Merge master into staging-next

.github/workflows/no-channel.yml

@@ -6,8 +6,13 @@ on:
       - 'nixos-**'
       - 'nixpkgs-**'
 
+permissions:
+  contents: read
+
 jobs:
   fail:
+    permissions:
+      contents: none
     name: "This PR is is targeting a channel branch"
     runs-on: ubuntu-latest
     steps:

.github/workflows/update-terraform-providers.yml

@@ -5,8 +5,15 @@ on:
     - cron: "14 3 * * 1"
   workflow_dispatch:
 
+permissions:
+  contents: read
+
 jobs:
   tf-providers:
+    permissions:
+      contents: write  # for peter-evans/create-pull-request to create branch
+      issues: write  # for peter-evans/create-or-update-comment to create or update comment
+      pull-requests: write  # for peter-evans/create-pull-request to create a PR
     if: github.repository_owner == 'NixOS' && github.ref == 'refs/heads/master' # ensure workflow_dispatch only runs on master
     runs-on: ubuntu-latest
     steps:

nixos/modules/installer/netboot/netboot.nix

@@ -81,7 +81,7 @@ with lib;
 
 
     # Create the initrd
-    system.build.netbootRamdisk = pkgs.makeInitrd {
+    system.build.netbootRamdisk = pkgs.makeInitrdNG {
       inherit (config.boot.initrd) compressor;
       prepend = [ "${config.system.build.initialRamdisk}/initrd" ];
 

nixos/modules/virtualisation/qemu-vm.nix

@@ -684,6 +684,21 @@ in
           '';
       };
 
+    virtualisation.useDefaultFilesystems =
+      mkOption {
+        type = types.bool;
+        default = true;
+        description =
+          ''
+            If enabled, the boot disk of the virtual machine will be
+            formatted and mounted with the default filesystems for
+            testing. Swap devices and LUKS will be disabled.
+
+            If disabled, a root filesystem has to be specified and
+            formatted (for example in the initial ramdisk).
+          '';
+      };
+
     virtualisation.efiVars =
       mkOption {
         type = types.str;
@@ -754,13 +769,13 @@ in
     );
     boot.loader.grub.gfxmodeBios = with cfg.resolution; "${toString x}x${toString y}";
 
-    boot.initrd.extraUtilsCommands = lib.mkIf (!config.boot.initrd.systemd.enable)
+    boot.initrd.extraUtilsCommands = lib.mkIf (cfg.useDefaultFilesystems && !config.boot.initrd.systemd.enable)
       ''
         # We need mke2fs in the initrd.
         copy_bin_and_libs ${pkgs.e2fsprogs}/bin/mke2fs
       '';
 
-    boot.initrd.postDeviceCommands = lib.mkIf (!config.boot.initrd.systemd.enable)
+    boot.initrd.postDeviceCommands = lib.mkIf (cfg.useDefaultFilesystems && !config.boot.initrd.systemd.enable)
       ''
         # If the disk image appears to be empty, run mke2fs to
         # initialise.
@@ -930,38 +945,41 @@ in
         };
     in
       mkVMOverride (cfg.fileSystems //
-      {
+      optionalAttrs cfg.useDefaultFilesystems {
         "/".device = cfg.bootDevice;
         "/".fsType = "ext4";
         "/".autoFormat = true;
-
-        "/tmp" = mkIf config.boot.tmpOnTmpfs
-          { device = "tmpfs";
-            fsType = "tmpfs";
-            neededForBoot = true;
-            # Sync with systemd's tmp.mount;
-            options = [ "mode=1777" "strictatime" "nosuid" "nodev" "size=${toString config.boot.tmpOnTmpfsSize}" ];
-          };
-
-        "/nix/${if cfg.writableStore then ".ro-store" else "store"}" =
-          mkIf cfg.useNixStoreImage
-            { device = "${lookupDriveDeviceName "nix-store" cfg.qemu.drives}";
-              neededForBoot = true;
-              options = [ "ro" ];
-            };
-
-        "/nix/.rw-store" = mkIf (cfg.writableStore && cfg.writableStoreUseTmpfs)
-          { fsType = "tmpfs";
-            options = [ "mode=0755" ];
-            neededForBoot = true;
-          };
-
-        "/boot" = mkIf cfg.useBootLoader
-          # see note [Disk layout with `useBootLoader`]
-          { device = "${lookupDriveDeviceName "boot" cfg.qemu.drives}2"; # 2 for e.g. `vdb2`, as created in `bootDisk`
-            fsType = "vfat";
-            noCheck = true; # fsck fails on a r/o filesystem
-          };
+      } //
+      optionalAttrs config.boot.tmpOnTmpfs {
+        "/tmp" = {
+          device = "tmpfs";
+          fsType = "tmpfs";
+          neededForBoot = true;
+          # Sync with systemd's tmp.mount;
+          options = [ "mode=1777" "strictatime" "nosuid" "nodev" "size=${toString config.boot.tmpOnTmpfsSize}" ];
+        };
+      } //
+      optionalAttrs cfg.useNixStoreImage {
+        "/nix/${if cfg.writableStore then ".ro-store" else "store"}" = {
+          device = "${lookupDriveDeviceName "nix-store" cfg.qemu.drives}";
+          neededForBoot = true;
+          options = [ "ro" ];
+        };
+      } //
+      optionalAttrs (cfg.writableStore && cfg.writableStoreUseTmpfs) {
+        "/nix/.rw-store" = {
+          fsType = "tmpfs";
+          options = [ "mode=0755" ];
+          neededForBoot = true;
+        };
+      } //
+      optionalAttrs cfg.useBootLoader {
+        # see note [Disk layout with `useBootLoader`]
+        "/boot" = {
+          device = "${lookupDriveDeviceName "boot" cfg.qemu.drives}2"; # 2 for e.g. `vdb2`, as created in `bootDisk`
+          fsType = "vfat";
+          noCheck = true; # fsck fails on a r/o filesystem
+        };
       } // lib.mapAttrs' mkSharedDir cfg.sharedDirectories);
 
     boot.initrd.systemd = lib.mkIf (config.boot.initrd.systemd.enable && cfg.writableStore) {
@@ -986,8 +1004,8 @@ in
       };
     };
 
-    swapDevices = mkVMOverride [ ];
-    boot.initrd.luks.devices = mkVMOverride {};
+    swapDevices = (if cfg.useDefaultFilesystems then mkVMOverride else mkDefault) [ ];
+    boot.initrd.luks.devices = (if cfg.useDefaultFilesystems then mkVMOverride else mkDefault) {};
 
     # Don't run ntpd in the guest.  It should get the correct time from KVM.
     services.timesyncd.enable = false;

nixos/tests/all-tests.nix

@@ -384,6 +384,7 @@ in {
   nixpkgs = pkgs.callPackage ../modules/misc/nixpkgs/test.nix { inherit evalMinimalConfig; };
   node-red = handleTest ./node-red.nix {};
   nomad = handleTest ./nomad.nix {};
+  non-default-filesystems = handleTest ./non-default-filesystems.nix {};
   noto-fonts = handleTest ./noto-fonts.nix {};
   novacomd = handleTestOn ["x86_64-linux"] ./novacomd.nix {};
   nsd = handleTest ./nsd.nix {};
@@ -519,6 +520,7 @@ in {
   step-ca = handleTestOn ["x86_64-linux"] ./step-ca.nix {};
   strongswan-swanctl = handleTest ./strongswan-swanctl.nix {};
   sudo = handleTest ./sudo.nix {};
+  swap-partition = handleTest ./swap-partition.nix {};
   sway = handleTest ./sway.nix {};
   switchTest = handleTest ./switch-test.nix {};
   sympa = handleTest ./sympa.nix {};

nixos/tests/non-default-filesystems.nix

@@ -0,0 +1,54 @@
+import ./make-test-python.nix ({ lib, pkgs, ... }:
+{
+  name = "non-default-filesystems";
+
+  nodes.machine =
+    { config, pkgs, lib, ... }:
+    let
+      disk = config.virtualisation.bootDevice;
+    in
+    {
+      virtualisation.useDefaultFilesystems = false;
+
+      boot.initrd.availableKernelModules = [ "btrfs" ];
+      boot.supportedFilesystems = [ "btrfs" ];
+
+      boot.initrd.postDeviceCommands = ''
+        FSTYPE=$(blkid -o value -s TYPE ${disk} || true)
+        if test -z "$FSTYPE"; then
+          modprobe btrfs
+          ${pkgs.btrfs-progs}/bin/mkfs.btrfs ${disk}
+
+          mkdir /nixos
+          mount -t btrfs ${disk} /nixos
+
+          ${pkgs.btrfs-progs}/bin/btrfs subvolume create /nixos/root
+          ${pkgs.btrfs-progs}/bin/btrfs subvolume create /nixos/home
+
+          umount /nixos
+        fi
+      '';
+
+      virtualisation.fileSystems = {
+        "/" = {
+          device = disk;
+          fsType = "btrfs";
+          options = [ "subvol=/root" ];
+        };
+
+        "/home" = {
+          device = disk;
+          fsType = "btrfs";
+          options = [ "subvol=/home" ];
+        };
+      };
+    };
+
+  testScript = ''
+    machine.wait_for_unit("multi-user.target")
+
+    with subtest("BTRFS filesystems are mounted correctly"):
+      machine.succeed("grep -E '/dev/vda / btrfs rw,relatime,space_cache=v2,subvolid=[0-9]+,subvol=/root 0 0' /proc/mounts")
+      machine.succeed("grep -E '/dev/vda /home btrfs rw,relatime,space_cache=v2,subvolid=[0-9]+,subvol=/home 0 0' /proc/mounts")
+  '';
+})

nixos/tests/swap-partition.nix

@@ -0,0 +1,48 @@
+import ./make-test-python.nix ({ lib, pkgs, ... }:
+{
+  name = "swap-partition";
+
+  nodes.machine =
+    { config, pkgs, lib, ... }:
+    {
+      virtualisation.useDefaultFilesystems = false;
+
+      virtualisation.bootDevice = "/dev/vda1";
+
+      boot.initrd.postDeviceCommands = ''
+        if ! test -b /dev/vda1; then
+          ${pkgs.parted}/bin/parted --script /dev/vda -- mklabel msdos
+          ${pkgs.parted}/bin/parted --script /dev/vda -- mkpart primary 1MiB -250MiB
+          ${pkgs.parted}/bin/parted --script /dev/vda -- mkpart primary -250MiB 100%
+          sync
+        fi
+
+        FSTYPE=$(blkid -o value -s TYPE /dev/vda1 || true)
+        if test -z "$FSTYPE"; then
+          ${pkgs.e2fsprogs}/bin/mke2fs -t ext4 -L root /dev/vda1
+          ${pkgs.util-linux}/bin/mkswap --label swap /dev/vda2
+        fi
+      '';
+
+      virtualisation.fileSystems = {
+        "/" = {
+          device = "/dev/disk/by-label/root";
+          fsType = "ext4";
+        };
+      };
+
+      swapDevices = [
+        {
+          device = "/dev/disk/by-label/swap";
+        }
+      ];
+    };
+
+  testScript = ''
+    machine.wait_for_unit("multi-user.target")
+
+    with subtest("Swap is active"):
+      # Doesn't matter if the numbers reported by `free` are slightly off due to unit conversions.
+      machine.succeed("free -h | grep -E 'Swap:\s+2[45][0-9]Mi'")
+  '';
+})

pkgs/applications/editors/neovim/neovim-qt.nix

@@ -3,13 +3,13 @@
 
 mkDerivation rec {
   pname = "neovim-qt-unwrapped";
-  version = "0.2.16.1";
+  version = "0.2.17";
 
   src = fetchFromGitHub {
     owner  = "equalsraf";
     repo   = "neovim-qt";
     rev    = "v${version}";
-    sha256 = "0x5brrim3f21bzdmh6wyrhrislwpx1248wbx56csvic6v78hzqny";
+    sha256 = "sha256-UJXaHENqau5EEe5c94pJuNxZU5rutJs642w9Cof8Sa4=";
   };
 
   cmakeFlags = [

pkgs/applications/science/electronics/archimedes/default.nix

@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl }:
+{ lib, stdenv, fetchurl, fetchpatch }:
 
 stdenv.mkDerivation rec {
   pname = "archimedes";
@@ -9,6 +9,16 @@ stdenv.mkDerivation rec {
     sha256 = "0jfpnd3pns5wxcxbiw49v5sgpmm5b4v8s4q1a5292hxxk2hzmb3z";
   };
 
+  patches = [
+    # Pull patch pending upstream inclusion to support c99 toolchains:
+    #   https://savannah.gnu.org/bugs/index.php?62703
+    (fetchpatch {
+      name = "c99.patch";
+      url = "https://savannah.gnu.org/bugs/download.php?file_id=53393";
+      sha256 = "1xmy1w4ln1gynldk3srdi2h0fxpx465dsa1yxc3rzrrjpxh6087f";
+    })
+  ];
+
   meta = {
     description = "GNU package for semiconductor device simulations";
     homepage = "https://www.gnu.org/software/archimedes";

pkgs/applications/version-management/gitqlient/default.nix

@@ -8,14 +8,46 @@
 
 mkDerivation rec {
   pname = "gitqlient";
-  version = "1.4.3";
+  version = "1.5.0";
 
-  src = fetchFromGitHub {
-    owner = "francescmm";
-    repo = pname;
-    rev = "v${version}";
-    sha256 = "018jz6b28zwr205jmgw13ddlfvlhxqf0cw1pfjiwsi6i8gay7w6s";
-  };
+  srcs = [
+    (fetchFromGitHub {
+      owner = "francescmm";
+      repo = pname;
+      rev = "v${version}";
+      sha256 = "sha256-Mq29HbmPABrRIJjWC5AAKIOKbGngeJdkZkWeJw8BFuw=";
+    })
+    (fetchFromGitHub rec {
+      owner = "francescmm";
+      repo = "AuxiliarCustomWidgets";
+      rev = "835f538b4a79e4d6bb70eef37a32103e7b2a1fd1";
+      sha256 = "sha256-b1gb/7UcLS6lI92dBfTenGXA064t4dZufs3S9lu/lQA=";
+      name = repo;
+    })
+    (fetchFromGitHub rec {
+      owner = "francescmm";
+      repo = "QLogger";
+      rev = "d1ed24e080521a239d5d5e2c2347fe211f0f3e4f";
+      sha256 = "sha256-NVlFYmm7IIkf8LhQrAYXil9kH6DFq1XjOEHQiIWmER4=";
+      name = repo;
+    })
+    (fetchFromGitHub rec {
+      owner = "francescmm";
+      repo = "QPinnableTabWidget";
+      rev = "cc937794e910d0452f0c07b4961c6014a7358831";
+      sha256 = "sha256-2KzzBv/s2t665axeBxWrn8aCMQQArQLlUBOAlVhU+wE=";
+      name = repo;
+    })
+    (fetchFromGitHub rec {
+      owner = "francescmm";
+      repo = "git";
+      rev = "b62750f4da4b133faff49e6f53950d659b18c948";
+      sha256 = "sha256-4FqA+kkHd0TqD6ZuB4CbJ+IhOtQG9uWN+qhSAT0dXGs=";
+      name = repo;
+    })
+  ];
+
+  sourceRoot = "source";
 
   nativeBuildInputs = [
     qmake
@@ -25,11 +57,21 @@ mkDerivation rec {
     qtwebengine
   ];
 
+  postUnpack = ''
+    for dep in AuxiliarCustomWidgets QPinnableTabWidget QLogger git; do
+      rmdir "source/src/$dep"
+      ln -sf "../../$dep" "source/src/$dep"
+    done
+  '';
+
   qmakeFlags = [
     "GitQlient.pro"
   ];
 
-  passthru.updateScript = gitUpdater { inherit pname version; };
+  passthru.updateScript = gitUpdater {
+    inherit pname version;
+    rev-prefix = "v";
+  };
 
   meta = with lib; {
     homepage = "https://github.com/francescmm/GitQlient";

pkgs/applications/virtualization/colima/default.nix

@@ -1,43 +1,47 @@
 { lib
-, buildGo118Module
+, buildGoModule
 , fetchFromGitHub
 , installShellFiles
 , lima
 , makeWrapper
+, qemu
+, testers
+, colima
 }:
 
-buildGo118Module rec {
+buildGoModule rec {
   pname = "colima";
-  version = "0.4.2";
+  version = "0.4.4";
 
   src = fetchFromGitHub {
     owner = "abiosoft";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-66nKH5jxTzLB9bg2lH1E8Cc0GZ6C/N/+yPYhCVEKOBY=";
-
+    sha256 = "bSBaSS+rVkFqTSdyegdE/F0X5u7yvF/nHslAO3xgD6I=";
     # We need the git revision
     leaveDotGit = true;
     postFetch = ''
-      git -C $out rev-parse HEAD > $out/.git-revision
+      git -C $out rev-parse --short HEAD > $out/.git-revision
       rm -rf $out/.git
     '';
   };
 
   nativeBuildInputs = [ installShellFiles makeWrapper ];
 
-  vendorSha256 = "sha256-91Ex3RPWxOHyZcR3Bo+bRdDAFw2mEGiC/uNKjdX2kuw=";
+  vendorSha256 = "sha256-jDzDwK7qA9lKP8CfkKzfooPDrHuHI4OpiLXmX9vOpOg=";
 
-  doCheck = false;
+  CGO_ENABLED = 1;
 
   preConfigure = ''
-    ldflags="-X github.com/abiosoft/colima/config.appVersion=${version}
-              -X github.com/abiosoft/colima/config.revision=$(cat .git-revision)"
+    ldflags="-s -w -X github.com/abiosoft/colima/config.appVersion=${version} \
+    -X github.com/abiosoft/colima/config.revision=$(cat .git-revision)"
   '';
 
+  subPackages = [ "cmd/colima" ];
+
   postInstall = ''
     wrapProgram $out/bin/colima \
-      --prefix PATH : ${lib.makeBinPath [ lima ]}
+      --prefix PATH : ${lib.makeBinPath [ lima qemu ]}
 
     installShellCompletion --cmd colima \
       --bash <($out/bin/colima completion bash) \
@@ -45,10 +49,15 @@ buildGo118Module rec {
       --zsh <($out/bin/colima completion zsh)
   '';
 
+  passthru.tests.version = testers.testVersion {
+    package = colima;
+    command = "HOME=$(mktemp -d) colima version";
+  };
+
   meta = with lib; {
-    description = "Container runtimes on MacOS with minimal setup";
+    description = "Container runtimes with minimal setup";
     homepage = "https://github.com/abiosoft/colima";
     license = licenses.mit;
-    maintainers = with maintainers; [ aaschmid ];
+    maintainers = with maintainers; [ aaschmid tricktron ];
   };
 }

pkgs/data/fonts/amiri/default.nix

@@ -1,19 +1,21 @@
 { lib, fetchzip }:
 
 let
-  version = "0.114";
+  version = "0.117";
 
 in fetchzip rec {
   name = "Amiri-${version}";
 
   url = "https://github.com/alif-type/amiri/releases/download/${version}/${name}.zip";
 
-  sha256 = "sha256-6FA46j1shP0R8iEi/Xop2kXS0OKW1jaGUEOthT3Z5b4=";
+  sha256 = "sha256-TCdL4Am+mT7E9fHEagcR7i9kBziyJuO3r1kM+ekfvbU=";
 
   postFetch = ''
-    unzip $downloadedFile
-    install -m444 -Dt $out/share/fonts/truetype ${name}/*.ttf
-    install -m444 -Dt $out/share/doc/${name}    ${name}/{*.txt,*.pdf}
+    rm -rf $out/otf
+    mkdir -p $out/share/fonts/truetype
+    mv $out/*.ttf $out/share/fonts/truetype/
+    mkdir -p $out/share/doc/${name}
+    mv $out/{*.html,*.txt,*.md} $out/share/doc/${name}/
   '';
 
   meta = with lib; {

pkgs/desktops/gnome/core/gnome-remote-desktop/default.nix

@@ -28,11 +28,11 @@
 
 stdenv.mkDerivation rec {
   pname = "gnome-remote-desktop";
-  version = "42.2";
+  version = "42.3";
 
   src = fetchurl {
     url = "mirror://gnome/sources/${pname}/${lib.versions.major version}/${pname}-${version}.tar.xz";
-    hash = "sha256-wcy82MpwN+9ttz9r8rXdOKM2t9gKKpyY32/4g4eP+dU=";
+    hash = "sha256-opatWPizvawOLg2H2xKpOV5ydwqWDnh/vMG+PwBotkI=";
   };
 
   nativeBuildInputs = [

pkgs/development/interpreters/ruby/default.nix

@@ -260,6 +260,9 @@ let
     ) args; in self;
 
 in {
+  mkRubyVersion = rubyVersion;
+  mkRuby = generic;
+
   ruby_2_7 = generic {
     version = rubyVersion "2" "7" "6" "";
     sha256 = "042xrdk7hsv4072bayz3f8ffqh61i8zlhvck10nfshllq063n877";

pkgs/development/interpreters/sollya/default.nix

@@ -19,11 +19,13 @@ stdenv.mkDerivation rec {
 
   buildInputs = [ gmp mpfr mpfi libxml2 fplll ];
 
+  doCheck = true;
+
   meta = with lib; {
     description = "A tool environment for safe floating-point code development";
     homepage = "https://www.sollya.org/";
     license = licenses.cecill-c;
-    platforms = platforms.linux;
-    maintainers = with maintainers; [ ];
+    platforms = platforms.unix;
+    maintainers = with maintainers; [ wegank ];
   };
 }

pkgs/development/ocaml-modules/io-page/default.nix

@@ -2,14 +2,13 @@
 
 buildDunePackage rec {
   pname = "io-page";
-  version = "2.3.0";
+  version = "3.0.0";
 
-  useDune2 = true;
-  minimumOCamlVersion = "4.02.3";
+  minimalOCamlVersion = "4.08";
 
   src = fetchurl {
-    url = "https://github.com/mirage/${pname}/releases/download/v${version}/${pname}-v${version}.tbz";
-    sha256 = "1hx27pwf419hrhwaw9cphbnl8akz8yy73hqj49l15g2k7shah1cn";
+    url = "https://github.com/mirage/${pname}/releases/download/v${version}/${pname}-${version}.tbz";
+    sha256 = "sha256-DjbKdNkFa6YQgJDLmLsuvyrweb4/TNvqAiggcj/3hu4=";
   };
 
   propagatedBuildInputs = [ cstruct bigarray-compat ];

pkgs/development/ocaml-modules/io-page/unix.nix

@@ -1,17 +0,0 @@
-{ lib, buildDunePackage, io-page, cstruct, ounit }:
-
-buildDunePackage {
-  pname = "io-page-unix";
-
-  inherit (io-page) version src useDune2 minimumOCamlVersion;
-
-  propagatedBuildInputs = [ cstruct io-page ];
-  checkInputs = [ ounit ];
-  doCheck = true;
-
-  meta = with lib; {
-    inherit (io-page.meta) homepage license;
-    description = "Support for efficient handling of I/O memory pages on Unix";
-    maintainers = [ maintainers.sternenseemann ];
-  };
-}

pkgs/development/ocaml-modules/mirage-block-ramdisk/default.nix

@@ -1,29 +1,20 @@
-{ lib, fetchurl, buildDunePackage, io-page, io-page-unix, mirage-block, alcotest
-, mirage-block-combinators }:
+{ lib, fetchurl, buildDunePackage, io-page, mirage-block }:
 
 buildDunePackage rec {
   pname = "mirage-block-ramdisk";
   version = "0.5";
 
-  useDune2 = true;
-
   src = fetchurl {
     url =
       "https://github.com/mirage/mirage-block-ramdisk/releases/download/${version}/mirage-block-ramdisk-${version}.tbz";
     sha256 = "cc0e814fd54efe7a5b7a8c5eb1c04e2dece751b7d8dee2d95908a0768896e8af";
   };
 
-  # Make tests compatible with alcotest 1.4.0
-  postPatch = ''
-    substituteInPlace test/tests.ml --replace 'Fmt.kstrf Alcotest.fail' 'Fmt.kstrf (fun s -> Alcotest.fail s)'
-  '';
-
-  minimumOCamlVersion = "4.06";
+  minimalOCamlVersion = "4.06";
 
   propagatedBuildInputs = [ io-page mirage-block ];
 
-  doCheck = true;
-  checkInputs = [ alcotest io-page-unix mirage-block-combinators ];
+  doCheck = false;
 
   meta = with lib; {
     description = "In-memory BLOCK device for MirageOS";

pkgs/development/ocaml-modules/mirage-block-unix/default.nix

@@ -1,24 +1,22 @@
-{ lib, fetchurl, buildDunePackage, cstruct-lwt, diet, io-page-unix, logs
-, mirage-block, ounit, rresult, uri }:
+{ lib, fetchurl, buildDunePackage, cstruct-lwt, diet, io-page, logs
+, mirage-block, ounit2, rresult, uri }:
 
 buildDunePackage rec {
   pname = "mirage-block-unix";
-  version = "2.12.1";
-
-  useDune2 = true;
+  version = "2.14.1";
 
   src = fetchurl {
     url =
-      "https://github.com/mirage/mirage-block-unix/releases/download/v${version}/mirage-block-unix-v${version}.tbz";
-    sha256 = "4fc0ccea3c06c654e149c0f0e1c2a6f19be4e3fe1afd293c6a0dba1b56b3b8c4";
+      "https://github.com/mirage/mirage-block-unix/releases/download/v${version}/mirage-block-unix-${version}.tbz";
+    sha256 = "sha256-FcUhbjHKT11ePDXaAVzUdV/WOHoxMoXyZKG5ikKpBNU=";
   };
 
-  minimumOCamlVersion = "4.06";
+  minimalOCamlVersion = "4.06";
 
-  propagatedBuildInputs = [ cstruct-lwt logs mirage-block rresult uri ];
+  propagatedBuildInputs = [ cstruct-lwt io-page logs mirage-block rresult uri ];
 
   doCheck = true;
-  checkInputs = [ diet io-page-unix ounit ];
+  checkInputs = [ diet ounit2 ];
 
   meta = with lib; {
     description = "MirageOS disk block driver for Unix";

pkgs/development/ocaml-modules/mirage-block/combinators.nix

@@ -1,16 +1,8 @@
-{ buildDunePackage, fetchpatch, mirage-block, io-page, logs }:
+{ buildDunePackage, mirage-block, io-page, logs }:
 
 buildDunePackage rec {
   pname = "mirage-block-combinators";
-  inherit (mirage-block) version src useDune2;
-
-  patches = [
-    (fetchpatch {
-      name = "cstruct-6.0.0-compat.patch";
-      url = "https://github.com/mirage/mirage-block/pull/49/commits/ff54105b21fb32d0d6977b419db0776e6c2ea166.patch";
-      sha256 = "0bwgypnsyn4d9b46q6r7kh5qfcy58db7krs6z5zw83hc7y20y2sd";
-    })
-  ];
+  inherit (mirage-block) version src;
 
   propagatedBuildInputs = [ mirage-block io-page logs ];
 

pkgs/development/ocaml-modules/mirage-block/default.nix

@@ -1,19 +1,17 @@
 { lib, fetchurl, buildDunePackage
-, cstruct, lwt, mirage-device
+, cstruct, lwt, fmt
 }:
 
 buildDunePackage rec {
   pname = "mirage-block";
-  version = "2.0.1";
-
-  useDune2 = true;
+  version = "3.0.0";
 
   src = fetchurl {
     url = "https://github.com/mirage/mirage-block/releases/download/v${version}/mirage-block-v${version}.tbz";
-    sha256 = "1wp8wmixaz9i2sbvq6nkx903lbnpdgb2w404pz1wk8kcg9p3ilcc";
+    sha256 = "sha256-NB5nJpppMtdi0HDjKcCAqRjO4vIbAMfnP934P+SnzmU=";
   };
 
-  propagatedBuildInputs = [ cstruct lwt mirage-device ];
+  propagatedBuildInputs = [ cstruct lwt fmt ];
 
   meta = with lib; {
     description = "Block signatures and implementations for MirageOS";

pkgs/development/ocaml-modules/mirage-unix/default.nix

@@ -1,17 +1,15 @@
-{ lib, buildDunePackage, fetchurl, ocaml_lwt, duration, mirage-runtime, io-page-unix }:
+{ lib, buildDunePackage, fetchurl, lwt, duration, mirage-runtime, io-page }:
 
 buildDunePackage rec {
   pname = "mirage-unix";
-  version = "4.0.0";
-
-  useDune2 = true;
+  version = "4.0.1";
 
   src = fetchurl {
     url = "https://github.com/mirage/${pname}/releases/download/v${version}/${pname}-v${version}.tbz";
-    sha256 = "0kyd83bkpjhn382b4mw3a4325xr8vms78znxqvifpcyfvfnlx7hj";
+    sha256 = "sha256-9ymVBb3dkhb+MN97/sXe/oQ36CVx0kruj3sd19LiFZ4=";
   };
 
-  propagatedBuildInputs = [ ocaml_lwt duration mirage-runtime io-page-unix ];
+  propagatedBuildInputs = [ lwt duration mirage-runtime io-page ];
   doCheck = true;
 
   meta = with lib; {

pkgs/development/ocaml-modules/secp256k1-internal/default.nix

@@ -11,16 +11,14 @@
 
 buildDunePackage rec {
   pname = "secp256k1-internal";
-  version = "0.2";
+  version = "0.3";
   src = fetchFromGitLab {
     owner = "nomadic-labs";
     repo = "ocaml-secp256k1-internal";
-    rev = "v${version}";
-    sha256 = "1g9fyi78nmmm19l2cggwj14m4n80rz7gmnh1gq376zids71s6qxv";
+    rev = version;
+    sha256 = "sha256-1wvQ4RW7avcGsIc0qgDzhGrwOBY0KHrtNVHCj2cgNzo=";
   };
 
-  useDune2 = true;
-
   minimalOCamlVersion = "4.08";
 
   propagatedBuildInputs = [

pkgs/development/ocaml-modules/vchan/default.nix

@@ -1,19 +1,18 @@
 { lib, buildDunePackage, fetchurl
-, ppx_cstruct, ppx_sexp_conv, ounit, io-page-unix
+, ppx_cstruct, ppx_sexp_conv, ounit
 , lwt, cstruct, io-page, mirage-flow, xenstore, xenstore_transport
 , sexplib, cmdliner
 }:
 
 buildDunePackage rec {
   pname = "vchan";
-  version = "6.0.0";
+  version = "6.0.1";
 
-  useDune2 = true;
-  minimumOCamlVersion = "4.08";
+  minimalOCamlVersion = "4.08";
 
   src = fetchurl {
-    url = "https://github.com/mirage/ocaml-vchan/releases/download/v${version}/vchan-v${version}.tbz";
-    sha256 = "7a6cc89ff8ba7144d6cef3f36722f40deedb3cefff0f7be1b2f3b7b2a2b41747";
+    url = "https://github.com/mirage/ocaml-vchan/releases/download/v${version}/vchan-${version}.tbz";
+    sha256 = "sha256-5E7dITMVirYoxUkp8ZamRAolyhA6avXGJNAioxeBuV0=";
   };
 
   nativeBuildInputs = [
@@ -34,7 +33,6 @@ buildDunePackage rec {
   doCheck = true;
   checkInputs = [
     cmdliner
-    io-page-unix
     ounit
   ];
 

pkgs/development/ocaml-modules/wodan/irmin.nix

@@ -1,4 +1,4 @@
-{ lib, buildDunePackage, io-page-unix, irmin-chunk, irmin-git, irmin-unix
+{ lib, buildDunePackage, irmin-chunk, irmin-git, irmin-unix
 , mirage-block-ramdisk, mirage-block-unix, wodan }:
 
 buildDunePackage rec {
@@ -6,7 +6,7 @@ buildDunePackage rec {
   inherit (wodan) version src useDune2;
 
   propagatedBuildInputs = [
-    io-page-unix
+    /* io-page-unix */ # No longer available in nixpkgs
     irmin-chunk
     irmin-git
     irmin-unix

pkgs/development/ocaml-modules/wodan/unix.nix

@@ -1,5 +1,5 @@
 { lib, buildDunePackage, base64, benchmark, csv, cmdliner, wodan, afl-persistent
-, io-page-unix, mirage-block-ramdisk, mirage-block-unix }:
+, mirage-block-ramdisk, mirage-block-unix }:
 
 buildDunePackage rec {
   outputs = [ "bin" "out" ];
@@ -12,7 +12,7 @@ buildDunePackage rec {
     benchmark
     cmdliner
     csv
-    io-page-unix
+    /* io-page-unix */
     mirage-block-ramdisk
     mirage-block-unix
     wodan
@@ -23,6 +23,7 @@ buildDunePackage rec {
   '';
 
   meta = wodan.meta // {
+    broken = true; # io-page-unix is no longer available
     description = "Wodan clients with Unix integration";
     mainProgram = "wodanc";
   };

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

@@ -0,0 +1,59 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pytorch
+, ninja
+, scipy
+, which
+, pybind11
+, pytest-xdist
+, pytestCheckHook
+}:
+
+buildPythonPackage rec {
+  pname = "deepwave";
+  version = "0.0.11";
+  format = "pyproject";
+
+  src = fetchFromGitHub {
+    owner = "ar4";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "sha256-d4EahmzHACHaeKoNZy63OKwWZdlHbUydrbr4fD43X8s=";
+  };
+
+  # unable to find ninja although it is available, most likely because it looks for its pip version
+  postPatch = ''
+    substituteInPlace setup.cfg --replace "ninja" ""
+  '';
+
+  # The source files are compiled at runtime and cached at the
+  # $HOME/.cache folder, so for the check phase it is needed to
+  # have a temporary home. This is also the reason ninja is not
+  # needed at the nativeBuildInputs, since it will only be used
+  # at runtime. The user will have to add it to its nix-shell
+  # along with deepwave
+  preBuild = ''
+    export HOME=$(mktemp -d)
+  '';
+
+  propagatedBuildInputs = [ pytorch pybind11 ];
+
+  checkInputs = [
+    ninja
+    which
+    scipy
+    pytest-xdist
+    pytestCheckHook
+  ];
+
+  pythonImportsCheck = [ "deepwave" ];
+
+  meta = with lib; {
+    description = "Wave propagation modules for PyTorch";
+    homepage = "https://github.com/ar4/deepwave";
+    license = licenses.mit;
+    platforms = intersectLists platforms.x86_64 platforms.linux;
+    maintainers = with maintainers; [ atila ];
+  };
+}

pkgs/development/tools/check-jsonschema/default.nix

@@ -0,0 +1,41 @@
+{ lib, fetchFromGitHub, python3 }:
+
+with python3.pkgs;
+
+buildPythonApplication rec {
+  pname = "check-jsonschema";
+  version = "0.16.2";
+
+  src = fetchFromGitHub {
+    owner = "python-jsonschema";
+    repo = "check-jsonschema";
+    rev = version;
+    sha256 = "sha256-rPjXua5kITr+I+jqeAO2iGUFVhjkLnQkXlUzRvkXduA=";
+  };
+
+  propagatedBuildInputs = [
+    ruamel-yaml
+    jsonschema
+    identify
+    requests
+    click
+  ];
+
+  checkInputs = [
+    pytestCheckHook
+    pytest-xdist
+    responses
+  ];
+
+  preCheck = lib.optionalString (stdenv.isDarwin && stdenv.isAarch64) ''
+    # https://github.com/python/cpython/issues/74570#issuecomment-1093748531
+    export no_proxy='*';
+  '';
+
+  meta = with lib; {
+    description = "A jsonschema CLI and pre-commit hook";
+    homepage = "https://github.com/python-jsonschema/check-jsonschema";
+    license = licenses.apsl20;
+    maintainers = with maintainers; [ sudosubin ];
+  };
+}

pkgs/servers/atlassian/jira.nix

@@ -8,11 +8,11 @@
 
 stdenv.mkDerivation rec {
   pname = "atlassian-jira";
-  version = "8.22.2";
+  version = "8.22.4";
 
   src = fetchurl {
     url = "https://product-downloads.atlassian.com/software/jira/downloads/atlassian-jira-software-${version}.tar.gz";
-    sha256 = "sha256-j9JUIK4GOdY9rMLPZcWbjWUh/s2ZkoVEQBNAIqHhdYI=";
+    sha256 = "sha256-Zog0m8tsx8mDLU1rsW5zhhHgyRmi4JGWuy9DV8yp9nY=";
   };
 
   buildPhase = ''

pkgs/tools/misc/pls/default.nix

@@ -2,14 +2,14 @@
 
 python3.pkgs.buildPythonApplication rec {
   pname = "pls";
-  version = "5.1.2";
+  version = "5.2.0";
   format = "pyproject";
 
   src = fetchFromGitHub {
     owner = "dhruvkb";
     repo = "pls";
     rev = version;
-    sha256 = "sha256-xJvAAlRVKQHEOz8wbErHCUTcb8Y1otcPEUwTw2lgddo=";
+    sha256 = "sha256-nmADeOVS5qdWsun36eKmeT4kYml0sTXYNa+YUiyNGQY=";
   };
 
   nativeBuildInputs = [ python3.pkgs.poetry-core ];

pkgs/tools/networking/edgedb/0001-dynamically-patchelf-binaries.patch

@@ -0,0 +1,34 @@
+diff --git a/src/portable/install.rs b/src/portable/install.rs
+index dc0d932..5394fc1 100644
+--- a/src/portable/install.rs
++++ b/src/portable/install.rs
+@@ -133,8 +133,16 @@ fn unpack_package(cache_file: &Path, target_dir: &Path)
+     for entry in arch.entries()? {
+         let mut entry = entry?;
+         let path = entry.path()?;
++        let is_inside_bin = {
++            let mut path_iter = path.iter();
++            path_iter.next(); // discards first folder
++            path_iter.as_path().starts_with("bin")
++        };
+         if let Some(path) = build_path(&target_dir, &*path)? {
+-            entry.unpack(path)?;
++            entry.unpack(&path)?;
++            if is_inside_bin {
++                nix_patchelf_if_needed(&path);
++            }
+         }
+     }
+     bar.finish_and_clear();
+@@ -203,3 +211,11 @@ pub fn package(pkg_info: &PackageInfo) -> anyhow::Result<InstallInfo> {
+ 
+     Ok(info)
+ }
++
++fn nix_patchelf_if_needed(dest_path: &Path) {
++    let _ = ::std::process::Command::new("@patchelf@/bin/patchelf")
++        .arg("--set-interpreter")
++        .arg("@dynamicLinker@")
++        .arg(dest_path)
++        .output();
++}

pkgs/tools/networking/edgedb/default.nix

@@ -0,0 +1,55 @@
+{ stdenv
+, lib
+, runCommand
+, patchelf
+, fetchFromGitHub
+, rustPlatform
+, makeWrapper
+, pkg-config
+, curl
+, Security
+, CoreServices
+, libiconv
+, xz
+, perl
+, substituteAll
+}:
+
+rustPlatform.buildRustPackage rec {
+  pname = "edgedb";
+  version = "unstable-2022-06-27";
+
+  src = fetchFromGitHub {
+    owner = "edgedb";
+    repo = "edgedb-cli";
+    rev = "3c65c8bf0a09988356ad477d0ae234182f809b0a";
+    sha256 = "sha256-UqoRa5ZbPJEHo9wyyygrN1ssorgY3cLw/mMrCDXr4gw=";
+  };
+
+  cargoSha256 = "sha256-6HJkkem44+dat5bmVEM+7GSJFjCz1dYZeRIPEoEwNlI=";
+
+  nativeBuildInputs = [ makeWrapper pkg-config perl ];
+
+  buildInputs = [
+    curl
+  ] ++ lib.optionals stdenv.isDarwin [ CoreServices Security libiconv xz ];
+
+  checkFeatures = [ ];
+
+  patches = [
+    (substituteAll {
+      src = ./0001-dynamically-patchelf-binaries.patch;
+      inherit patchelf;
+      dynamicLinker = stdenv.cc.bintools.dynamicLinker;
+    })
+  ];
+
+  doCheck = false;
+
+  meta = with lib; {
+    description = "EdgeDB cli";
+    homepage = "https://www.edgedb.com/docs/cli/index";
+    license = with licenses; [ asl20 /* or */ mit ];
+    maintainers = [ maintainers.ranfdev ];
+  };
+}

pkgs/top-level/all-packages.nix

@@ -406,6 +406,10 @@ with pkgs;
 
   eclipse-mat = callPackage ../development/tools/eclipse-mat { };
 
+  edgedb = callPackage ../tools/networking/edgedb {
+    inherit (darwin.apple_sdk.frameworks) CoreServices Security;
+  };
+
   efficient-compression-tool = callPackage ../tools/compression/efficient-compression-tool { };
 
   evans = callPackage ../development/tools/evans { };
@@ -14768,6 +14772,8 @@ with pkgs;
 
   pythonDocs = recurseIntoAttrs (callPackage ../development/interpreters/python/cpython/docs {});
 
+  check-jsonschema = callPackage ../development/tools/check-jsonschema {};
+
   pypi2nix = callPackage ../development/tools/pypi2nix {};
 
   pypi-mirror = callPackage ../development/tools/pypi-mirror {};
@@ -14866,6 +14872,8 @@ with pkgs;
     inherit (darwin) libiconv libobjc libunwind;
     inherit (darwin.apple_sdk.frameworks) Foundation;
   })
+    mkRubyVersion
+    mkRuby
     ruby_2_7
     ruby_3_0
     ruby_3_1;
@@ -33144,9 +33152,7 @@ with pkgs;
 
   astral = callPackage ../applications/science/biology/astral { };
 
-  archimedes = callPackage ../applications/science/electronics/archimedes {
-    stdenv = gcc6Stdenv;
-  };
+  archimedes = callPackage ../applications/science/electronics/archimedes { };
 
   bayescan = callPackage ../applications/science/biology/bayescan { };
 
@@ -34507,7 +34513,7 @@ with pkgs;
 
   idsk = callPackage ../tools/filesystems/idsk { stdenv = gcc10StdenvCompat; };
 
-  colima = callPackage ../applications/virtualization/colima { };
+  colima = callPackage ../applications/virtualization/colima { buildGoModule = buildGo118Module; };
 
   lima = callPackage ../applications/virtualization/lima { };
 

pkgs/top-level/ocaml-packages.nix

@@ -529,8 +529,6 @@ let
 
     io-page = callPackage ../development/ocaml-modules/io-page { };
 
-    io-page-unix = callPackage ../development/ocaml-modules/io-page/unix.nix { };
-
     ipaddr = callPackage ../development/ocaml-modules/ipaddr { };
 
     ipaddr-cstruct = callPackage ../development/ocaml-modules/ipaddr/cstruct.nix { };

pkgs/top-level/python-packages.nix

@@ -2204,6 +2204,8 @@ in {
 
   deeptoolsintervals = callPackage ../development/python-modules/deeptoolsintervals { };
 
+  deepwave = callPackage ../development/python-modules/deepwave { };
+
   deep-translator = callPackage ../development/python-modules/deep-translator { };
 
   deezer-py = callPackage ../development/python-modules/deezer-py { };