Merge master into staging-next

nixos/tests/minio.nix

@@ -43,17 +43,17 @@ import ./make-test-python.nix ({ pkgs, ... }:
 
         # Minio requires at least 1GiB of free disk space to run.
         virtualisation.diskSize = 4 * 1024;
+
+        # Minio pre allocates 2GiB or memory, reserve some more
+        virtualisation.memorySize = 4096;
       };
     };
 
     testScript = ''
-      import time
 
       start_all()
       # simulate manually editing root credentials file
       machine.wait_for_unit("multi-user.target")
-      machine.copy_from_host("${credsPartial}", "${rootCredentialsFile}")
-      time.sleep(3)
       machine.copy_from_host("${credsFull}", "${rootCredentialsFile}")
 
       machine.wait_for_unit("minio.service")

pkgs/applications/misc/cartridges/default.nix

@@ -29,6 +29,9 @@ stdenv.mkDerivation (finalAttrs: {
     requests
   ];
 
+  # TODO: remove this when #286814 hits master
+  mesonFlags = [ "-Dtiff_compression=jpeg" ];
+
   buildInputs = [
     libadwaita
     (python3Packages.python.withPackages (_: finalAttrs.pythonPath))

pkgs/applications/misc/duden/default.nix

@@ -1,40 +0,0 @@
-{ lib
-, python3
-, fetchFromGitHub
-}:
-
-python3.pkgs.buildPythonPackage rec {
-  pname = "duden";
-  version = "0.18.0";
-  format = "pyproject";
-
-  src = fetchFromGitHub {
-    owner = "radomirbosak";
-    repo = "duden";
-    rev = version;
-    hash = "sha256-ZrarN09Znw4m6YiZxD7q7dTJ49WjmHDobLnOt8JCwvc=";
-  };
-
-  nativeBuildInputs = [
-    python3.pkgs.poetry-core
-  ];
-
-  propagatedBuildInputs = with python3.pkgs; [
-    beautifulsoup4
-    crayons
-    pyxdg
-    pyyaml
-    requests
-    setuptools
-  ];
-
-  pythonImportsCheck = [ "duden" ];
-
-  meta = with lib; {
-    description = "CLI for http://duden.de dictionary written in Python";
-    homepage = "https://github.com/radomirbosak/duden";
-    changelog = "https://github.com/radomirbosak/duden/blob/${src.rev}/CHANGELOG.md";
-    license = licenses.mit;
-    maintainers = with maintainers; [ ];
-  };
-}

pkgs/applications/science/molecular-dynamics/lammps/default.nix

@@ -46,14 +46,14 @@
 stdenv.mkDerivation (finalAttrs: {
   # LAMMPS has weird versioning convention. Updates should go smoothly with:
   # nix-update --commit lammps --version-regex 'stable_(.*)'
-  version = "2Aug2023_update2";
+  version = "2Aug2023_update3";
   pname = "lammps";
 
   src = fetchFromGitHub {
     owner = "lammps";
     repo = "lammps";
     rev = "stable_${finalAttrs.version}";
-    hash = "sha256-E918Jv6RAfXmHxyHZos2F7S8HFWzU6KjxDwXYNAYFMY=";
+    hash = "sha256-jx0hkiYxQlnE2sa4WTvluEgphF//sNbK91VGAQJMwjw=";
   };
   preConfigure = ''
     cd cmake

pkgs/by-name/pr/presenterm/package.nix

@@ -9,20 +9,20 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "presenterm";
-  version = "0.6.1";
+  version = "0.7.0";
 
   src = fetchFromGitHub {
     owner = "mfontanini";
     repo = "presenterm";
     rev = "refs/tags/v${version}";
-    hash = "sha256-+XESFDseRScWYOry58JLknGv+xhewTKx38lrzQu2mQ4=";
+    hash = "sha256-I5L+Wygj9ApQu/5fm55okwNbyxOiF++7BDl765MLnjY=";
   };
 
   buildInputs = [
     libsixel
   ];
 
-  cargoHash = "sha256-xZLGm+tGAmmo/OzDMrgQK0uH7GMG6fTkpPsXwLe94VM=";
+  cargoHash = "sha256-w1uXCH8Ybf78EPTIKrhPlPHAnNBp1iiBpFJHY98IPWY=";
 
   # Crashes at runtime on darwin with:
   # Library not loaded: .../out/lib/libsixel.1.dylib

pkgs/by-name/se/sequoia-sq/package.nix

@@ -1,31 +1,44 @@
 { stdenv
 , fetchFromGitLab
+, fetchpatch
 , lib
 , darwin
 , nettle
 , nix-update-script
 , rustPlatform
 , pkg-config
+, capnproto
+, installShellFiles
 , openssl
 , sqlite
 }:
 
 rustPlatform.buildRustPackage rec {
   pname = "sequoia-sq";
-  version = "0.32.0";
+  version = "0.34.0";
 
   src = fetchFromGitLab {
     owner = "sequoia-pgp";
     repo = "sequoia-sq";
     rev = "v${version}";
-    hash = "sha256-2a6LIW5ohSi7fbMwk/wmNJ0AOz5JIXiXJI7EoVKv1Sk=";
+    hash = "sha256-voFektWZnkmIQzI7s5nKzVVWQtEhzk2GKtxX926RtxU=";
   };
+  patches = [
+    # Fixes test failing on Darwin, see:
+    # https://gitlab.com/sequoia-pgp/sequoia-sq/-/issues/211
+    (fetchpatch {
+      url = "https://gitlab.com/sequoia-pgp/sequoia-sq/-/commit/21221a935e0d058ed269ae6c8f45c5fa7ea0d598.patch";
+      hash = "sha256-ZjTl3EumeFwMJUl+qMpX+P2maYz4Ow/Tn9KwYbHDbes=";
+    })
+  ];
 
-  cargoHash = "sha256-beA0viJVDjfANsPegkc/x2syVp8uGKTMnrPcM7jcvG4=";
+  cargoHash = "sha256-3ncBpRi0v6g6wwPkSASDwt0d8cOOAUv9BwZaYvnif1U=";
 
   nativeBuildInputs = [
     pkg-config
     rustPlatform.bindgenHook
+    capnproto
+    installShellFiles
   ];
 
   buildInputs = [
@@ -41,14 +54,19 @@ rustPlatform.buildRustPackage rec {
     "--skip=macros::time_it"
   ];
 
-  # Install manual pages, see https://gitlab.com/sequoia-pgp/sequoia-sq#building
+  env.ASSET_OUT_DIR = "/tmp/";
-  postInstall = ''
-    mkdir -p $out/share/man
-    SQ_MAN=$out/share/man/man1 cargo run
-  '';
 
   doCheck = true;
 
+  postInstall = ''
+    installManPage /tmp/man-pages/*.*
+    installShellCompletion \
+      --cmd sq \
+      --bash /tmp/shell-completions/sq.bash \
+      --fish /tmp/shell-completions/sq.fish \
+      --zsh /tmp/shell-completions/_sq
+  '';
+
   passthru.updateScript = nix-update-script { };
 
   meta = with lib; {

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

@@ -1,9 +1,12 @@
 { lib
 , fetchPypi
 , buildPythonPackage
+, fetchpatch
 , dask
 , urllib3
 , geojson
+, verlib2
+, pueblo
 , pandas
 , pythonOlder
 , sqlalchemy
@@ -13,20 +16,35 @@
 
 buildPythonPackage rec {
   pname = "crate";
-  version = "0.34.0";
+  version = "0.35.2";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-nEWrfCd2MQCcIM6dLkVYc/cWT5wcT/pvYaY2V3wfuto=";
+    hash = "sha256-4hGACtsK71hvcn8L9ggID7zR+umtTwvskBxSHBpLyME=";
   };
+  patches = [
+    # Fix a pandas issue https://github.com/crate/crate-python/commit/db7ba4d0e1f4f4087739a8f9ebe1d71946333979
+    (fetchpatch {
+      url = "https://github.com/crate/crate-python/commit/db7ba4d0e1f4f4087739a8f9ebe1d71946333979.patch";
+      hash = "sha256-20g8T0t5gPMbK6kRJ2bzc4BNbB1Dg4hvngXNUPvxi5I=";
+      name = "python-crate-fix-pandas-error.patch";
+      # Patch doesn't apply due to other changes to these files
+      excludes = [
+        "setup.py"
+        "docs/by-example/sqlalchemy/dataframe.rst"
+      ];
+    })
+  ];
 
   propagatedBuildInputs = [
     urllib3
     sqlalchemy
     geojson
+    verlib2
+    pueblo
   ];
 
   nativeCheckInputs = [

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

@@ -0,0 +1,56 @@
+{ lib
+, beautifulsoup4
+, buildPythonPackage
+, crayons
+, fetchFromGitHub
+, poetry-core
+, pyxdg
+, pyyaml
+, requests
+, setuptools
+}:
+
+let
+  finalAttrs = {
+    pname = "duden";
+    version = "0.19.1";
+    pyproject = true;
+
+    src = fetchFromGitHub {
+      owner = "radomirbosak";
+      repo = "duden";
+      rev = finalAttrs.version;
+      hash = "sha256-c6IItrjFVbsdYg3sDrExcxv7aRcKhd/M5hiZD+wBZ2Y=";
+    };
+
+    nativeBuildInputs = [
+      poetry-core
+    ];
+
+    propagatedBuildInputs = [
+      beautifulsoup4
+      crayons
+      pyxdg
+      pyyaml
+      requests
+      setuptools
+    ];
+
+    pythonImportsCheck = [ "duden" ];
+
+    meta = {
+      homepage = "https://github.com/radomirbosak/duden";
+      changelog = "https://github.com/radomirbosak/duden/blob/${finalAttrs.src.rev}/CHANGELOG.md";
+      description = "CLI for https://duden.de dictionary written in Python";
+      longDescription = ''
+        duden is a CLI-based program and python module, which can provide
+        various information about given german word. The provided data are
+        parsed from german dictionary duden.de.
+      '';
+      license = with lib.licenses; [ mit ];
+      mainProgram = "duden";
+      maintainers = with lib.maintainers; [ AndersonTorres linuxissuper ];
+    };
+  };
+in
+buildPythonPackage finalAttrs

pkgs/development/python-modules/langchain-core/default.nix

@@ -16,7 +16,7 @@
 
 buildPythonPackage rec {
   pname = "langchain-core";
-  version = "0.1.27";
+  version = "0.1.28";
   pyproject = true;
 
   disabled = pythonOlder "3.8";
@@ -24,7 +24,7 @@ buildPythonPackage rec {
   src = fetchPypi {
     pname = "langchain_core";
     inherit version;
-    hash = "sha256-aYQUIjUlwLwTDYWmFOFJOQXViKty/gya07U3sdxiBn8=";
+    hash = "sha256-BOdhpRMgC25bWBhhOCGUV5nAe8U0kIfXaS5QgjEHydY=";
   };
 
   pythonRelaxDeps = [

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

@@ -0,0 +1,44 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, setuptools
+, versioningit
+, platformdirs
+}:
+
+buildPythonPackage rec {
+  pname = "pueblo";
+  version = "0.0.8";
+  pyproject = true;
+
+  # This tarball doesn't include tests unfortuneatly, and the GitHub tarball
+  # could have been an alternative, but versioningit fails to detect the
+  # version of it correctly, even with setuptools-scm and
+  # SETUPTOOLS_SCM_PRETEND_VERSION = version added. Since this is a pure Python
+  # package, we can rely on upstream to run the tests before releasing, and it
+  # should work for us as well.
+  src = fetchPypi {
+    inherit pname version;
+    hash = "sha256-iM8Ea2ym7ZM0wInkCZ76yUjvOPRF5MVbT4WhpWz70UU=";
+  };
+
+  nativeBuildInputs = [
+    setuptools
+    versioningit
+  ];
+
+  propagatedBuildInputs = [
+  #  contextlib-chdir
+  #  importlib-metadata
+    platformdirs
+  ];
+
+  pythonImportsCheck = [ "pueblo" ];
+
+  meta = with lib; {
+    description = "Pueblo - a Python toolbox library";
+    homepage = "https://pypi.org/project/pueblo/";
+    license = licenses.lgpl3Only;
+    maintainers = with maintainers; [ doronbehar ];
+  };
+}

pkgs/development/python-modules/verlib2/default.nix

@@ -0,0 +1,37 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, setuptools
+, versioningit
+}:
+
+buildPythonPackage rec {
+  pname = "verlib2";
+  version = "0.2.0";
+  pyproject = true;
+
+  # This tarball doesn't include tests unfortuneatly, and the GitHub tarball
+  # could have been an alternative, but versioningit fails to detect the
+  # version of it correctly, even with setuptools-scm and
+  # SETUPTOOLS_SCM_PRETEND_VERSION = version added. Since this is a pure Python
+  # package, we can rely on upstream to run the tests before releasing, and it
+  # should work for us as well.
+  src = fetchPypi {
+    inherit pname version;
+    hash = "sha256-CrlAh8CU4nFjlI36gXyY1itr3QEibM5RiPjMPNaDRbk=";
+  };
+
+  nativeBuildInputs = [
+    setuptools
+    versioningit
+  ];
+
+  pythonImportsCheck = [ "verlib2" ];
+
+  meta = with lib; {
+    description = "A standalone variant of packaging.version, without anything else";
+    homepage = "https://pypi.org/project/verlib2/";
+    license = licenses.bsd2;
+    maintainers = with maintainers; [ doronbehar ];
+  };
+}

pkgs/development/tools/language-servers/vhdl-ls/default.nix

@@ -5,16 +5,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "vhdl-ls";
-  version = "0.77.0";
+  version = "0.78.0";
 
   src = fetchFromGitHub {
     owner = "VHDL-LS";
     repo = "rust_hdl";
     rev = "v${version}";
-    hash = "sha256-IAe4m/GC6ubCcZZESC6fToWVQT73XrhjJOiGCGzNxnQ=";
+    hash = "sha256-R1ACYsN2GxpWkUd8kocbv3tnBOiu7PzjtSG8hWbCYfE=";
   };
 
-  cargoHash = "sha256-p7BL8WuQiB1KihwAl5aeO6Fa9INYRTQgoQPHcSMnaiQ=";
+  cargoHash = "sha256-xt9v0QvHgej+YTIKGWfsEmLNy9RZp/mahPjKz3QWPrk=";
 
   postPatch = ''
     substituteInPlace vhdl_lang/src/config.rs \

pkgs/development/tools/rust/cargo-cyclonedx/default.nix

@@ -12,16 +12,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "cargo-cyclonedx";
-  version = "0.4.1";
+  version = "0.5.0";
 
   src = fetchFromGitHub {
     owner = "CycloneDX";
     repo = "cyclonedx-rust-cargo";
     rev = "${pname}-${version}";
-    hash = "sha256-JrusJsMjaWAsWAssU+q87BCH2ouLfthIw47ypwBkR9o=";
+    hash = "sha256-791FZR9dmwVjORrkpm8el+2VMEEKJG+yKKqq+R1I9U4=";
   };
 
-  cargoHash = "sha256-QzEojbwBF7s3C+LlFWle0+8DVtyEljuqAcMAyRJqFcs=";
+  cargoHash = "sha256-Cbi1cnUy6HKkgBXVjK0xItx2pzuYVob/Qz4o8eT6Fws=";
 
   nativeBuildInputs = [
     pkg-config

pkgs/games/sgt-puzzles/default.nix

@@ -6,11 +6,11 @@
 
 stdenv.mkDerivation rec {
   pname = "sgt-puzzles";
-  version = "20240103.7a93ae5";
+  version = "20240302.80aac31";
 
   src = fetchurl {
     url = "http://www.chiark.greenend.org.uk/~sgtatham/puzzles/puzzles-${version}.tar.gz";
-    hash = "sha256-1pTruSF+Kl1wqTFIaYYHrvbD9p+k+1PGa5PpV4jvgEk=";
+    hash = "sha256-0+bmGq4wM+0/ldQz8ieKdkuG0HHazctQr9ul/qLT0gg=";
   };
 
   sgt-puzzles-menu = fetchurl {

pkgs/servers/minio/default.nix

@@ -21,13 +21,13 @@ let
 in
 buildGoModule rec {
   pname = "minio";
-  version = "2024-02-24T17-11-14Z";
+  version = "2024-02-26T09-33-48Z";
 
   src = fetchFromGitHub {
     owner = "minio";
     repo = "minio";
     rev = "RELEASE.${version}";
-    hash = "sha256-LD32cNKvW0mfYeXHNOqgiWXAiHjWJrorRqbQkosjaNE=";
+    hash = "sha256-V5Pmp36YA0u1Z2SBNdJZAHQuA3PgVKHmIJlDElhS24s=";
   };
 
   vendorHash = "sha256-0EymK7jQhr+NJDg1zgWpcniV5zZ33Av6zpq0IDuWw7M=";

pkgs/servers/squid/default.nix

@@ -5,11 +5,11 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "squid";
-  version = "6.6";
+  version = "6.7";
 
   src = fetchurl {
     url = "http://www.squid-cache.org/Versions/v6/${finalAttrs.pname}-${finalAttrs.version}.tar.xz";
-    hash = "sha256-Vb1/n0iYFTFh6hIomYrLVRv4QIMrnluQ/I7NKUJCAxg=";
+    hash = "sha256-4U2qTq5Bkl0a4/COZEOaaqowEb3O1oZii43ml9WrhCg=";
   };
 
   nativeBuildInputs = [ pkg-config ];

pkgs/tools/misc/blahaj/default.nix

@@ -1,6 +1,10 @@
 { lib
+, stdenv
 , crystal
 , fetchFromGitHub
+  # https://crystal-lang.org/2019/09/06/parallelism-in-crystal/
+, multithreading ? true
+, static ? stdenv.hostPlatform.isStatic
 }:
 
 crystal.buildCrystalPackage rec {
@@ -14,6 +18,8 @@ crystal.buildCrystalPackage rec {
     hash = "sha256-CmMF9jDKUo+c8dYc2UEHKdBDE4dgwExcRS5sSUsUJik=";
   };
 
+  buildTargets = [ "${if static then "static" else "build"}${if multithreading then "_mt" else ""}" ];
+
   meta = with lib; {
     description = "Gay sharks at your local terminal - lolcat-like CLI tool";
     homepage = "https://blahaj.queer.software";

pkgs/tools/networking/minio-client/default.nix

@@ -2,16 +2,16 @@
 
 buildGoModule rec {
   pname = "minio-client";
-  version = "2024-02-16T11-05-48Z";
+  version = "2024-02-24T01-33-20Z";
 
   src = fetchFromGitHub {
     owner = "minio";
     repo = "mc";
     rev = "RELEASE.${version}";
-    sha256 = "sha256-Kqv48krXiDi/8QtCEpn0uGvuLS2P6BYAtSnY5sNrCQ0=";
+    sha256 = "sha256-WWQwrrsYyJ96rVORSmxqid2bhYvkOREpP03uQ/Bbj9Q=";
   };
 
-  vendorHash = "sha256-wxFhj+oqj5WV/UkPZlmeJHF2WC4oLlZOql1qgSFs+zU=";
+  vendorHash = "sha256-yteWhm9GxNIiYhuCxrlLqP2OzZ1iv1UmpEj8GH8LIWY=";
 
   subPackages = [ "." ];
 

pkgs/tools/wayland/swayrbar/default.nix

@@ -2,16 +2,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "swayrbar";
-  version = "0.3.7";
+  version = "0.3.8";
 
   src = fetchFromSourcehut {
     owner = "~tsdh";
     repo = "swayr";
     rev = "swayrbar-${version}";
-    sha256 = "sha256-41zlVT060Fu90N4oiZ6lWSZdJJSZjyk3GEA/u+bVNCI=";
+    sha256 = "sha256-pCXkgIesHqXI/m8ecytlq+U62lIrf7bOv95Hi/nyf/g=";
   };
 
-  cargoHash = "sha256-/MUolnEdYlBTfmUB/j9vHaVpU63upeMoScjHl38cGjo=";
+  cargoHash = "sha256-RSdNYr6l9ayn9anczeGGh2rkKt6COqj+H71d14Gb8r0=";
 
   # don't build swayr
   buildAndTestSubdir = pname;

pkgs/top-level/all-packages.nix

@@ -13022,8 +13022,6 @@ with pkgs;
 
   seqdiag = with python3Packages; toPythonApplication seqdiag;
 
-  sequoia-sq = callPackage ../tools/security/sequoia-sq { };
-
   sequoia-sqv = callPackage ../tools/security/sequoia-sqv { };
 
   sequoia-sqop = callPackage ../tools/security/sequoia-sqop { };
@@ -41726,7 +41724,7 @@ with pkgs;
 
   udict = callPackage ../applications/misc/udict { };
 
-  duden = callPackage ../applications/misc/duden { };
+  duden = python3Packages.toPythonApplication python3Packages.duden;
 
   zf = callPackage ../tools/misc/zf { };
 

pkgs/top-level/python-packages.nix

@@ -1310,6 +1310,8 @@ self: super: with self; {
 
   paddlepaddle = callPackage ../development/python-modules/paddlepaddle { };
 
+  pueblo = callPackage ../development/python-modules/pueblo { };
+
   pulumi = callPackage ../development/python-modules/pulumi { inherit (pkgs) pulumi; };
 
   pulumi-aws = callPackage ../development/python-modules/pulumi-aws { };
@@ -3500,6 +3502,8 @@ self: super: with self; {
 
   duct-py = callPackage ../development/python-modules/duct-py { };
 
+  duden = callPackage ../development/python-modules/duden { };
+
   duecredit = callPackage ../development/python-modules/duecredit { };
 
   duet = callPackage ../development/python-modules/duet { };
@@ -16144,6 +16148,8 @@ self: super: with self; {
 
   verboselogs = callPackage ../development/python-modules/verboselogs { };
 
+  verlib2 = callPackage ../development/python-modules/verlib2 { };
+
   versioneer = callPackage ../development/python-modules/versioneer { };
 
   versionfinder = callPackage ../development/python-modules/versionfinder { };