Merge staging-next into staging

NixOS · Feb 13, 2025 · 3dbb877 · 3dbb877
2 parents 7f493d2 + 7e43cbe
commit 3dbb877
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diff --git a/maintainers/maintainer-list.nix b/maintainers/maintainer-list.nix
@@ -10752,7 +10752,7 @@
     name = "Jeffrey David Johnson";
   };
   jefflabonte = {
-    email = "[email protected]";
+    email = "[email protected]";
     github = "JeffLabonte";
     githubId = 9425955;
     name = "Jean-François Labonté";

diff --git a/pkgs/applications/editors/vscode/vscode.nix b/pkgs/applications/editors/vscode/vscode.nix
@@ -36,22 +36,22 @@ let
 
   sha256 =
     {
-      x86_64-linux = "0a4siy3is9bzbzmhhaf4l2djabv1yxjb20yp48i094wk0lpwbgcm";
-      x86_64-darwin = "1pdx07ibylfk8zx71cjfjmsd8650kpd8rvkknixg1nm1jar9zsb3";
-      aarch64-linux = "0x2qg7ixgkq637qvd218zk8ykfq97l55az17fqgp9dm9g73xn85f";
-      aarch64-darwin = "0jlfkkc99wv875n2h5v3lnyhjhh74w53yd07jp02fbg4hs8sds92";
-      armv7l-linux = "13a7s1il860g7v41wwdac3zdawc9w0bkrg9yif99s5ll0nakfs88";
+      x86_64-linux = "0gr2z4vzms6fv4kcc8dzc7l3inpb5hasnzdfr1zc2n4i3nl8z8vw";
+      x86_64-darwin = "1qplpjazjds5kns0kmp5qa6zfix30cqa93bl4bcpvblb2x9fh1v8";
+      aarch64-linux = "1jhrmwrnxzwvhqgfrs35kyd5hhg2b7dyq3p5k88jhm8607nkds79";
+      aarch64-darwin = "072lg4nvq3cdjzrwngaxnz9p952zkxsknsb39zjh55vzrij55g9x";
+      armv7l-linux = "06bvh72bq4ippr2k8ifcfqhkhhh6na4vxsz1k50swr1k2kzwwr5d";
     }
     .${system} or throwSystem;
 in
 callPackage ./generic.nix rec {
   # Please backport all compatible updates to the stable release.
   # This is important for the extension ecosystem.
-  version = "1.97.0";
+  version = "1.97.1";
   pname = "vscode" + lib.optionalString isInsiders "-insiders";
 
   # This is used for VS Code - Remote SSH test
-  rev = "33fc5a94a3f99ebe7087e8fe79fbe1d37a251016";
+  rev = "e249dada235c2083c83813bd65b7f4707fb97b76";
 
   executableName = "code" + lib.optionalString isInsiders "-insiders";
   longName = "Visual Studio Code" + lib.optionalString isInsiders " - Insiders";
@@ -75,7 +75,7 @@ callPackage ./generic.nix rec {
     src = fetchurl {
       name = "vscode-server-${rev}.tar.gz";
       url = "https://update.code.visualstudio.com/commit:${rev}/server-linux-x64/stable";
-      sha256 = "1vqqrcyrb8kigdwap5rkpil8lrahngix16hyqpvsmf0gsyjh46h0";
+      sha256 = "01snzahh794ygpgwh4r57c8mnisp6a4fc3v5x76cdhxw2hd9s26n";
     };
     stdenv = stdenvNoCC;
   };
@@ -110,6 +110,7 @@ callPackage ./generic.nix rec {
       synthetica
       bobby285271
       johnrtitor
+      jefflabonte
     ];
     platforms = [
       "x86_64-linux"

diff --git a/pkgs/by-name/co/containerlab/package.nix b/pkgs/by-name/co/containerlab/package.nix
@@ -7,16 +7,16 @@
 
 buildGoModule rec {
   pname = "containerlab";
-  version = "0.62.2";
+  version = "0.64.0";
 
   src = fetchFromGitHub {
     owner = "srl-labs";
     repo = "containerlab";
     rev = "v${version}";
-    hash = "sha256-RUe/IHHhZKbxtNVxiS29/OPvpCCOzaz2d5Qh3vVll3U=";
+    hash = "sha256-ijqylVQKt7N3rc+HVc34XfU3LMXAtn+mhVWIzZZIikw=";
   };
 
-  vendorHash = "sha256-G9W4iC04R5Rvl3hAJtMlUKJKo7AAIE33Y2c+0HedXU8=";
+  vendorHash = "sha256-9p4J9qkIQCubn3W4b3qNHfq1M2kMiqG0eGFaBxGdrAk=";
 
   nativeBuildInputs = [ installShellFiles ];
 

diff --git a/pkgs/by-name/de/deeptools/package.nix b/pkgs/by-name/de/deeptools/package.nix
@@ -1,46 +1,43 @@
 {
   lib,
-  python3,
+  python3Packages,
   fetchFromGitHub,
+  addBinToPathHook,
 }:
 
-python3.pkgs.buildPythonApplication rec {
+python3Packages.buildPythonApplication rec {
   pname = "deeptools";
-  version = "3.5.5";
+  version = "3.5.6";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "deeptools";
     repo = "deepTools";
     tag = version;
-    hash = "sha256-2kSlL7Y5f/FjVtStnmz+GlTw2oymrtxOCaXlqgbQ7FU=";
+    hash = "sha256-dxXlOvOjF4KSc5YO+1A5hlp95sfeyPSbmp93tihm7Vo=";
   };
 
-  nativeBuildInputs = with python3.pkgs; [
+  build-system = with python3Packages; [
     setuptools
   ];
 
-  propagatedBuildInputs = with python3.pkgs; [
+  dependencies = with python3Packages; [
     numpy
-    numpydoc
     scipy
-    py2bit
-    pybigwig
-    pysam
     matplotlib
+    pysam
+    numpydoc
+    pybigwig
+    py2bit
     plotly
     deeptoolsintervals
-    importlib-metadata
   ];
 
-  nativeCheckInputs = with python3.pkgs; [
+  nativeCheckInputs = with python3Packages; [
     pytestCheckHook
+    addBinToPathHook
   ];
 
-  preCheck = ''
-    export PATH="$out/bin:$PATH"
-  '';
-
   disabledTestPaths = [
     # tests trip on `len(sys.argv) == 1`
     "deeptools/test/test_bigwigAverage.py"
@@ -49,7 +46,7 @@ python3.pkgs.buildPythonApplication rec {
     "deeptools/test/test_multiBamSummary.py"
   ];
 
-  meta = with lib; {
+  meta = {
     homepage = "https://deeptools.readthedocs.io/en/develop";
     description = "Tools for exploring deep DNA sequencing data";
     longDescription = ''
@@ -60,10 +57,10 @@ python3.pkgs.buildPythonApplication rec {
       publication-ready visualizations to identify enrichments and for functional
       annotations of the genome.
     '';
-    license = with licenses; [
+    license = with lib.licenses; [
       mit
       bsd3
     ];
-    maintainers = with maintainers; [ scalavision ];
+    maintainers = with lib.maintainers; [ scalavision ];
   };
 }
diff --git a/pkgs/by-name/de/desktop-file-utils/package.nix b/pkgs/by-name/de/desktop-file-utils/package.nix
@@ -38,7 +38,7 @@ stdenv.mkDerivation rec {
   meta = with lib; {
     homepage = "https://www.freedesktop.org/wiki/Software/desktop-file-utils";
     description = "Command line utilities for working with .desktop files";
-    platforms = platforms.linux ++ platforms.darwin;
+    platforms = platforms.linux ++ platforms.darwin ++ platforms.freebsd;
     license = licenses.gpl2Plus;
   };
 }
diff --git a/pkgs/by-name/go/google-amber/package.nix b/pkgs/by-name/go/google-amber/package.nix
@@ -18,8 +18,8 @@ let
   glslang = fetchFromGitHub {
     owner = "KhronosGroup";
     repo = "glslang";
-    rev = "e8dd0b6903b34f1879520b444634c75ea2deedf5";
-    hash = "sha256-B6jVCeoFjd2H6+7tIses+Kj8DgHS6E2dkVzQAIzDHEc=";
+    rev = "340bf88f3fdb4f4a25b7071cd2c1205035fc6eaa";
+    hash = "sha256-3h27yE6k4BgUAugQCkpUYO5aIHpK6Anyh90y3q+aYpM=";
   };
 
   lodepng = fetchFromGitHub {
@@ -32,34 +32,34 @@ let
   shaderc = fetchFromGitHub {
     owner = "google";
     repo = "shaderc";
-    rev = "f59f0d11b80fd622383199c867137ededf89d43b";
-    hash = "sha256-kHz8Io5GZDWv1FjPyBWRpnKhGygKhSU4L9zl/AKXZlU=";
+    rev = "690d259384193c90c01b52288e280b05a8481121";
+    hash = "sha256-p4tP/8lRy0tpdDHIuh2/tWPIBBr2ludFRSr+Q2TbUic=";
   };
 
   spirv-headers = fetchFromGitHub {
     owner = "KhronosGroup";
     repo = "SPIRV-Headers";
-    rev = "5e3ad389ee56fca27c9705d093ae5387ce404df4";
-    hash = "sha256-gjF5mVTXqU/GZzr2S6oKGChgvqqHcQSrEq/ePP2yJys=";
+    rev = "3f17b2af6784bfa2c5aa5dbb8e0e74a607dd8b3b";
+    hash = "sha256-MCQ+i9ymjnxRZP/Agk7rOGdHcB4p67jT4J4athWUlcI=";
   };
 
   spirv-tools = fetchFromGitHub {
     owner = "KhronosGroup";
     repo = "SPIRV-Tools";
-    rev = "9241a58a8028c49510bc174b6c970e3c2b4b8e51";
-    hash = "sha256-0qHUpwNDJI2jV4h68QaTNPIwTPxwTt0iAUnMXqFCiJE=";
+    rev = "13b59bf1d84054b8ccd29cdc6b1303f69e8f9e77";
+    hash = "sha256-k/mTHiLbZdnslC24fjcrzqsZYMyVaAADGEqngqJcC2c=";
   };
 
 in
 stdenv.mkDerivation (finalAttrs: {
   pname = "amber";
-  version = "unstable-2024-08-21";
+  version = "unstable-2025-02-03";
 
   src = fetchFromGitHub {
     owner = "google";
     repo = "amber";
-    rev = "66399a35927606a435bf7a59756e87e6cb5a0013";
-    hash = "sha256-PCO64zI/vzp4HyGz5WpeYpCBeaWjTvz1punWsTz1yiM=";
+    rev = "3f078e41d86ca1a5881560f00e26198f59bb8ac0";
+    hash = "sha256-pAotVFmtEGp9GKmDD0vrbfbO+Xt2URmM8gYCjl0LEnk=";
   };
 
   buildInputs = [

diff --git a/pkgs/by-name/pu/pulldown-cmark/package.nix b/pkgs/by-name/pu/pulldown-cmark/package.nix
@@ -6,15 +6,15 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "pulldown-cmark";
-  version = "0.12.2";
+  version = "0.13.0";
 
   src = fetchCrate {
     inherit pname version;
-    hash = "sha256-dsSt0JC3e1IItyY16tosxD83XUdttHVIT40QsW9iUFU=";
+    hash = "sha256-lp0ywX/3phfC30QvYkO2wFZNSinP4cdm4HY744EZ02o=";
   };
 
   useFetchCargoVendor = true;
-  cargoHash = "sha256-5AXEXuw3aKT8ghzEclwZYSOQvKcy90OvZbAVVkNJq1U=";
+  cargoHash = "sha256-ek6Eczqb/kxxoZFakGcwrgqXAtNCtQxDX2PHdOcIUjU=";
 
   meta = {
     description = "Pull parser for CommonMark written in Rust";

diff --git a/pkgs/by-name/wy/wyoming-satellite/package.nix b/pkgs/by-name/wy/wyoming-satellite/package.nix
@@ -2,6 +2,7 @@
   lib,
   python3Packages,
   fetchFromGitHub,
+  fetchpatch2,
 }:
 
 let
@@ -21,16 +22,24 @@ let
 in
 python.pkgs.buildPythonApplication rec {
   pname = "wyoming-satellite";
-  version = "1.3.0";
+  version = "1.4.1";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "rhasspy";
     repo = "wyoming-satellite";
     tag = "v${version}";
-    hash = "sha256-9UgfD0Hs/IgOszd/QBbe6DYY6kBWh7q/e57gghQ1/Bk=";
+    hash = "sha256-sAtyyS60Fr6iFE3tTxEgAjhmX6O5WjWwb9rk+phzrtM=";
   };
 
+  patches = [
+    (fetchpatch2 {
+      # https://github.com/rhasspy/wyoming-satellite/pull/285
+      url = "https://github.com/rhasspy/wyoming-satellite/commit/69465fd56011179cb92e7ce95da2e79fb06a83fb.patch";
+      hash = "sha256-njJ8kIVGOpYK6bDeGow3OSNHxKQ9NsUKAR3+lEUH3GE=";
+    })
+  ];
+
   build-system = with python.pkgs; [
     setuptools
   ];
@@ -46,14 +55,19 @@ python.pkgs.buildPythonApplication rec {
     zeroconf
   ];
 
-  optional-dependencies = {
+  optional-dependencies = lib.fix (self: {
+    all = self.silerovad ++ self.webrtc;
+    respeaker = with python3Packages; [
+      gpiozero
+      spidev
+    ];
     silerovad = with python3Packages; [
       pysilero-vad
     ];
     webrtc = with python3Packages; [
       webrtc-noise-gain
     ];
-  };
+  });
 
   pythonImportsCheck = [
     "wyoming_satellite"

diff --git a/pkgs/development/interpreters/python/cpython/3.12/CVE-2024-12254.patch b/pkgs/development/interpreters/python/cpython/3.12/CVE-2024-12254.patch
diff --git a/pkgs/development/interpreters/python/cpython/default.nix b/pkgs/development/interpreters/python/cpython/default.nix
@@ -254,7 +254,7 @@ in with passthru; stdenv.mkDerivation (finalAttrs: {
     # (since it will do a futile invocation of gcc (!) to find
     # libuuid, slowing down program startup a lot).
     noldconfigPatch
-  ] ++ optionals (!isPy312 && !isPy313) [
+  ] ++ optionals (pythonOlder "3.12") [
     # https://www.cve.org/CVERecord?id=CVE-2025-0938
     ./CVE-2025-0938.patch
   ] ++ optionals (stdenv.hostPlatform != stdenv.buildPlatform && stdenv.hostPlatform.isFreeBSD) [
@@ -299,8 +299,6 @@ in with passthru; stdenv.mkDerivation (finalAttrs: {
   ] ++ optionals (pythonOlder "3.12") [
     # https://github.com/python/cpython/issues/90656
     ./loongarch-support.patch
-  ] ++ optionals isPy314 [
-    ./3.12/CVE-2024-12254.patch
   ] ++ optionals (pythonAtLeast "3.11" && pythonOlder "3.13") [
     # backport fix for https://github.com/python/cpython/issues/95855
     ./platform-triplet-detection.patch

diff --git a/pkgs/development/interpreters/python/default.nix b/pkgs/development/interpreters/python/default.nix
@@ -100,9 +100,9 @@ in {
       major = "3";
       minor = "14";
       patch = "0";
-      suffix = "a4";
+      suffix = "a5";
     };
-    hash = "sha256-wk8HiBhzwdRgIoeVymyoyZEw4wx3PJFGPTDX6o/w5ws=";
+    hash = "sha256-dOg/Jt4eT7nu8bVkks/5JQiDS7cawT9cWAQ4zp8JNoI=";
     inherit passthruFun;
   };
   # Minimal versions of Python (built without optional dependencies)

diff --git a/pkgs/development/python-modules/awkward-cpp/default.nix b/pkgs/development/python-modules/awkward-cpp/default.nix
@@ -11,13 +11,13 @@
 
 buildPythonPackage rec {
   pname = "awkward-cpp";
-  version = "43";
+  version = "44";
   pyproject = true;
 
   src = fetchPypi {
     pname = "awkward_cpp";
     inherit version;
-    hash = "sha256-we11WW7IKvZm2ghLW/gF2bcsg1MtA10rZeB5WQXSXq0=";
+    hash = "sha256-jcSZKI1tFrLqILUaJ9UEflGiR7aqz8vLOzAsrW08h9g=";
   };
 
   build-system = [