Merge commit '87807e64a5ef5206b745a40af118c7be8db73681'

17 files changed, 135 insertions, 72 deletions

diff --git a/nixpkgs/pkgs/applications/science/astronomy/phd2/default.nix b/nixpkgs/pkgs/applications/science/astronomy/phd2/default.nix
index 0e0ad06bbe9f..543e6820a763 100644
--- a/nixpkgs/pkgs/applications/science/astronomy/phd2/default.nix
+++ b/nixpkgs/pkgs/applications/science/astronomy/phd2/default.nix
@@ -1,19 +1,32 @@
-{ lib, stdenv, fetchFromGitHub, pkg-config, cmake, gtk3, wxGTK30-gtk3,
-  curl, gettext, glib, indi-full, libnova, wrapGAppsHook }:
+{ lib, stdenv, fetchFromGitHub, pkg-config, cmake, gtk3, wxGTK30-gtk3
+, curl, gettext, glib, indi-full, libnova, wrapGAppsHook }:
 
 stdenv.mkDerivation rec {
   pname = "phd2";
-  version = "2.6.9dev1";
+  version = "2.6.10";
 
   src = fetchFromGitHub {
     owner = "OpenPHDGuiding";
     repo = "phd2";
     rev = "v${version}";
-    sha256 = "1ih7m9lilh12xbhmwm9kkicaqy72mi3firl6df7m5x38n2zj3zm4";
+    sha256 = "sha256-2ZiPjhlguWXFcC53xG1aqAode7twtoHWszFUMQkK5xU=";
   };
 
-  nativeBuildInputs = [ cmake pkg-config wrapGAppsHook ];
-  buildInputs = [ gtk3 wxGTK30-gtk3 curl gettext glib indi-full libnova ];
+  nativeBuildInputs = [
+    cmake
+    pkg-config
+    wrapGAppsHook
+  ];
+
+  buildInputs = [
+    gtk3
+    wxGTK30-gtk3
+    curl
+    gettext
+    glib
+    indi-full
+    libnova
+  ];
 
   cmakeFlags = [
     "-DOPENSOURCE_ONLY=1"
@@ -27,8 +40,9 @@ stdenv.mkDerivation rec {
   meta = with lib; {
     homepage = "https://openphdguiding.org/";
     description = "Telescope auto-guidance application";
+    changelog = "https://github.com/OpenPHDGuiding/phd2/releases/tag/v${version}";
     license = licenses.bsd3;
     maintainers = with maintainers; [ hjones2199 ];
-    platforms = [ "x86_64-linux" ];
+    platforms = platforms.linux;
   };
 }
diff --git a/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix b/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix
index ca80262eb76a..43007cb1f0f5 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix
@@ -35,10 +35,10 @@ in
 
 stdenv.mkDerivation rec {
   pname = "gwyddion";
-   version = "2.58";
+   version = "2.59";
   src = fetchurl {
     url = "mirror://sourceforge/gwyddion/gwyddion-${version}.tar.xz";
-    sha256 = "sha256-0xNnzYkuW3nEsO2o+0WEA+Z71XWoq6FYXm342OWO9Sw=";
+    sha256 = "sha256-APMOJeZt/zp8JvXghKZ5lQFRKWO/4TVDORok8qAgEBk=";
   };
 
   nativeBuildInputs = [ pkg-config file ];
diff --git a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
index c645693e19a1..5d2158843ede 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
@@ -17,14 +17,14 @@ let
   };
 in
 stdenv.mkDerivation rec {
-  version = "14.31.41";
+  version = "14.31.44";
   pname = "jmol";
 
   src = let
     baseVersion = "${lib.versions.major version}.${lib.versions.minor version}";
   in fetchurl {
     url = "mirror://sourceforge/jmol/Jmol/Version%20${baseVersion}/Jmol%20${version}/Jmol-${version}-binary.tar.gz";
-    sha256 = "sha256-dI1WkQgFikxaIjjqVKZcsGvc3QIu/NMIcRW3N8PGbkY=";
+    sha256 = "sha256-MHfqoQzUEL7nje7Y/hbaA8iktxfN7464TJXum5B6OCc=";
   };
 
   patchPhase = ''
diff --git a/nixpkgs/pkgs/applications/science/electronics/gtkwave/default.nix b/nixpkgs/pkgs/applications/science/electronics/gtkwave/default.nix
index af5441f07e21..b539df7592a5 100644
--- a/nixpkgs/pkgs/applications/science/electronics/gtkwave/default.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/gtkwave/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "gtkwave";
-  version = "3.3.109";
+  version = "3.3.110";
 
   src = fetchurl {
     url    = "mirror://sourceforge/gtkwave/${pname}-gtk3-${version}.tar.gz";
-    sha256 = "sha256-NUYezNm4tEcMqnirmo8U7Ky8ye/2MDPY3OWAk+eG3rc=";
+    sha256 = "sha256-Ku25IVa8ot3SWxODeMrOaxBY5X022TnvD3l2kAa3Wao=";
   };
 
   nativeBuildInputs = [ pkg-config wrapGAppsHook ];
diff --git a/nixpkgs/pkgs/applications/science/logic/coq/default.nix b/nixpkgs/pkgs/applications/science/logic/coq/default.nix
index 9d6212fef112..b5c66289c9d3 100644
--- a/nixpkgs/pkgs/applications/science/logic/coq/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/coq/default.nix
@@ -129,14 +129,15 @@ self = stdenv.mkDerivation {
     ++ optionals buildIde
       (if versionAtLeast "8.10"
        then [ ocamlPackages.lablgtk3-sourceview3 glib gnome.adwaita-icon-theme wrapGAppsHook ]
-       else [ ocamlPackages.lablgtk ]);
+       else [ ocamlPackages.lablgtk ])
+    ++ optional (versionAtLeast "8.14") ocamlPackages.dune_2
+  ;
 
   postPatch = ''
     UNAME=$(type -tp uname)
     RM=$(type -tp rm)
-    substituteInPlace configure --replace "/bin/uname" "$UNAME"
     substituteInPlace tools/beautify-archive --replace "/bin/rm" "$RM"
-    substituteInPlace configure.ml --replace '"md5 -q"' '"md5sum"'
+    ${if !versionAtLeast "8.7" then "substituteInPlace configure.ml --replace \"md5 -q\" \"md5sum\"" else ""}
     ${csdpPatch}
   '';
 
diff --git a/nixpkgs/pkgs/applications/science/logic/elan/default.nix b/nixpkgs/pkgs/applications/science/logic/elan/default.nix
index d20be86daf0b..a49262e7cb65 100644
--- a/nixpkgs/pkgs/applications/science/logic/elan/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/elan/default.nix
@@ -7,16 +7,16 @@ in
 
 rustPlatform.buildRustPackage rec {
   pname = "elan";
-  version = "1.0.2";
+  version = "1.0.6";
 
   src = fetchFromGitHub {
     owner = "leanprover";
     repo = "elan";
     rev = "v${version}";
-    sha256 = "sha256-nK4wvxK5Ne1+4kaMts6pIr5FvXBgXJsGdn68gGEZUdk=";
+    sha256 = "sha256-Ns8vSS/PDlfopigW4Nz3fdR9PCMG8gDoL36+/s0Qkeo=";
   };
 
-  cargoSha256 = "sha256-ptSbpq1ePNWmdBGfKtqFGfkdimDjU0YEo4F8VPtQMt4=";
+  cargoSha256 = "sha256-NDtldiVo4SyE88f6ntKn1WJDFdvwN5Ps4DxQH15iNZE=";
 
   nativeBuildInputs = [ pkg-config makeWrapper ];
 
diff --git a/nixpkgs/pkgs/applications/science/logic/hol/default.nix b/nixpkgs/pkgs/applications/science/logic/hol/default.nix
index 569c455e6532..8427249c4ce9 100644
--- a/nixpkgs/pkgs/applications/science/logic/hol/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/hol/default.nix
@@ -81,7 +81,7 @@ stdenv.mkDerivation {
     '';
     homepage = "http://hol.sourceforge.net/";
     license = licenses.bsd3;
-    platforms = [ "x86_64-linux" ];
+    platforms = platforms.unix;
     maintainers = with maintainers; [ mudri ];
   };
 }
diff --git a/nixpkgs/pkgs/applications/science/logic/lean/default.nix b/nixpkgs/pkgs/applications/science/logic/lean/default.nix
index 214f4e218fd3..ea2cd356e315 100644
--- a/nixpkgs/pkgs/applications/science/logic/lean/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/lean/default.nix
@@ -2,7 +2,7 @@
 
 stdenv.mkDerivation rec {
   pname = "lean";
-  version = "3.30.0";
+  version = "3.31.0";
 
   src = fetchFromGitHub {
     owner  = "leanprover-community";
@@ -11,8 +11,8 @@ stdenv.mkDerivation rec {
     # from. this is then used to check whether an olean file should be
     # rebuilt. don't use a tag as rev because this will get replaced into
     # src/githash.h.in in preConfigure.
-    rev    = "a5822ea47ebc52eec6323d8f1b60f6ec025daf99";
-    sha256 = "sha256-gJhbkl19iilNyfCt2TfPmghYA3yCjg6kS+yk/x/k14Y=";
+    rev    = "333783350cd3fe38f25fed1da7d6a433d8f85b77";
+    sha256 = "sha256-N8Ju7pSGssvt84/0e1o6G/p7fWM1c0Mzw+ftL1/++J4=";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/nixpkgs/pkgs/applications/science/logic/tlaplus/toolbox.nix b/nixpkgs/pkgs/applications/science/logic/tlaplus/toolbox.nix
index defe218b119e..ef2d97ef6bfc 100644
--- a/nixpkgs/pkgs/applications/science/logic/tlaplus/toolbox.nix
+++ b/nixpkgs/pkgs/applications/science/logic/tlaplus/toolbox.nix
@@ -1,5 +1,5 @@
 { lib, fetchzip, makeWrapper, makeDesktopItem, stdenv
-, gtk3, libXtst, glib, zlib
+, gtk3, libXtst, glib, zlib, wrapGAppsHook
 }:
 
 let
@@ -25,7 +25,11 @@ in stdenv.mkDerivation rec {
     sha256 = "02a2y2mkfab5cczw8g604m61h4xr0apir49zbd1aq6mmgcgngw80";
   };
 
-  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ gtk3 ];
+
+  nativeBuildInputs = [ makeWrapper wrapGAppsHook ];
+
+  dontWrapGApps = true;
 
   phases = [ "installPhase" ];
 
@@ -36,6 +40,9 @@ in stdenv.mkDerivation rec {
     cp -r "$src" "$out/toolbox"
     chmod -R +w "$out/toolbox"
 
+    fixupPhase
+    gappsWrapperArgsHook
+
     patchelf \
       --set-interpreter $(cat $NIX_CC/nix-support/dynamic-linker) \
       "$out/toolbox/toolbox"
@@ -52,7 +59,8 @@ in stdenv.mkDerivation rec {
     makeWrapper $out/toolbox/toolbox $out/bin/tla-toolbox \
       --run "set -x; cd $out/toolbox" \
       --add-flags "-data ~/.tla-toolbox" \
-      --prefix LD_LIBRARY_PATH : "${lib.makeLibraryPath [ gtk3 libXtst glib zlib ]}"
+      --prefix LD_LIBRARY_PATH : "${lib.makeLibraryPath [ gtk3 libXtst glib zlib ]}"  \
+      "''${gappsWrapperArgs[@]}"
 
     echo -e "\nCreating TLA Toolbox icons..."
     pushd "$src"
diff --git a/nixpkgs/pkgs/applications/science/math/caffe/default.nix b/nixpkgs/pkgs/applications/science/math/caffe/default.nix
index 565c6a17672d..08bf84be7c89 100644
--- a/nixpkgs/pkgs/applications/science/math/caffe/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/caffe/default.nix
@@ -76,7 +76,7 @@ stdenv.mkDerivation rec {
     let pp = python.pkgs; in ([
       pp.numpy pp.scipy pp.scikitimage pp.h5py
       pp.matplotlib pp.ipython pp.networkx pp.nose
-      pp.pandas pp.dateutil pp.protobuf pp.gflags
+      pp.pandas pp.python-dateutil pp.protobuf pp.gflags
       pp.pyyaml pp.pillow pp.six
     ] ++ lib.optional leveldbSupport pp.leveldb)
   );
diff --git a/nixpkgs/pkgs/applications/science/math/glsurf/default.nix b/nixpkgs/pkgs/applications/science/math/glsurf/default.nix
index 208bb95f930e..58b2a617bd63 100644
--- a/nixpkgs/pkgs/applications/science/math/glsurf/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/glsurf/default.nix
@@ -1,7 +1,12 @@
-{ lib, stdenv, fetchurl, ocamlPackages, libGLU, libGL, freeglut, giflib
-, libmysqlclient, mpfr, gmp, libtiff, libjpeg, libpng
+{ lib, stdenv, fetchurl, ocamlPackages, makeWrapper
+, libGLU, libGL, freeglut, mpfr, gmp
+, pkgsHostTarget
 }:
 
+let
+  inherit (pkgsHostTarget.targetPackages.stdenv) cc;
+in
+
 stdenv.mkDerivation {
   name = "glsurf-3.3.1";
 
@@ -10,17 +15,32 @@ stdenv.mkDerivation {
     sha256 = "0w8xxfnw2snflz8wdr2ca9f5g91w5vbyp1hwlx1v7vg83d4bwqs7";
   };
 
-  buildInputs = [ freeglut libGLU libGL libmysqlclient mpfr giflib gmp
-    libtiff libjpeg libpng ]
-  ++ (with ocamlPackages; [
-    ocaml findlib ocaml_mysql lablgl camlimages_4_1_2 mlgmpidl
+  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 = {
diff --git a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix
index 56b6df94e8fb..7807ae613e8c 100644
--- a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "qalculate-gtk";
-  version = "3.18.0";
+  version = "3.19.0";
 
   src = fetchFromGitHub {
     owner = "qalculate";
     repo = "qalculate-gtk";
     rev = "v${version}";
-    sha256 = "sha256-hE0di7B6dCnMmMBLgFkb6vPS4hS/7zD6BbviIucrn1I=";
+    sha256 = "1nrx7gp6f1yalbdda1gb97azhbr4xclq2xf08vvbvsk8jfd6fd2v";
   };
 
   hardeningDisable = [ "format" ];
diff --git a/nixpkgs/pkgs/applications/science/math/sage/patches/sphinx-3.5-code-output.patch b/nixpkgs/pkgs/applications/science/math/sage/patches/sphinx-3.5-code-output.patch
deleted file mode 100644
index f17897d4c89f..000000000000
--- a/nixpkgs/pkgs/applications/science/math/sage/patches/sphinx-3.5-code-output.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/src/sage/misc/sagedoc.py b/src/sage/misc/sagedoc.py
-index 6bad826a88..f4d7b8651c 100644
---- a/src/sage/misc/sagedoc.py
-+++ b/src/sage/misc/sagedoc.py
-@@ -24,7 +24,7 @@ see :trac:`12849`::
-     ....:     for line in fobj:
-     ....:         if "#sage.symbolic.expression.Expression.numerical_approx" in line:
-     ....:             print(line)
--    <code class="sig-name descname">numerical_approx</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">prec</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">digits</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">algorithm</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span>...
-+    <code class="sig-name descname"><span class="pre">numerical_approx</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">prec</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">digits</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">algorithm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span>...
- 
- Check that sphinx is not imported at Sage start-up::
- 
diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
index 57234c660a5a..218ab920a872 100644
--- a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
+++ b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
@@ -16,7 +16,12 @@ let
   fetchSageDiff = { base, name, rev, sha256, ...}@args: (
     fetchpatch ({
       inherit name sha256;
-      url = "https://git.sagemath.org/sage.git/patch?id2=${base}&id=${rev}";
+
+      # We used to use
+      # "https://git.sagemath.org/sage.git/patch?id2=${base}&id=${rev}"
+      # but the former way does not squash multiple patches together.
+      url = "https://github.com/sagemath/sage/compare/${base}...${rev}.diff";
+
       # We don't care about sage's own build system (which builds all its dependencies).
       # Exclude build system changes to avoid conflicts.
       excludes = [ "build/*" ];
@@ -79,13 +84,6 @@ stdenv.mkDerivation rec {
     # ignore a deprecation warning for usage of `cmp` in the attrs library in the doctests
     ./patches/ignore-cmp-deprecation.patch
 
-    # sphinx 3.5 pretty-prints code slightly differently than sphinx
-    # 3.1--3.3. a similar patch is available at the sphinx 4 ticket
-    # (https://trac.sagemath.org/ticket/31696), but sphinx 3.5 uses
-    # <code> tags while sphinx 4 uses <span> tags so we cannot just
-    # import the patch from trac.
-    ./patches/sphinx-3.5-code-output.patch
-
     # remove use of matplotlib function deprecated in 3.4
     # https://trac.sagemath.org/ticket/31827
     (fetchSageDiff {
@@ -95,16 +93,47 @@ stdenv.mkDerivation rec {
       sha256 = "sha256-SXcUGBMOoE9HpuBzgKC3P6cUmM5MiktXbe/7dVdrfWo=";
     })
 
-    # https://trac.sagemath.org/ticket/30801. this patch has
-    # positive_review but has not been merged upstream yet, so we
-    # don't use fetchSageDiff because it returns a file that contains
-    # each commit as a separate patch instead of a single diff, and
-    # some commits from the pari update branch are already in 9.3.rc5
-    # (auto-resolvable merge conflicts).
-    (fetchpatch {
+    # pari 2.13 update
+    # https://trac.sagemath.org/ticket/30801
+    #
+    # the last commit in that ticket is
+    # c78b1470fccd915e2fa93f95f2fefba6220fb1f7, but commits after
+    # 10a4531721d2700fd717e2b3a1364508ffd971c3 only deal with 32-bit
+    # and post-26635 breakage, none of which is relevant to us. since
+    # there are post-9.4.beta0 rebases after that, we just skip later
+    # commits.
+    (fetchSageDiff {
+      base = "9.3";
       name = "pari-2.13.1.patch";
-      url = "https://github.com/sagemath/sagetrac-mirror/compare/d6c5cd9be78cc448ee4c54bac93385b1244a234c...10a4531721d2700fd717e2b3a1364508ffd971c3.diff";
-      sha256 = "sha256-zMjRMEReoiTvmt+vvV0Ij1jtyLSLwSXBEVXqgvmq1D4=";
+      rev = "10a4531721d2700fd717e2b3a1364508ffd971c3";
+      sha256 = "sha256-gffWKK9CMREaNOb5zb63iZUgON4FvsPrMQNqe+5ZU9E=";
+    })
+
+    # sympy 1.8 update
+    # https://trac.sagemath.org/ticket/31647
+    (fetchSageDiff {
+      base = "9.4.beta0";
+      name = "sympy-1.8.patch";
+      rev = "fa864b36e15696450c36d54215b1e68183b29d25";
+      sha256 = "sha256-fj/9QEZlVF0fw9NpWflkTuBSKpGjCE6b96ECBgdn77o=";
+    })
+
+    # sphinx 4 update
+    # https://trac.sagemath.org/ticket/31696
+    (fetchSageDiff {
+      base = "9.4.beta3";
+      name = "sphinx-4.patch";
+      rev = "bc84af8c795b7da433d2000afc3626ee65ba28b8";
+      sha256 = "sha256-5Kvs9jarC8xRIU1rdmvIWxQLC25ehiTLJpg5skh8WNM=";
+    })
+
+    # eclib 20210625 update
+    # https://trac.sagemath.org/ticket/31443
+    (fetchSageDiff {
+      base = "9.4.beta3";
+      name = "eclib-20210625.patch";
+      rev = "789550ca04c94acfb1e803251538996a34962038";
+      sha256 = "sha256-VlyEn5hg3joG8t/GwiRfq9TzJ54AoHxLolsNQ3shc2c=";
     })
   ];
 
diff --git a/nixpkgs/pkgs/applications/science/misc/root/default.nix b/nixpkgs/pkgs/applications/science/misc/root/default.nix
index b3d0e96a5648..a97be6ec76fd 100644
--- a/nixpkgs/pkgs/applications/science/misc/root/default.nix
+++ b/nixpkgs/pkgs/applications/science/misc/root/default.nix
@@ -2,7 +2,7 @@
 , libX11, libXpm, libXft, libXext, libGLU, libGL, libxml2, lz4, xz, pcre, nlohmann_json
 , pkg-config, python, xxHash, zlib, zstd
 , libAfterImage, giflib, libjpeg, libtiff, libpng
-, Cocoa, OpenGL, noSplash ? false }:
+, Cocoa, CoreSymbolication, OpenGL, noSplash ? false }:
 
 stdenv.mkDerivation rec {
   pname = "root";
@@ -16,7 +16,7 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ makeWrapper cmake pkg-config git ];
   buildInputs = [ ftgl gl2ps glew pcre zlib zstd libxml2 lz4 xz gsl xxHash libAfterImage giflib libjpeg libtiff libpng nlohmann_json python.pkgs.numpy ]
     ++ lib.optionals (!stdenv.isDarwin) [ libX11 libXpm libXft libXext libGLU libGL ]
-    ++ lib.optionals (stdenv.isDarwin) [ Cocoa OpenGL ]
+    ++ lib.optionals (stdenv.isDarwin) [ Cocoa CoreSymbolication OpenGL ]
     ;
 
   patches = [
@@ -38,6 +38,10 @@ stdenv.mkDerivation rec {
     patchShebangs build/unix/
   '' + lib.optionalString noSplash ''
     substituteInPlace rootx/src/rootx.cxx --replace "gNoLogo = false" "gNoLogo = true"
+  '' + lib.optionalString stdenv.isDarwin ''
+    # Eliminate impure reference to /System/Library/PrivateFrameworks
+    substituteInPlace core/CMakeLists.txt \
+      --replace "-F/System/Library/PrivateFrameworks" ""
   '';
 
   cmakeFlags = [
diff --git a/nixpkgs/pkgs/applications/science/networking/sumo/default.nix b/nixpkgs/pkgs/applications/science/networking/sumo/default.nix
index af252da04f81..9cdf576b9c68 100644
--- a/nixpkgs/pkgs/applications/science/networking/sumo/default.nix
+++ b/nixpkgs/pkgs/applications/science/networking/sumo/default.nix
@@ -5,13 +5,13 @@
 
 stdenv.mkDerivation rec {
   pname = "sumo";
-  version = "1.8.0";
+  version = "1.9.2";
 
   src = fetchFromGitHub {
     owner = "eclipse";
     repo = "sumo";
     rev = "v${lib.replaceStrings ["."] ["_"] version}";
-    sha256 = "1w9im1zz8xnkdwmv4v11kn1xcqm889268g1fw4y2s9f6shi41mxx";
+    sha256 = "0zpd331vy1kfi4hfiszv3m8wl4m0wdfr3zzza200kkaakw5hjxhs";
     fetchSubmodules = true;
   };
 
@@ -33,7 +33,6 @@ stdenv.mkDerivation rec {
     jdk
     libGL
     libGLU
-    libX11
     libjpeg
     libpng
     libtiff
@@ -44,6 +43,7 @@ stdenv.mkDerivation rec {
     zlib
     python3
   ] ++ (with xorg; [
+    libX11
     libXcursor
     libXext
     libXfixes
diff --git a/nixpkgs/pkgs/applications/science/robotics/emuflight-configurator/default.nix b/nixpkgs/pkgs/applications/science/robotics/emuflight-configurator/default.nix
index 2b89a00eb4bd..ab94df9ef18f 100644
--- a/nixpkgs/pkgs/applications/science/robotics/emuflight-configurator/default.nix
+++ b/nixpkgs/pkgs/applications/science/robotics/emuflight-configurator/default.nix
@@ -3,11 +3,11 @@
 
 stdenv.mkDerivation rec {
   pname = "emuflight-configurator";
-  version = "0.3.5";
+  version = "0.3.6";
 
   src = fetchurl {
     url = "https://github.com/emuflight/EmuConfigurator/releases/download/${version}/emuflight-configurator_${version}_linux64.zip";
-    sha256 = "d55bdc52cf93d58c728ccb296ef912a5fc0f42c57ed95f3ded5f85d1c10838c4";
+    sha256 = "sha256-egSUd/+RNo0vr2EJibgk9nNnql5sHC11gctUMK+DzW0=";
   };
 
   nativeBuildInputs = [ wrapGAppsHook unzip copyDesktopItems ];