FIXME which sage
+      "--python"
+      "-m"
+      "sage.repl.ipython_kernel"
+      "-f"
+      "{connection_file}"
+    ];
+    language = "sagemath";
+    # just one 16x16 logo is available
+    logo32 = "${sage-src}/src/doc/common/themes/sage/static/sageicon.png";
+    logo64 = "${sage-src}/src/doc/common/themes/sage/static/sageicon.png";
+  };
+
+  jupyter-kernel-specs = pkgs.jupyter-kernel.create {
+    definitions = pkgs.jupyter-kernel.default // {
+      sagemath = jupyter-kernel-definition;
+    };
+  };
+
+  three = callPackage ./threejs-sage.nix { };
+
+  # 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;
+    inherit singular maxima;
+    inherit three;
+    cysignals = python3.pkgs.cysignals;
+    mathjax = nodePackages.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 = python3.pkgs.sagelib;
+    sage-docbuild = python3.pkgs.sage-docbuild;
+    inherit env-locations;
+    inherit python3 singular palp flint pythonEnv maxima;
+    pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config
+  };
+
+  # The documentation for sage, building it takes a lot of ram.
+  sagedoc = callPackage ./sagedoc.nix {
+    inherit sage-with-env jupyter-kernel-specs;
+  };
+
+  # 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 python3 pythonEnv;
+    inherit sage-env;
+    inherit singular maxima;
+    inherit three;
+    pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config
+  };
+
+  # 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;
+  };
+
+  sage-src = callPackage ./sage-src.nix {};
+
+  pythonRuntimeDeps = with python3.pkgs; [
+    sagelib
+    sage-docbuild
+    cvxopt
+    networkx
+    service-identity
+    psutil
+    sympy
+    fpylll
+    matplotlib
+    tkinter # optional, as a matplotlib backend (use with `%matplotlib tk`)
+    scipy
+    ipywidgets
+    rpy2
+    sphinx
+    pillow
+  ] ++ extraPythonPackages python3.pkgs;
+
+  pythonEnv = python3.buildEnv.override {
+    extraLibs = pythonRuntimeDeps;
+    ignoreCollisions = true;
+  } // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible
+
+  arb = pkgs.arb.override { inherit flint; };
+
+  singular = pkgs.singular.override { inherit flint; };
+
+  maxima = pkgs.maxima.override {
+    lisp-compiler = pkgs.ecl.override {
+      # "echo syntax error | ecl > /dev/full 2>&1" segfaults in
+      # ECL. We apply a patch to fix it (write_error.patch), but it
+      # only works if threads are disabled.  sage 9.2 tests this
+      # (src/sage/interfaces/tests.py) and ships ecl like so.
+      # https://gitlab.com/embeddable-common-lisp/ecl/-/merge_requests/1#note_1657275
+      threadSupport = false;
+
+      # if we don't use the system boehmgc, sending a SIGINT to ecl
+      # can segfault if we it happens during memory allocation.
+      # src/sage/libs/ecl.pyx would intermittently fail in this case.
+      useBoehmgc = true;
+    };
+  };
+
+  # 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 = 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-${pkgs.palp.version}";
+    paths = [
+      (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 pkgs; [
+      pari-galdata
+      pari-seadata-small
+    ];
+  };
+in
+# 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 jupyter-kernel-definition jupyter-kernel-specs;
+  inherit withDoc requireSageTests;
+}
--- a/pkgs/applications/science/math/sage/dist-tests.nix
+++ b/pkgs/applications/science/math/sage/dist-tests.nix
@ -0,0 +1,17 @@
+# Lists past failures and files associated with it. The intention is to build
+# up a subset of a testsuite that catches 95% of failures that are relevant for
+# distributions while only taking ~5m to run. This in turn makes it more
+# reasonable to re-test sage on dependency changes and makes it easier for
+# users to override the sage derivation.
+# This is an experiment for now. If it turns out that there really is a small
+# subset of files responsible for the vast majority of packaging tests, we can
+# think about moving this upstream.
+[
+	"src/sage/env.py" # [1]
+	"src/sage/misc/persist.pyx" # [1]
+	"src/sage/misc/inline_fortran.py" # [1]
+	"src/sage/repl/ipython_extension.py" # [1]
+]
+
+# Numbered list of past failures to annotate files with
+# [1] PYTHONPATH related issue https://github.com/NixOS/nixpkgs/commit/ec7f569211091282410050e89e68832d4fe60528
--- a/pkgs/applications/science/math/sage/env-locations.nix
+++ b/pkgs/applications/science/math/sage/env-locations.nix
@ -0,0 +1,48 @@
+{ writeTextFile
+, pari_data
+, pari
+, singular
+, maxima
+, conway_polynomials
+, graphs
+, elliptic_curves
+, polytopes_db
+, gap
+, combinatorial_designs
+, jmol
+, mathjax
+, three
+, cysignals
+}:
+
+# A bash script setting various environment variables to tell sage where
+# the files its looking fore are located. Also see `sage-env`.
+writeTextFile rec {
+  name = "sage-env-locations";
+  destination = "/${name}";
+  text = ''
+    export GP_DATA_DIR="${pari_data}/share/pari"
+    export PARI_DATA_DIR="${pari_data}"
+    export GPHELP="${pari}/bin/gphelp"
+    export GPDOCDIR="${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='${polytopes_db}/share/reflexive_polytopes'
+    export GAP_ROOT_DIR='${gap}/share/gap/build-dir'
+    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="${elliptic_curves}/share/cremona"
+    export JMOL_DIR="${jmol}/share/jmol" # point to the directory that contains JmolData.jar
+    export JSMOL_DIR="${jmol}/share/jsmol"
+    export MATHJAX_DIR="${mathjax}/lib/node_modules/mathjax"
+    export THREEJS_DIR="${three}/lib/node_modules/three"
+    export SAGE_INCLUDE_DIRECTORIES="${cysignals}/${cysignals.pythonModule.sitePackages}"
+  '';
+}
--- a/pkgs/applications/science/math/sage/patches/configurationpy-error-verbose.patch
+++ b/pkgs/applications/science/math/sage/patches/configurationpy-error-verbose.patch
@ -0,0 +1,19 @@
+diff --git a/src/sage/repl/configuration.py b/src/sage/repl/configuration.py
+index 67d7d2accf..18279581e2 100644
+--- a/src/sage/repl/configuration.py
+++ b/src/sage/repl/configuration.py
+@@ -9,10 +9,11 @@ the IPython simple prompt is being used::
+     sage: cmd = 'print([sys.stdin.isatty(), sys.stdout.isatty()])'
+     sage: import pexpect
+     sage: output = pexpect.run(
+-    ....:     'bash -c \'echo "{0}" | sage\''.format(cmd),
+    ....:     'bash -c \'export SAGE_BANNER=no; echo "{0}" | sage\''.format(cmd),
+     ....: ).decode('utf-8', 'surrogateescape')
+-    sage: 'sage: [False, True]' in output
+-    True
+    sage: print(output)
+    sage...[False, True]
+    ...
+ """
+ 
+ #*****************************************************************************
--- a/pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch
+++ b/pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch
@ -0,0 +1,87 @@
+diff --git a/src/sage/env.py b/src/sage/env.py
+index c4953cfa65..47b880f9ad 100644
+--- a/src/sage/env.py
+++ b/src/sage/env.py
+@@ -244,81 +244,8 @@ os.environ['MPMATH_SAGE'] = '1'
+ SAGE_BANNER = var("SAGE_BANNER", "")
+ SAGE_IMPORTALL = var("SAGE_IMPORTALL", "yes")
+ 
+-
+-def _get_shared_lib_path(*libnames: str) -> Optional[str]:
+-    """
+-    Return the full path to a shared library file installed in
+-    ``$SAGE_LOCAL/lib`` or the directories associated with the
+-    Python sysconfig.
+-
+-    This can also be passed more than one library name (e.g. for cases where
+-    some library may have multiple names depending on the platform) in which
+-    case the first one found is returned.
+-
+-    This supports most *NIX variants (in which ``lib<libname>.so`` is found
+-    under ``$SAGE_LOCAL/lib``), macOS (same, but with the ``.dylib``
+-    extension), and Cygwin (under ``$SAGE_LOCAL/bin/cyg<libname>.dll``,
+-    or ``$SAGE_LOCAL/bin/cyg<libname>-*.dll`` for versioned DLLs).
+-
+-    For distributions like Debian that use a multiarch layout, we also try the
+-    multiarch lib paths (i.e. ``/usr/lib/<arch>/``).
+-
+-    This returns ``None`` if no matching library file could be found.
+-
+-    EXAMPLES::
+-
+-        sage: from sage.env import _get_shared_lib_path
+-        sage: "gap" in _get_shared_lib_path("gap")
+-        True
+-        sage: _get_shared_lib_path("an_absurd_lib") is None
+-        True
+-
+-    """
+-
+-    for libname in libnames:
+-        search_directories: List[Path] = []
+-        patterns: List[str] = []
+-        if sys.platform == 'cygwin':
+-            # Later down we take the first matching DLL found, so search
+-            # SAGE_LOCAL first so that it takes precedence
+-            if SAGE_LOCAL:
+-                search_directories.append(Path(SAGE_LOCAL) / 'bin')
+-            search_directories.append(Path(sysconfig.get_config_var('BINDIR')))
+-            # Note: The following is not very robust, since if there are multible
+-            # versions for the same library this just selects one more or less
+-            # at arbitrary. However, practically speaking, on Cygwin, there
+-            # will only ever be one version
+-            patterns = [f'cyg{libname}.dll', f'cyg{libname}-*.dll']
+-        else:
+-            if sys.platform == 'darwin':
+-                ext = 'dylib'
+-            else:
+-                ext = 'so'
+-
+-            if SAGE_LOCAL:
+-                search_directories.append(Path(SAGE_LOCAL) / 'lib')
+-            libdir = sysconfig.get_config_var('LIBDIR')
+-            if libdir is not None:
+-                libdir = Path(libdir)
+-                search_directories.append(libdir)
+-
+-                multiarchlib = sysconfig.get_config_var('MULTIARCH')
+-                if multiarchlib is not None:
+-                    search_directories.append(libdir / multiarchlib),
+-
+-            patterns = [f'lib{libname}.{ext}']
+-
+-        for directory in search_directories:
+-            for pattern in patterns:
+-                path = next(directory.glob(pattern), None)
+-                if path is not None:
+-                    return str(path.resolve())
+-
+-    # Just return None if no files were found
+-    return None
+-
+ # locate libgap shared object
+-GAP_SO = var("GAP_SO", _get_shared_lib_path("gap", ""))
+GAP_SO = var("GAP_SO", '/default')
+ 
+ # post process
+ if DOT_SAGE is not None and ' ' in DOT_SAGE:
--- a/pkgs/applications/science/math/sage/patches/docutils-0.18.1-deprecation.patch
+++ b/pkgs/applications/science/math/sage/patches/docutils-0.18.1-deprecation.patch
@ -0,0 +1,13 @@
+diff --git a/src/sage/misc/sagedoc.py b/src/sage/misc/sagedoc.py
+index 08c4225b87..3a9bbe4ed0 100644
+--- a/src/sage/misc/sagedoc.py
+++ b/src/sage/misc/sagedoc.py
+@@ -1402,6 +1402,8 @@ class _sage_doc:
+             sage: identity_matrix.__doc__ in browse_sage_doc(identity_matrix, 'rst')
+             True
+             sage: browse_sage_doc(identity_matrix, 'html', False)             # optional - sphinx sagemath_doc_html
+            ...
+            FutureWarning: The configuration setting "embed_images" will be removed in Docutils 1.2. Use "image_loading: link".
+             '...div...File:...Type:...Definition:...identity_matrix...'
+ 
+         In the 'text' version, double colons have been replaced with
--- a/pkgs/applications/science/math/sage/patches/fix-ecl-race.patch
+++ b/pkgs/applications/science/math/sage/patches/fix-ecl-race.patch
@ -0,0 +1,19 @@
+diff --git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py
+index 02e18e67e7..2ebf6eb35f 100644
+--- a/src/sage/doctest/forker.py
+++ b/src/sage/doctest/forker.py
+@@ -1075,6 +1075,14 @@ class SageDocTestRunner(doctest.DocTestRunner, object):
+             sage: set(ex2.predecessors) == set([ex0,ex1])
+             True
+         """
+
+        # Fix ECL dir race conditions by using a separate dir for each process
+        # (https://trac.sagemath.org/ticket/26968)
+        os.environ['MAXIMA_USERDIR'] = "{}/sage-maxima-{}".format(
+            tempfile.gettempdir(),
+            os.getpid()
+        )
+
+         if isinstance(globs, RecordingDict):
+             globs.start()
+         example.sequence_number = len(self.history)
--- a/pkgs/applications/science/math/sage/patches/linbox-1.7-upgrade.patch
+++ b/pkgs/applications/science/math/sage/patches/linbox-1.7-upgrade.patch
@ -0,0 +1,58 @@
+diff --git a/src/sage/libs/linbox/conversion.pxd b/src/sage/libs/linbox/conversion.pxd
+index 7794c9edc3..1753277b1f 100644
+--- a/src/sage/libs/linbox/conversion.pxd
+++ b/src/sage/libs/linbox/conversion.pxd
+@@ -177,9 +177,8 @@ cdef inline Vector_integer_dense new_sage_vector_integer_dense(P, DenseVector_in
+     - v -- linbox vector
+     """
+     cdef Vector_integer_dense res = P()
+-    cdef cppvector[Integer] * vec = &v.refRep()
+     cdef size_t i
+     for i in range(<size_t> res._degree):
+-        mpz_set(res._entries[i], vec[0][i].get_mpz_const())
+        mpz_set(res._entries[i], v.getEntry(i).get_mpz_const())
+ 
+     return res
+diff --git a/src/sage/libs/linbox/linbox.pxd b/src/sage/libs/linbox/linbox.pxd
+index 9112d151f8..dcc482960c 100644
+--- a/src/sage/libs/linbox/linbox.pxd
+++ b/src/sage/libs/linbox/linbox.pxd
+@@ -32,7 +32,7 @@ cdef extern from "linbox/matrix/dense-matrix.h":
+         ctypedef Modular_double Field
+         ctypedef double Element
+         DenseMatrix_Modular_double(Field F, size_t m, size_t n)
+-        DenseMatrix_Modular_double(Field F, Element*, size_t m, size_t n)
+        DenseMatrix_Modular_double(Field F, size_t m, size_t n, Element*)
+         void setEntry(size_t i, size_t j, Element& a)
+         Element &getEntry(size_t i, size_t j)
+ 
+@@ -42,7 +42,7 @@ cdef extern from "linbox/matrix/dense-matrix.h":
+         ctypedef Modular_float Field
+         ctypedef float Element
+         DenseMatrix_Modular_float(Field F, size_t m, size_t n)
+-        DenseMatrix_Modular_float(Field F, Element*, size_t m, size_t n)
+        DenseMatrix_Modular_float(Field F, size_t m, size_t n, Element*)
+         void setEntry(size_t i, size_t j, Element& a)
+         Element &getEntry(size_t i, size_t j)
+ 
+@@ -101,7 +101,6 @@ cdef extern from "linbox/vector/vector.h":
+         DenseVector_integer (Field &F)
+         DenseVector_integer (Field &F, long& m)
+         DenseVector_integer (Field &F, cppvector[Integer]&)
+-        cppvector[Element]& refRep()
+         size_t size()
+         void resize(size_t)
+         void resize(size_t n, const Element&)
+diff --git a/src/sage/matrix/matrix_modn_dense_template.pxi b/src/sage/matrix/matrix_modn_dense_template.pxi
+index 010365d76f..3d60726ff9 100644
+--- a/src/sage/matrix/matrix_modn_dense_template.pxi
+++ b/src/sage/matrix/matrix_modn_dense_template.pxi
+@@ -219,7 +219,7 @@ cdef inline linbox_echelonize_efd(celement modulus, celement* entries, Py_ssize_
+         return 0,[]
+ 
+     cdef ModField *F = new ModField(<long>modulus)
+-    cdef DenseMatrix *A = new DenseMatrix(F[0], <ModField.Element*>entries,<Py_ssize_t>nrows, <Py_ssize_t>ncols)
+    cdef DenseMatrix *A = new DenseMatrix(F[0], <Py_ssize_t>nrows, <Py_ssize_t>ncols, <ModField.Element*>entries)
+     cdef Py_ssize_t r = reducedRowEchelonize(A[0])
+     cdef Py_ssize_t i,j
+     for i in range(nrows):
--- a/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch
+++ b/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch
@ -0,0 +1,61 @@
+diff --git a/src/sage_docbuild/__init__.py b/src/sage_docbuild/__init__.py
+index b12d56a3c9..df9d949ed1 100644
+--- a/src/sage_docbuild/__init__.py
+++ b/src/sage_docbuild/__init__.py
+@@ -88,30 +88,6 @@ def builder_helper(type):
+     """
+     Return a function which builds the documentation for
+     output type ``type``.
+-
+-    TESTS:
+-
+-    Check that :trac:`25161` has been resolved::
+-
+-        sage: from sage_docbuild import DocBuilder, setup_parser
+-        sage: DocBuilder._options = setup_parser().parse_args([]) # builder_helper needs _options to be set
+-
+-        sage: import sage_docbuild.sphinxbuild
+-        sage: def raiseBaseException():
+-        ....:     raise BaseException("abort pool operation")
+-        sage: original_runsphinx, sage_docbuild.sphinxbuild.runsphinx = sage_docbuild.sphinxbuild.runsphinx, raiseBaseException
+-
+-        sage: from sage.misc.temporary_file import tmp_dir
+-        sage: os.environ['SAGE_DOC'] = tmp_dir()
+-        sage: sage.env.var('SAGE_DOC') # random
+-        sage: from sage_docbuild import builder_helper, build_ref_doc
+-        sage: from sage_docbuild import _build_many as build_many
+-        sage: helper = builder_helper("html")
+-        sage: try:  # optional - sagemath_doc_html
+-        ....:     build_many(build_ref_doc, [("docname", "en", "html", {})])
+-        ....: except Exception as E:
+-        ....:     "Non-exception during docbuild: abort pool operation" in str(E)
+-        True
+     """
+     def f(self, *args, **kwds):
+         output_dir = self._output_dir(type)
+@@ -139,10 +115,9 @@ def builder_helper(type):
+         logger.debug(build_command)
+ 
+         # Run Sphinx with Sage's special logger
+-        sys.argv = ["sphinx-build"] + build_command.split()
+-        from .sphinxbuild import runsphinx
+        args = "python3 -um sage_docbuild.sphinxbuild -N".split() + build_command.split()
+         try:
+-            runsphinx()
+            subprocess.check_call(args)
+         except Exception:
+             if ABORT_ON_ERROR:
+                 raise
+diff --git a/src/sage_docbuild/sphinxbuild.py b/src/sage_docbuild/sphinxbuild.py
+index a39c99ffe9..73be823684 100644
+--- a/src/sage_docbuild/sphinxbuild.py
+++ b/src/sage_docbuild/sphinxbuild.py
+@@ -330,3 +330,8 @@ def runsphinx():
+         sys.stderr = saved_stderr
+         sys.stdout.flush()
+         sys.stderr.flush()
+
+if __name__ == '__main__':
+    import sys
+    sys.argv[0] = "sphinx-build"
+    runsphinx()
--- a/pkgs/applications/science/math/sage/patches/sympow-cache.patch
+++ b/pkgs/applications/science/math/sage/patches/sympow-cache.patch
@ -0,0 +1,21 @@
+diff --git a/src/sage/lfunctions/sympow.py b/src/sage/lfunctions/sympow.py
+index 92cb01fd73..b123e6accc 100644
+--- a/src/sage/lfunctions/sympow.py
+++ b/src/sage/lfunctions/sympow.py
+@@ -50,6 +50,7 @@ from __future__ import print_function, absolute_import
+ 
+ import os
+ 
+from sage.env import DOT_SAGE
+ from sage.structure.sage_object import SageObject
+ from sage.misc.all import pager
+ from sage.misc.verbose import verbose
+@@ -78,7 +79,7 @@ class Sympow(SageObject):
+         """
+         Used to call sympow with given args
+         """
+-        cmd = 'sympow %s' % args
+        cmd = 'env SYMPOW_CACHEDIR="%s/sympow///" sympow %s' % (DOT_SAGE, args)
+         with os.popen(cmd) as f:
+             v = f.read().strip()
+         verbose(v, level=2)
--- a/pkgs/applications/science/math/sage/patches/tachyon-renamed-focallength.patch
+++ b/pkgs/applications/science/math/sage/patches/tachyon-renamed-focallength.patch
@ -0,0 +1,81 @@
+diff --git a/src/sage/interfaces/tachyon.py b/src/sage/interfaces/tachyon.py
+index 3f1dcdb538..b6fa8d1fbd 100644
+--- a/src/sage/interfaces/tachyon.py
+++ b/src/sage/interfaces/tachyon.py
+@@ -261,13 +261,13 @@ written in the sequence they are listed in the examples in this section.
+   The {\bf PROJECTION} keyword must be followed by one of the supported
+ camera projection mode identifiers {\bf PERSPECTIVE}, {\bf PERSPECTIVE_DOF},
+ {\bf ORTHOGRAPHIC}, or {\bf FISHEYE}.  The {\bf FISHEYE} projection mode
+-requires two extra parameters {\bf FOCALLENGTH} and {\bf APERTURE}
+requires two extra parameters {\bf FOCALDIST} and {\bf APERTURE}
+ which precede the regular camera options.
+ 
+ \begin{verbatim}
+ Camera
+   projection perspective_dof
+-  focallength 0.75
+  focaldist 0.75
+   aperture 0.02
+   Zoom 0.666667
+   Aspectratio 1.000000
+diff --git a/src/sage/plot/plot3d/tachyon.py b/src/sage/plot/plot3d/tachyon.py
+index 08caf38d67..3e827411ce 100644
+--- a/src/sage/plot/plot3d/tachyon.py
+++ b/src/sage/plot/plot3d/tachyon.py
+@@ -92,7 +92,7 @@ angle, right angle)::
+ Finally there is the ``projection='perspective_dof'`` option. ::
+ 
+     sage: T = Tachyon(xres=800, antialiasing=4, raydepth=10,
+-    ....: projection='perspective_dof', focallength='1.0', aperture='.0025')
+    ....: projection='perspective_dof', focaldist='1.0', aperture='.0025')
+     sage: T.light((0,5,7), 1.0, (1,1,1))
+     sage: T.texture('t1', opacity=1, specular=.3)
+     sage: T.texture('t2', opacity=1, specular=.3, color=(0,0,1))
+@@ -186,7 +186,7 @@ class Tachyon(WithEqualityById, SageObject):
+       or ``'fisheye'``.
+     - ``frustum`` - (default ''), otherwise list of four numbers. Only
+       used with projection='fisheye'.
+-    - ``focallength`` - (default ''), otherwise a number. Only used
+    - ``focaldist`` - (default ''), otherwise a number. Only used
+       with projection='perspective_dof'.
+     - ``aperture`` - (default ''), otherwise a number.  Only used
+       with projection='perspective_dof'.
+@@ -331,7 +331,7 @@ class Tachyon(WithEqualityById, SageObject):
+     Use of the ``projection='perspective_dof'`` option.  This may not be
+     implemented correctly. ::
+ 
+-        sage: T = Tachyon(xres=800,antialiasing=4, raydepth=10, projection='perspective_dof', focallength='1.0', aperture='.0025')
+        sage: T = Tachyon(xres=800,antialiasing=4, raydepth=10, projection='perspective_dof', focaldist='1.0', aperture='.0025')
+         sage: T.light((0,5,7), 1.0, (1,1,1))
+         sage: T.texture('t1', opacity=1, specular=.3)
+         sage: T.texture('t2', opacity=1, specular=.3, color=(0,0,1))
+@@ -365,7 +365,7 @@ class Tachyon(WithEqualityById, SageObject):
+                  look_at=[0, 0, 0],
+                  viewdir=None,
+                  projection='PERSPECTIVE',
+-                 focallength='',
+                 focaldist='',
+                  aperture='',
+                  frustum=''):
+         r"""
+@@ -391,7 +391,7 @@ class Tachyon(WithEqualityById, SageObject):
+             self._camera_position = (-3, 0, 0) # default value
+         self._updir = updir
+         self._projection = projection
+-        self._focallength = focallength
+        self._focaldist = focaldist
+         self._aperture = aperture
+         self._frustum = frustum
+         self._objects = []
+@@ -624,9 +624,9 @@ class Tachyon(WithEqualityById, SageObject):
+         camera_out = r"""
+            camera
+               projection %s""" % (tostr(self._projection))
+-        if self._focallength != '':
+        if self._focaldist != '':
+             camera_out = camera_out + r"""
+-              focallength %s""" % (float(self._focallength))
+              focaldist %s""" % (float(self._focaldist))
+         if self._aperture != '':
+             camera_out = camera_out + r"""
+               aperture %s""" % (float(self._aperture))
--- a/pkgs/applications/science/math/sage/python-modules/sage-docbuild.nix
+++ b/pkgs/applications/science/math/sage/python-modules/sage-docbuild.nix
@ -0,0 +1,30 @@
+{ lib
+, buildPythonPackage
+, sage-src
+, sphinx
+, jupyter-sphinx
+}:
+
+buildPythonPackage rec {
+  version = src.version;
+  pname = "sage-docbuild";
+  src = sage-src;
+
+  propagatedBuildInputs = [
+    sphinx
+    jupyter-sphinx
+  ];
+
+  preBuild = ''
+    cd pkgs/sage-docbuild
+  '';
+
+  doCheck = false; # we will run tests in sagedoc.nix
+
+  meta = with lib; {
+    description = "Build system of the Sage documentation";
+    homepage = "https://www.sagemath.org";
+    license = licenses.gpl2Plus;
+    maintainers = teams.sage.members;
+  };
+}
--- a/pkgs/applications/science/math/sage/python-modules/sage-setup.nix
+++ b/pkgs/applications/science/math/sage/python-modules/sage-setup.nix
@ -0,0 +1,28 @@
+{ lib
+, buildPythonPackage
+, sage-src
+, pkgconfig # the python module, not the pkg-config alias
+}:
+
+buildPythonPackage rec {
+  version = src.version;
+  pname = "sage-setup";
+  src = sage-src;
+
+  buildInputs = [
+    pkgconfig
+  ];
+
+  preBuild = ''
+    cd pkgs/sage-setup
+  '';
+
+  doCheck = false; # sagelib depends on sage-setup, but sage-setup's tests depend on sagelib
+
+  meta = with lib; {
+    description = "Build system of the Sage library";
+    homepage = "https://www.sagemath.org";
+    license = licenses.gpl2Plus;
+    maintainers = teams.sage.members;
+  };
+}
--- a/pkgs/applications/science/math/sage/sage-env.nix
+++ b/pkgs/applications/science/math/sage/sage-env.nix
@ -0,0 +1,194 @@
+{ stdenv
+, lib
+, writeTextFile
+, sagelib
+, sage-docbuild
+, env-locations
+, gfortran
+, bash
+, coreutils
+, gnused
+, gnugrep
+, binutils
+, pythonEnv
+, python3
+, pkg-config
+, pari
+, gap
+, maxima
+, singular
+, fflas-ffpack
+, givaro
+, gd
+, libpng
+, linbox
+, m4ri
+, giac
+, palp
+, rWrapper
+, gfan
+, cddlib
+, jmol
+, tachyon
+, glpk
+, eclib
+, sympow
+, nauty
+, sqlite
+, ppl
+, ecm
+, lcalc
+, rubiks
+, flintqs
+, blas
+, lapack
+, flint
+, gmp
+, mpfr
+, zlib
+, gsl
+, ntl
+, jdk
+, less
+}:
+
+assert (!blas.isILP64) && (!lapack.isILP64);
+
+# This generates a `sage-env` shell file that will be sourced by sage on startup.
+# It sets up various environment variables, telling sage where to find its
+# dependencies.
+
+let
+  runtimepath = (lib.makeBinPath ([
+    "@sage-local@"
+    "@sage-local@/build"
+    pythonEnv
+    gfortran # for inline fortran
+    stdenv.cc # for cython
+    bash
+    coreutils
+    gnused
+    gnugrep
+    binutils.bintools
+    pkg-config
+    pari
+    gap
+    maxima.lisp-compiler
+    maxima
+    singular
+    giac
+    palp
+    # needs to be rWrapper since the default `R` doesn't include R's default libraries
+    rWrapper
+    gfan
+    cddlib
+    jmol
+    tachyon
+    glpk
+    eclib
+    sympow
+    nauty
+    sqlite
+    ppl
+    ecm
+    lcalc
+    rubiks
+    flintqs
+    jdk # only needed for `jmol` which may be replaced in the future
+    less # needed to prevent transient test errors until https://github.com/ipython/ipython/pull/11864 is resolved
+  ]
+  ));
+in
+writeTextFile rec {
+  name = "sage-env";
+  destination = "/${name}";
+  text = ''
+    export PKG_CONFIG_PATH='${lib.makeSearchPathOutput "dev" "lib/pkgconfig" [
+        # This should only be needed during build. However, since the  doctests
+        # also test the cython build (for example in src/sage/misc/cython.py),
+        # it is also needed for the testsuite to pass. We could fix the
+        # testsuite instead, but since all the packages are also runtime
+        # dependencies it doesn't really hurt to include them here.
+        singular
+        blas lapack
+        fflas-ffpack givaro
+        gd
+        libpng zlib
+        gsl
+        linbox
+        m4ri
+      ]
+    }'
+    export SAGE_ROOT='${sagelib.src}'
+  '' +
+    # TODO: is using pythonEnv instead of @sage-local@ here a good
+    # idea? there is a test in src/sage/env.py that checks if the values
+    # SAGE_ROOT and SAGE_LOCAL set here match the ones set in env.py.
+    # we fix up env.py's SAGE_ROOT in sage-src.nix (which does not
+    # have access to sage-with-env), but env.py autodetects
+    # SAGE_LOCAL to be pythonEnv.
+    # setting SAGE_LOCAL to pythonEnv also avoids having to create
+    # python3, ipython, ipython3 and jupyter symlinks in
+    # sage-with-env.nix.
+  ''
+    export SAGE_LOCAL='${pythonEnv}'
+
+    export SAGE_SHARE='${sagelib}/share'
+    export SAGE_ENV_CONFIG_SOURCED=1 # sage-env complains if sage-env-config is not sourced beforehand
+    orig_path="$PATH"
+    export PATH='${runtimepath}'
+
+    # set dependent vars, like JUPYTER_CONFIG_DIR
+    source "${sagelib.src}/src/bin/sage-env"
+    export PATH="$RUNTIMEPATH_PREFIX:${runtimepath}:$orig_path" # sage-env messes with PATH
+
+    export SAGE_LOGS="$TMPDIR/sage-logs"
+    export SAGE_DOC="''${SAGE_DOC_OVERRIDE:-doc-placeholder}"
+    export SAGE_DOC_SRC="''${SAGE_DOC_SRC_OVERRIDE:-${sagelib.src}/src/doc}"
+
+    # set locations of dependencies
+    . ${env-locations}/sage-env-locations
+
+    # needed for cython
+    export CC='${stdenv.cc}/bin/${stdenv.cc.targetPrefix}cc'
+    export CXX='${stdenv.cc}/bin/${stdenv.cc.targetPrefix}c++'
+    # cython needs to find these libraries, otherwise will fail with `ld: cannot find -lflint` or similar
+    export LDFLAGS='${
+      lib.concatStringsSep " " (map (pkg: "-L${pkg}/lib") [
+        flint
+        gap
+        glpk
+        gmp
+        mpfr
+        pari
+        zlib
+        eclib
+        gsl
+        ntl
+        jmol
+        sympow
+      ])
+    }'
+    export CFLAGS='${
+      lib.concatStringsSep " " (map (pkg: "-isystem ${pkg}/include") [
+        singular
+        gmp.dev
+        glpk
+        flint
+        gap
+        mpfr.dev
+      ])
+    }'
+    export CXXFLAGS=$CFLAGS
+
+    export SAGE_LIB='${sagelib}/${python3.sitePackages}'
+
+    export SAGE_EXTCODE='${sagelib.src}/src/sage/ext_data'
+
+  # for find_library
+    export DYLD_LIBRARY_PATH="${lib.makeLibraryPath [stdenv.cc.libc singular giac]}''${DYLD_LIBRARY_PATH:+:}$DYLD_LIBRARY_PATH"
+  '';
+} // { # equivalent of `passthru`, which `writeTextFile` doesn't support
+  lib = sagelib;
+  docbuild = sage-docbuild;
+}
--- a/pkgs/applications/science/math/sage/sage-src.nix
+++ b/pkgs/applications/science/math/sage/sage-src.nix
@ -0,0 +1,150 @@
+{ stdenv
+, fetchFromGitHub
+, fetchpatch
+, runtimeShell
+}:
+
+# This file is responsible for fetching the sage source and adding necessary patches.
+# It does not actually build anything, it just copies the patched sources to $out.
+# This is done because multiple derivations rely on these sources and they should
+# all get the same sources with the same patches applied.
+
+let
+  # Fetch a diff between `base` and `rev` on sage's git server.
+  # Used to fetch trac tickets by setting the `base` to the last release and the
+  # `rev` to the last commit of the ticket.
+  #
+  # We don't use sage's own build system (which builds all its
+  # dependencies), so we exclude changes to "build/" from patches by
+  # default to avoid conflicts.
+  fetchSageDiff = { base, name, rev, sha256, squashed ? false, excludes ? [ "build/*" ]
+                  , ...}@args: (
+    fetchpatch ({
+      inherit name sha256 excludes;
+
+      # There are three places to get changes from:
+      #
+      # 1) From Sage's Trac. Contains all release tags (like "9.4") and all developer
+      # branches (wip patches from tickets), but exports each commit as a separate
+      # patch, so merge commits can lead to conflicts. Used if squashed == false.
+      #
+      # The above is the preferred option. To use it, find a Trac ticket and pass the
+      # "Commit" field from the ticket as "rev", choosing "base" as an appropriate
+      # release tag, i.e. a tag that doesn't cause the patch to include a lot of
+      # unrelated changes. If there is no such tag (due to nonlinear history, for
+      # example), there are two other options, listed below.
+      #
+      # 2) From GitHub's sagemath/sage repo. This lets us use a GH feature that allows
+      # us to choose between a .patch file, with one patch per commit, or a .diff file,
+      # which squashes all commits into a single diff. This is used if squashed ==
+      # true. This repo has all release tags. However, it has no developer branches, so
+      # this option can't be used if a change wasn't yet shipped in a (possibly beta)
+      # release.
+      #
+      # 3) From GitHub's sagemath/sagetrac-mirror repo. Mirrors all developer branches,
+      # but has no release tags. The only use case not covered by 1 or 2 is when we need
+      # to apply a patch from an open ticket that contains merge commits.
+      #
+      # Item 3 could cover all use cases if the sagemath/sagetrack-mirror repo had
+      # release tags, but it requires a sha instead of a release number in "base", which
+      # is inconvenient.
+      urls = if squashed
+             then [
+               "https://github.com/sagemath/sage/compare/${base}...${rev}.diff"
+               "https://github.com/sagemath/sagetrac-mirror/compare/${base}...${rev}.diff"
+             ]
+             else [ "https://git.sagemath.org/sage.git/patch?id2=${base}&id=${rev}" ];
+    } // builtins.removeAttrs args [ "rev" "base" "sha256" "squashed" "excludes" ])
+  );
+in
+stdenv.mkDerivation rec {
+  version = "9.6";
+  pname = "sage-src";
+
+  src = fetchFromGitHub {
+    owner = "sagemath";
+    repo = "sage";
+    rev = version;
+    sha256 = "sha256-QY8Yga3hD1WhSCtA2/PVry8hHlMmC31J8jCBFtWgIU0=";
+  };
+
+  # Patches needed because of particularities of nix or the way this is packaged.
+  # The goal is to upstream all of them and get rid of this list.
+  nixPatches = [
+    # Fixes a potential race condition which can lead to transient doctest failures.
+    ./patches/fix-ecl-race.patch
+
+    # Not necessary since library location is set explicitly
+    # https://trac.sagemath.org/ticket/27660#ticket
+    ./patches/do-not-test-find-library.patch
+
+    # Parallelize docubuild using subprocesses, fixing an isolation issue. See
+    # https://groups.google.com/forum/#!topic/sage-packaging/YGOm8tkADrE
+    ./patches/sphinx-docbuild-subprocesses.patch
+  ];
+
+  # Since sage unfortunately does not release bugfix releases, packagers must
+  # fix those bugs themselves. This is for critical bugfixes, where "critical"
+  # == "causes (transient) doctest failures / somebody complained".
+  bugfixPatches = [
+    # To help debug the transient error in
+    # https://trac.sagemath.org/ticket/23087 when it next occurs.
+    ./patches/configurationpy-error-verbose.patch
+  ];
+
+  # Patches needed because of package updates. We could just pin the versions of
+  # dependencies, but that would lead to rebuilds, confusion and the burdons of
+  # maintaining multiple versions of dependencies. Instead we try to make sage
+  # compatible with never dependency versions when possible. All these changes
+  # should come from or be proposed to upstream. This list will probably never
+  # be empty since dependencies update all the time.
+  packageUpgradePatches = [
+    # After updating smypow to (https://trac.sagemath.org/ticket/3360) we can
+    # now set the cache dir to be within the .sage directory. This is not
+    # strictly necessary, but keeps us from littering in the user's HOME.
+    ./patches/sympow-cache.patch
+
+    # Upstream will wait until Sage 9.7 to upgrade to linbox 1.7 because it
+    # does not support gcc 6. We can upgrade earlier.
+    # https://trac.sagemath.org/ticket/32959
+    ./patches/linbox-1.7-upgrade.patch
+
+    # adapted from https://trac.sagemath.org/ticket/23712#comment:22
+    ./patches/tachyon-renamed-focallength.patch
+
+    # docutils 0.18.1 now triggers Sphinx warnings. tolerate them for
+    # now, because patching Sphinx is not feasible. remove when Sphinx
+    # 5.0 hits nixpkgs.
+    # https://github.com/sphinx-doc/sphinx/pull/10372
+    ./patches/docutils-0.18.1-deprecation.patch
+  ];
+
+  patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;
+
+  postPatch = ''
+    # Make sure sage can at least be imported without setting any environment
+    # variables. It won't be close to feature complete though.
+    sed -i \
+      "s|var(\"SAGE_ROOT\".*|var(\"SAGE_ROOT\", \"$out\")|" \
+      src/sage/env.py
+
+    # src/doc/en/reference/spkg/conf.py expects index.rst in its directory,
+    # a list of external packages in the sage distribution (build/pkgs)
+    # generated by the bootstrap script (which we don't run).  this is not
+    # relevant for other distributions, so remove it.
+    rm src/doc/en/reference/spkg/conf.py
+    sed -i "/spkg/d" src/doc/en/reference/index.rst
+
+    # the bootstrap script also generates installation instructions for
+    # arch, debian, fedora, cygwin and homebrew using data from build/pkgs.
+    # we don't run the bootstrap script, so disable including the generated
+    # files. docbuilding fails otherwise.
+    sed -i "/literalinclude/d" src/doc/en/installation/source.rst
+  '';
+
+  buildPhase = "# do nothing";
+
+  installPhase = ''
+    cp -r . "$out"
+  '';
+}
--- a/pkgs/applications/science/math/sage/sage-tests.nix
+++ b/pkgs/applications/science/math/sage/sage-tests.nix
@ -0,0 +1,61 @@
+{ stdenv
+, lib
+, sage-with-env
+, makeWrapper
+, files ? null # "null" means run all tests
+, longTests ? true # run tests marked as "long time" (roughly doubles runtime)
+# Run as many tests as possible in approximately n seconds. This will give each
+# file to test a "time budget" and stop tests if it is exceeded. 300 is the
+# upstream default value.
+# https://trac.sagemath.org/ticket/25270 for details.
+, timeLimit ? null
+}:
+
+# for a quick test of some source files:
+# nix-build -E 'with (import ./. {}); sage.tests.override { files = [ "src/sage/misc/cython.py" ];}'
+
+let
+  src = sage-with-env.env.lib.src;
+  runAllTests = files == null;
+  testArgs = if runAllTests then "--all" else testFileList;
+  patienceSpecifier = if longTests then "--long" else "";
+  timeSpecifier = if timeLimit == null then "" else "--short ${toString timeLimit}";
+  relpathToArg = relpath: lib.escapeShellArg "${src}/${relpath}"; # paths need to be absolute
+  testFileList = lib.concatStringsSep " " (map relpathToArg files);
+in
+stdenv.mkDerivation {
+  version = src.version;
+  pname = "sage-tests";
+  inherit src;
+
+  buildInputs = [
+    makeWrapper
+    sage-with-env
+  ];
+
+  dontUnpack = true;
+  configurePhase = "#do nothing";
+  buildPhase = "#do nothing";
+
+  installPhase = ''
+    # This output is not actually needed for anything, the package just
+    # exists to decouple the sage build from its t ests.
+
+    mkdir -p "$out/bin"
+    # Like a symlink, but make sure that $0 points to the original.
+    makeWrapper "${sage-with-env}/bin/sage" "$out/bin/sage"
+  '';
+
+  doInstallCheck = true;
+  installCheckPhase = ''
+    export HOME="$TMPDIR/sage-home"
+    mkdir -p "$HOME"
+
+    # avoid running out of memory with many threads in subprocesses, see
+    # https://github.com/NixOS/nixpkgs/pull/65802
+    export GLIBC_TUNABLES=glibc.malloc.arena_max=4
+
+    echo "Running sage tests with arguments ${timeSpecifier} ${patienceSpecifier} ${testArgs}"
+    "sage" -t --timeout=0 --nthreads "$NIX_BUILD_CORES" --optional=sage ${timeSpecifier} ${patienceSpecifier} ${testArgs}
+  '';
+}
--- a/pkgs/applications/science/math/sage/sage-with-env.nix
+++ b/pkgs/applications/science/math/sage/sage-with-env.nix
@ -0,0 +1,139 @@
+{ stdenv
+, lib
+, makeWrapper
+, sage-env
+, blas
+, lapack
+, pkg-config
+, three
+, singular
+, gap
+, giac
+, maxima
+, pari
+, gmp
+, gfan
+, python3
+, flintqs
+, eclib
+, ntl
+, ecm
+, pythonEnv
+}:
+
+# lots of segfaults with (64 bit) blas
+assert (!blas.isILP64) && (!lapack.isILP64);
+
+# Wrapper that combined `sagelib` with `sage-env` to produce an actually
+# executable sage. No tests are run yet and no documentation is built.
+
+let
+  buildInputs = [
+    pythonEnv # for patchShebangs
+    makeWrapper
+    pkg-config
+    blas lapack
+    singular
+    three
+    giac
+    gap
+    pari
+    gmp
+    gfan
+    maxima
+    eclib
+    flintqs
+    ntl
+    ecm
+  ];
+
+  # remove python prefix, replace "-" in the name by "_", apply patch_names
+  # python3.8-some-pkg-1.0 -> some_pkg-1.0
+  pkg_to_spkg_name = pkg: patch_names: let
+    parts = lib.splitString "-" pkg.name;
+    # remove python3.8-
+    stripped_parts = if (builtins.head parts) == python3.libPrefix then builtins.tail parts else parts;
+    version = lib.last stripped_parts;
+    orig_pkgname = lib.init stripped_parts;
+    pkgname = patch_names (lib.concatStringsSep "_" orig_pkgname);
+  in pkgname + "-" + version;
+
+
+  # return the names of all dependencies in the transitive closure
+  transitiveClosure = dep:
+  if dep == null then
+    # propagatedBuildInputs might contain null
+    # (although that might be considered a programming error in the derivation)
+    []
+  else
+    [ dep ] ++ (
+      if builtins.hasAttr "propagatedBuildInputs" dep then
+        lib.unique (builtins.concatLists (map transitiveClosure dep.propagatedBuildInputs))
+      else
+      []
+    );
+
+  allInputs = lib.remove null (buildInputs ++ pythonEnv.extraLibs);
+  transitiveDeps = lib.unique (builtins.concatLists (map transitiveClosure allInputs ));
+  # fix differences between spkg and sage names
+  # (could patch sage instead, but this is more lightweight and also works for packages depending on sage)
+  patch_names = builtins.replaceStrings [
+    "zope.interface"
+    "node_three"
+  ] [
+    "zope_interface"
+    "threejs"
+  ];
+  # spkg names (this_is_a_package-version) of all transitive deps
+  input_names = map (dep: pkg_to_spkg_name dep patch_names) transitiveDeps;
+in
+stdenv.mkDerivation rec {
+  version = src.version;
+  pname = "sage-with-env";
+  src = sage-env.lib.src;
+
+  inherit buildInputs;
+
+  configurePhase = "#do nothing";
+
+  buildPhase = ''
+    mkdir installed
+    for pkg in ${lib.concatStringsSep " " input_names}; do
+      touch "installed/$pkg"
+    done
+
+    # threejs version is in format 0.<version>.minor, but sage currently still
+    # relies on installed_packages for the online version of threejs to work
+    # and expects the format r<version>. This is a hotfix for now.
+    # upstream: https://trac.sagemath.org/ticket/26434
+    rm "installed/threejs"*
+    touch "installed/threejs-r${lib.versions.minor three.version}"
+  '';
+
+  installPhase = ''
+    mkdir -p "$out/var/lib/sage"
+    cp -r installed "$out/var/lib/sage"
+
+    mkdir -p "$out/etc"
+    # sage tests will try to create this file if it doesn't exist
+    touch "$out/etc/sage-started.txt"
+
+    mkdir -p "$out/build"
+
+    # the scripts in src/bin will find the actual sage source files using environment variables set in `sage-env`
+    cp -r src/bin "$out/bin"
+    cp -r build/bin "$out/build/bin"
+
+    # sage assumes the existence of sage-src-env-config.in means it's being executed in-tree. in this case, it
+    # adds SAGE_SRC/bin to PATH, breaking our wrappers
+    rm "$out/bin"/*.in "$out/build/bin"/*.in
+
+    cp -f '${sage-env}/sage-env' "$out/bin/sage-env"
+    substituteInPlace "$out/bin/sage-env" \
+      --subst-var-by sage-local "$out"
+  '';
+
+  passthru = {
+    env = sage-env;
+  };
+}
--- a/pkgs/applications/science/math/sage/sage.nix
+++ b/pkgs/applications/science/math/sage/sage.nix
@ -0,0 +1,62 @@
+{ lib, stdenv
+, makeWrapper
+, sage-tests
+, sage-with-env
+, jupyter-kernel-definition
+, jupyter-kernel-specs
+, sagedoc
+, withDoc
+, requireSageTests
+}:
+
+# A wrapper that makes sure sage finds its docs (if they were build) and the
+# jupyter kernel spec.
+
+stdenv.mkDerivation rec {
+  version = src.version;
+  pname = "sage";
+  src = sage-with-env.env.lib.src;
+
+  buildInputs = [
+    makeWrapper
+  ] ++ lib.optionals requireSageTests [
+    # This is a hack to make sure sage-tests is evaluated. It doesn't acutally
+    # produce anything of value, it just decouples the tests from the build.
+    sage-tests
+  ];
+
+  dontUnpack = true;
+  configurePhase = "#do nothing";
+  buildPhase = "#do nothing";
+
+  installPhase = ''
+    mkdir -p "$out/bin"
+    makeWrapper "${sage-with-env}/bin/sage" "$out/bin/sage" \
+      --set SAGE_DOC_SRC_OVERRIDE "${src}/src/doc" ${
+        lib.optionalString withDoc "--set SAGE_DOC_OVERRIDE ${sagedoc}/share/doc/sage"
+      } \
+      --prefix JUPYTER_PATH : "${jupyter-kernel-specs}"
+  '';
+
+  doInstallCheck = withDoc;
+  installCheckPhase = ''
+    export HOME="$TMPDIR/sage-home"
+    mkdir -p "$HOME"
+    "$out/bin/sage" -c 'browse_sage_doc._open("reference", testing=True)'
+  '';
+
+  passthru = {
+    tests = sage-tests;
+    quicktest = sage-tests.override { longTests = false; timeLimit = 600; }; # as many tests as possible in ~10m
+    doc = sagedoc;
+    lib = sage-with-env.env.lib;
+    kernelspec = jupyter-kernel-definition;
+  };
+
+  meta = with lib; {
+    description = "Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab";
+    homepage = "https://www.sagemath.org";
+    license = licenses.gpl2Plus;
+    maintainers = teams.sage.members;
+  };
+}
--- a/pkgs/applications/science/math/sage/sagedoc.nix
+++ b/pkgs/applications/science/math/sage/sagedoc.nix
@ -0,0 +1,71 @@
+{ stdenv
+, sage-with-env
+, python3
+, jupyter-kernel-specs
+}:
+
+stdenv.mkDerivation rec {
+  version = src.version;
+  pname = "sagedoc";
+  src = sage-with-env.env.lib.src;
+
+  strictDeps = true;
+
+  unpackPhase = ''
+    export SAGE_DOC_OVERRIDE="$PWD/share/doc/sage"
+    export SAGE_DOC_SRC_OVERRIDE="$PWD/docsrc"
+
+    cp -r "${src}/src/doc" "$SAGE_DOC_SRC_OVERRIDE"
+    chmod -R 755 "$SAGE_DOC_SRC_OVERRIDE"
+  '';
+
+  buildPhase = ''
+    export SAGE_NUM_THREADS="$NIX_BUILD_CORES"
+    export HOME="$TMPDIR/sage_home"
+    mkdir -p "$HOME"
+
+    # needed to link them in the sage docs using intersphinx
+    export PPLPY_DOCS=${python3.pkgs.pplpy.doc}/share/doc/pplpy
+
+    # adapted from src/doc/bootstrap (which we don't run)
+    OUTPUT_DIR="$SAGE_DOC_SRC_OVERRIDE/en/reference/repl"
+    mkdir -p "$OUTPUT_DIR"
+    OUTPUT="$OUTPUT_DIR/options.txt"
+    ${sage-with-env}/bin/sage -advanced > "$OUTPUT"
+
+    # jupyter-sphinx calls the sagemath jupyter kernel during docbuild
+    export JUPYTER_PATH=${jupyter-kernel-specs}
+
+    # sage --docbuild unsets JUPYTER_PATH, so we call sage_docbuild directly
+    # https://trac.sagemath.org/ticket/33650#comment:32
+    ${sage-with-env}/bin/sage --python3 -m sage_docbuild \
+      --mathjax \
+      --no-pdf-links \
+      all html < /dev/null
+  '';
+
+  installPhase = ''
+    cd "$SAGE_DOC_OVERRIDE"
+
+    mkdir -p "$out/share/doc/sage"
+    cp -r html "$out"/share/doc/sage
+
+    # Replace duplicated files by symlinks (Gentoo)
+    cd "$out"/share/doc/sage
+    mv html/en/_static{,.tmp}
+    for _dir in `find -name _static` ; do
+          rm -r $_dir
+          ln -rs html/en/_static $_dir
+    done
+    mv html/en/_static{.tmp,}
+  '';
+
+  doCheck = true;
+  checkPhase = ''
+    # sagemath_doc_html tests assume sage tests are being run, so we
+    # compromise: we run standard tests, but only on files containing
+    # relevant tests. as of Sage 9.6, there are only 4 such files.
+    grep -PRl "#.*optional.*sagemath_doc_html" ${src}/src/sage{,_docbuild} | \
+      xargs ${sage-with-env}/bin/sage -t --optional=sage,sagemath_doc_html
+  '';
+}
--- a/pkgs/applications/science/math/sage/sagelib.nix
+++ b/pkgs/applications/science/math/sage/sagelib.nix
@ -0,0 +1,213 @@
+{ sage-src
+, env-locations
+, perl
+, buildPythonPackage
+, m4
+, arb
+, blas
+, lapack
+, brial
+, cliquer
+, cypari2
+, cysignals
+, cython
+, lisp-compiler
+, eclib
+, ecm
+, flint
+, gd
+, giac
+, givaro
+, glpk
+, gsl
+, iml
+, jinja2
+, lcalc
+, lrcalc
+, gap
+, linbox
+, m4ri
+, m4rie
+, memory-allocator
+, libmpc
+, mpfi
+, ntl
+, numpy
+, pari
+, pkgconfig # the python module, not the pkg-config alias
+, pkg-config
+, planarity
+, ppl
+, primecountpy
+, python
+, ratpoints
+, readline
+, rankwidth
+, symmetrica
+, zn_poly
+, fflas-ffpack
+, boost
+, singular
+, pip
+, jupyter_core
+, sage-setup
+, libhomfly
+, libbraiding
+, gmpy2
+, pplpy
+, sqlite
+, jupyter-client
+, ipywidgets
+, mpmath
+, rpy2
+, fpylll
+, scipy
+, sympy
+, matplotlib
+, pillow
+, ipykernel
+, networkx
+, ptyprocess
+, lrcalc-python
+, sphinx # TODO: this is in setup.cfg, should we override it?
+}:
+
+assert (!blas.isILP64) && (!lapack.isILP64);
+
+# This is the core sage python package. Everything else is just wrappers gluing
+# stuff together. It is not very useful on its own though, since it will not
+# find many of its dependencies without `sage-env`, will not be tested without
+# `sage-tests` and will not have html docs without `sagedoc`.
+
+buildPythonPackage rec {
+  version = src.version;
+  pname = "sagelib";
+  src = sage-src;
+
+  nativeBuildInputs = [
+    iml
+    perl
+    jupyter_core
+    pkg-config
+    sage-setup
+    pip # needed to query installed packages
+    lisp-compiler
+    m4
+  ];
+
+  buildInputs = [
+    gd
+    readline
+    iml
+  ];
+
+  propagatedBuildInputs = [
+    cypari2
+    jinja2
+    numpy
+    pkgconfig
+    boost
+    arb
+    brial
+    cliquer
+    lisp-compiler
+    eclib
+    ecm
+    fflas-ffpack
+    flint
+    giac
+    givaro
+    glpk
+    gsl
+    lcalc
+    gap
+    libmpc
+    linbox
+    lrcalc
+    m4ri
+    m4rie
+    memory-allocator
+    mpfi
+    ntl
+    blas
+    lapack
+    pari
+    planarity
+    ppl
+    primecountpy
+    rankwidth
+    ratpoints
+    singular
+    symmetrica
+    zn_poly
+    pip
+    cython
+    cysignals
+    libhomfly
+    libbraiding
+    gmpy2
+    pplpy
+    sqlite
+    mpmath
+    rpy2
+    scipy
+    sympy
+    matplotlib
+    pillow
+    ipykernel
+    fpylll
+    networkx
+    jupyter-client
+    ipywidgets
+    ptyprocess
+    lrcalc-python
+    sphinx
+  ];
+
+  preBuild = ''
+    export SAGE_ROOT="$PWD"
+    export SAGE_LOCAL="$SAGE_ROOT"
+    export SAGE_SHARE="$SAGE_LOCAL/share"
+
+    # set locations of dependencies (needed for nbextensions like threejs)
+    . ${env-locations}/sage-env-locations
+
+    export JUPYTER_PATH="$SAGE_LOCAL/jupyter"
+    export PATH="$SAGE_ROOT/build/bin:$SAGE_ROOT/src/bin:$PATH"
+
+    export SAGE_NUM_THREADS="$NIX_BUILD_CORES"
+
+    mkdir -p "$SAGE_SHARE/sage/ext/notebook-ipython"
+    mkdir -p "var/lib/sage/installed"
+
+    cd build/pkgs/sagelib
+
+    # some files, like Pipfile, pyproject.toml, requirements.txt and setup.cfg
+    # are generated by the bootstrap script using m4. these can fetch data from
+    # build/pkgs, either directly or via sage-get-system-packages.
+    sed -i '/sage_conf/d' src/setup.cfg.m4
+    sed -i '/sage_conf/d' src/requirements.txt.m4
+
+    # version lower bounds are useful, but upper bounds are a hassle because
+    # Sage tests already catch any relevant API breakage.
+    # according to the discussion at https://trac.sagemath.org/ticket/33520,
+    # upper bounds will be less noisy starting from Sage 9.6.
+    sed -i 's/==0.5.1/>=0.5.1/' ../ptyprocess/install-requires.txt
+    sed -i 's/, <[^, ]*//' ../*/install-requires.txt
+
+    for infile in src/*.m4; do
+        if [ -f "$infile" ]; then
+            outfile="src/$(basename $infile .m4)"
+            m4 "$infile" > "$outfile"
+        fi
+    done
+
+    cd src
+  '';
+
+  postInstall = ''
+    rm -r "$out/${python.sitePackages}/sage/cython_debug"
+  '';
+
+  doCheck = false; # we will run tests in sage-tests.nix
+}
--- a/pkgs/applications/science/math/sage/threejs-sage.nix
+++ b/pkgs/applications/science/math/sage/threejs-sage.nix
@ -0,0 +1,19 @@
+{ stdenv, fetchFromGitHub }:
+
+stdenv.mkDerivation rec {
+  pname = "threejs-sage";
+  version = "r122";
+
+  src = fetchFromGitHub {
+    owner = "sagemath";
+    repo = "threejs-sage";
+    rev = version;
+    sha256 = "sha256-xPAPt36Fon3hYQq6SOmGkIyUzAII2LMl10nqYG4UPI0=";
+  };
+
+  installPhase = ''
+    mkdir -p "$out/lib/node_modules/three/"
+    cp version "$out/lib/node_modules/three"
+    cp -r build "$out/lib/node_modules/three/$(cat version)"
+  '';
+}
--- a/Show more
+++ b/Show more