Merge master into staging-next

17 files changed, 177 insertions, 303 deletions

diff --git a/pkgs/applications/audio/cmus/option-debugging.patch b/pkgs/applications/audio/cmus/option-debugging.patch
deleted file mode 100644
index 84115e1480e13..0000000000000
--- a/pkgs/applications/audio/cmus/option-debugging.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-Shows build and link errors in configure for ease of debugging which
-options require what.
-diff --git a/scripts/checks.sh b/scripts/checks.sh
-index 64cbbf3..fab4d9b 100644
---- a/scripts/checks.sh
-+++ b/scripts/checks.sh
-@@ -425,7 +425,7 @@ try_compile()
- 		echo "$1" > $__src || exit 1
- 		shift
- 		__cmd="$CC -c $CFLAGS $@ $__src -o $__obj"
--		$CC -c $CFLAGS "$@" $__src -o $__obj 2>/dev/null
-+		$CC -c $CFLAGS "$@" $__src -o $__obj
- 		;;
- 	cxx)
- 		__src=`tmp_file prog.cc`
-@@ -433,7 +433,7 @@ try_compile()
- 		echo "$1" > $__src || exit 1
- 		shift
- 		__cmd="$CXX -c $CXXFLAGS $@ $__src -o $__obj"
--		$CXX -c $CXXFLAGS "$@" $__src -o $__obj 2>/dev/null
-+		$CXX -c $CXXFLAGS "$@" $__src -o $__obj
- 		;;
- 	esac
- 	return $?
-@@ -451,7 +451,7 @@ try_compile_link()
- 		echo "$1" > $__src || exit 1
- 		shift
- 		__cmd="$CC $__src -o $__exe $CFLAGS $LDFLAGS $@"
--		$CC $__src -o $__exe $CFLAGS $LDFLAGS "$@" 2>/dev/null
-+		$CC $__src -o $__exe $CFLAGS $LDFLAGS "$@"
- 		;;
- 	cxx)
- 		__src=`tmp_file prog.cc`
-@@ -459,7 +459,7 @@ try_compile_link()
- 		echo "$1" > $__src || exit 1
- 		shift
- 		__cmd="$CXX $__src -o $__exe $CXXFLAGS $CXXLDFLAGS $@"
--		$CXX $__src -o $__exe $CXXFLAGS $CXXLDFLAGS "$@" 2>/dev/null
-+		$CXX $__src -o $__exe $CXXFLAGS $CXXLDFLAGS "$@"
- 		;;
- 	esac
- 	return $?
diff --git a/pkgs/applications/audio/vcv-rack/default.nix b/pkgs/applications/audio/vcv-rack/default.nix
index 907cd09961489..7a1ded3e2f82a 100644
--- a/pkgs/applications/audio/vcv-rack/default.nix
+++ b/pkgs/applications/audio/vcv-rack/default.nix
@@ -250,6 +250,7 @@ stdenv.mkDerivation rec {
     # no-derivatives clause
     license = with licenses; [ gpl3Plus cc-by-nc-40 unfreeRedistributable ];
     maintainers = with maintainers; [ nathyong jpotier ddelabru ];
+    mainProgram = "Rack";
     platforms = platforms.linux;
   };
 }
diff --git a/pkgs/applications/blockchains/bitcoin-abc/default.nix b/pkgs/applications/blockchains/bitcoin-abc/default.nix
index 1cc43a059e204..948645d60006b 100644
--- a/pkgs/applications/blockchains/bitcoin-abc/default.nix
+++ b/pkgs/applications/blockchains/bitcoin-abc/default.nix
@@ -25,13 +25,13 @@
 
 mkDerivation rec {
   pname = "bitcoin" + lib.optionalString (!withGui) "d" + "-abc";
-  version = "0.29.2";
+  version = "0.29.3";
 
   src = fetchFromGitHub {
     owner = "bitcoin-ABC";
     repo = "bitcoin-abc";
     rev = "v${version}";
-    hash = "sha256-og9hMQdDXGdUQN+A+z0064E6svF+qPd9CWtDQsdvNYQ=";
+    hash = "sha256-hYA0O7nDT8J1EnpW4i1+eBzkNw77JC6M7GwO3BdBh3U=";
   };
 
   nativeBuildInputs = [ pkg-config cmake ];
diff --git a/pkgs/applications/editors/vscode/extensions/default.nix b/pkgs/applications/editors/vscode/extensions/default.nix
index cfb14bd2cfe73..260711bd4880b 100644
--- a/pkgs/applications/editors/vscode/extensions/default.nix
+++ b/pkgs/applications/editors/vscode/extensions/default.nix
@@ -970,7 +970,7 @@ let
             version = "0.8.25";
           }
           // sources.${stdenv.system};
-        nativeBuildInputs = [ autoPatchelfHook ];
+        nativeBuildInputs = lib.optionals stdenv.isLinux [ autoPatchelfHook ];
         buildInputs = [ stdenv.cc.cc.lib ];
         meta = {
           description = "Open-source autopilot for software development - bring the power of ChatGPT to your IDE";
diff --git a/pkgs/applications/emulators/craftos-pc/default.nix b/pkgs/applications/emulators/craftos-pc/default.nix
index 12c86c3680f83..9ad54f00d4e8e 100644
--- a/pkgs/applications/emulators/craftos-pc/default.nix
+++ b/pkgs/applications/emulators/craftos-pc/default.nix
@@ -1,10 +1,8 @@
 { lib
 , stdenv
 , fetchFromGitHub
-, fetchpatch
 , callPackage
 , patchelf
-, unzip
 , poco
 , openssl
 , SDL2
@@ -16,18 +14,18 @@
 }:
 
 let
-  version = "2.8.1";
+  version = "2.8.2";
   craftos2-lua = fetchFromGitHub {
     owner = "MCJack123";
     repo = "craftos2-lua";
     rev = "v${version}";
-    hash = "sha256-8bl83AOIWtUQ06F2unYEF08VT13o9EGo9YDZpdNxd8w=";
+    hash = "sha256-Kv0supnYKWLaVqOeZAzQNd3tQRP2KJugZqytyoj8QtY=";
   };
   craftos2-rom = fetchFromGitHub {
     owner = "McJack123";
     repo = "craftos2-rom";
     rev = "v${version}";
-    hash = "sha256-aCRJ3idSrRM8ydt8hP8nA1RR0etPnWpQKphXcOGgTfk=";
+    hash = "sha256-5ZsLsqrkO02NLJCzsgf0k/ifsqNybTi4DcB9GLmWDHw=";
   };
 in
 
@@ -39,7 +37,7 @@ stdenv.mkDerivation rec {
     owner = "MCJack123";
     repo = "craftos2";
     rev = "v${version}";
-    hash = "sha256-iQCv4EDdqmnU0fYxMwpCZ2Z5p43P0MGBNIG/dZrWndg=";
+    hash = "sha256-ozebHgUgwdqYtWAyL+EdwpjEvZC+PkWcLYCPWz2FjSw=";
   };
 
   buildInputs = [ patchelf poco openssl SDL2 SDL2_mixer ncurses libpng pngpp libwebp ];
diff --git a/pkgs/applications/misc/urlscan/default.nix b/pkgs/applications/misc/urlscan/default.nix
index 3715ef27524e9..2247344ba765a 100644
--- a/pkgs/applications/misc/urlscan/default.nix
+++ b/pkgs/applications/misc/urlscan/default.nix
@@ -5,14 +5,14 @@
 
 python3.pkgs.buildPythonApplication rec {
   pname = "urlscan";
-  version = "1.0.1";
+  version = "1.0.2";
   format = "pyproject";
 
   src = fetchFromGitHub {
     owner = "firecat53";
     repo = pname;
     rev = "refs/tags/${version}";
-    hash = "sha256-OzcoOIgEiadWrsUPIxBJTuZQYjScJBYKyqCu1or6fz8=";
+    hash = "sha256-nyq4BrpfbZwK/nOnB8ZEN1wlM8CssYVRvV7ytpX7k40=";
   };
 
   nativeBuildInputs = with python3.pkgs; [
diff --git a/pkgs/applications/networking/cluster/opentofu/default.nix b/pkgs/applications/networking/cluster/opentofu/default.nix
index a378a7486b713..2d9b07a3f88dc 100644
--- a/pkgs/applications/networking/cluster/opentofu/default.nix
+++ b/pkgs/applications/networking/cluster/opentofu/default.nix
@@ -14,22 +14,22 @@
 let
   package =  buildGoModule rec {
     pname = "opentofu";
-    version = "1.6.2";
+    version = "1.7.0";
 
     src = fetchFromGitHub {
       owner = "opentofu";
       repo = "opentofu";
       rev = "v${version}";
-      hash = "sha256-CYiwn2NDIAx30J8tmbrV45dbCIGoA3U+yBdMj4RX5Ho=";
+      hash = "sha256-e0u8aFua3oMsBafwRPYuWQ9M6DtC7f9LlCDGJ5vdAWE=";
     };
 
-    vendorHash = "sha256-kSm5RZqQRgbmPaKt5IWmuMhHwAu+oJKTX1q1lbE7hWk=";
+    vendorHash = "sha256-cML742FfWFNIwGyIdRd3JWcfDlOXnJVgUXz4j5fa74Q=";
     ldflags = [ "-s" "-w" "-X" "github.com/opentofu/opentofu/version.dev=no" ];
 
     postConfigure = ''
       # speakeasy hardcodes /bin/stty https://github.com/bgentry/speakeasy/issues/22
       substituteInPlace vendor/github.com/bgentry/speakeasy/speakeasy_unix.go \
-        --replace "/bin/stty" "${coreutils}/bin/stty"
+        --replace-fail "/bin/stty" "${coreutils}/bin/stty"
     '';
 
     nativeBuildInputs = [ installShellFiles ];
diff --git a/pkgs/applications/office/clockify/default.nix b/pkgs/applications/office/clockify/default.nix
index efd20632a2a31..7b2faa6b7d203 100644
--- a/pkgs/applications/office/clockify/default.nix
+++ b/pkgs/applications/office/clockify/default.nix
@@ -1,40 +1,27 @@
-{ stdenv, lib, fetchurl, dpkg, makeWrapper, electron }:
+{ lib
+, appimageTools
+, fetchurl }:
 
-stdenv.mkDerivation rec {
+appimageTools.wrapType2 rec {
   pname = "clockify";
-  version = "2.1.6";
+  version = "2.1.17.1354";
 
   src = fetchurl {
-    url = "https://web.archive.org/web/20231110130133/https://clockify.me/downloads/Clockify_Setup_x64.deb";
-    hash = "sha256-jndoMk3vqk8a5jMzKVo6ThovSISmcu+hef9IJcg3reQ=";
+    url = "https://web.archive.org/web/20240406052908/https://clockify.me/downloads/Clockify_Setup.AppImage";
+    hash = "sha256-G5VOAf6PrjHUsnk7IlXdqJ2D941cnggjuHkkgrOaVaA=";
   };
 
-  nativeBuildInputs = [
-    dpkg
-    makeWrapper
-  ];
+  extraInstallCommands =
+    let appimageContents = appimageTools.extract { inherit pname version src; };
+    in ''
+      mv $out/bin/${pname}-${version} $out/bin/${pname}
 
-  dontBuild = true;
-  dontConfigure = true;
+      install -Dm 444 ${appimageContents}/clockify.desktop -t $out/share/applications
+      install -Dm 444 ${appimageContents}/clockify.png -t $out/share/pixmaps
 
-  unpackPhase = ''
-    dpkg-deb -x ${src} ./
-  '';
-
-  installPhase = ''
-    runHook preInstall
-
-    mv usr $out
-    mv opt $out
-
-    substituteInPlace $out/share/applications/clockify.desktop \
-      --replace "/opt/Clockify/" ""
-
-    makeWrapper ${electron}/bin/electron $out/bin/clockify \
-      --add-flags $out/opt/Clockify/resources/app.asar
-
-    runHook postInstall
-  '';
+      substituteInPlace $out/share/applications/clockify.desktop \
+        --replace 'Exec=AppRun' 'Exec=${pname}'
+    '';
 
   meta = with lib; {
     description = "Free time tracker and timesheet app that lets you track work hours across projects";
diff --git a/pkgs/applications/radio/gnuradio/wrapper.nix b/pkgs/applications/radio/gnuradio/wrapper.nix
index 9e2430334231c..9ec00058f1b8c 100644
--- a/pkgs/applications/radio/gnuradio/wrapper.nix
+++ b/pkgs/applications/radio/gnuradio/wrapper.nix
@@ -58,6 +58,10 @@ let
   # may wish to wrap GR without python support.
   pythonPkgs = extraPythonPackages
     ++ [ (unwrapped.python.pkgs.toPythonModule unwrapped) ]
+    ++ unwrapped.passthru.uhd.pythonPath
+    ++ lib.optionals (unwrapped.passthru.uhd.pythonPath != []) [
+      (unwrapped.python.pkgs.toPythonModule unwrapped.passthru.uhd)
+    ]
     # Add the extraPackages as python modules as well
     ++ (builtins.map unwrapped.python.pkgs.toPythonModule extraPackages)
     ++ lib.flatten (lib.mapAttrsToList (
diff --git a/pkgs/applications/radio/uhd/default.nix b/pkgs/applications/radio/uhd/default.nix
index c3f7b58fa1ba6..947d7d48108d2 100644
--- a/pkgs/applications/radio/uhd/default.nix
+++ b/pkgs/applications/radio/uhd/default.nix
@@ -8,15 +8,8 @@
 , boost
 , ncurses
 , enableCApi ? true
-# Although we handle the Python API's dependencies in pythonEnvArg, this
-# feature is currently disabled as upstream attempts to run `python setup.py
-# install` by itself, and it fails because the Python's environment's prefix is
-# not a writable directly. Adding support for this feature would require using
-# python's pypa/build nad pypa/install hooks directly, and currently it is hard
-# to do that because it all happens after a long buildPhase of the C API.
-, enablePythonApi ? false
+, enablePythonApi ? true
 , python3
-, buildPackages
 , enableExamples ? false
 , enableUtils ? true
 , libusb1
@@ -38,13 +31,7 @@
 }:
 
 let
-  onOffBool = b: if b then "ON" else "OFF";
-  inherit (lib) optionals;
-  # Later used in pythonEnv generation. Python + mako are always required for the build itself but not necessary for runtime.
-  pythonEnvArg = (ps: with ps; [ mako ]
-    ++ optionals (enablePythonApi) [ numpy setuptools ]
-    ++ optionals (enableUtils) [ requests six ]
-  );
+  inherit (lib) optionals cmakeBool;
 in
 
 stdenv.mkDerivation (finalAttrs: {
@@ -72,7 +59,30 @@ stdenv.mkDerivation (finalAttrs: {
     # hash.
     sha256 = "17g503mhndaabrdl7qai3rdbafr8xx8awsyr7h2bdzwzprzmh4m3";
   };
+  # This are the minimum required Python dependencies, this attribute might
+  # be useful if you want to build a development environment with a python
+  # interpreter able to import the uhd module.
+  pythonPath = optionals (enablePythonApi || enableUtils) [
+    python3.pkgs.numpy
+    python3.pkgs.setuptools
+  ] ++ optionals (enableUtils) [
+    python3.pkgs.requests
+    python3.pkgs.six
+
+    /* These deps are needed for the usrp_hwd.py utility, however even if they
+    would have been added here, the utility wouldn't have worked because it
+    depends on an old python library mprpc that is not supported for Python >
+    3.8. See also report upstream:
+    https://github.com/EttusResearch/uhd/issues/744
+
+    python3.pkgs.gevent
+    python3.pkgs.pyudev
+    python3.pkgs.pyroute2
+
+    */
+  ];
   passthru = {
+    runtimePython = python3.withPackages (ps: finalAttrs.pythonPath);
     updateScript = [
       ./update.sh
       # Pass it this file name as argument
@@ -83,66 +93,91 @@ stdenv.mkDerivation (finalAttrs: {
   cmakeFlags = [
     "-DENABLE_LIBUHD=ON"
     "-DENABLE_USB=ON"
-    "-DENABLE_TESTS=ON" # This installs tests as well so we delete them via postPhases
-    "-DENABLE_EXAMPLES=${onOffBool enableExamples}"
-    "-DENABLE_UTILS=${onOffBool enableUtils}"
-    "-DENABLE_C_API=${onOffBool enableCApi}"
-    "-DENABLE_PYTHON_API=${onOffBool enablePythonApi}"
-    "-DENABLE_DPDK=${onOffBool enableDpdk}"
+    # Regardless of doCheck, we want to build the tests to help us gain
+    # confident that the package is OK.
+    "-DENABLE_TESTS=ON"
+    (cmakeBool "ENABLE_EXAMPLES" enableExamples)
+    (cmakeBool "ENABLE_UTILS" enableUtils)
+    (cmakeBool "ENABLE_C_API" enableCApi)
+    (cmakeBool "ENABLE_PYTHON_API" enablePythonApi)
+    /*
+
+    Otherwise python tests fail. Using a dedicated pythonEnv for either or both
+    nativeBuildInputs and buildInputs makes upstream's cmake scripts fail to
+    install the Python API as reported on our end at [1] (we don't want
+    upstream to think we are in a virtual environment because we use
+    python3.withPackages...).
+
+    Putting simply the python dependencies in the nativeBuildInputs and
+    buildInputs as they are now from some reason makes the `python` in the
+    checkPhase fail to find the python dependencies, as reported at [2]. Even
+    using nativeCheckInputs with the python dependencies, or using a
+    `python3.withPackages` wrapper in nativeCheckInputs, doesn't help, as the
+    `python` found in $PATH first is the one from nativeBuildInputs.
+
+    [1]: https://github.com/NixOS/nixpkgs/pull/307435
+    [2]: https://discourse.nixos.org/t/missing-python-package-in-checkphase/9168/
+
+    Hence we use upstream's provided cmake flag to control which python
+    interpreter they will use to run the the python tests.
+
+    */
+    "-DRUNTIME_PYTHON_EXECUTABLE=${lib.getExe finalAttrs.passthru.runtimePython}"
+    (cmakeBool "ENABLE_DPDK" enableDpdk)
     # Devices
-    "-DENABLE_OCTOCLOCK=${onOffBool enableOctoClock}"
-    "-DENABLE_MPMD=${onOffBool enableMpmd}"
-    "-DENABLE_B100=${onOffBool enableB100}"
-    "-DENABLE_B200=${onOffBool enableB200}"
-    "-DENABLE_USRP1=${onOffBool enableUsrp1}"
-    "-DENABLE_USRP2=${onOffBool enableUsrp2}"
-    "-DENABLE_X300=${onOffBool enableX300}"
-    "-DENABLE_N300=${onOffBool enableN300}"
-    "-DENABLE_N320=${onOffBool enableN320}"
-    "-DENABLE_E300=${onOffBool enableE300}"
-    "-DENABLE_E320=${onOffBool enableE320}"
-  ]
+    (cmakeBool "ENABLE_OCTOCLOCK" enableOctoClock)
+    (cmakeBool "ENABLE_MPMD" enableMpmd)
+    (cmakeBool "ENABLE_B100" enableB100)
+    (cmakeBool "ENABLE_B200" enableB200)
+    (cmakeBool "ENABLE_USRP1" enableUsrp1)
+    (cmakeBool "ENABLE_USRP2" enableUsrp2)
+    (cmakeBool "ENABLE_X300" enableX300)
+    (cmakeBool "ENABLE_N300" enableN300)
+    (cmakeBool "ENABLE_N320" enableN320)
+    (cmakeBool "ENABLE_E300" enableE300)
+    (cmakeBool "ENABLE_E320" enableE320)
     # TODO: Check if this still needed
     # ABI differences GCC 7.1
     # /nix/store/wd6r25miqbk9ia53pp669gn4wrg9n9cj-gcc-7.3.0/include/c++/7.3.0/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<uhd::range_t>::iterator {aka __gnu_cxx::__normal_iterator<uhd::range_t*, std::vector<uhd::range_t> >}' changed in GCC 7.1
-    ++ [ (lib.optionalString stdenv.isAarch32 "-DCMAKE_CXX_FLAGS=-Wno-psabi") ]
-  ;
-
-  pythonEnv = python3.withPackages pythonEnvArg;
+  ] ++ optionals stdenv.isAarch32 [
+    "-DCMAKE_CXX_FLAGS=-Wno-psabi"
+  ];
 
   nativeBuildInputs = [
     cmake
     pkg-config
     # Present both here and in buildInputs for cross compilation.
-    (buildPackages.python3.withPackages pythonEnvArg)
+    python3
+    python3.pkgs.mako
+    # We add this unconditionally, but actually run wrapPythonPrograms only if
+    # python utilities are enabled
+    python3.pkgs.wrapPython
   ];
-  buildInputs = [
+  buildInputs = finalAttrs.pythonPath ++ [
     boost
     libusb1
-  ]
-    # However, if enableLibuhd_Python_api *or* enableUtils is on, we need
-    # pythonEnv for runtime as well. The utilities' runtime dependencies are
-    # handled at the environment
-    ++ optionals (enableExamples) [ ncurses ncurses.dev ]
-    ++ optionals (enablePythonApi || enableUtils) [ finalAttrs.pythonEnv ]
-    ++ optionals (enableDpdk) [ dpdk ]
-  ;
+  ] ++ optionals (enableExamples) [
+    ncurses ncurses.dev
+  ] ++ optionals (enableDpdk) [
+    dpdk
+  ];
 
   # many tests fails on darwin, according to ofborg
   doCheck = !stdenv.isDarwin;
 
   # Build only the host software
   preConfigure = "cd host";
-  # TODO: Check if this still needed, perhaps relevant:
-  # https://files.ettus.com/manual_archive/v3.15.0.0/html/page_build_guide.html#build_instructions_unix_arm
   patches = [
-    # Disable tests that fail in the sandbox
+    # Disable tests that fail in the sandbox, last checked at version 4.6.0.0
     ./no-adapter-tests.patch
   ];
 
-  postPhases = [ "installFirmware" "removeInstalledTests" ]
-    ++ optionals (enableUtils && stdenv.hostPlatform.isLinux) [ "moveUdevRules" ]
-  ;
+  postPhases = [
+    "installFirmware"
+    "removeInstalledTests"
+  ] ++ optionals (enableUtils && stdenv.hostPlatform.isLinux) [
+    "moveUdevRules"
+  ];
 
   # UHD expects images in `$CMAKE_INSTALL_PREFIX/share/uhd/images`
   installFirmware = ''
@@ -162,6 +197,10 @@ stdenv.mkDerivation (finalAttrs: {
     mv $out/lib/uhd/utils/uhd-usrp.rules $out/lib/udev/rules.d/
   '';
 
+  # Wrap the python utilities with our pythonPath definition
+  postFixup = lib.optionalString (enablePythonApi && enableUtils) ''
+    wrapPythonPrograms
+  '';
   disallowedReferences = optionals (!enablePythonApi && !enableUtils) [
     python3
   ];
diff --git a/pkgs/applications/science/electronics/digital/default.nix b/pkgs/applications/science/electronics/digital/default.nix
index 41deecbb62247..7619e43e80332 100644
--- a/pkgs/applications/science/electronics/digital/default.nix
+++ b/pkgs/applications/science/electronics/digital/default.nix
@@ -3,17 +3,18 @@
 }:
 
 let
+  pname = "digital";
   pkgDescription = "A digital logic designer and circuit simulator.";
   version = "0.30";
   buildDate = "2023-02-03T08:00:56+01:00"; # v0.30 commit date
 
   desktopItem = makeDesktopItem {
     type = "Application";
-    name = "Digital";
-    desktopName = pkgDescription;
+    name = pname;
+    desktopName = "Digital";
     comment = "Easy-to-use digital logic designer and circuit simulator";
-    exec = "digital";
-    icon = "digital";
+    exec = pname;
+    icon = pname;
     categories = [ "Education" "Electronics" ];
     mimeTypes = [ "text/x-digital" ];
     terminal = false;
@@ -28,8 +29,7 @@ let
   mvnParameters = "-Pno-git-rev -Dgit.commit.id.describe=${version} -Dproject.build.outputTimestamp=${buildDate} -DbuildTimestamp=${buildDate}";
 in
 maven.buildMavenPackage rec {
-  pname = "digital";
-  inherit version jre;
+  inherit pname version jre;
 
   src = fetchFromGitHub {
     owner = "hneemann";
@@ -44,6 +44,8 @@ maven.buildMavenPackage rec {
   nativeBuildInputs = [ copyDesktopItems makeWrapper ];
 
   installPhase = ''
+    runHook preInstall
+
     mkdir -p $out/bin
     mkdir -p $out/share/java
 
@@ -53,6 +55,13 @@ maven.buildMavenPackage rec {
     makeWrapper ${jre}/bin/java $out/bin/${pname} \
       --add-flags "-classpath $out/share/java/${pname}-${version}.jar:''${classpath#:}" \
       --add-flags "-jar $out/share/java/Digital.jar"
+
+    install -Dm644 src/main/svg/icon.svg $out/share/icons/hicolor/scalable/apps/${pname}.svg
+    for size in 16 32 48 64 128; do
+      install -Dm644 src/main/resources/icons/icon"$size".png $out/share/icons/hicolor/"$size"x"$size"/apps/${pname}.png
+    done
+
+    runHook postInstall
   '';
 
   desktopItems = [ desktopItem ];
diff --git a/pkgs/applications/science/math/sage/patches/linbox-1.7-upgrade.patch b/pkgs/applications/science/math/sage/patches/linbox-1.7-upgrade.patch
deleted file mode 100644
index 91e080aa294a0..0000000000000
--- a/pkgs/applications/science/math/sage/patches/linbox-1.7-upgrade.patch
+++ /dev/null
@@ -1,58 +0,0 @@
-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):
diff --git a/pkgs/applications/science/misc/gplates/boost-placeholders.patch b/pkgs/applications/science/misc/gplates/boost-placeholders.patch
deleted file mode 100644
index 7166b92f646af..0000000000000
--- a/pkgs/applications/science/misc/gplates/boost-placeholders.patch
+++ /dev/null
@@ -1,75 +0,0 @@
-diff --unified --recursive a/src/gui/TopologyTools.cc b/src/gui/TopologyTools.cc
---- a/src/gui/TopologyTools.cc	2021-07-05 05:11:47.000000000 +0200
-+++ b/src/gui/TopologyTools.cc	2022-12-07 22:35:20.444054124 +0100
-@@ -3448,7 +3448,7 @@
- 			std::find_if(
- 					d_visible_boundary_section_seq.begin(),
- 					d_visible_boundary_section_seq.end(),
--					boost::bind(&VisibleSection::d_section_info_index, _1) ==
-+					boost::bind(&VisibleSection::d_section_info_index, boost::placeholders::_1) ==
- 						boost::cref(section_index));
- 
- 	if (visible_section_iter == d_visible_boundary_section_seq.end())
-@@ -3467,7 +3467,7 @@
- 			std::find_if(
- 					d_visible_interior_section_seq.begin(),
- 					d_visible_interior_section_seq.end(),
--					boost::bind(&VisibleSection::d_section_info_index, _1) ==
-+					boost::bind(&VisibleSection::d_section_info_index, boost::placeholders::_1) ==
- 						boost::cref(section_index));
- 
- 	if (visible_section_iter == d_visible_interior_section_seq.end())
-diff --unified --recursive a/src/presentation/ReconstructionGeometryRenderer.cc b/src/presentation/ReconstructionGeometryRenderer.cc
---- a/src/presentation/ReconstructionGeometryRenderer.cc	2021-07-05 05:11:50.000000000 +0200
-+++ b/src/presentation/ReconstructionGeometryRenderer.cc	2022-12-07 22:36:11.117884262 +0100
-@@ -274,7 +274,7 @@
- GPlatesPresentation::ReconstructionGeometryRenderer::RenderParamsPopulator::visit_reconstruct_visual_layer_params(
- 		const ReconstructVisualLayerParams &params)
- {
--	d_render_params.show_vgp = boost::bind(&ReconstructVisualLayerParams::show_vgp, &params, _1, _2);
-+	d_render_params.show_vgp = boost::bind(&ReconstructVisualLayerParams::show_vgp, &params, boost::placeholders::_1, boost::placeholders::_2);
- 	d_render_params.vgp_draw_circular_error = params.get_vgp_draw_circular_error();
- 	d_render_params.fill_polygons = params.get_fill_polygons();
- 	d_render_params.fill_polylines = params.get_fill_polylines();
-diff --unified --recursive a/src/presentation/VisualLayerRegistry.cc b/src/presentation/VisualLayerRegistry.cc
---- a/src/presentation/VisualLayerRegistry.cc	2021-07-05 05:11:50.000000000 +0200
-+++ b/src/presentation/VisualLayerRegistry.cc	2022-12-07 22:38:12.950877614 +0100
-@@ -448,7 +448,7 @@
- 			&GPlatesQtWidgets::ReconstructScalarCoverageLayerOptionsWidget::create,
- 			boost::bind(
- 					&ReconstructScalarCoverageVisualLayerParams::create,
--					_1),
-+					boost::placeholders::_1),
- 			true);
- 
- 	registry.register_visual_layer_type(
-@@ -498,7 +498,7 @@
- 					// NOTE: We pass in ViewState and not the GlobeAndMapWidget, obtained from
- 					// ViewportWindow, because ViewportWindow is not yet available (a reference to
- 					// it not yet been initialised inside ViewState) so accessing it would crash...
--					_1, boost::ref(view_state)),
-+					boost::placeholders::_1, boost::ref(view_state)),
- 			true);
- 
- 	// DERIVED_DATA group.
-@@ -549,7 +549,7 @@
- 			&GPlatesQtWidgets::VelocityFieldCalculatorLayerOptionsWidget::create,
- 			boost::bind(
- 					&VelocityFieldCalculatorVisualLayerParams::create,
--					_1, boost::cref(view_state.get_rendered_geometry_parameters())),
-+					boost::placeholders::_1, boost::cref(view_state.get_rendered_geometry_parameters())),
- 			true);
- 
- 	using namespace  GPlatesUtils;
-diff --unified --recursive a/src/qt-widgets/ViewportWindow.cc b/src/qt-widgets/ViewportWindow.cc
---- a/src/qt-widgets/ViewportWindow.cc	2021-08-05 05:44:01.000000000 +0200
-+++ b/src/qt-widgets/ViewportWindow.cc	2022-12-07 22:39:20.487981302 +0100
-@@ -326,7 +326,7 @@
- 			*d_geometry_operation_state_ptr,
- 			*d_modify_geometry_state,
- 			*d_measure_distance_state_ptr,
--			boost::bind(&canvas_tool_status_message, boost::ref(*this), _1),
-+			boost::bind(&canvas_tool_status_message, boost::ref(*this), boost::placeholders::_1),
- 			get_view_state(),
- 			*this);
- 
diff --git a/pkgs/applications/science/misc/graphia/breakpad-sigstksz.patch b/pkgs/applications/science/misc/graphia/breakpad-sigstksz.patch
deleted file mode 100644
index 6e90faf9f0373..0000000000000
--- a/pkgs/applications/science/misc/graphia/breakpad-sigstksz.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/source/thirdparty/breakpad/src/client/linux/handler/exception_handler.cc b/source/thirdparty/breakpad/src/client/linux/handler/exception_handler.cc
-index ca353c4099..499be0a986 100644
---- a/source/thirdparty/breakpad/src/client/linux/handler/exception_handler.cc
-+++ b/source/thirdparty/breakpad/src/client/linux/handler/exception_handler.cc
-@@ -138,7 +138,7 @@ void InstallAlternateStackLocked() {
-   // SIGSTKSZ may be too small to prevent the signal handlers from overrunning
-   // the alternative stack. Ensure that the size of the alternative stack is
-   // large enough.
--  static const unsigned kSigStackSize = std::max(16384, SIGSTKSZ);
-+  const unsigned kSigStackSize = std::max<unsigned>(16384, SIGSTKSZ);
- 
-   // Only set an alternative stack if there isn't already one, or if the current
-   // one is too small.
diff --git a/pkgs/applications/terminal-emulators/tym/default.nix b/pkgs/applications/terminal-emulators/tym/default.nix
index acfbbb48943d0..562e06176130c 100644
--- a/pkgs/applications/terminal-emulators/tym/default.nix
+++ b/pkgs/applications/terminal-emulators/tym/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "tym";
-  version = "3.5.0";
+  version = "3.5.1";
 
   src = fetchFromGitHub {
     owner = "endaaman";
     repo = "${pname}";
     rev = version;
-    sha256 = "sha256-aXV3TNjHxg/9Lb2o+ci5/cCAPbkWhxqOka3wv21ajSA=";
+    sha256 = "sha256-53XAHyDiFPUTmw/rgoEoSoh+c/t4rS12gxwH1yKHqvw=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/applications/version-management/git-vanity-hash/default.nix b/pkgs/applications/version-management/git-vanity-hash/default.nix
index 915ef38307b2f..55332c6c7287b 100644
--- a/pkgs/applications/version-management/git-vanity-hash/default.nix
+++ b/pkgs/applications/version-management/git-vanity-hash/default.nix
@@ -1,17 +1,22 @@
-{ lib, fetchFromGitHub, rustPlatform }:
+{
+  lib,
+  fetchFromGitHub,
+  rustPlatform,
+}:
 
-rustPlatform.buildRustPackage rec {
+rustPlatform.buildRustPackage {
   pname = "git-vanity-hash";
   version = "1.0.0";
 
   src = fetchFromGitHub {
     owner = "prasmussen";
     repo = "git-vanity-hash";
-    rev = "v${version}";
-    hash = "sha256-jD8cSFXf9UNBZ9d8JTnuwhs6nPHY/xGd5RyqF+mQOlo=";
+    # v1.0.0 + build fix
+    rev = "a80e7725ac6d0b7e6807cd7315cfdc7eaf0584f6";
+    hash = "sha256-1z4jbtzUB3SH79dDXAITf7Vup1YZdTLHBieSrhrvSXc=";
   };
 
-  cargoHash = "sha256-8oW6gRtdQdmSmdwKlcU2EhHsyhk9hFhKl7RtsYwC7Ps=";
+  cargoHash = "sha256-+SQ0HpURBjnnwH1Ue7IUReOtI4LxVPK9AGSAihs0qsc=";
 
   postInstall = ''
     mkdir -p $out/share/doc/git-vanity-hash
diff --git a/pkgs/applications/window-managers/jay/default.nix b/pkgs/applications/window-managers/jay/default.nix
index 6718caf1ada23..6b7951c14c374 100644
--- a/pkgs/applications/window-managers/jay/default.nix
+++ b/pkgs/applications/window-managers/jay/default.nix
@@ -7,20 +7,30 @@
 , mesa
 , pango
 , udev
+, shaderc
+, libglvnd
+, vulkan-loader
+, autoPatchelfHook
 }:
 
 rustPlatform.buildRustPackage rec {
   pname = "jay";
-  version = "unstable-2022-11-20";
+  version = "1.1.0";
 
   src = fetchFromGitHub {
     owner = "mahkoh";
     repo = pname;
-    rev = "09b4668a5363a6e93dfb8ba35b244835f4edb0f2";
-    sha256 = "sha256-0IIzXY7AFTGEe0TzJVKOtTPUZee0Wz40yKgEWLeIYJw=";
+    rev = "v${version}";
+    sha256 = "sha256-9fWwVUqeYADt33HGaJRRFmM20WM7qRWbNGpt3rk9xQM=";
   };
 
-  cargoSha256 = "sha256-zSq6YBlm6gJXGlF9xZ8gWSTMewdNqrJzwP58a0x8QIU=";
+  cargoSha256 = "sha256-oPGY/rVx94BkWgKkwwyDjfASMyGGU32R5IZuNjOv+EM=";
+
+  SHADERC_LIB_DIR = "${lib.getLib shaderc}/lib";
+
+  nativeBuildInputs = [
+    autoPatchelfHook
+  ];
 
   buildInputs = [
     libGL
@@ -29,9 +39,18 @@ rustPlatform.buildRustPackage rec {
     pango
     udev
     libinput
+    shaderc
+  ];
+
+  runtimeDependencies = [
+    libglvnd
+    vulkan-loader
   ];
 
-  RUSTC_BOOTSTRAP = 1;
+  postInstall = ''
+    install -D etc/jay.portal $out/usr/share/xdg-desktop-portal/portals/jay.portal
+    install -D etc/jay-portals.conf $out/usr/share/xdg-desktop-portal/jay-portals.conf
+  '';
 
   meta = with lib; {
     description = "A Wayland compositor written in Rust";