From cbc1db7b1ab12db3303da0067633c252b8279ee6 Mon Sep 17 00:00:00 2001
From: jfvillablanca <31008330+jfvillablanca@users.noreply.github.com>
Date: Mon, 16 Oct 2023 19:31:12 +0800
Subject: [PATCH 01/24] pythonPackages.repl-python-wakatime: init at 0.0.6

---
 .../repl-python-wakatime/default.nix          | 48 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 +
 2 files changed, 50 insertions(+)
 create mode 100644 pkgs/development/python-modules/repl-python-wakatime/default.nix

diff --git a/pkgs/development/python-modules/repl-python-wakatime/default.nix b/pkgs/development/python-modules/repl-python-wakatime/default.nix
new file mode 100644
index 000000000000..929a51dbce98
--- /dev/null
+++ b/pkgs/development/python-modules/repl-python-wakatime/default.nix
@@ -0,0 +1,48 @@
+{ lib
+, buildPythonPackage
+, pythonOlder
+, fetchPypi
+, ptpython
+, ipython
+, setuptools
+, setuptools-scm
+, setuptools-generate
+}:
+
+let
+  pname = "repl-python-wakatime";
+  version = "0.0.6";
+in
+
+buildPythonPackage {
+  inherit pname version;
+  format = "pyproject";
+  disabled = pythonOlder "3.6";
+
+  src = fetchPypi {
+    inherit pname version;
+    hash = "sha256-s2UelniMn4+wWILbVIIKidRCFaOvo/nNNofA7yf2+9c=";
+  };
+
+  nativeBuildInputs = [
+    setuptools
+    setuptools-scm
+    setuptools-generate
+  ];
+
+  propagatedBuildInputs = [
+    ptpython
+    ipython
+  ];
+
+  pythonImportsCheck = [
+    "repl_python_wakatime"
+  ];
+
+  meta = with lib; {
+    description = "Python REPL plugin for automatic time tracking and metrics generated from your programming activity";
+    homepage = "https://github.com/wakatime/repl-python-wakatime";
+    license = licenses.gpl3Only;
+    maintainers = with maintainers; [ jfvillablanca ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 06d5d17d87b8..76fe6939b957 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -12079,6 +12079,8 @@ self: super: with self; {
 
   repeated-test = callPackage ../development/python-modules/repeated-test { };
 
+  repl-python-wakatime = callPackage ../development/python-modules/repl-python-wakatime { };
+
   repocheck = callPackage ../development/python-modules/repocheck { };
 
   reportengine = callPackage ../development/python-modules/reportengine { };

From 1e7765143c74873f695e588873b432a1207d6c20 Mon Sep 17 00:00:00 2001
From: raspher <raspher@posteo.me>
Date: Sun, 4 Feb 2024 00:18:51 +0100
Subject: [PATCH 02/24] dnss: init at 0-unstable-2023-10-22

---
 pkgs/by-name/dn/dnss/package.nix | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 pkgs/by-name/dn/dnss/package.nix

diff --git a/pkgs/by-name/dn/dnss/package.nix b/pkgs/by-name/dn/dnss/package.nix
new file mode 100644
index 000000000000..00796cf8df17
--- /dev/null
+++ b/pkgs/by-name/dn/dnss/package.nix
@@ -0,0 +1,25 @@
+{ buildGoModule
+, fetchFromGitHub
+, lib
+}:
+
+buildGoModule {
+  pname = "dnss";
+  version = "0-unstable-2024-03-17";
+  src = fetchFromGitHub {
+    owner = "albertito";
+    repo = "dnss";
+    rev = "da8986dd432870f5710e3e8652c92c95f34b830b";
+    hash = "sha256-YjBt+22fc9yHcORRmd//rejNVvf6eK+FAYAcT0fABuI=";
+  };
+
+  vendorHash = "sha256-d9aGSBRblkvH5Ixw3jpbgC8lMW/qEYNJfLTVeUlos7A=";
+
+  meta = with lib; {
+    description = "A daemon for using DNS over HTTPS";
+    homepage = "https://blitiri.com.ar/git/r/dnss/";
+    license = licenses.asl20;
+    mainProgram = "dnss";
+    maintainers = with maintainers; [ raspher ];
+  };
+}

From 095ba4fdc3fe7dd5894833cd1446a2ad348ff39b Mon Sep 17 00:00:00 2001
From: Jeremy Baxter <jeremy@baxters.nz>
Date: Tue, 28 May 2024 11:21:52 +1200
Subject: [PATCH 03/24] ldc: merge into single file

---
 pkgs/development/compilers/ldc/binary.nix    |  43 ------
 pkgs/development/compilers/ldc/bootstrap.nix |  43 +++++-
 pkgs/development/compilers/ldc/default.nix   | 136 +++++++++++++++++-
 pkgs/development/compilers/ldc/generic.nix   | 137 -------------------
 4 files changed, 175 insertions(+), 184 deletions(-)
 delete mode 100644 pkgs/development/compilers/ldc/binary.nix
 delete mode 100644 pkgs/development/compilers/ldc/generic.nix

diff --git a/pkgs/development/compilers/ldc/binary.nix b/pkgs/development/compilers/ldc/binary.nix
deleted file mode 100644
index ca7fb4f04de3..000000000000
--- a/pkgs/development/compilers/ldc/binary.nix
+++ /dev/null
@@ -1,43 +0,0 @@
-{ lib, stdenv, fetchurl, curl, tzdata, autoPatchelfHook, fixDarwinDylibNames, libxml2
-, version, hashes }:
-
-let
-  inherit (stdenv) hostPlatform;
-  OS = if hostPlatform.isDarwin then "osx" else hostPlatform.parsed.kernel.name;
-  ARCH = if hostPlatform.isDarwin && hostPlatform.isAarch64 then "arm64" else hostPlatform.parsed.cpu.name;
-in stdenv.mkDerivation {
-  pname = "ldc-bootstrap";
-  inherit version;
-
-  src = fetchurl rec {
-    name = "ldc2-${version}-${OS}-${ARCH}.tar.xz";
-    url = "https://github.com/ldc-developers/ldc/releases/download/v${version}/${name}";
-    sha256 = hashes."${OS}-${ARCH}" or (throw "missing bootstrap sha256 for ${OS}-${ARCH}");
-  };
-
-  dontConfigure = true;
-  dontBuild = true;
-
-  nativeBuildInputs = lib.optionals hostPlatform.isLinux [
-    autoPatchelfHook
-  ] ++ lib.optional hostPlatform.isDarwin fixDarwinDylibNames;
-
-  buildInputs = lib.optionals stdenv.hostPlatform.isLinux [ libxml2 stdenv.cc.cc ];
-
-  propagatedBuildInputs = [ curl tzdata ];
-
-  installPhase = ''
-    mkdir -p $out
-
-    mv bin etc import lib LICENSE README $out/
-  '';
-
-  meta = with lib; {
-    description = "The LLVM-based D Compiler";
-    homepage = "https://github.com/ldc-developers/ldc";
-    # from https://github.com/ldc-developers/ldc/blob/master/LICENSE
-    license = with licenses; [ bsd3 boost mit ncsa gpl2Plus ];
-    maintainers = with maintainers; [ lionello ];
-    platforms = [ "x86_64-linux" "x86_64-darwin" "aarch64-linux" "aarch64-darwin" ];
-  };
-}
diff --git a/pkgs/development/compilers/ldc/bootstrap.nix b/pkgs/development/compilers/ldc/bootstrap.nix
index aa25fb77fc52..0325eada2982 100644
--- a/pkgs/development/compilers/ldc/bootstrap.nix
+++ b/pkgs/development/compilers/ldc/bootstrap.nix
@@ -1,5 +1,9 @@
-{ callPackage }:
-callPackage ./binary.nix {
+{ lib, stdenv, fetchurl, curl, tzdata, autoPatchelfHook, fixDarwinDylibNames, libxml2 }:
+
+let
+  inherit (stdenv) hostPlatform;
+  OS = if hostPlatform.isDarwin then "osx" else hostPlatform.parsed.kernel.name;
+  ARCH = if hostPlatform.isDarwin && hostPlatform.isAarch64 then "arm64" else hostPlatform.parsed.cpu.name;
   version = "1.30.0";
   hashes = {
     # Get these from `nix store prefetch-file https://github.com/ldc-developers/ldc/releases/download/v1.19.0/ldc2-1.19.0-osx-x86_64.tar.xz` etc..
@@ -8,4 +12,39 @@ callPackage ./binary.nix {
     linux-aarch64  = "sha256-kTeglub75iv/jWWNPCn15aCGAbmck0RQl6L7bFOUu7Y=";
     osx-arm64  = "sha256-Nb/owBdIeroB9jLMDvwjo8bvsTC9vFyJPLMTOMsSAd4=";
   };
+in stdenv.mkDerivation {
+  pname = "ldc-bootstrap";
+  inherit version;
+
+  src = fetchurl rec {
+    name = "ldc2-${version}-${OS}-${ARCH}.tar.xz";
+    url = "https://github.com/ldc-developers/ldc/releases/download/v${version}/${name}";
+    sha256 = hashes."${OS}-${ARCH}" or (throw "missing bootstrap sha256 for ${OS}-${ARCH}");
+  };
+
+  dontConfigure = true;
+  dontBuild = true;
+
+  nativeBuildInputs = lib.optionals hostPlatform.isLinux [
+    autoPatchelfHook
+  ] ++ lib.optional hostPlatform.isDarwin fixDarwinDylibNames;
+
+  buildInputs = lib.optionals stdenv.hostPlatform.isLinux [ libxml2 stdenv.cc.cc ];
+
+  propagatedBuildInputs = [ curl tzdata ];
+
+  installPhase = ''
+    mkdir -p $out
+
+    mv bin etc import lib LICENSE README $out/
+  '';
+
+  meta = with lib; {
+    description = "The LLVM-based D Compiler";
+    homepage = "https://github.com/ldc-developers/ldc";
+    # from https://github.com/ldc-developers/ldc/blob/master/LICENSE
+    license = with licenses; [ bsd3 boost mit ncsa gpl2Plus ];
+    maintainers = with maintainers; [ lionello ];
+    platforms = [ "x86_64-linux" "x86_64-darwin" "aarch64-linux" "aarch64-darwin" ];
+  };
 }
diff --git a/pkgs/development/compilers/ldc/default.nix b/pkgs/development/compilers/ldc/default.nix
index 6b0761217703..490e52a9a813 100644
--- a/pkgs/development/compilers/ldc/default.nix
+++ b/pkgs/development/compilers/ldc/default.nix
@@ -1,4 +1,136 @@
-import ./generic.nix {
+{ lib, stdenv, fetchurl, cmake, ninja, llvm_17, curl, tzdata
+, libconfig, lit, gdb, unzip, darwin, bash
+, callPackage, makeWrapper, runCommand, targetPackages
+, ldcBootstrap ? callPackage ./bootstrap.nix { }
+}:
+
+let
+  pathConfig = runCommand "ldc-lib-paths" {} ''
+    mkdir $out
+    echo ${tzdata}/share/zoneinfo/ > $out/TZDatabaseDirFile
+    echo ${curl.out}/lib/libcurl${stdenv.hostPlatform.extensions.sharedLibrary} > $out/LibcurlPathFile
+  '';
+
+in
+
+stdenv.mkDerivation rec {
+  pname = "ldc";
   version = "1.36.0";
-  sha256 = "sha256-oAx5BzEjqIfBf0Rsd4KklVajUSo9Natna31Trhu41u8=";
+
+  src = fetchurl {
+    url = "https://github.com/ldc-developers/ldc/releases/download/v${version}/ldc-${version}-src.tar.gz";
+    sha256 = "sha256-oAx5BzEjqIfBf0Rsd4KklVajUSo9Natna31Trhu41u8=";
+  };
+
+  # https://issues.dlang.org/show_bug.cgi?id=19553
+  hardeningDisable = [ "fortify" ];
+
+  postUnpack = ''
+    patchShebangs .
+  ''
+  + ''
+      rm ldc-${version}-src/tests/dmd/fail_compilation/mixin_gc.d
+      rm ldc-${version}-src/tests/dmd/runnable/xtest46_gc.d
+      rm ldc-${version}-src/tests/dmd/runnable/testptrref_gc.d
+
+      # test depends on current year
+      rm ldc-${version}-src/tests/dmd/compilable/ddocYear.d
+  ''
+  + lib.optionalString stdenv.hostPlatform.isDarwin ''
+      # https://github.com/NixOS/nixpkgs/issues/34817
+      rm -r ldc-${version}-src/tests/plugins/addFuncEntryCall
+  '';
+
+  postPatch = ''
+    # Setting SHELL=$SHELL when dmd testsuite is run doesn't work on Linux somehow
+    substituteInPlace tests/dmd/Makefile --replace "SHELL=/bin/bash" "SHELL=${bash}/bin/bash"
+  ''
+  + lib.optionalString stdenv.hostPlatform.isLinux ''
+      substituteInPlace runtime/phobos/std/socket.d --replace "assert(ih.addrList[0] == 0x7F_00_00_01);" ""
+  ''
+  + lib.optionalString stdenv.hostPlatform.isDarwin ''
+      substituteInPlace runtime/phobos/std/socket.d --replace "foreach (name; names)" "names = []; foreach (name; names)"
+  '';
+
+  nativeBuildInputs = [
+    cmake ldcBootstrap lit lit.python llvm_17.dev makeWrapper ninja unzip
+  ]
+  ++ lib.optionals stdenv.hostPlatform.isDarwin [
+    darwin.apple_sdk.frameworks.Foundation
+  ]
+  ++ lib.optionals (!stdenv.hostPlatform.isDarwin) [
+    # https://github.com/NixOS/nixpkgs/pull/36378#issuecomment-385034818
+    gdb
+  ];
+
+  buildInputs = [ curl tzdata ];
+
+  cmakeFlags = [
+    "-DD_FLAGS=-d-version=TZDatabaseDir;-d-version=LibcurlPath;-J${pathConfig}"
+  ];
+
+  postConfigure = ''
+    export DMD=$PWD/bin/ldmd2
+  '';
+
+  makeFlags = [ "DMD=$DMD" ];
+
+  fixNames = lib.optionalString stdenv.hostPlatform.isDarwin  ''
+    fixDarwinDylibNames() {
+      local flags=()
+
+      for fn in "$@"; do
+        flags+=(-change "$(basename "$fn")" "$fn")
+      done
+
+      for fn in "$@"; do
+        if [ -L "$fn" ]; then continue; fi
+        echo "$fn: fixing dylib"
+        install_name_tool -id "$fn" "''${flags[@]}" "$fn"
+      done
+    }
+
+    fixDarwinDylibNames $(find "$(pwd)/lib" -name "*.dylib")
+    export DYLD_LIBRARY_PATH=$(pwd)/lib
+  '';
+
+  # https://github.com/ldc-developers/ldc/issues/2497#issuecomment-459633746
+  additionalExceptions = lib.optionalString stdenv.hostPlatform.isDarwin
+    "|druntime-test-shared";
+
+  checkPhase = ''
+    # Build default lib test runners
+    ninja -j$NIX_BUILD_CORES all-test-runners
+
+    ${fixNames}
+
+    # Run dmd testsuite
+    export DMD_TESTSUITE_MAKE_ARGS="-j$NIX_BUILD_CORES DMD=$DMD"
+    ctest -V -R "dmd-testsuite"
+
+    # Build and run LDC D unittests.
+    ctest --output-on-failure -R "ldc2-unittest"
+
+    # Run LIT testsuite.
+    ctest -V -R "lit-tests"
+
+    # Run default lib unittests
+    ctest -j$NIX_BUILD_CORES --output-on-failure -E "ldc2-unittest|lit-tests|dmd-testsuite${additionalExceptions}"
+  '';
+
+  postInstall = ''
+    wrapProgram $out/bin/ldc2 \
+        --prefix PATH ":" "${targetPackages.stdenv.cc}/bin" \
+        --set-default CC "${targetPackages.stdenv.cc}/bin/cc"
+   '';
+
+  meta = with lib; {
+    description = "The LLVM-based D compiler";
+    homepage = "https://github.com/ldc-developers/ldc";
+    # from https://github.com/ldc-developers/ldc/blob/master/LICENSE
+    license = with licenses; [ bsd3 boost mit ncsa gpl2Plus ];
+    mainProgram = "ldc2";
+    maintainers = with maintainers; [ lionello jtbx ];
+    platforms = [ "x86_64-linux" "i686-linux" "aarch64-linux" "x86_64-darwin" "aarch64-darwin" ];
+  };
 }
diff --git a/pkgs/development/compilers/ldc/generic.nix b/pkgs/development/compilers/ldc/generic.nix
deleted file mode 100644
index 07b6986189c0..000000000000
--- a/pkgs/development/compilers/ldc/generic.nix
+++ /dev/null
@@ -1,137 +0,0 @@
-{ version, sha256 }:
-{ lib, stdenv, fetchurl, cmake, ninja, llvm_17, curl, tzdata
-, libconfig, lit, gdb, unzip, darwin, bash
-, callPackage, makeWrapper, runCommand, targetPackages
-, ldcBootstrap ? callPackage ./bootstrap.nix { }
-}:
-
-let
-  pathConfig = runCommand "ldc-lib-paths" {} ''
-    mkdir $out
-    echo ${tzdata}/share/zoneinfo/ > $out/TZDatabaseDirFile
-    echo ${curl.out}/lib/libcurl${stdenv.hostPlatform.extensions.sharedLibrary} > $out/LibcurlPathFile
-  '';
-
-in
-
-stdenv.mkDerivation rec {
-  pname = "ldc";
-  inherit version;
-
-  src = fetchurl {
-    url = "https://github.com/ldc-developers/ldc/releases/download/v${version}/ldc-${version}-src.tar.gz";
-    inherit sha256;
-  };
-
-  # https://issues.dlang.org/show_bug.cgi?id=19553
-  hardeningDisable = [ "fortify" ];
-
-  postUnpack = ''
-    patchShebangs .
-  ''
-  + ''
-      rm ldc-${version}-src/tests/dmd/fail_compilation/mixin_gc.d
-      rm ldc-${version}-src/tests/dmd/runnable/xtest46_gc.d
-      rm ldc-${version}-src/tests/dmd/runnable/testptrref_gc.d
-
-      # test depends on current year
-      rm ldc-${version}-src/tests/dmd/compilable/ddocYear.d
-  ''
-  + lib.optionalString stdenv.hostPlatform.isDarwin ''
-      # https://github.com/NixOS/nixpkgs/issues/34817
-      rm -r ldc-${version}-src/tests/plugins/addFuncEntryCall
-  '';
-
-  postPatch = ''
-    # Setting SHELL=$SHELL when dmd testsuite is run doesn't work on Linux somehow
-    substituteInPlace tests/dmd/Makefile --replace "SHELL=/bin/bash" "SHELL=${bash}/bin/bash"
-  ''
-  + lib.optionalString stdenv.hostPlatform.isLinux ''
-      substituteInPlace runtime/phobos/std/socket.d --replace "assert(ih.addrList[0] == 0x7F_00_00_01);" ""
-  ''
-  + lib.optionalString stdenv.hostPlatform.isDarwin ''
-      substituteInPlace runtime/phobos/std/socket.d --replace "foreach (name; names)" "names = []; foreach (name; names)"
-  '';
-
-  nativeBuildInputs = [
-    cmake ldcBootstrap lit lit.python llvm_17.dev makeWrapper ninja unzip
-  ]
-  ++ lib.optionals stdenv.hostPlatform.isDarwin [
-    darwin.apple_sdk.frameworks.Foundation
-  ]
-  ++ lib.optionals (!stdenv.hostPlatform.isDarwin) [
-    # https://github.com/NixOS/nixpkgs/pull/36378#issuecomment-385034818
-    gdb
-  ];
-
-  buildInputs = [ curl tzdata ];
-
-  cmakeFlags = [
-    "-DD_FLAGS=-d-version=TZDatabaseDir;-d-version=LibcurlPath;-J${pathConfig}"
-  ];
-
-  postConfigure = ''
-    export DMD=$PWD/bin/ldmd2
-  '';
-
-  makeFlags = [ "DMD=$DMD" ];
-
-  fixNames = lib.optionalString stdenv.hostPlatform.isDarwin  ''
-    fixDarwinDylibNames() {
-      local flags=()
-
-      for fn in "$@"; do
-        flags+=(-change "$(basename "$fn")" "$fn")
-      done
-
-      for fn in "$@"; do
-        if [ -L "$fn" ]; then continue; fi
-        echo "$fn: fixing dylib"
-        install_name_tool -id "$fn" "''${flags[@]}" "$fn"
-      done
-    }
-
-    fixDarwinDylibNames $(find "$(pwd)/lib" -name "*.dylib")
-    export DYLD_LIBRARY_PATH=$(pwd)/lib
-  '';
-
-  # https://github.com/ldc-developers/ldc/issues/2497#issuecomment-459633746
-  additionalExceptions = lib.optionalString stdenv.hostPlatform.isDarwin
-    "|druntime-test-shared";
-
-  checkPhase = ''
-    # Build default lib test runners
-    ninja -j$NIX_BUILD_CORES all-test-runners
-
-    ${fixNames}
-
-    # Run dmd testsuite
-    export DMD_TESTSUITE_MAKE_ARGS="-j$NIX_BUILD_CORES DMD=$DMD"
-    ctest -V -R "dmd-testsuite"
-
-    # Build and run LDC D unittests.
-    ctest --output-on-failure -R "ldc2-unittest"
-
-    # Run LIT testsuite.
-    ctest -V -R "lit-tests"
-
-    # Run default lib unittests
-    ctest -j$NIX_BUILD_CORES --output-on-failure -E "ldc2-unittest|lit-tests|dmd-testsuite${additionalExceptions}"
-  '';
-
-  postInstall = ''
-    wrapProgram $out/bin/ldc2 \
-        --prefix PATH ":" "${targetPackages.stdenv.cc}/bin" \
-        --set-default CC "${targetPackages.stdenv.cc}/bin/cc"
-   '';
-
-  meta = with lib; {
-    description = "The LLVM-based D compiler";
-    homepage = "https://github.com/ldc-developers/ldc";
-    # from https://github.com/ldc-developers/ldc/blob/master/LICENSE
-    license = with licenses; [ bsd3 boost mit ncsa gpl2Plus ];
-    mainProgram = "ldc2";
-    maintainers = with maintainers; [ lionello jtbx ];
-    platforms = [ "x86_64-linux" "i686-linux" "aarch64-linux" "x86_64-darwin" "aarch64-darwin" ];
-  };
-}

From ad4a42b2ce5089d39c3a1fd11b027dec2da73f17 Mon Sep 17 00:00:00 2001
From: Jeremy Baxter <jeremy@baxters.nz>
Date: Tue, 28 May 2024 11:22:27 +1200
Subject: [PATCH 04/24] ldc: migrate to pkgs/by-name

---
 pkgs/{development/compilers => by-name/ld}/ldc/bootstrap.nix    | 0
 .../compilers/ldc/default.nix => by-name/ld/ldc/package.nix}    | 0
 pkgs/top-level/all-packages.nix                                 | 2 --
 3 files changed, 2 deletions(-)
 rename pkgs/{development/compilers => by-name/ld}/ldc/bootstrap.nix (100%)
 rename pkgs/{development/compilers/ldc/default.nix => by-name/ld/ldc/package.nix} (100%)

diff --git a/pkgs/development/compilers/ldc/bootstrap.nix b/pkgs/by-name/ld/ldc/bootstrap.nix
similarity index 100%
rename from pkgs/development/compilers/ldc/bootstrap.nix
rename to pkgs/by-name/ld/ldc/bootstrap.nix
diff --git a/pkgs/development/compilers/ldc/default.nix b/pkgs/by-name/ld/ldc/package.nix
similarity index 100%
rename from pkgs/development/compilers/ldc/default.nix
rename to pkgs/by-name/ld/ldc/package.nix
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 1ad8d6d20c1c..97c7e0b44b29 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -9620,8 +9620,6 @@ with pkgs;
 
   last-resort = callPackage ../data/fonts/last-resort { };
 
-  ldc = callPackage ../development/compilers/ldc { };
-
   ligo =
     let ocaml_p = ocaml-ng.ocamlPackages_4_14_janeStreet_0_15; in
     callPackage ../development/compilers/ligo {

From 42029a9e641b3743e44da22382719e124ccf7fc8 Mon Sep 17 00:00:00 2001
From: zendo <linzway@qq.com>
Date: Thu, 30 May 2024 23:22:21 +0800
Subject: [PATCH 05/24] mangareader: move to by-name

---
 .../default.nix => by-name/ma/mangareader/package.nix}          | 0
 pkgs/top-level/all-packages.nix                                 | 2 --
 2 files changed, 2 deletions(-)
 rename pkgs/{applications/graphics/mangareader/default.nix => by-name/ma/mangareader/package.nix} (100%)

diff --git a/pkgs/applications/graphics/mangareader/default.nix b/pkgs/by-name/ma/mangareader/package.nix
similarity index 100%
rename from pkgs/applications/graphics/mangareader/default.nix
rename to pkgs/by-name/ma/mangareader/package.nix
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index b644950f1661..81a8389dfbb4 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -10491,8 +10491,6 @@ with pkgs;
 
   mandoc = callPackage ../tools/misc/mandoc { };
 
-  mangareader = libsForQt5.callPackage ../applications/graphics/mangareader { };
-
   mangohud = callPackage ../tools/graphics/mangohud {
     libXNVCtrl = linuxPackages.nvidia_x11.settings.libXNVCtrl;
     mangohud32 = pkgsi686Linux.mangohud;

From 4ce21890829b1ff5955a4941c23c512c5f326b85 Mon Sep 17 00:00:00 2001
From: Jonas Heinrich <onny@project-insanity.org>
Date: Mon, 3 Jun 2024 11:18:59 +0200
Subject: [PATCH 06/24] nixos/davfs2: Remove deprecated extraConfig

---
 .../services/network-filesystems/davfs2.nix   | 50 ++-----------------
 1 file changed, 4 insertions(+), 46 deletions(-)

diff --git a/nixos/modules/services/network-filesystems/davfs2.nix b/nixos/modules/services/network-filesystems/davfs2.nix
index 23c04658031f..9a7d0daa6421 100644
--- a/nixos/modules/services/network-filesystems/davfs2.nix
+++ b/nixos/modules/services/network-filesystems/davfs2.nix
@@ -20,14 +20,10 @@ let
     else toString value;
 
   configFile = pkgs.writeText "davfs2.conf" (
-    if (cfg.settings != { }) then
-      (toINIWithGlobalSection {
-        mkSectionName = escapeString;
-        mkKeyValue = k: v: "${k} ${formatValue v}";
-      } cfg.settings)
-    else
-      cfg.extraConfig
-  );
+    toINIWithGlobalSection {
+      mkSectionName = escapeString;
+      mkKeyValue = k: v: "${k} ${formatValue v}";
+    } cfg.settings);
 in
 {
 
@@ -53,29 +49,6 @@ in
       '';
     };
 
-    extraConfig = mkOption {
-      type = lines;
-      default = "";
-      example = ''
-        proxy foo.bar:8080
-        use_locks 0
-
-        [/media/dav]
-        use_locks 1
-
-        [/home/otto/mywebspace]
-        gui_optimize 1
-      '';
-      description = ''
-        Extra lines appended to the configuration of davfs2.
-        See {manpage}`davfs2.conf(5)` for available settings.
-
-        **Note**: Please pass structured settings via
-        {option}`settings` instead, this option
-        will get deprecated in the future.
-      ''  ;
-    };
-
     settings = mkOption {
       type = submodule {
         freeformType = let
@@ -109,21 +82,6 @@ in
 
   config = mkIf cfg.enable {
 
-    assertions = [
-      {
-        assertion = cfg.extraConfig != "" -> cfg.settings == { };
-        message = ''
-          services.davfs2.extraConfig and services.davfs2.settings cannot be used together.
-          Please prefer using services.davfs2.settings.
-        '';
-      }
-    ];
-
-    warnings = optional (cfg.extraConfig != "") ''
-      services.davfs2.extraConfig will be deprecated in future releases;
-      please use services.davfs2.settings instead.
-    '';
-
     environment.systemPackages = [ pkgs.davfs2 ];
     environment.etc."davfs2/davfs2.conf".source = configFile;
 

From 44b69c0ad248e2cdcf1097c9a38499325b8b8952 Mon Sep 17 00:00:00 2001
From: Jeremy Baxter <jeremy@baxters.nz>
Date: Thu, 6 Jun 2024 15:25:21 +1200
Subject: [PATCH 07/24] ldc: modernize

---
 pkgs/by-name/ld/ldc/bootstrap.nix |  2 +-
 pkgs/by-name/ld/ldc/package.nix   | 92 +++++++++++++++++--------------
 2 files changed, 51 insertions(+), 43 deletions(-)

diff --git a/pkgs/by-name/ld/ldc/bootstrap.nix b/pkgs/by-name/ld/ldc/bootstrap.nix
index 0325eada2982..4355277e8863 100644
--- a/pkgs/by-name/ld/ldc/bootstrap.nix
+++ b/pkgs/by-name/ld/ldc/bootstrap.nix
@@ -19,7 +19,7 @@ in stdenv.mkDerivation {
   src = fetchurl rec {
     name = "ldc2-${version}-${OS}-${ARCH}.tar.xz";
     url = "https://github.com/ldc-developers/ldc/releases/download/v${version}/${name}";
-    sha256 = hashes."${OS}-${ARCH}" or (throw "missing bootstrap sha256 for ${OS}-${ARCH}");
+    hash = hashes."${OS}-${ARCH}" or (throw "missing bootstrap hash for ${OS}-${ARCH}");
   };
 
   dontConfigure = true;
diff --git a/pkgs/by-name/ld/ldc/package.nix b/pkgs/by-name/ld/ldc/package.nix
index 490e52a9a813..dc11b092f5aa 100644
--- a/pkgs/by-name/ld/ldc/package.nix
+++ b/pkgs/by-name/ld/ldc/package.nix
@@ -1,6 +1,22 @@
-{ lib, stdenv, fetchurl, cmake, ninja, llvm_17, curl, tzdata
-, libconfig, lit, gdb, unzip, darwin, bash
-, callPackage, makeWrapper, runCommand, targetPackages
+{ lib
+, stdenv
+, fetchFromGitHub
+, cmake
+, ninja
+, llvm_17
+, curl
+, tzdata
+, libconfig
+, lit
+, gdb
+, unzip
+, darwin
+, bash
+, callPackage
+, makeWrapper
+, runCommand
+, targetPackages
+
 , ldcBootstrap ? callPackage ./bootstrap.nix { }
 }:
 
@@ -13,52 +29,44 @@ let
 
 in
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "ldc";
   version = "1.36.0";
 
-  src = fetchurl {
-    url = "https://github.com/ldc-developers/ldc/releases/download/v${version}/ldc-${version}-src.tar.gz";
-    sha256 = "sha256-oAx5BzEjqIfBf0Rsd4KklVajUSo9Natna31Trhu41u8=";
+  src = fetchFromGitHub {
+    owner = "ldc-developers";
+    repo = "ldc";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-tFc+vgC9Iq3VvlKEn3c1yHFEbgbz6/zP8S9IEDz8Qvw=";
+    fetchSubmodules = true;
   };
 
   # https://issues.dlang.org/show_bug.cgi?id=19553
   hardeningDisable = [ "fortify" ];
 
-  postUnpack = ''
-    patchShebangs .
-  ''
-  + ''
-      rm ldc-${version}-src/tests/dmd/fail_compilation/mixin_gc.d
-      rm ldc-${version}-src/tests/dmd/runnable/xtest46_gc.d
-      rm ldc-${version}-src/tests/dmd/runnable/testptrref_gc.d
-
-      # test depends on current year
-      rm ldc-${version}-src/tests/dmd/compilable/ddocYear.d
-  ''
-  + lib.optionalString stdenv.hostPlatform.isDarwin ''
-      # https://github.com/NixOS/nixpkgs/issues/34817
-      rm -r ldc-${version}-src/tests/plugins/addFuncEntryCall
-  '';
-
   postPatch = ''
-    # Setting SHELL=$SHELL when dmd testsuite is run doesn't work on Linux somehow
-    substituteInPlace tests/dmd/Makefile --replace "SHELL=/bin/bash" "SHELL=${bash}/bin/bash"
-  ''
-  + lib.optionalString stdenv.hostPlatform.isLinux ''
-      substituteInPlace runtime/phobos/std/socket.d --replace "assert(ih.addrList[0] == 0x7F_00_00_01);" ""
-  ''
-  + lib.optionalString stdenv.hostPlatform.isDarwin ''
-      substituteInPlace runtime/phobos/std/socket.d --replace "foreach (name; names)" "names = []; foreach (name; names)"
+    patchShebangs runtime tools tests
+
+    rm tests/dmd/fail_compilation/mixin_gc.d
+    rm tests/dmd/runnable/xtest46_gc.d
+    rm tests/dmd/runnable/testptrref_gc.d
+
+    # test depends on current year
+    rm tests/dmd/compilable/ddocYear.d
+  '' + lib.optionalString stdenv.hostPlatform.isLinux ''
+    substituteInPlace runtime/phobos/std/socket.d --replace-fail "assert(ih.addrList[0] == 0x7F_00_00_01);" ""
+  '' + lib.optionalString stdenv.hostPlatform.isDarwin ''
+    substituteInPlace runtime/phobos/std/socket.d --replace-fail "foreach (name; names)" "names = []; foreach (name; names)"
+
+    # https://github.com/NixOS/nixpkgs/issues/34817
+    rm -r tests/plugins/addFuncEntryCall
   '';
 
   nativeBuildInputs = [
     cmake ldcBootstrap lit lit.python llvm_17.dev makeWrapper ninja unzip
-  ]
-  ++ lib.optionals stdenv.hostPlatform.isDarwin [
+  ] ++ lib.optionals stdenv.hostPlatform.isDarwin [
     darwin.apple_sdk.frameworks.Foundation
-  ]
-  ++ lib.optionals (!stdenv.hostPlatform.isDarwin) [
+  ] ++ lib.optionals (!stdenv.hostPlatform.isDarwin) [
     # https://github.com/NixOS/nixpkgs/pull/36378#issuecomment-385034818
     gdb
   ];
@@ -75,7 +83,7 @@ stdenv.mkDerivation rec {
 
   makeFlags = [ "DMD=$DMD" ];
 
-  fixNames = lib.optionalString stdenv.hostPlatform.isDarwin  ''
+  fixNames = lib.optionalString stdenv.hostPlatform.isDarwin ''
     fixDarwinDylibNames() {
       local flags=()
 
@@ -102,7 +110,7 @@ stdenv.mkDerivation rec {
     # Build default lib test runners
     ninja -j$NIX_BUILD_CORES all-test-runners
 
-    ${fixNames}
+    ${finalAttrs.fixNames}
 
     # Run dmd testsuite
     export DMD_TESTSUITE_MAKE_ARGS="-j$NIX_BUILD_CORES DMD=$DMD"
@@ -115,14 +123,14 @@ stdenv.mkDerivation rec {
     ctest -V -R "lit-tests"
 
     # Run default lib unittests
-    ctest -j$NIX_BUILD_CORES --output-on-failure -E "ldc2-unittest|lit-tests|dmd-testsuite${additionalExceptions}"
+    ctest -j$NIX_BUILD_CORES --output-on-failure -E "ldc2-unittest|lit-tests|dmd-testsuite${finalAttrs.additionalExceptions}"
   '';
 
   postInstall = ''
     wrapProgram $out/bin/ldc2 \
-        --prefix PATH ":" "${targetPackages.stdenv.cc}/bin" \
-        --set-default CC "${targetPackages.stdenv.cc}/bin/cc"
-   '';
+      --prefix PATH : ${targetPackages.stdenv.cc}/bin \
+      --set-default CC ${targetPackages.stdenv.cc}/bin/cc
+  '';
 
   meta = with lib; {
     description = "The LLVM-based D compiler";
@@ -133,4 +141,4 @@ stdenv.mkDerivation rec {
     maintainers = with maintainers; [ lionello jtbx ];
     platforms = [ "x86_64-linux" "i686-linux" "aarch64-linux" "x86_64-darwin" "aarch64-darwin" ];
   };
-}
+})

From ef4d4906557333792999433d4035677e34f83598 Mon Sep 17 00:00:00 2001
From: Jeremy Baxter <jeremy@baxters.nz>
Date: Fri, 7 Jun 2024 09:49:21 +1200
Subject: [PATCH 08/24] ldc: add meta.changelog

---
 pkgs/by-name/ld/ldc/package.nix | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pkgs/by-name/ld/ldc/package.nix b/pkgs/by-name/ld/ldc/package.nix
index dc11b092f5aa..207c660b62c9 100644
--- a/pkgs/by-name/ld/ldc/package.nix
+++ b/pkgs/by-name/ld/ldc/package.nix
@@ -135,6 +135,7 @@ stdenv.mkDerivation (finalAttrs: {
   meta = with lib; {
     description = "The LLVM-based D compiler";
     homepage = "https://github.com/ldc-developers/ldc";
+    changelog = "https://github.com/ldc-developers/ldc/releases/tag/v${finalAttrs.version}";
     # from https://github.com/ldc-developers/ldc/blob/master/LICENSE
     license = with licenses; [ bsd3 boost mit ncsa gpl2Plus ];
     mainProgram = "ldc2";

From b8eef4c70d1ceb52f89bf5fa2c0acbcb459b9828 Mon Sep 17 00:00:00 2001
From: Jeremy Baxter <jeremy@baxters.nz>
Date: Fri, 7 Jun 2024 09:49:27 +1200
Subject: [PATCH 09/24] ldc: 1.36.0 -> 1.38.0

---
 pkgs/by-name/ld/ldc/package.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/by-name/ld/ldc/package.nix b/pkgs/by-name/ld/ldc/package.nix
index 207c660b62c9..77be57e83632 100644
--- a/pkgs/by-name/ld/ldc/package.nix
+++ b/pkgs/by-name/ld/ldc/package.nix
@@ -31,13 +31,13 @@ in
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "ldc";
-  version = "1.36.0";
+  version = "1.38.0";
 
   src = fetchFromGitHub {
     owner = "ldc-developers";
     repo = "ldc";
     rev = "v${finalAttrs.version}";
-    hash = "sha256-tFc+vgC9Iq3VvlKEn3c1yHFEbgbz6/zP8S9IEDz8Qvw=";
+    hash = "sha256-d/UREh+fHRRh0r3H60uPjHute+qspcm9TBFWZMbGDxk=";
     fetchSubmodules = true;
   };
 

From 81641e04a02cf11d17b943a8354e73d7d5dbbb07 Mon Sep 17 00:00:00 2001
From: "R. Ryantm" <ryantm-bot@ryantm.com>
Date: Fri, 7 Jun 2024 05:26:09 +0000
Subject: [PATCH 10/24] edge-runtime: 1.53.3 -> 1.53.4

---
 pkgs/development/web/edge-runtime/Cargo.lock  | 2 ++
 pkgs/development/web/edge-runtime/default.nix | 4 ++--
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/web/edge-runtime/Cargo.lock b/pkgs/development/web/edge-runtime/Cargo.lock
index d21116d0f79b..6f3f1aa872b0 100644
--- a/pkgs/development/web/edge-runtime/Cargo.lock
+++ b/pkgs/development/web/edge-runtime/Cargo.lock
@@ -1956,6 +1956,7 @@ dependencies = [
  "deno_core",
  "log",
  "serde",
+ "strum",
  "tokio",
  "uuid",
 ]
@@ -4795,6 +4796,7 @@ name = "sb_module_loader"
 version = "0.1.0"
 dependencies = [
  "anyhow",
+ "base64 0.21.7",
  "deno_ast",
  "deno_core",
  "deno_fs",
diff --git a/pkgs/development/web/edge-runtime/default.nix b/pkgs/development/web/edge-runtime/default.nix
index 07d7cb59785d..cae336b3b081 100644
--- a/pkgs/development/web/edge-runtime/default.nix
+++ b/pkgs/development/web/edge-runtime/default.nix
@@ -11,7 +11,7 @@
 
 let
   pname = "edge-runtime";
-  version = "1.53.3";
+  version = "1.53.4";
 in
 rustPlatform.buildRustPackage {
   inherit pname version;
@@ -20,7 +20,7 @@ rustPlatform.buildRustPackage {
     owner = "supabase";
     repo = pname;
     rev = "v${version}";
-    hash = "sha256-eGFLwypLgoTKUapG3kbI9J9jSyR39JtKgM0dwtkR9zk=";
+    hash = "sha256-sDgGfQiAUuI+JaF0BRB5lwvjbWWIoTV/k/tbQsBBc4E=";
     fetchSubmodules = true;
   };
 

From 5e74195b45bec881ca00c52c3ef786266e75bf50 Mon Sep 17 00:00:00 2001
From: "R. Ryantm" <ryantm-bot@ryantm.com>
Date: Fri, 7 Jun 2024 13:22:55 +0000
Subject: [PATCH 11/24] python311Packages.langfuse: 2.33.1 -> 2.35.0

---
 pkgs/development/python-modules/langfuse/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/langfuse/default.nix b/pkgs/development/python-modules/langfuse/default.nix
index ba8cb7db308f..e820964e5e1e 100644
--- a/pkgs/development/python-modules/langfuse/default.nix
+++ b/pkgs/development/python-modules/langfuse/default.nix
@@ -17,14 +17,14 @@
 
 buildPythonPackage rec {
   pname = "langfuse";
-  version = "2.33.1";
+  version = "2.35.0";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "langfuse";
     repo = "langfuse-python";
     rev = "refs/tags/v${version}";
-    hash = "sha256-ZPCL3Xle4qEw2pNIcja252meep26W/RbVEk2suzywYI=";
+    hash = "sha256-u1gnv2eDYhF0C4r88VMIedxUEk6WU88Q0mlweVKLaoc=";
   };
 
   build-system = [ poetry-core ];

From d88d0acd2b418bc87b5fd5795659e5209a40f374 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=B6rg=20Thalheim?= <joerg@thalheim.io>
Date: Fri, 7 Jun 2024 15:28:54 +0200
Subject: [PATCH 12/24] nixos-anywhere: 1.2.0 -> 1.3.0

Diff: https://github.com/numtide/nixos-anywhere/compare/1.2.0...1.3.0
---
 pkgs/by-name/ni/nixos-anywhere/package.nix | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/pkgs/by-name/ni/nixos-anywhere/package.nix b/pkgs/by-name/ni/nixos-anywhere/package.nix
index 36ee25429b81..55a7deb1b442 100644
--- a/pkgs/by-name/ni/nixos-anywhere/package.nix
+++ b/pkgs/by-name/ni/nixos-anywhere/package.nix
@@ -2,7 +2,6 @@
 , fetchFromGitHub
 , openssh
 , gitMinimal
-, rsync
 , nix
 , coreutils
 , curl
@@ -13,6 +12,7 @@
 , lib
 , makeWrapper
 , sshpass
+, gnutar
 }:
 let
   runtimeDeps = [
@@ -25,17 +25,17 @@ let
     findutils
     gnused # needed by ssh-copy-id
     sshpass # used to provide password for ssh-copy-id
-    rsync # used to upload extra-files
+    gnutar # used to upload extra-files
   ];
 in
 stdenv.mkDerivation (finalAttrs: {
   pname = "nixos-anywhere";
-  version = "1.2.0";
+  version = "1.3.0";
   src = fetchFromGitHub {
     owner = "numtide";
     repo = "nixos-anywhere";
     rev = finalAttrs.version;
-    hash = "sha256-u3PFJup/XOz2MBhvqCzm94iH6Z4nrE0KmBgT/OnNDqU=";
+    hash = "sha256-AdSrhQhJb9ObCgM1iXnoIBBl+6cjRbuTST4Lt02AP5Q=";
   };
   nativeBuildInputs = [ makeWrapper ];
   installPhase = ''

From 855185c2aafee6f2bca2e04fa2ba25b7734610d8 Mon Sep 17 00:00:00 2001
From: "R. Ryantm" <ryantm-bot@ryantm.com>
Date: Fri, 7 Jun 2024 18:44:56 +0000
Subject: [PATCH 13/24] retroarchBare: 1.19.0 -> 1.19.1

---
 pkgs/applications/emulators/retroarch/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/applications/emulators/retroarch/default.nix b/pkgs/applications/emulators/retroarch/default.nix
index 79fa7648fbe7..7e7090a87a64 100644
--- a/pkgs/applications/emulators/retroarch/default.nix
+++ b/pkgs/applications/emulators/retroarch/default.nix
@@ -47,12 +47,12 @@ let
 in
 stdenv.mkDerivation rec {
   pname = "retroarch-bare";
-  version = "1.19.0";
+  version = "1.19.1";
 
   src = fetchFromGitHub {
     owner = "libretro";
     repo = "RetroArch";
-    hash = "sha256-xn6lFknL5y9WozGZtqiZVyVzOuNheGhwxWlfFOYVFzU=";
+    hash = "sha256-NVe5dhH3w7RL1C7Z736L5fdi/+aO+Ah9Dpa4u4kn0JY=";
     rev = "v${version}";
   };
 

From 06afa6e026d80788895a4baf68d3f14b9108ff1b Mon Sep 17 00:00:00 2001
From: "R. Ryantm" <ryantm-bot@ryantm.com>
Date: Fri, 7 Jun 2024 19:02:41 +0000
Subject: [PATCH 14/24] fastfetch: 2.14.0 -> 2.15.0

---
 pkgs/by-name/fa/fastfetch/package.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/by-name/fa/fastfetch/package.nix b/pkgs/by-name/fa/fastfetch/package.nix
index 2441f765482e..5a3c6d488210 100644
--- a/pkgs/by-name/fa/fastfetch/package.nix
+++ b/pkgs/by-name/fa/fastfetch/package.nix
@@ -47,13 +47,13 @@ let
 in
 stdenv'.mkDerivation (finalAttrs: {
   pname = "fastfetch";
-  version = "2.14.0";
+  version = "2.15.0";
 
   src = fetchFromGitHub {
     owner = "fastfetch-cli";
     repo = "fastfetch";
     rev = finalAttrs.version;
-    hash = "sha256-RJDRxH9VKNxBSfoFl1rDTeKKyLC3C09F0Z3ksJoMDRk=";
+    hash = "sha256-0kReN7FKrcRhxUuwZoArLTW2F1q40Wbp9/hRoDjKZHs=";
   };
 
   outputs = [ "out" "man" ];

From 64494ffef1b7913cf50ca8cc0228907abfe4bf46 Mon Sep 17 00:00:00 2001
From: Jeffrey Harmon <contact@jeffreyharmon.dev>
Date: Thu, 7 Mar 2024 16:00:14 -0500
Subject: [PATCH 15/24] gdtoolkit_4: init at 4.2.2

---
 pkgs/by-name/gd/gdtoolkit_4/package.nix | 73 +++++++++++++++++++++++++
 1 file changed, 73 insertions(+)
 create mode 100644 pkgs/by-name/gd/gdtoolkit_4/package.nix

diff --git a/pkgs/by-name/gd/gdtoolkit_4/package.nix b/pkgs/by-name/gd/gdtoolkit_4/package.nix
new file mode 100644
index 000000000000..6f4a25602ee2
--- /dev/null
+++ b/pkgs/by-name/gd/gdtoolkit_4/package.nix
@@ -0,0 +1,73 @@
+{ lib
+, python3
+, fetchFromGitHub
+}:
+
+let
+  python = python3.override {
+    packageOverrides = self: super: {
+      lark = super.lark.overridePythonAttrs (old: rec {
+        # gdtoolkit needs exactly this lark version
+        version = "1.1.9";
+        src = fetchFromGitHub {
+          owner = "lark-parser";
+          repo = "lark";
+          rev = version;
+          hash = "sha256-vDu+VPAXONY8J+A6oS7EiMeOMgzGms0nWpE+DKI1MVU=";
+          fetchSubmodules = true;
+        };
+        patches = [ ];
+      });
+    };
+  };
+in
+python.pkgs.buildPythonApplication rec {
+  pname = "gdtoolkit";
+  version = "4.2.2";
+
+  src = fetchFromGitHub {
+    owner = "Scony";
+    repo = "godot-gdscript-toolkit";
+    rev = version;
+    hash = "sha256-SvEKKuDnfxV+5AArg5ssrQzgIwRITdek4KYEs3d0n4Y=";
+  };
+
+  disabled = python.pythonOlder "3.7";
+
+  propagatedBuildInputs = with python.pkgs; [
+    docopt
+    lark
+    pyyaml
+    setuptools
+  ];
+
+  doCheck = true;
+
+  nativeCheckInputs = with python.pkgs; [
+    pytestCheckHook
+    hypothesis
+  ];
+
+  preCheck = ''
+      # The tests want to run the installed executables
+      export PATH=$out/bin:$PATH
+
+      # gdtoolkit tries to write cache variables to $HOME/.cache
+      export HOME=$TMP
+    '';
+
+  # The tests are not working on NixOS
+  disabledTestPaths = [
+    "tests/generated/test_expression_parsing.py"
+    "tests/gdradon/test_executable.py"
+  ];
+
+  pythonImportsCheck = [ "gdtoolkit" "gdtoolkit.formatter" "gdtoolkit.linter" "gdtoolkit.parser" ];
+
+  meta = with lib; {
+    description = "Independent set of tools for working with Godot's GDScript - parser, linter and formatter";
+    homepage = "https://github.com/Scony/godot-gdscript-toolkit";
+    license = licenses.mit;
+    maintainers = with maintainers; [ squarepear ];
+  };
+}

From c01927fc82a06fdd81f76947b1341a7ee66e35c1 Mon Sep 17 00:00:00 2001
From: Jeffrey Harmon <contact@jeffreyharmon.dev>
Date: Thu, 7 Mar 2024 16:06:38 -0500
Subject: [PATCH 16/24] gdtoolkit: rename to gdtoolkit_3

---
 .../default.nix => by-name/gd/gdtoolkit_3/package.nix}       | 5 +++--
 pkgs/top-level/aliases.nix                                   | 2 ++
 pkgs/top-level/all-packages.nix                              | 2 --
 3 files changed, 5 insertions(+), 4 deletions(-)
 rename pkgs/{development/tools/gdtoolkit/default.nix => by-name/gd/gdtoolkit_3/package.nix} (96%)

diff --git a/pkgs/development/tools/gdtoolkit/default.nix b/pkgs/by-name/gd/gdtoolkit_3/package.nix
similarity index 96%
rename from pkgs/development/tools/gdtoolkit/default.nix
rename to pkgs/by-name/gd/gdtoolkit_3/package.nix
index ea5e5ec8de9a..608d86493217 100644
--- a/pkgs/development/tools/gdtoolkit/default.nix
+++ b/pkgs/by-name/gd/gdtoolkit_3/package.nix
@@ -23,7 +23,7 @@ let
   };
 in
 python.pkgs.buildPythonApplication rec {
-  pname = "gdtoolkit";
+  pname = "gdtoolkit3";
   version = "3.3.1";
 
   # If we try to get using fetchPypi it requires GeoIP (but the package dont has that dep!?)
@@ -62,7 +62,8 @@ python.pkgs.buildPythonApplication rec {
          - disable doCheck for gdtoolkit, or
          - provide a compatible godot-server version to gdtoolkit"
       '';
-    in lib.throwIf (godotServerMajorVersion != gdtoolkitMajorVersion) msg ''
+    in
+    lib.throwIf (godotServerMajorVersion != gdtoolkitMajorVersion) msg ''
       # The tests want to run the installed executables
       export PATH=$out/bin:$PATH
 
diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix
index fc9248b519a8..486e8c5fdb0a 100644
--- a/pkgs/top-level/aliases.nix
+++ b/pkgs/top-level/aliases.nix
@@ -414,6 +414,8 @@ mapAliases ({
   godot-headless = throw "godot-headless has been renamed to godot3-headless to distinguish from version 4"; # Added 2023-07-16
   godot-server = throw "godot-server has been renamed to godot3-server to distinguish from version 4"; # Added 2023-07-16
 
+  gdtoolkit = throw "gdtoolkit has been renamed to gdtoolkit_3 to distinguish from version 4"; # Added 2024-02-17
+
   google-chrome-beta = throw "'google-chrome-beta' has been removed due to the lack of maintenance in nixpkgs. Consider using 'google-chrome' instead."; # Added 2023-10-18
   google-chrome-dev = throw "'google-chrome-dev' has been removed due to the lack of maintenance in nixpkgs. Consider using 'google-chrome' instead."; # Added 2023-10-18
   google-gflags = throw "'google-gflags' has been renamed to/replaced by 'gflags'"; # Converted to throw 2023-09-10
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 87916f7f9666..43cec31676c8 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -8423,8 +8423,6 @@ with pkgs;
 
   gdmap = callPackage ../tools/system/gdmap { };
 
-  gdtoolkit = callPackage ../development/tools/gdtoolkit { };
-
   gef = callPackage ../development/tools/misc/gef { };
 
   gelasio = callPackage ../data/fonts/gelasio { };

From 471f48a215b61ba5fea0c5bfc15448e375465b52 Mon Sep 17 00:00:00 2001
From: Jeffrey Harmon <contact@jeffreyharmon.dev>
Date: Thu, 7 Mar 2024 16:09:40 -0500
Subject: [PATCH 17/24] gdtoolkit_3: 3.3.1 -> 3.5.0

---
 pkgs/by-name/gd/gdtoolkit_3/package.nix | 39 +++++++------------------
 1 file changed, 10 insertions(+), 29 deletions(-)

diff --git a/pkgs/by-name/gd/gdtoolkit_3/package.nix b/pkgs/by-name/gd/gdtoolkit_3/package.nix
index 608d86493217..6b6abbfc4026 100644
--- a/pkgs/by-name/gd/gdtoolkit_3/package.nix
+++ b/pkgs/by-name/gd/gdtoolkit_3/package.nix
@@ -1,7 +1,6 @@
 { lib
 , python3
 , fetchFromGitHub
-, godot3-server
 }:
 
 let
@@ -24,14 +23,14 @@ let
 in
 python.pkgs.buildPythonApplication rec {
   pname = "gdtoolkit3";
-  version = "3.3.1";
+  version = "3.5.0";
 
   # If we try to get using fetchPypi it requires GeoIP (but the package dont has that dep!?)
   src = fetchFromGitHub {
     owner = "Scony";
     repo = "godot-gdscript-toolkit";
     rev = version;
-    sha256 = "13nnpwy550jf5qnm9ixpxl1bwfnhhbiys8vqfd25g3aim4bm3gnn";
+    hash = "sha256-cMGD5Xdf9ElS1NT7Q0NPB//EvUO0MI0VTtps5JRisZ4=";
   };
 
   disabled = python.pythonOlder "3.7";
@@ -48,36 +47,18 @@ python.pkgs.buildPythonApplication rec {
   nativeCheckInputs = with python.pkgs; [
     pytestCheckHook
     hypothesis
-    godot3-server
   ];
 
-  preCheck =
-    let
-      godotServerMajorVersion = lib.versions.major godot3-server.version;
-      gdtoolkitMajorVersion = lib.versions.major version;
-      msg = ''
-        gdtoolkit major version ${gdtoolkitMajorVersion} does not match godot-server major version ${godotServerMajorVersion}!
-        gdtoolkit needs a matching godot-server for its tests.
-        If you see this error, you can either:
-         - disable doCheck for gdtoolkit, or
-         - provide a compatible godot-server version to gdtoolkit"
-      '';
-    in
-    lib.throwIf (godotServerMajorVersion != gdtoolkitMajorVersion) msg ''
-      # The tests want to run the installed executables
-      export PATH=$out/bin:$PATH
+  preCheck = ''
+    # The tests want to run the installed executables
+    export PATH=$out/bin:$PATH
 
-      # gdtoolkit tries to write cache variables to $HOME/.cache
-      export HOME=$TMP
+    # gdtoolkit tries to write cache variables to $HOME/.cache
+    export HOME=$TMP
+  '';
 
-      # Work around https://github.com/godotengine/godot/issues/20503
-      # Without this, Godot will complain about a missing project file
-      touch project.godot
-
-      # Remove broken test case
-      # (hard to skip via disabledTests since the test name contains an absolute path)
-      rm tests/potential-godot-bugs/multiline-subscription-expression.gd
-    '';
+  # The tests are not working on NixOS
+  disabledTests = [ "test_cc_on_empty_file_succeeds" "test_cc_on_file_with_single_function_succeeds" ];
 
   pythonImportsCheck = [ "gdtoolkit" "gdtoolkit.formatter" "gdtoolkit.linter" "gdtoolkit.parser" ];
 

From c0381f6b72e648e894617a34881d77490e6359ce Mon Sep 17 00:00:00 2001
From: Azat Bahawi <azat@bahawi.net>
Date: Fri, 7 Jun 2024 23:13:50 +0300
Subject: [PATCH 18/24] radare2: 5.9.0 -> 5.9.2

---
 .../tools/analysis/radare2/default.nix        | 55 ++++++++++++-------
 1 file changed, 34 insertions(+), 21 deletions(-)

diff --git a/pkgs/development/tools/analysis/radare2/default.nix b/pkgs/development/tools/analysis/radare2/default.nix
index 0efbd75773ff..8d75f994aee6 100644
--- a/pkgs/development/tools/analysis/radare2/default.nix
+++ b/pkgs/development/tools/analysis/radare2/default.nix
@@ -29,8 +29,8 @@
 }:
 
 let
-  # FIXME: Compare revision with
-  # https://github.com/radareorg/radare2/blob/master/libr/arch/p/arm/v35/Makefile#L26-L27
+  # NOTE: Check these revision changes when updating the package.
+  # https://github.com/radareorg/radare2/blob/master/libr/arch/p/arm/v35/Makefile#L25-L26
   arm64 = fetchFromGitHub {
     owner = "radareorg";
     repo = "vector35-arch-arm64";
@@ -44,15 +44,15 @@ let
     hash = "sha256-YhfgJ7M8ys53jh1clOzj0I2yfJshXQm5zP0L9kMYsmk=";
   };
 in
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "radare2";
-  version = "5.9.0";
+  version = "5.9.2";
 
   src = fetchFromGitHub {
     owner = "radare";
     repo = "radare2";
-    rev = "refs/tags/${version}";
-    hash = "sha256-h2IYOGr+yCgCJR1gB4jibcUt1A+8IuNVoTUcJ83lKHw=";
+    rev = "refs/tags/${finalAttrs.version}";
+    hash = "sha256-smsjGfTvSTVwd7nhWhptYpkus2fEQ2EVdT5bDt/rHZE=";
   };
 
   preBuild = ''
@@ -66,30 +66,27 @@ stdenv.mkDerivation rec {
   '';
 
   postFixup = lib.optionalString stdenv.isDarwin ''
-    install_name_tool -add_rpath $out/lib $out/lib/libr_io.${version}.dylib
+    install_name_tool -add_rpath $out/lib $out/lib/libr_io.${finalAttrs.version}.dylib
   '';
 
   mesonFlags = [
+   "-Dr2_gittap=${finalAttrs.version}"
    "-Duse_sys_capstone=true"
-   "-Duse_sys_magic=true"
-   "-Duse_sys_zip=true"
-   "-Duse_sys_xxhash=true"
    "-Duse_sys_lz4=true"
-   "-Dr2_gittap=${version}"
+   "-Duse_sys_magic=true"
+   "-Duse_sys_openssl=true"
+   "-Duse_sys_xxhash=true"
+   "-Duse_sys_zip=true"
   ];
 
-  # TODO: remove when upstream fixes the issue
-  # https://github.com/radareorg/radare2/issues/22793
-  env.NIX_CFLAGS_COMPILE = toString (lib.optionals stdenv.isDarwin [
-     "-DTHREAD_CONVERT_THREAD_STATE_TO_SELF=1"
-  ]);
-
   enableParallelBuilding = true;
+
   depsBuildBuild = [ buildPackages.stdenv.cc ];
 
   strictDeps = true;
 
   nativeBuildInputs = [ pkg-config meson ninja python3 ];
+
   buildInputs = [
     capstone
     file
@@ -113,11 +110,27 @@ stdenv.mkDerivation rec {
   ];
 
   meta = with lib; {
-    description = "UNIX-like reverse engineering framework and command-line tools";
+    description = "UNIX-like reverse engineering framework and command-line toolset";
+    longDescription = ''
+      r2 is a complete rewrite of radare. It provides a set of libraries, tools
+      and plugins to ease reverse engineering tasks. Distributed mostly under
+      LGPLv3, each plugin can have different licenses.
+
+      The radare project started as a simple command-line hexadecimal editor
+      focused on forensics. Today, r2 is a featureful low-level command-line
+      tool with support for scripting with the embedded JavaScript interpreter
+      or via r2pipe.
+
+      r2 can edit files on local hard drives, view kernel memory, and debug
+      programs locally or via a remote gdb/windbg servers. r2's wide
+      architecture support allows you to analyze, emulate, debug, modify, and
+      disassemble any binary.
+    '';
     homepage = "https://radare.org";
-    changelog = "https://github.com/radareorg/radare2/releases/tag/${version}";
-    license = licenses.gpl2Plus;
+    changelog = "https://github.com/radareorg/radare2/releases/tag/${finalAttrs.version}";
+    license = with licenses; [ gpl3Only lgpl3Only ];
     maintainers = with maintainers; [ azahi raskin makefu mic92 arkivm ];
+    mainProgram = "radare2";
     platforms = platforms.unix;
   };
-}
+})

From 791c2414e3b3b674685052f588894b8441c2944d Mon Sep 17 00:00:00 2001
From: Azat Bahawi <azat@bahawi.net>
Date: Fri, 7 Jun 2024 23:14:09 +0300
Subject: [PATCH 19/24] iaito: 5.9.0 -> 5.9.2

---
 pkgs/tools/security/iaito/default.nix | 26 +++++++++++---------------
 1 file changed, 11 insertions(+), 15 deletions(-)

diff --git a/pkgs/tools/security/iaito/default.nix b/pkgs/tools/security/iaito/default.nix
index 2ba6dd0aec26..79d9a65136c5 100644
--- a/pkgs/tools/security/iaito/default.nix
+++ b/pkgs/tools/security/iaito/default.nix
@@ -13,13 +13,13 @@
 
 let
   pname = "iaito";
-  version = "5.9.0";
+  version = "5.9.2";
 
   main_src = fetchFromGitHub rec {
     owner = "radareorg";
     repo = pname;
-    rev = version;
-    hash = "sha256-Ep3Cbi0qjY4PKG0urr12y0DgX/l/Tsq8w1qlyH0lu3s=";
+    rev = "refs/tags/${version}";
+    hash = "sha256-bq4kaP3BmDprKAxMxO+OvTceEQFeAxJ7aGDnRFHjVDA=";
     name = repo;
   };
 
@@ -31,8 +31,7 @@ let
     name = repo;
   };
 in
-
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   inherit pname version;
 
   srcs = [ main_src translations_src ];
@@ -61,9 +60,6 @@ stdenv.mkDerivation rec {
     radare2
   ];
 
-  # the radare2 binary package seems to not install all necessary headers.
-  env.NIX_CFLAGS_COMPILE = toString [ "-I" "${radare2.src}/shlr/sdb/include/sdb" ];
-
   postBuild = ''
     pushd ../../../${translations_src.name}
     make build -j$NIX_BUILD_CORES PREFIX=$out
@@ -86,16 +82,16 @@ stdenv.mkDerivation rec {
   '';
 
   meta = with lib; {
-    description = "An official graphical interface of radare2";
-    mainProgram = "iaito";
+    description = "Official Qt frontend of radare2";
     longDescription = ''
-      iaito is the official graphical interface of radare2. It's the
-      continuation of Cutter for radare2 after the Rizin fork.
+      iaito is the official graphical interface for radare2, a libre reverse
+      engineering framework.
     '';
     homepage = "https://radare.org/n/iaito.html";
-    changelog = "https://github.com/radareorg/iaito/releases/tag/${version}";
-    license = licenses.gpl3Plus;
+    changelog = "https://github.com/radareorg/iaito/releases/tag/${finalAttrs.version}";
+    license = licenses.gpl3Only;
     maintainers = with maintainers; [ azahi ];
+    mainProgram = "iaito";
     platforms = platforms.linux;
   };
-}
+})

From 98ab6d76b07718b32eaf9c9957cf4bca6c997c46 Mon Sep 17 00:00:00 2001
From: "R. Ryantm" <ryantm-bot@ryantm.com>
Date: Fri, 7 Jun 2024 21:00:07 +0000
Subject: [PATCH 20/24] ananicy-rules-cachyos: 0-unstable-2024-05-28 ->
 0-unstable-2024-06-07

---
 pkgs/by-name/an/ananicy-rules-cachyos/package.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/by-name/an/ananicy-rules-cachyos/package.nix b/pkgs/by-name/an/ananicy-rules-cachyos/package.nix
index 58de0bd61e89..3329b40dfbf7 100644
--- a/pkgs/by-name/an/ananicy-rules-cachyos/package.nix
+++ b/pkgs/by-name/an/ananicy-rules-cachyos/package.nix
@@ -7,13 +7,13 @@
 
 stdenvNoCC.mkDerivation {
   pname = "ananicy-rules-cachyos";
-  version = "0-unstable-2024-05-28";
+  version = "0-unstable-2024-06-07";
 
   src = fetchFromGitHub {
     owner = "CachyOS";
     repo = "ananicy-rules";
-    rev = "5718579addbd733a4ab190fb9355a78e8b19b0b4";
-    hash = "sha256-SD15wFUWryL3sRBbREr94A8oKf8KXVBaiI2bmWxbMx4=";
+    rev = "38b3e8c12801df68ba15c2d96ee96d7d2362b576";
+    hash = "sha256-yVKzkASMzJDmgzS0CxEFky2Y4Bs4vlbRJgUI+uG3muY=";
   };
 
   dontConfigure = true;

From 727cac162f8753ba346bdf23a53b74b85770e218 Mon Sep 17 00:00:00 2001
From: zendo <linzway@qq.com>
Date: Thu, 30 May 2024 23:49:28 +0800
Subject: [PATCH 21/24] mangareader: 2.1.0 -> 2.2.1

---
 pkgs/by-name/ma/mangareader/package.nix | 46 ++++++++++++-------------
 1 file changed, 22 insertions(+), 24 deletions(-)

diff --git a/pkgs/by-name/ma/mangareader/package.nix b/pkgs/by-name/ma/mangareader/package.nix
index 37a58ea0ba45..456803218816 100644
--- a/pkgs/by-name/ma/mangareader/package.nix
+++ b/pkgs/by-name/ma/mangareader/package.nix
@@ -1,37 +1,31 @@
-{ lib
-, stdenv
-, fetchFromGitHub
-, wrapQtAppsHook
-, extra-cmake-modules
-, cmake
-, kio
-, ki18n
-, kxmlgui
-, kconfig
-, karchive
-, kcoreaddons
-, kconfigwidgets
-, nix-update-script
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  cmake,
+  kdePackages,
+  nix-update-script,
 }:
 
 stdenv.mkDerivation rec {
   pname = "mangareader";
-  version = "2.1.0";
+  version = "2.2.1";
 
   src = fetchFromGitHub {
     owner = "g-fb";
-    repo = pname;
+    repo = "mangareader";
     rev = version;
-    hash = "sha256-YZZcp+HS/P/GxWYyOpO35nByJSzv4HahzzrZSVRcCRs=";
+    hash = "sha256-XX0VaXVYmAs5vmgwslflKIYx1peITp4VmReLkv1nV3I=";
   };
 
   nativeBuildInputs = [
     cmake
-    extra-cmake-modules
-    wrapQtAppsHook
+    kdePackages.extra-cmake-modules
+    kdePackages.wrapQtAppsHook
   ];
 
-  buildInputs = [
+  buildInputs = with kdePackages; [
+    qtbase
     kio
     ki18n
     kxmlgui
@@ -43,12 +37,16 @@ stdenv.mkDerivation rec {
 
   passthru.updateScript = nix-update-script { };
 
-  meta = with lib; {
+  meta = {
     description = "Qt manga reader for local files";
     homepage = "https://github.com/g-fb/mangareader";
     changelog = "https://github.com/g-fb/mangareader/releases/tag/${src.rev}";
-    platforms = platforms.linux;
-    license = with licenses; [ gpl3Plus cc-by-nc-sa-40 ];
-    maintainers = with maintainers; [ zendo ];
+    mainProgram = "mangareader";
+    platforms = lib.platforms.linux;
+    license = with lib.licenses; [
+      gpl3Plus
+      cc-by-sa-40
+    ];
+    maintainers = with lib.maintainers; [ zendo ];
   };
 }

From 07509a06adfc66f871c15fd9a1060b5813fa6850 Mon Sep 17 00:00:00 2001
From: "imad.nyc" <me@imad.nyc>
Date: Sun, 25 Feb 2024 19:00:01 -0500
Subject: [PATCH 22/24] numworks-epsilon: 15.5.0 -> 22.2.0

real
---
 .../numworks-epsilon/0001-ion-linux-makerules.patch  | 12 ------------
 .../science/math/numworks-epsilon/default.nix        | 12 ++++--------
 2 files changed, 4 insertions(+), 20 deletions(-)
 delete mode 100644 pkgs/applications/science/math/numworks-epsilon/0001-ion-linux-makerules.patch

diff --git a/pkgs/applications/science/math/numworks-epsilon/0001-ion-linux-makerules.patch b/pkgs/applications/science/math/numworks-epsilon/0001-ion-linux-makerules.patch
deleted file mode 100644
index 0bc29b9aab5f..000000000000
--- a/pkgs/applications/science/math/numworks-epsilon/0001-ion-linux-makerules.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-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 \
- )
- 
diff --git a/pkgs/applications/science/math/numworks-epsilon/default.nix b/pkgs/applications/science/math/numworks-epsilon/default.nix
index a90ebc67b65b..98d5d0d4560a 100644
--- a/pkgs/applications/science/math/numworks-epsilon/default.nix
+++ b/pkgs/applications/science/math/numworks-epsilon/default.nix
@@ -9,17 +9,18 @@
 , imagemagick
 , gcc-arm-embedded
 , pkg-config
+, python3Packages
 }:
 
 stdenv.mkDerivation rec {
   pname = "numworks-epsilon";
-  version = "15.5.0";
+  version = "22.2.0";
 
   src = fetchFromGitHub {
     owner = "numworks";
     repo = "epsilon";
     rev = version;
-    sha256 = "fPBO3FzZ4k5OxG+Ifc6R/au4Te974HNKAEdHz+aFdSg=";
+    hash = "sha256-E2WaXTn8+Ky9kdZxvQmEt63Ggo6Ns0fZ0Za+rQGIMSg=";
   };
 
   nativeBuildInputs = [ pkg-config ];
@@ -31,18 +32,13 @@ stdenv.mkDerivation rec {
     python3
     imagemagick
     gcc-arm-embedded
+    python3Packages.lz4
   ];
 
   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
 

From 17f548b4322d473800e2deafd9acf532b8bdc1ea Mon Sep 17 00:00:00 2001
From: "R. Ryantm" <ryantm-bot@ryantm.com>
Date: Sat, 8 Jun 2024 01:00:48 +0000
Subject: [PATCH 23/24] python311Packages.snakemake: 8.11.6 -> 8.13.0

---
 pkgs/applications/science/misc/snakemake/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/applications/science/misc/snakemake/default.nix b/pkgs/applications/science/misc/snakemake/default.nix
index 56d1d7206249..ade523976251 100644
--- a/pkgs/applications/science/misc/snakemake/default.nix
+++ b/pkgs/applications/science/misc/snakemake/default.nix
@@ -6,14 +6,14 @@
 
 python3.pkgs.buildPythonApplication rec {
   pname = "snakemake";
-  version = "8.11.6";
+  version = "8.13.0";
   format = "setuptools";
 
   src = fetchFromGitHub {
     owner = "snakemake";
     repo = pname;
     rev = "refs/tags/v${version}";
-    hash = "sha256-00Zh8NenBikdingmx34WYYH5SF+yazeAs+7h1/3UIJY=";
+    hash = "sha256-Xd8mZ8tsemJ53hAMED2biRyDlEw/gG/Hh1iZSwSB1vY=";
     # https://github.com/python-versioneer/python-versioneer/issues/217
     postFetch = ''
       sed -i "$out"/snakemake/_version.py -e 's#git_refnames = ".*"#git_refnames = " (tag: v${version})"#'

From 9e4e5d96f16f7539ae8020b4b1ea71ddba9b6f3d Mon Sep 17 00:00:00 2001
From: Tom Fitzhenry <tom@tom-fitzhenry.me.uk>
Date: Thu, 6 Jun 2024 23:06:29 +1000
Subject: [PATCH 24/24] tests/openssh: use upstream's algorithms in "no
 openssl" example

When I initially wrote this test, I wasn't aware that services.openssh
could opt into using OpenSSH's default algorithms by just setting the
relevant settings to null.

That's a better approach since:
* it's a simpler setting for this test to have to worry about
* it introduces test coverage for the null case
* the null case should be demonstrated as an example for those that
  want to compile without OpenSSL
---
 nixos/tests/openssh.nix | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/nixos/tests/openssh.nix b/nixos/tests/openssh.nix
index 3929522a39e7..d420c482ca7f 100644
--- a/nixos/tests/openssh.nix
+++ b/nixos/tests/openssh.nix
@@ -120,12 +120,14 @@ in {
             { type = "ed25519"; path = "/etc/ssh/ssh_host_ed25519_key"; }
           ];
           settings = {
-            # Must not specify the OpenSSL provided algorithms.
-            Ciphers = [ "chacha20-poly1305@openssh.com" ];
-            KexAlgorithms = [
-              "curve25519-sha256"
-              "curve25519-sha256@libssh.org"
-            ];
+            # Since this test is against an OpenSSH-without-OpenSSL,
+            # we have to override NixOS's defaults ciphers (which require OpenSSL)
+            # and instead set these to null, which will mean OpenSSH uses its defaults.
+            # Expectedly, OpenSSH's defaults don't require OpenSSL when it's compiled
+            # without OpenSSL.
+            Ciphers = null;
+            KexAlgorithms = null;
+            Macs = null;
           };
         };
         users.users.root.openssh.authorizedKeys.keys = [