Merge staging-next into staging

nixos/modules/services/continuous-integration/buildkite-agents.nix

···
       default = null;
       description = lib.mdDoc description;
       type = types.nullOr types.lines;
-    } // (if example == null then {} else { inherit example; });
+    } // (lib.optionalAttrs (example != null) { inherit example; });
   };
   mkHookOptions = hooks: listToAttrs (map mkHookOption hooks);
 

nixos/modules/services/mail/rspamd.nix

···
       text = v.extraConfig;
     })
     (filterAttrs (n: v: v.extraConfig != "") cfg.workers))
-    // (if cfg.extraConfig == "" then {} else {
+    // (lib.optionalAttrs (cfg.extraConfig != "") {
       "extra-config.inc".text = cfg.extraConfig;
     });
 in

nixos/modules/services/web-apps/mattermost.nix

···
   mattermostConf = recursiveUpdate
     mattermostConfWithoutPlugins
     (
-      if mattermostPlugins == null then {}
-      else {
+      lib.optionalAttrs (mattermostPlugins != null) {
         PluginSettings = {
           Enable = true;
         };

pkgs/applications/networking/nextcloud-client/default.nix

···
 
 mkDerivation rec {
   pname = "nextcloud-client";
-  version = "3.8.2";
+  version = "3.9.0";
 
   outputs = [ "out" "dev" ];
 
···
     owner = "nextcloud";
     repo = "desktop";
     rev = "v${version}";
-    sha256 = "sha256-V5g6+Ci2MjBKnitY6IIaMY4gpoeMK+sd7HGZ1U87xL4=";
+    sha256 = "sha256-XcQYttd5dl2TCbBxOlRBg8/mEiHekoxayPi81ot7N7o=";
   };
 
   patches = [

pkgs/applications/science/biology/MACS2/default.nix

···
-{ lib, python3, fetchPypi }:
-
-python3.pkgs.buildPythonPackage rec {
-  pname = "MACS2";
-  version = "2.2.7.1";
-
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "1rcxj943kgzs746f5jrb72x1cp4v50rk3qmad0m99a02vndscb5d";
-  };
-
-  postPatch = ''
-    # remove version check which breaks on 3.10
-    substituteInPlace setup.py \
-      --replace 'if float(sys.version[:3])<3.6:' 'if False:'
-  '';
-
-  propagatedBuildInputs = with python3.pkgs; [ numpy ];
-
-  # To prevent ERROR: diffpeak_cmd (unittest.loader._FailedTest) for obsolete
-  # function (ImportError: Failed to import test module: diffpeak_cmd)
-  doCheck = false;
-  pythonImportsCheck = [ "MACS2" ];
-
-  meta = with lib; {
-    description = "Model-based Analysis for ChIP-Seq";
-    license = licenses.bsd3;
-    maintainers = with maintainers; [ gschwartz ];
-    platforms = platforms.linux;
-    # error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘use_tracing’; did you mean ‘tracing’?
-    broken = true;
-  };
-}

pkgs/applications/science/biology/macs2/default.nix

···
+{ lib, python3, fetchPypi }:
+
+python3.pkgs.buildPythonPackage rec {
+  pname = "macs2";
+  version = "2.2.8";
+  format = "pyproject";
+
+  src = fetchPypi {
+    pname = lib.toUpper pname;
+    inherit version;
+    hash = "sha256-KgpDasidj4yUoeQQaQA3dg5eN5Ka1xnFRpbnTvhKmOA=";
+  };
+
+  postPatch = ''
+    # prevent setup.py from installing numpy
+    substituteInPlace setup.py \
+      --replace "subprocess.call([sys.executable, \"-m\", 'pip', 'install', f'numpy{numpy_requires}'],cwd=cwd)" "0"
+  '';
+
+  nativeBuildInputs = with python3.pkgs; [
+    cython
+    setuptools
+  ];
+
+  propagatedBuildInputs = with python3.pkgs; [ numpy ];
+
+  nativeCheckInputs = [
+    python3.pkgs.unittestCheckHook
+  ];
+
+  unittestFlagsArray = [
+    "-s"
+    "test"
+  ];
+
+  pythonImportsCheck = [ "MACS2" ];
+
+  meta = with lib; {
+    description = "Model-based Analysis for ChIP-Seq";
+    homepage = "https://github.com/macs3-project/MACS/";
+    changelog = "https://github.com/macs3-project/MACS/releases/tag/v${version}";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ gschwartz ];
+  };
+}

pkgs/applications/science/misc/gplates/boost-placeholders.patch

···
+diff --unified --recursive a/src/gui/TopologyTools.cc b/src/gui/TopologyTools.cc
+--- a/src/gui/TopologyTools.cc	2021-07-05 05:11:47.000000000 +0200
++++ b/src/gui/TopologyTools.cc	2022-12-07 22:35:20.444054124 +0100
+@@ -3448,7 +3448,7 @@
+ 			std::find_if(
+ 					d_visible_boundary_section_seq.begin(),
+ 					d_visible_boundary_section_seq.end(),
+-					boost::bind(&VisibleSection::d_section_info_index, _1) ==
++					boost::bind(&VisibleSection::d_section_info_index, boost::placeholders::_1) ==
+ 						boost::cref(section_index));
+ 
+ 	if (visible_section_iter == d_visible_boundary_section_seq.end())
+@@ -3467,7 +3467,7 @@
+ 			std::find_if(
+ 					d_visible_interior_section_seq.begin(),
+ 					d_visible_interior_section_seq.end(),
+-					boost::bind(&VisibleSection::d_section_info_index, _1) ==
++					boost::bind(&VisibleSection::d_section_info_index, boost::placeholders::_1) ==
+ 						boost::cref(section_index));
+ 
+ 	if (visible_section_iter == d_visible_interior_section_seq.end())
+diff --unified --recursive a/src/presentation/ReconstructionGeometryRenderer.cc b/src/presentation/ReconstructionGeometryRenderer.cc
+--- a/src/presentation/ReconstructionGeometryRenderer.cc	2021-07-05 05:11:50.000000000 +0200
++++ b/src/presentation/ReconstructionGeometryRenderer.cc	2022-12-07 22:36:11.117884262 +0100
+@@ -274,7 +274,7 @@
+ GPlatesPresentation::ReconstructionGeometryRenderer::RenderParamsPopulator::visit_reconstruct_visual_layer_params(
+ 		const ReconstructVisualLayerParams &params)
+ {
+-	d_render_params.show_vgp = boost::bind(&ReconstructVisualLayerParams::show_vgp, &params, _1, _2);
++	d_render_params.show_vgp = boost::bind(&ReconstructVisualLayerParams::show_vgp, &params, boost::placeholders::_1, boost::placeholders::_2);
+ 	d_render_params.vgp_draw_circular_error = params.get_vgp_draw_circular_error();
+ 	d_render_params.fill_polygons = params.get_fill_polygons();
+ 	d_render_params.fill_polylines = params.get_fill_polylines();
+diff --unified --recursive a/src/presentation/VisualLayerRegistry.cc b/src/presentation/VisualLayerRegistry.cc
+--- a/src/presentation/VisualLayerRegistry.cc	2021-07-05 05:11:50.000000000 +0200
++++ b/src/presentation/VisualLayerRegistry.cc	2022-12-07 22:38:12.950877614 +0100
+@@ -448,7 +448,7 @@
+ 			&GPlatesQtWidgets::ReconstructScalarCoverageLayerOptionsWidget::create,
+ 			boost::bind(
+ 					&ReconstructScalarCoverageVisualLayerParams::create,
+-					_1),
++					boost::placeholders::_1),
+ 			true);
+ 
+ 	registry.register_visual_layer_type(
+@@ -498,7 +498,7 @@
+ 					// NOTE: We pass in ViewState and not the GlobeAndMapWidget, obtained from
+ 					// ViewportWindow, because ViewportWindow is not yet available (a reference to
+ 					// it not yet been initialised inside ViewState) so accessing it would crash...
+-					_1, boost::ref(view_state)),
++					boost::placeholders::_1, boost::ref(view_state)),
+ 			true);
+ 
+ 	// DERIVED_DATA group.
+@@ -549,7 +549,7 @@
+ 			&GPlatesQtWidgets::VelocityFieldCalculatorLayerOptionsWidget::create,
+ 			boost::bind(
+ 					&VelocityFieldCalculatorVisualLayerParams::create,
+-					_1, boost::cref(view_state.get_rendered_geometry_parameters())),
++					boost::placeholders::_1, boost::cref(view_state.get_rendered_geometry_parameters())),
+ 			true);
+ 
+ 	using namespace  GPlatesUtils;
+diff --unified --recursive a/src/qt-widgets/ViewportWindow.cc b/src/qt-widgets/ViewportWindow.cc
+--- a/src/qt-widgets/ViewportWindow.cc	2021-08-05 05:44:01.000000000 +0200
++++ b/src/qt-widgets/ViewportWindow.cc	2022-12-07 22:39:20.487981302 +0100
+@@ -326,7 +326,7 @@
+ 			*d_geometry_operation_state_ptr,
+ 			*d_modify_geometry_state,
+ 			*d_measure_distance_state_ptr,
+-			boost::bind(&canvas_tool_status_message, boost::ref(*this), _1),
++			boost::bind(&canvas_tool_status_message, boost::ref(*this), boost::placeholders::_1),
+ 			get_view_state(),
+ 			*this);
+ 

pkgs/applications/science/misc/gplates/default.nix

···
     sha256 = "0lrcmcxc924ixddii8cyglqlwwxvk7f00g4yzbss5i3fgcbh8n96";
   };
 
+  patches = [
+    ./boost-placeholders.patch
+  ];
+
   nativeBuildInputs = [
     cmake
     doxygen

pkgs/applications/window-managers/sway/default.nix

···
 { lib, stdenv, fetchFromGitHub, fetchpatch, substituteAll, swaybg
 , meson, ninja, pkg-config, wayland-scanner, scdoc
 , wayland, libxkbcommon, pcre2, json_c, libevdev
-, pango, cairo, libinput, libcap, pam, gdk-pixbuf, librsvg
+, pango, cairo, libinput, gdk-pixbuf, librsvg
 , wlroots_0_16, wayland-protocols, libdrm
 , nixosTests
 # Used by the NixOS module:
 , isNixOS ? false
 , enableXWayland ? true, xorg
 , systemdSupport ? lib.meta.availableOn stdenv.hostPlatform systemd, systemd
-, dbusSupport ? true
-, dbus
-, trayEnabled ? systemdSupport && dbusSupport
+, trayEnabled ? systemdSupport
 }:
 
 # The "sd-bus-provider" meson option does not include a "none" option,
 # but it is silently ignored iff "-Dtray=disabled".  We use "basu"
 # (which is not in nixpkgs) instead of "none" to alert us if this
 # changes: https://github.com/swaywm/sway/issues/6843#issuecomment-1047288761
-assert trayEnabled -> systemdSupport && dbusSupport;
+assert trayEnabled -> systemdSupport;
 let sd-bus-provider = if systemdSupport then "libsystemd" else "basu"; in
 
 stdenv.mkDerivation rec {
···
 
   buildInputs = [
     wayland libxkbcommon pcre2 json_c libevdev
-    pango cairo libinput libcap pam gdk-pixbuf librsvg
+    pango cairo libinput gdk-pixbuf librsvg
     wayland-protocols libdrm
     (wlroots_0_16.override { inherit enableXWayland; })
-  ] ++ lib.optionals dbusSupport [
-    dbus
   ] ++ lib.optionals enableXWayland [
     xorg.xcbutilwm
   ];

pkgs/data/icons/numix-icon-theme-circle/default.nix

···
 
 stdenvNoCC.mkDerivation rec {
   pname = "numix-icon-theme-circle";
-  version = "23.05.15";
+  version = "23.06.11";
 
   src = fetchFromGitHub {
     owner = "numixproject";
     repo = pname;
     rev = version;
-    sha256 = "sha256-jZ++x2xtwmCYqv1jdJuNM2sHpmvkv6gj8Xo4PN2Vjsk=";
+    sha256 = "sha256-bEUT6hBAKyilbUWSbyvGRuIwatooJ3k/mvVJg1PncjA=";
   };
 
   nativeBuildInputs = [ gtk3 ];

pkgs/data/icons/numix-icon-theme-square/default.nix

···
 
 stdenvNoCC.mkDerivation rec {
   pname = "numix-icon-theme-square";
-  version = "23.05.15";
+  version = "23.06.11";
 
   src = fetchFromGitHub {
     owner = "numixproject";
     repo = pname;
     rev = version;
-    sha256 = "sha256-tcEVwc3Ez0h9JwiHyYfMvdTfUaivy4sH3QJR9tP1LSk=";
+    sha256 = "sha256-pm3sEx3OJkS4sz+sg09HeTSdQZTdjyxJCsjYWCA4mN0=";
   };
 
   nativeBuildInputs = [ gtk3 ];

pkgs/development/coq-modules/tlc/default.nix

···
     maintainers = [ maintainers.vbgl ];
   };
 }).overrideAttrs (x:
-  if lib.versionAtLeast x.version "20210316"
-  then {}
-  else {
+  lib.optionalAttrs (lib.versionOlder x.version "20210316") {
     installFlags = [ "CONTRIB=$(out)/lib/coq/${coq.coq-version}/user-contrib" ];
   }
 )

pkgs/development/libraries/httplib/default.nix

···
 
 stdenv.mkDerivation rec {
   pname = "httplib";
-  version = "0.12.5";
+  version = "0.12.6";
 
   src = fetchFromGitHub {
     owner = "yhirose";
     repo = "cpp-httplib";
     rev = "v${version}";
-    hash = "sha256-9qCquF6DXpgtrfXVd/hc8n1Eu1nOxf/Lm+R13QI0N9Q=";
+    hash = "sha256-7bH7bq6lsobf5ZEyxPXPqPopZyn9NKInlqmuNzmHkkM=";
   };
 
   nativeBuildInputs = [ cmake ];

pkgs/development/libraries/qtkeychain/0002-Fix-install-name-Darwin.patch

···
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -215,7 +215,6 @@
-     VERSION ${QTKEYCHAIN_VERSION}
-     SOVERSION ${QTKEYCHAIN_SOVERSION}
-     MACOSX_RPATH 1
--    INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}"
-     INSTALL_RPATH_USE_LINK_PATH TRUE
- )
- 

pkgs/development/libraries/qtkeychain/default.nix

···
 
 stdenv.mkDerivation rec {
   pname = "qtkeychain";
-  version = "0.12.0";
+  version = "0.14.1";
 
   src = fetchFromGitHub {
     owner = "frankosterfeld";
     repo = "qtkeychain";
-    rev = "v${version}";
-    sha256 = "0gi1nx4bcc1vwfw41cif3xi2i59229vy0kc2r5959d8n6yv31kfr"; # v0.9.1
+    rev = "${version}";
+    sha256 = "sha256-LclYOuIYn+jYCvg69uHFlV3VcZ2KWdr8lFyCSBIB7Kw=";
   };
 
   dontWrapQtApps = true;
-
-  patches = [ ./0002-Fix-install-name-Darwin.patch ];
 
   cmakeFlags = [
     "-DBUILD_WITH_QT6=${if lib.versions.major qtbase.version == "6" then "ON" else "OFF"}"

pkgs/development/lisp-modules-obsolete/quicklisp-to-nix-overrides.nix

···
   skipBuildPhase = x: {
     overrides = y: ((x.overrides y) // { buildPhase = "true"; });
   };
-  multiOverride = l: x: if l == [] then {} else
-    ((builtins.head l) x) // (multiOverride (builtins.tail l) x);
+  multiOverride = l: x: pkgs.lib.optionalAttrs (l != []) (((builtins.head l) x) // (multiOverride (builtins.tail l) x));
   lispName = (clwrapper.lisp.pname or (builtins.parseDrvName clwrapper.lisp.name).name);
   ifLispIn = l: f: if (pkgs.lib.elem lispName l) then f else (x: {});
   ifLispNotIn = l: f: if ! (pkgs.lib.elem lispName l) then f else (x: {});

pkgs/development/tools/codespelunker/default.nix

···
 
 buildGoModule rec {
   pname = "codespelunker";
-  version = "1.0.0";
+  version = "1.2.0";
 
   src = fetchFromGitHub {
     owner = "boyter";
     repo = "cs";
     rev = "v${version}";
-    hash = "sha256-NN/78paePdvYHQ4J2aQu56PvEciOXY8DxHd4ajfVCFU=";
+    hash = "sha256-kWKDr8KKD3M5MyRuEMMZXvTqflDidkMsu2fN9N0s50w=";
   };
 
   vendorHash = null;

pkgs/games/openttd/default.nix

···
 in
 stdenv.mkDerivation rec {
   pname = "openttd";
-  version = "13.1";
+  version = "13.3";
 
   src = fetchurl {
     url = "https://cdn.openttd.org/openttd-releases/${version}/${pname}-${version}-source.tar.xz";
-    hash = "sha256-Xt8i03A1I4KF72cql9WeZCgL66sj5YR4CDTM1r4KWLs=";
+    hash = "sha256-qvoW0vtnFlE0xzqIj3n3pe19oXoEz26ez2csnLiecZI=";
   };
 
   nativeBuildInputs = [ cmake makeWrapper ];

pkgs/games/openttd/jgrpp.nix

···
 
 openttd.overrideAttrs (oldAttrs: rec {
   pname = "openttd-jgrpp";
-  version = "0.53.1";
+  version = "0.54.1";
 
   src = fetchFromGitHub rec {
     owner = "JGRennison";
     repo = "OpenTTD-patches";
     rev = "jgrpp-${version}";
-    hash = "sha256-+5AOsop3x1fkX5UfxMFLhrTLeSnt+E0PYoU5n31N3f4=";
+    hash = "sha256-MfYh2a3wjWB/5zgTE8AAIREI2OEhykqF0Rad7I+912U=";
   };
 
   buildInputs = oldAttrs.buildInputs ++ [ zstd ];

pkgs/servers/bird-lg/default.nix

···
   generic = { modRoot, vendorSha256 }:
     buildGoModule rec {
       pname = "bird-lg-${modRoot}";
-      version = "1.2.0";
+      version = "1.3.0";
 
       src = fetchFromGitHub {
         owner = "xddxdd";
         repo = "bird-lg-go";
         rev = "v${version}";
-        sha256 = "sha256-Ldp/c1UU5EFnKjlUqQ+Hh6rVEOYEX7kaDL36edr9pNA=";
+        hash = "sha256-VQJHrC9ag697QfCEre1KvwbotfMm8f1otJ6SPg5zRYM=";
       };
 
       doDist = false;
···
 
   bird-lg-frontend = generic {
     modRoot = "frontend";
-    vendorSha256 = "sha256-lYOi3tfXYhsFaWgikDUoJYRm8sxFNFKiFQMlVx/8AkA=";
+    vendorSha256 = "sha256-4ajQp425SFciTi2DV3ITW4iQkq6kUJFK2BabTTb87Zo=";
   };
 
   bird-lg-proxy = generic {
     modRoot = "proxy";
-    vendorSha256 = "sha256-QHLq4RuQaCMjefs7Vl7zSVgjLMDXvIZcM8d6/B5ECZc=";
+    vendorSha256 = "sha256-o8F3uNGpz1fZr15HCY2PC7xRx9NakmvYrVQKe42ElOA=";
   };
 in
 symlinkJoin {

pkgs/servers/code-server/default.nix

···
-{ lib, stdenv, fetchFromGitHub, buildGoModule, makeWrapper
-, cacert, moreutils, jq, git, rsync, pkg-config, yarn, python3
-, esbuild, nodejs_16, node-gyp, libsecret, xorg, ripgrep
-, AppKit, Cocoa, CoreServices, Security, cctools, xcbuild, quilt, nixosTests }:
+{ lib
+, stdenv
+, fetchFromGitHub
+, buildGoModule
+, makeWrapper
+, cacert
+, moreutils
+, jq
+, git
+, rsync
+, pkg-config
+, yarn
+, python3
+, esbuild
+, nodejs
+, node-gyp
+, libsecret
+, xorg
+, ripgrep
+, AppKit
+, Cocoa
+, CoreServices
+, Security
+, cctools
+, xcbuild
+, quilt
+, nixosTests
+}:
 
 let
   system = stdenv.hostPlatform.system;
 
-  nodejs = nodejs_16;
   python = python3;
   yarn' = yarn.override { inherit nodejs; };
   defaultYarnOpts = [ ];
···
   };
 
   # replaces esbuild's download script with a binary from nixpkgs
-  patchEsbuild = path : version : ''
+  patchEsbuild = path: version: ''
     mkdir -p ${path}/node_modules/esbuild/bin
     jq "del(.scripts.postinstall)" ${path}/node_modules/esbuild/package.json | sponge ${path}/node_modules/esbuild/package.json
     sed -i 's/${version}/${esbuild'.version}/g' ${path}/node_modules/esbuild/lib/main.js
     ln -s -f ${esbuild'}/bin/esbuild ${path}/node_modules/esbuild/bin/esbuild
   '';
-
-in stdenv.mkDerivation rec {
+in
+stdenv.mkDerivation (finalAttrs: {
   pname = "code-server";
   version = "4.12.0";
 
   src = fetchFromGitHub {
     owner = "coder";
     repo = "code-server";
-    rev = "v${version}";
+    rev = "v${finalAttrs.version}";
     fetchSubmodules = true;
     hash = "sha256-PQp5dji2Ynp+LJRWBka41umwe1/IR76C+at/wyOWGcI=";
   };
 
-  cloudAgent = buildGoModule rec {
-    pname = "cloud-agent";
-    version = "0.2.6";
+  yarnCache = stdenv.mkDerivation {
+    name = "${finalAttrs.pname}-${finalAttrs.version}-${system}-yarn-cache";
+    inherit (finalAttrs) src;
 
-    src = fetchFromGitHub {
-      owner = "coder";
-      repo = "cloud-agent";
-      rev = "v${version}";
-      sha256 = "1s3jpgvzizc9skc27c3x35sya2p4ywhvdi3l73927z3j47wszy7f";
-    };
-
-    vendorSha256 = "14xzlbmki8fk8mbcci62q8sklyd0nyga07ww1ap0vdrv7d1g31hn";
-
-    postPatch = ''
-      # the cloud-agent release tag has an empty version string, so add it back in
-      substituteInPlace internal/version/version.go \
-        --replace 'var Version string' 'var Version string = "v${version}"'
-    '';
-  };
+    nativeBuildInputs = [ yarn' git cacert ];
 
-  yarnCache = stdenv.mkDerivation {
-    name = "${pname}-${version}-${system}-yarn-cache";
-    inherit src;
-    nativeBuildInputs = [ yarn' git cacert ];
     buildPhase = ''
       export HOME=$PWD
       export GIT_SSL_CAINFO="${cacert}/etc/ssl/certs/ca-bundle.crt"
···
         xargs -I {} yarn --cwd {} \
           --ignore-scripts --ignore-engines
     '';
+
     outputHashMode = "recursive";
     outputHashAlgo = "sha256";
-
-    # to get hash values use nix-build -A code-server.prefetchYarnCache
     outputHash = "sha256-4Vr9u3+W/IhbbTc39jyDyDNQODlmdF+M/N8oJn0Z4+w=";
   };
 
   nativeBuildInputs = [
-    nodejs yarn' python pkg-config makeWrapper git rsync jq moreutils quilt
+    nodejs
+    yarn'
+    python
+    pkg-config
+    makeWrapper
+    git
+    rsync
+    jq
+    moreutils
+    quilt
   ];
+
   buildInputs = lib.optionals (!stdenv.isDarwin) [ libsecret ]
     ++ (with xorg; [ libX11 libxkbfile ])
     ++ lib.optionals stdenv.isDarwin [
-      AppKit Cocoa CoreServices Security cctools xcbuild
-    ];
+    AppKit
+    Cocoa
+    CoreServices
+    Security
+    cctools
+    xcbuild
+  ];
 
   patches = [
     # remove git calls from vscode build script
···
   '';
 
   configurePhase = ''
+    runHook preConfigure
+
     # run yarn offline by default
     echo '--install.offline true' >> .yarnrc
 
···
     '') defaultYarnOpts}
 
     # set offline mirror to yarn cache we created in previous steps
-    yarn --offline config set yarn-offline-mirror "${yarnCache}"
+    yarn --offline config set yarn-offline-mirror "${finalAttrs.yarnCache}"
 
     # skip unnecessary electron download
     export ELECTRON_SKIP_BINARY_DOWNLOAD=1
···
     # use updated node-gyp. fixes the following error on Darwin:
     # PermissionError: [Errno 1] Operation not permitted: '/usr/sbin/pkgutil'
     export npm_config_node_gyp=${node-gyp}/lib/node_modules/node-gyp/bin/node-gyp.js
+
+    runHook postConfigure
   '';
 
   buildPhase = ''
+    runHook preBuild
+
     # install code-server dependencies
     yarn --offline --ignore-scripts
 
···
 
     ${patchEsbuild "./lib/vscode/build" "0.12.6"}
     ${patchEsbuild "./lib/vscode/extensions" "0.11.23"}
-    '' + lib.optionalString stdenv.isDarwin ''
+  '' + lib.optionalString stdenv.isDarwin ''
     # use prebuilt binary for @parcel/watcher, which requires macOS SDK 10.13+
     # (see issue #101229)
     pushd ./lib/vscode/remote/node_modules/@parcel/watcher
···
     yarn build
 
     # build vscode
-    VERSION=${version} yarn build:vscode
+    VERSION=${finalAttrs.version} yarn build:vscode
 
     # create release
     yarn release
+
+    runHook postBuild
   '';
 
   installPhase = ''
+    runHook preInstall
+
     mkdir -p $out/libexec/code-server $out/bin
 
     # copy release to libexec path
···
     # install only production dependencies
     yarn --offline --cwd "$out/libexec/code-server" --production
 
-    # link coder-cloud agent from nix store
-    mkdir -p $out/libexec/code-server/lib
-    ln -s "${cloudAgent}/bin/cloud-agent" $out/libexec/code-server/lib/coder-cloud-agent
-
     # create wrapper
-    makeWrapper "${nodejs_16}/bin/node" "$out/bin/code-server" \
+    makeWrapper "${nodejs}/bin/node" "$out/bin/code-server" \
       --add-flags "$out/libexec/code-server/out/node/entry.js"
+
+    runHook postInstall
   '';
 
   passthru = {
-    prefetchYarnCache = lib.overrideDerivation yarnCache (d: {
+    prefetchYarnCache = lib.overrideDerivation finalAttrs.yarnCache (d: {
       outputHash = lib.fakeSha256;
     });
     tests = {
···
     };
   };
 
-  meta = with lib; {
+  meta = {
     description = "Run VS Code on a remote server";
     longDescription = ''
       code-server is VS Code running on a remote server, accessible through the
       browser.
     '';
     homepage = "https://github.com/coder/code-server";
-    license = licenses.mit;
-    maintainers = with maintainers; [ offline henkery ];
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ offline henkery ];
     platforms = [ "x86_64-linux" "aarch64-linux" "x86_64-darwin" ];
   };
-}
+})

pkgs/servers/plex/raw.nix

···
 # server, and the FHS userenv and corresponding NixOS module should
 # automatically pick up the changes.
 stdenv.mkDerivation rec {
-  version = "1.32.3.7162-b0a36929b";
+  version = "1.32.3.7192-7aa441827";
   pname = "plexmediaserver";
 
   # Fetch the source
   src = if stdenv.hostPlatform.system == "aarch64-linux" then fetchurl {
     url = "https://downloads.plex.tv/plex-media-server-new/${version}/debian/plexmediaserver_${version}_arm64.deb";
-    sha256 = "sha256-y1H1DmgMCYEzmhN01LgFHPzN/as2z457tZMdEJ0lgxk=";
+    sha256 = "sha256-sqlvJIMlyrRfvtQB+IpbmWwdQBA2lEGNPEc3zTfwr4s=";
   } else fetchurl {
     url = "https://downloads.plex.tv/plex-media-server-new/${version}/debian/plexmediaserver_${version}_amd64.deb";
-    sha256 = "sha256-q95xyp+XJbDuT+SRP+EbcFDqqdcvRP4P1rnX8RO1egQ=";
+    sha256 = "sha256-F3djGd03yD64TtjnB/S8HWDNmY1kA3OgctpamGNxPZ0=";
   };
 
   outputs = [ "out" "basedb" ];

pkgs/tools/misc/jfrog-cli/default.nix

···
 
 buildGoModule rec {
   pname = "jfrog-cli";
-  version = "2.38.5";
+  version = "2.40.0";
 
   src = fetchFromGitHub {
     owner = "jfrog";
     repo = "jfrog-cli";
     rev = "refs/tags/v${version}";
-    hash = "sha256-fd5YJCaqT78TjhC3CkX7+iPTxW278U7GTiXLH46L2m4=";
+    hash = "sha256-Fhpg78IV+NEkKXWk0Xw58uE6G2qfaYhgKfhmTVAGvEo=";
   };
 
-  vendorHash = "sha256-6sUifqqryPrlwOFYPKp1VrgGE+xF/ELz8s7eLrMJnr4=";
+  vendorHash = "sha256-zzqXl6i1ZrxIU9ePzTd+drOtPU76DcfLY8RDu/rVNzE=";
 
   postInstall = ''
     # Name the output the same way as the original build script does

pkgs/tools/security/cariddi/default.nix

···
 
 buildGoModule rec {
   pname = "cariddi";
-  version = "1.3.1";
+  version = "1.3.2";
 
   src = fetchFromGitHub {
     owner = "edoardottt";
     repo = pname;
     rev = "refs/tags/v${version}";
-    hash = "sha256-zz9p35Wk5jwp5Cn4+FgJCwG2KKgBuOQsH4lJeAVhpCM=";
+    hash = "sha256-oM4A4chSBTiCMr3bW0AvjAFlyuqvKKKY2Ji4PYRsUqA=";
   };
 
-  vendorHash = "sha256-s6aEq3LzCj9xzieLD1aC69KV3aeav+bQ5VUZ3TbFetw=";
+  vendorHash = "sha256-EeoJssX/OkIJKltANfvMirvDVmVVIe9hDj+rThKpd10=";
 
   meta = with lib; {
     description = "Crawler for URLs and endpoints";

pkgs/top-level/aliases.nix

···
   ### M ###
 
   m3d-linux = throw "'m3d-linux' has been renamed to/replaced by 'm33-linux'"; # Converted to throw 2022-02-22
+  MACS2 = macs2; # Added 2023-06-12
   mail-notification = throw "mail-notification has been removed from nixpkgs, as it's unmaintained and has dependencies on old gnome libraries we want to remove"; # Added 2021-08-21
   mailpile = throw "mailpile was removed from nixpkgs, as it is stuck on python2"; # Added 2022-01-12
   man_db = throw "'man_db' has been renamed to/replaced by 'man-db'"; # Converted to throw 2022-02-22

pkgs/top-level/all-packages.nix

···
   };
 
   code-server = callPackage ../servers/code-server {
+    nodejs = nodejs_16;
     inherit (darwin.apple_sdk.frameworks) AppKit Cocoa CoreServices Security;
     inherit (darwin) cctools;
     inherit (nodePackages) node-gyp;
···
 
   macse = callPackage ../applications/science/biology/macse { };
 
-  MACS2 = callPackage ../applications/science/biology/MACS2 { };
+  macs2 = callPackage ../applications/science/biology/macs2 { };
 
   mafft = callPackage ../applications/science/biology/mafft { };
 
···
 
   gildas = callPackage ../applications/science/astronomy/gildas { };
 
-  gplates = libsForQt5.callPackage ../applications/science/misc/gplates {
-    boost = boost175;
-    # build with Python 3.10 fails, because boost <= 1.78 can't find
-    # pythons with double digits in minor versions, like X.YZ
-    python3 = python39;
-  };
+  gplates = libsForQt5.callPackage ../applications/science/misc/gplates { };
 
   grap = callPackage ../tools/security/grap { };