Merge remote-tracking branch 'origin/master' into staging-next

pkgs/by-name/bi/bind/package.nix

@@ -26,11 +26,11 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "bind";
-  version = "9.18.28";
+  version = "9.18.33";
 
   src = fetchurl {
     url = "https://downloads.isc.org/isc/bind9/${finalAttrs.version}/${finalAttrs.pname}-${finalAttrs.version}.tar.xz";
-    hash = "sha256-58zpoWX3thnu/Egy8KjcFrAF0p44kK7WAIxQbqKGpec=";
+    hash = "sha256-+zc/rF67xBxkUWCv1an7RRkY9sDmmrHZR0FU4rUV3kA=";
   };
 
   outputs = [
@@ -150,7 +150,9 @@ stdenv.mkDerivation (finalAttrs: {
     homepage = "https://www.isc.org/bind/";
     description = "Domain name server";
     license = licenses.mpl20;
-    changelog = "https://downloads.isc.org/isc/bind9/cur/${lib.versions.majorMinor finalAttrs.version}/CHANGES";
+    changelog = "https://downloads.isc.org/isc/bind9/cur/${lib.versions.majorMinor finalAttrs.version}/doc/arm/html/notes.html#notes-for-bind-${
+      lib.replaceStrings [ "." ] [ "-" ] finalAttrs.version
+    }";
     maintainers = with maintainers; [ globin ];
     platforms = platforms.unix;
 

pkgs/by-name/mc/mcpelauncher-client/package.nix

@@ -1,6 +1,7 @@
 {
   lib,
   clangStdenv,
+  stdenv,
   fetchFromGitHub,
   fetchpatch,
   cmake,
@@ -18,6 +19,8 @@
   withQtWebview ? true,
   withQtErrorWindow ? true,
   fetchzip,
+  zenity,
+  xdg-utils,
 }:
 
 # gcc doesn't support __has_feature
@@ -51,6 +54,16 @@ clangStdenv.mkDerivation (finalAttrs: {
     })
   ];
 
+  # Path hard-coded paths.
+  postPatch = lib.optionalString stdenv.isLinux ''
+    substituteInPlace mcpelauncher-client/src/jni/main_activity.cpp \
+      --replace-fail /usr/bin/xdg-open ${xdg-utils}/bin/xdg-open \
+      --replace-fail /usr/bin/zenity ${zenity}/bin/zenity
+
+    substituteInPlace file-picker/src/file_picker_zenity.cpp \
+      --replace-fail /usr/bin/zenity ${zenity}/bin/zenity
+  '';
+
   # FORTIFY_SOURCE breaks libc_shim and the project will fail to compile
   hardeningDisable = [ "fortify" ];
 

pkgs/by-name/mm/mmdbctl/package.nix

@@ -11,16 +11,16 @@
 
 buildGoModule rec {
   pname = "mmdbctl";
-  version = "1.4.6";
+  version = "1.4.7";
 
   src = fetchFromGitHub {
     owner = "ipinfo";
     repo = "mmdbctl";
     tag = "mmdbctl-${version}";
-    hash = "sha256-6hJ9V8fHs84Lq48l3mB9nZka4rLneyxD4HMhWQYZ0cI=";
+    hash = "sha256-drYtuL4TzutzitLVKyUotxgyDjL7AMNnt0vVtfQhu4A=";
   };
 
-  vendorHash = "sha256-5vd39j/gpRRkUccctKGU8+QL0vANm2FMyw6jTtoqJmw=";
+  vendorHash = "sha256-4T3HEzRerC4KrGQnMNSW3OVzChUIf4yJ7qS9v8mWIX4=";
 
   ldflags = [
     "-s"

pkgs/by-name/mo/moralerspace-hw/package.nix

@@ -0,0 +1,28 @@
+{
+  lib,
+  stdenvNoCC,
+  fetchzip,
+  moralerspace,
+}:
+
+stdenvNoCC.mkDerivation (finalAttrs: {
+  pname = "moralerspace-hw";
+  inherit (moralerspace) version meta;
+
+  src = fetchzip {
+    url = "https://github.com/yuru7/moralerspace/releases/download/v${finalAttrs.version}/MoralerspaceHW_v${finalAttrs.version}.zip";
+    hash = "sha256-V02Lp7bWKjUGhFJ5fOTVrk74ei0T5UtITQeHZ4OHytw=";
+  };
+
+  installPhase = ''
+    runHook preInstall
+
+    install -Dm644 *.ttf -t $out/share/fonts/moralerspace-hw
+
+    runHook postInstall
+  '';
+
+  passthru = {
+    inherit (moralerspace) updateScript;
+  };
+})

pkgs/by-name/mo/moralerspace-hwjpdoc/package.nix

@@ -0,0 +1,28 @@
+{
+  lib,
+  stdenvNoCC,
+  fetchzip,
+  moralerspace,
+}:
+
+stdenvNoCC.mkDerivation (finalAttrs: {
+  pname = "moralerspace-hwjpdoc";
+  inherit (moralerspace) version meta;
+
+  src = fetchzip {
+    url = "https://github.com/yuru7/moralerspace/releases/download/v${finalAttrs.version}/MoralerspaceHWJPDOC_v${finalAttrs.version}.zip";
+    hash = "sha256-rYDx3MMjxnmp/o6nRc5/bIEkwvMP9gmwm6R//3KwoLk=";
+  };
+
+  installPhase = ''
+    runHook preInstall
+
+    install -Dm644 *.ttf -t $out/share/fonts/moralerspace-hwjpdoc
+
+    runHook postInstall
+  '';
+
+  passthru = {
+    inherit (moralerspace) updateScript;
+  };
+})

pkgs/by-name/mo/moralerspace-hwnf/package.nix

@@ -0,0 +1,28 @@
+{
+  lib,
+  stdenvNoCC,
+  fetchzip,
+  moralerspace,
+}:
+
+stdenvNoCC.mkDerivation (finalAttrs: {
+  pname = "moralerspace-hwnf";
+  inherit (moralerspace) version meta;
+
+  src = fetchzip {
+    url = "https://github.com/yuru7/moralerspace/releases/download/v${finalAttrs.version}/MoralerspaceHWNF_v${finalAttrs.version}.zip";
+    hash = "sha256-XRdDcfgwbP5g26xh9rlHRp9i//k5PdRhMExMy3ibN/4=";
+  };
+
+  installPhase = ''
+    runHook preInstall
+
+    install -Dm644 *.ttf -t $out/share/fonts/moralerspace-hwnf
+
+    runHook postInstall
+  '';
+
+  passthru = {
+    inherit (moralerspace) updateScript;
+  };
+})

pkgs/by-name/mo/moralerspace-jpdoc/package.nix

@@ -0,0 +1,28 @@
+{
+  lib,
+  stdenvNoCC,
+  fetchzip,
+  moralerspace,
+}:
+
+stdenvNoCC.mkDerivation (finalAttrs: {
+  pname = "moralerspace-jpdoc";
+  inherit (moralerspace) version meta;
+
+  src = fetchzip {
+    url = "https://github.com/yuru7/moralerspace/releases/download/v${finalAttrs.version}/MoralerspaceJPDOC_v${finalAttrs.version}.zip";
+    hash = "sha256-oeTRnDSp9sbicMmaybX7xue1u7dSpAqUv8XTOUrzEjE=";
+  };
+
+  installPhase = ''
+    runHook preInstall
+
+    install -Dm644 *.ttf -t $out/share/fonts/moralerspace-jpdoc
+
+    runHook postInstall
+  '';
+
+  passthru = {
+    inherit (moralerspace) updateScript;
+  };
+})

pkgs/by-name/mo/moralerspace-nf/package.nix

@@ -0,0 +1,28 @@
+{
+  lib,
+  stdenvNoCC,
+  fetchzip,
+  moralerspace,
+}:
+
+stdenvNoCC.mkDerivation (finalAttrs: {
+  pname = "moralerspace-nf";
+  inherit (moralerspace) version meta;
+
+  src = fetchzip {
+    url = "https://github.com/yuru7/moralerspace/releases/download/v${finalAttrs.version}/MoralerspaceNF_v${finalAttrs.version}.zip";
+    hash = "sha256-zpJ6I/4WMiVfDbowcvw1JAup0RdvylJCzQbwa5qWM44=";
+  };
+
+  installPhase = ''
+    runHook preInstall
+
+    install -Dm644 *.ttf -t $out/share/fonts/moralerspace-nf
+
+    runHook postInstall
+  '';
+
+  passthru = {
+    inherit (moralerspace) updateScript;
+  };
+})

pkgs/by-name/mo/moralerspace/package.nix

@@ -0,0 +1,58 @@
+{
+  lib,
+  stdenvNoCC,
+  fetchzip,
+  _experimental-update-script-combinators,
+  nix-update-script,
+}:
+
+stdenvNoCC.mkDerivation (finalAttrs: {
+  pname = "moralerspace";
+  version = "1.1.0";
+
+  src = fetchzip {
+    url = "https://github.com/yuru7/moralerspace/releases/download/v${finalAttrs.version}/Moralerspace_v${finalAttrs.version}.zip";
+    hash = "sha256-sItgkidfmOPKtMx8+eaVFn8hK9cRxYShIsNXTh5dJfk=";
+  };
+
+  installPhase = ''
+    runHook preInstall
+
+    install -Dm644 *.ttf -t $out/share/fonts/moralerspace
+
+    runHook postInstall
+  '';
+
+  passthru.updateScript = _experimental-update-script-combinators.sequence [
+    (nix-update-script { })
+    (nix-update-script {
+      attrPath = "moralerspace-hw";
+      extraArgs = [ "--version=skip" ];
+    })
+    (nix-update-script {
+      attrPath = "moralerspace-hwjpdoc";
+      extraArgs = [ "--version=skip" ];
+    })
+    (nix-update-script {
+      attrPath = "moralerspace-hwnf";
+      extraArgs = [ "--version=skip" ];
+    })
+    (nix-update-script {
+      attrPath = "moralerspace-jpdoc";
+      extraArgs = [ "--version=skip" ];
+    })
+    (nix-update-script {
+      attrPath = "moralerspace-nf";
+      extraArgs = [ "--version=skip" ];
+    })
+  ];
+
+  meta = {
+    description = "Composite font of Monaspace and IBM Plex Sans JP";
+    homepage = "https://github.com/yuru7/moralerspace";
+    changelog = "https://github.com/yuru7/moralerspace/releases/tag/v${finalAttrs.version}";
+    license = lib.licenses.ofl;
+    maintainers = with lib.maintainers; [ natsukium ];
+    platforms = lib.platforms.all;
+  };
+})

pkgs/by-name/mu/multiqc/package.nix

@@ -0,0 +1,117 @@
+{
+  lib,
+  python3Packages,
+  fetchFromGitHub,
+  procps,
+  stdenv,
+  versionCheckHook,
+}:
+
+python3Packages.buildPythonApplication rec {
+  pname = "multiqc";
+  version = "1.26";
+
+  # Two data sources. One for the code, another for the test data
+  srcs = [
+    (fetchFromGitHub {
+      name = "multiqc";
+      owner = "MultiQC";
+      repo = "MultiQC";
+      tag = "v${version}";
+      hash = "sha256-MPAw6gG/3LzdskkDXOTDEM1NpG0sH9GvklYFQ1ZXWIs=";
+    })
+    (fetchFromGitHub {
+      owner = "MultiQC";
+      repo = "test-data";
+      rev = "67435083a8bfa228dca3dda7d835facef15fc2c7";
+      hash = "sha256-oYmPIJSy6dOKPcMr3B4foGoWcerA29x0XeGoU4dSYsA=";
+      name = "test-data";
+    })
+  ];
+
+  sourceRoot = "multiqc";
+
+  dependencies = with python3Packages; [
+    click
+    humanize
+    importlib-metadata
+    jinja2
+    kaleido
+    markdown
+    natsort
+    numpy
+    packaging
+    requests
+    pillow
+    plotly
+    pyyaml
+    rich
+    rich-click
+    coloredlogs
+    spectra
+    pydantic
+    typeguard
+    tqdm
+  ];
+
+  optional-dependencies = {
+    dev = with python3Packages; [
+      pre-commit-hooks
+      pdoc3
+      pytest
+      pytest-cov-stub
+      pytest-xdist
+      syrupy
+      pygithub
+      mypy
+      types-pyyaml
+      types-tqdm
+      types-requests
+      types-markdown
+      types-beautifulsoup4
+      types-pillow
+    ];
+  };
+
+  # Some tests run subprocess.run() with "multiqc"
+  preCheck = ''
+    chmod -R u+w ../test-data
+    ln -s ../test-data .
+    export PATH=$out/bin:$PATH
+  '';
+
+  # Some tests run subprocess.run() with "ps"
+  nativeCheckInputs = with python3Packages; [
+    procps
+    pytest-cov
+    pytest-xdist
+    pytestCheckHook
+    syrupy
+    pygithub
+    versionCheckHook
+  ];
+
+  versionCheckProgramArg = [ "--version" ];
+
+  disabledTests =
+    # On darwin, kaleido fails to starts
+    lib.optionals (stdenv.hostPlatform.isDarwin) [
+      "test_flat_plot"
+    ];
+
+  meta = {
+    description = "Aggregates bioinformatics results from multiple samples into a unified report";
+    longDescription = ''
+      MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
+
+      Reports are generated by scanning given directories for recognised log files. These are parsed and a single HTML report is generated summarising the statistics for all logs found. MultiQC reports can describe multiple analysis steps and large numbers of samples within a single plot, and multiple analysis tools making it ideal for routine fast quality control.
+    '';
+    homepage = "https://multiqc.info";
+    changelog = "https://github.com/MultiQC/MultiQC/releases/tag/v${version}/";
+    license = [ lib.licenses.gpl3Plus ];
+    maintainers = [ lib.maintainers.apraga ];
+    mainProgram = "multiqc";
+    platforms = lib.platforms.unix;
+  };
+
+}

pkgs/by-name/op/openlinkhub/package.nix

@@ -9,13 +9,13 @@
 
 buildGoModule rec {
   pname = "openlinkhub";
-  version = "0.4.8";
+  version = "0.5.0";
 
   src = fetchFromGitHub {
     owner = "jurkovic-nikola";
     repo = "OpenLinkHub";
     tag = version;
-    hash = "sha256-gsMzquVK4QVXZPHIeAuZW/vHW8tRBWcVAX+/fORDp+U=";
+    hash = "sha256-2dsdswtpKXHEiPOdGS1gIyx8r3xx3Bjr2i4WyX4hmVY=";
   };
 
   proxyVendor = true;

pkgs/by-name/se/sequoia-chameleon-gnupg/package.nix

@@ -11,17 +11,17 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "sequoia-chameleon-gnupg";
-  version = "0.11.2";
+  version = "0.12.0";
 
   src = fetchFromGitLab {
     owner = "sequoia-pgp";
     repo = pname;
     rev = "v${version}";
-    hash = "sha256-XoZA8X6lwziKFECJDPCSpqcFtJe5TsDGWvM+EgpBU3U=";
+    hash = "sha256-2EJDpiNYrNh8Ojhs6jSsaLV5zKExShiIor3/Tjue+y8=";
   };
 
   useFetchCargoVendor = true;
-  cargoHash = "sha256-BuUyOI0skXViwYTPP9/AVoqtLHCIrdRKJF/4Zq6aTD8=";
+  cargoHash = "sha256-DKMz8unxxH4crjN8X1Ulh61jBtFSTVNrzFBkEs0RnGM=";
 
   nativeBuildInputs = [
     rustPlatform.bindgenHook

pkgs/by-name/ta/tailwindcss-language-server/package.nix

@@ -2,12 +2,13 @@
   lib,
   stdenv,
   fetchFromGitHub,
-  nodejs_22,
+  nodejs_23,
   pnpm_9,
+  cacert,
 }:
 
 let
-  version = "0.0.27";
+  version = "0.14.1";
 in
 stdenv.mkDerivation (finalAttrs: {
   pname = "tailwindcss-language-server";
@@ -16,8 +17,8 @@ stdenv.mkDerivation (finalAttrs: {
   src = fetchFromGitHub {
     owner = "tailwindlabs";
     repo = "tailwindcss-intellisense";
-    rev = "@tailwindcss/language-server@v${finalAttrs.version}";
+    rev = "v${finalAttrs.version}";
-    hash = "sha256-FphKiGMTMQj/tBmrwkPVlb+dEGjf+N4EgZtOVg7iL2M=";
+    hash = "sha256-8hP61zBsNWolA60yzSBb+fPlRuHCTvRfnC1DduB4KkA=";
   };
 
   pnpmDeps = pnpm_9.fetchDeps {
@@ -28,21 +29,24 @@ stdenv.mkDerivation (finalAttrs: {
       pnpmWorkspaces
       prePnpmInstall
       ;
-    hash = "sha256-kLB84P2Zb3gXpNlXCnQFIxz8xibACB39URIhy6Na9p8=";
+    hash = "sha256-bxapagJcVPFxtKUuS4ATKr6rpAaDIFiccSANG0p3Ybc=";
   };
 
   nativeBuildInputs = [
-    nodejs_22
+    nodejs_23
     pnpm_9.configHook
   ];
 
-  buildInputs = [ nodejs_22 ];
+  buildInputs = [
+    nodejs_23
+  ];
 
   pnpmWorkspaces = [ "@tailwindcss/language-server..." ];
   prePnpmInstall = ''
     # Warning section for "pnpm@v8"
     # https://pnpm.io/cli/install#--filter-package_selector
     pnpm config set dedupe-peer-dependents false
+    export NODE_EXTRA_CA_CERTS="${cacert}/etc/ssl/certs/ca-bundle.crt"
   '';
 
   buildPhase = ''

pkgs/development/python-modules/llm/default.nix

@@ -22,7 +22,7 @@
 let
   llm = buildPythonPackage rec {
     pname = "llm";
-    version = "0.19.1";
+    version = "0.20";
     pyproject = true;
 
     build-system = [ setuptools ];
@@ -33,7 +33,7 @@ let
       owner = "simonw";
       repo = "llm";
       tag = version;
-      hash = "sha256-MMqlcKSvBAdM6Xfz3MQTIbCfWEqzVeCPzuJJzFVpxb4=";
+      hash = "sha256-nNwhsdix65i19f7JHvSLydDufP7nAUjV1YYQspsHT8s=";
     };
 
     patches = [ ./001-disable-install-uninstall-commands.patch ];

pkgs/development/python-modules/spectra/default.nix

@@ -0,0 +1,49 @@
+{
+  buildPythonPackage,
+  colormath,
+  fetchFromGitHub,
+  fetchpatch2,
+  lib,
+  pytestCheckHook,
+  setuptools,
+}:
+
+buildPythonPackage rec {
+  pname = "spectra";
+  version = "0.0.11";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "jsvine";
+    repo = "spectra";
+    tag = "v${version}";
+    hash = "sha256-4A2TWTxYqckJ3DX5cd2KN3KXcmO/lQdXmOEnGi76RsA=";
+  };
+
+  patches = [
+    # https://github.com/jsvine/spectra/pull/21
+    (fetchpatch2 {
+      name = "nose-to-pytest.patch";
+      url = "https://github.com/jsvine/spectra/commit/50037aba16dac4bf0fb7ffbd787d0e6b906e8a4b.patch";
+      hash = "sha256-cMoIbjRwcZjvhiIOcJR7NmIAOaqpr/e5eh9+sPGKqos=";
+      excludes = [ ".github/*" ];
+    })
+  ];
+
+  build-system = [
+    setuptools
+  ];
+
+  propagatedBuildInputs = [ colormath ];
+
+  nativeCheckInputs = [
+    pytestCheckHook
+  ];
+
+  meta = {
+    description = "Python library that makes color math, color scales, and color-space conversion easy";
+    homepage = "https://github.com/jsvine/spectra";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ apraga ];
+  };
+}

pkgs/top-level/python-packages.nix

@@ -15270,6 +15270,8 @@ self: super: with self; {
 
   speaklater3 = callPackage ../development/python-modules/speaklater3 { };
 
+  spectra = callPackage ../development/python-modules/spectra { };
+
   spectral-cube = callPackage ../development/python-modules/spectral-cube { };
 
   speechbrain = callPackage ../development/python-modules/speechbrain { };