Merge master into staging-next

12 files changed, 52 insertions, 25 deletions

diff --git a/nixos/modules/services/networking/bind.nix b/nixos/modules/services/networking/bind.nix
index 20eef2c3455..33da4071638 100644
--- a/nixos/modules/services/networking/bind.nix
+++ b/nixos/modules/services/networking/bind.nix
@@ -6,6 +6,8 @@ let
 
   cfg = config.services.bind;
 
+  bindPkg = config.services.bind.package;
+
   bindUser = "named";
 
   bindZoneCoerce = list: builtins.listToAttrs (lib.forEach list (zone: { name = zone.name; value = zone; }));
@@ -104,6 +106,14 @@ in
 
       enable = mkEnableOption "BIND domain name server";
 
+
+      package = mkOption {
+        type = types.package;
+        default = pkgs.bind;
+        defaultText = "pkgs.bind";
+        description = "The BIND package to use.";
+      };
+
       cacheNetworks = mkOption {
         default = [ "127.0.0.0/24" ];
         type = types.listOf types.str;
@@ -225,7 +235,7 @@ in
       preStart = ''
         mkdir -m 0755 -p /etc/bind
         if ! [ -f "/etc/bind/rndc.key" ]; then
-          ${pkgs.bind.out}/sbin/rndc-confgen -c /etc/bind/rndc.key -u ${bindUser} -a -A hmac-sha256 2>/dev/null
+          ${bindPkg.out}/sbin/rndc-confgen -c /etc/bind/rndc.key -u ${bindUser} -a -A hmac-sha256 2>/dev/null
         fi
 
         ${pkgs.coreutils}/bin/mkdir -p /run/named
@@ -233,9 +243,9 @@ in
       '';
 
       serviceConfig = {
-        ExecStart = "${pkgs.bind.out}/sbin/named -u ${bindUser} ${optionalString cfg.ipv4Only "-4"} -c ${cfg.configFile} -f";
-        ExecReload = "${pkgs.bind.out}/sbin/rndc -k '/etc/bind/rndc.key' reload";
-        ExecStop = "${pkgs.bind.out}/sbin/rndc -k '/etc/bind/rndc.key' stop";
+        ExecStart = "${bindPkg.out}/sbin/named -u ${bindUser} ${optionalString cfg.ipv4Only "-4"} -c ${cfg.configFile} -f";
+        ExecReload = "${bindPkg.out}/sbin/rndc -k '/etc/bind/rndc.key' reload";
+        ExecStop = "${bindPkg.out}/sbin/rndc -k '/etc/bind/rndc.key' stop";
       };
 
       unitConfig.Documentation = "man:named(8)";
diff --git a/pkgs/applications/misc/logseq/default.nix b/pkgs/applications/misc/logseq/default.nix
index d28a12396ee..f281ab5a4cb 100644
--- a/pkgs/applications/misc/logseq/default.nix
+++ b/pkgs/applications/misc/logseq/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "logseq";
-  version = "0.2.2";
+  version = "0.2.3";
 
   src = fetchurl {
     url = "https://github.com/logseq/logseq/releases/download/${version}/logseq-linux-x64-${version}.AppImage";
-    sha256 = "03l5w0fg3laiz85k4g4w98ngaziyfr9s24xshjrfl71q6r9s813m";
+    sha256 = "LTwgLG/jUVOSR29LkLJ9q5wpPMK78yFvGtglzMG0ZC0=";
     name = "${pname}-${version}.AppImage";
   };
 
diff --git a/pkgs/applications/science/chemistry/octopus/default.nix b/pkgs/applications/science/chemistry/octopus/default.nix
index 74ed1873efe..1927950c4fc 100644
--- a/pkgs/applications/science/chemistry/octopus/default.nix
+++ b/pkgs/applications/science/chemistry/octopus/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitLab, symlinkJoin, gfortran, perl, procps
+{ lib, stdenv, fetchFromGitLab, gfortran, perl, procps
 , libyaml, libxc, fftw, blas, lapack, gsl, netcdf, arpack, autoreconfHook
 , python3
 }:
@@ -7,19 +7,24 @@ assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation rec {
   pname = "octopus";
-  version = "10.3";
+  version = "10.5";
 
   src = fetchFromGitLab {
     owner = "octopus-code";
     repo = "octopus";
     rev = version;
-    sha256 = "1axr3j53mi30gm3f645ga5jkhxbc7rbx432w2k2lgg6g9dv3fcs4";
+    sha256 = "1bgdkmsp6pwq3b6nxxkimrdmz71wqr8qi25gdzwpcv9wmcf1q27v";
   };
 
-  nativeBuildInputs = [ perl procps autoreconfHook ];
+  nativeBuildInputs = [
+    perl
+    procps
+    autoreconfHook
+    gfortran
+  ];
+
   buildInputs = [
     libyaml
-    gfortran
     libxc
     blas
     lapack
diff --git a/pkgs/applications/science/math/engauge-digitizer/default.nix b/pkgs/applications/science/math/engauge-digitizer/default.nix
index 5b529ca4b30..4c26dc2887c 100644
--- a/pkgs/applications/science/math/engauge-digitizer/default.nix
+++ b/pkgs/applications/science/math/engauge-digitizer/default.nix
@@ -4,13 +4,13 @@
 
 stdenv.mkDerivation rec {
   pname = "engauge-digitizer";
-  version = "12.1";
+  version = "12.2.2";
 
   src = fetchFromGitHub {
     owner = "markummitchell";
     repo = pname;
     rev = "v${version}";
-    sha256 = "12gflxqaa4w6vifwpaqwl0l3f9qq5pbrh45s1rpc584nmr0897a7";
+    sha256 = "sha256-Wj9o3wWbtHsEi6LFH4xDpwVR9BwcWc472jJ/QFDQZvY=";
   };
 
   nativeBuildInputs = [ qmake wrapQtAppsHook ];
diff --git a/pkgs/data/fonts/andika/default.nix b/pkgs/data/fonts/andika/default.nix
index 5fa2f1b2710..4799804b9ec 100644
--- a/pkgs/data/fonts/andika/default.nix
+++ b/pkgs/data/fonts/andika/default.nix
@@ -1,7 +1,7 @@
 { lib, fetchzip }:
 
 let
-  version = "5.000";
+  version = "6.000";
 in
   fetchzip rec {
     name = "andika-${version}";
@@ -14,7 +14,7 @@ in
       unzip -j $downloadedFile \*OFL.txt \*OFL-FAQ.txt \*README.txt \*FONTLOG.txt -d "$out/share/doc/${name}"
     '';
 
-    sha256 = "1jy9vpcprpd1k48p20wh6jhyn909ibia8lr5i747p41l0s8a7lqy";
+    sha256 = "sha256-5ymTBFssoEhmc2Z+JyEcMqw2p91i9/R44GRzEzUzK9Q=";
 
     meta = with lib; {
       homepage = "https://software.sil.org/andika";
diff --git a/pkgs/data/fonts/doulos-sil/default.nix b/pkgs/data/fonts/doulos-sil/default.nix
index 3de4cfc0cae..a1e686a320e 100644
--- a/pkgs/data/fonts/doulos-sil/default.nix
+++ b/pkgs/data/fonts/doulos-sil/default.nix
@@ -1,7 +1,7 @@
 { lib, fetchzip }:
 
 let
-  version = "5.000";
+  version = "6.001";
 in
   fetchzip rec {
     name = "doulos-sil-${version}";
@@ -14,7 +14,7 @@ in
       unzip -j $downloadedFile \*OFL.txt \*OFL-FAQ.txt \*README.txt \*FONTLOG.txt -d "$out/share/doc/${name}"
     '';
 
-    sha256 = "04a9cr7jbw7d8llcj8xsqp9rp8w6gcgbd9sdwvi02kz7jhqa0vad";
+    sha256 = "sha256-MkeLLT7EAeSuCMxVVxVfajHufxr+xMLIz2hf3wF3U4o=";
 
     meta = with lib; {
       homepage = "https://software.sil.org/doulos";
diff --git a/pkgs/development/tools/pandoc/default.nix b/pkgs/development/tools/pandoc/default.nix
index 4f65d5fa5db..7c286218d8e 100644
--- a/pkgs/development/tools/pandoc/default.nix
+++ b/pkgs/development/tools/pandoc/default.nix
@@ -8,6 +8,14 @@ in
     configureFlags = drv.configureFlags or [] ++ ["-fembed_data_files"];
     buildDepends = drv.buildDepends or [] ++ [haskellPackages.file-embed];
     buildTools = (drv.buildTools or []) ++ [ removeReferencesTo ];
+    patches = (drv.patches or []) ++ [
+      # Support citerefentry DocBook element.
+      # https://github.com/jgm/pandoc/pull/7437
+      (fetchpatch {
+        url = "https://github.com/jgm/pandoc/commit/06408d08e5ccf06a6a04c9b77470e6a67d98e52c.patch";
+        sha256 = "gOtrWVylzwgu0YLD4SztqlXxtaXXGOf8nTqLwUBS7qs=";
+      })
+    ];
   })).overrideAttrs (drv: {
 
     # These libraries are still referenced, because they generate
diff --git a/pkgs/servers/http/jetty/default.nix b/pkgs/servers/http/jetty/default.nix
index d9830df4f45..f226e0ad7e4 100644
--- a/pkgs/servers/http/jetty/default.nix
+++ b/pkgs/servers/http/jetty/default.nix
@@ -2,10 +2,10 @@
 
 stdenv.mkDerivation rec {
   pname = "jetty";
-  version = "9.4.41.v20210516";
+  version = "9.4.43.v20210629";
   src = fetchurl {
     url = "https://repo1.maven.org/maven2/org/eclipse/jetty/jetty-distribution/${version}/jetty-distribution-${version}.tar.gz";
-    sha256 = "sha256-hFQC1UiqZbbvyMf1FC3eqvVga3QdPWh0fbotatkVHBI=";
+    sha256 = "sha256-AfrmVLCZMuRGAZqoWeevbgXifbreErVM17rjJJ/HI9k=";
   };
 
   dontBuild = true;
diff --git a/pkgs/tools/admin/exoscale-cli/default.nix b/pkgs/tools/admin/exoscale-cli/default.nix
index 477bac87b9a..b37f3ce465e 100644
--- a/pkgs/tools/admin/exoscale-cli/default.nix
+++ b/pkgs/tools/admin/exoscale-cli/default.nix
@@ -2,13 +2,13 @@
 
 buildGoPackage rec {
   pname = "exoscale-cli";
-  version = "1.35.1";
+  version = "1.36.0";
 
   src = fetchFromGitHub {
     owner  = "exoscale";
     repo   = "cli";
     rev    = "v${version}";
-    sha256 = "sha256-RF0ZLcQNBVEExzSaOBM9EbqP1wuY8yIWYV8uabyc40o=";
+    sha256 = "sha256-2pkSwr/8pmRedcsvl55wHskv0aSAjlIbmHFUoTXCTE0=";
   };
 
   goPackagePath = "github.com/exoscale/cli";
diff --git a/pkgs/tools/misc/bdf2psf/default.nix b/pkgs/tools/misc/bdf2psf/default.nix
index 5e91756413e..d6ee1720430 100644
--- a/pkgs/tools/misc/bdf2psf/default.nix
+++ b/pkgs/tools/misc/bdf2psf/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "bdf2psf";
-  version = "1.203";
+  version = "1.204";
 
   src = fetchurl {
     url = "mirror://debian/pool/main/c/console-setup/bdf2psf_${version}_all.deb";
-    sha256 = "sha256-jQJC3b+HsEeKYRKQUfI2w3xYDJHs9ajfN8lb6Upzgd8=";
+    sha256 = "sha256-oyBkt52mWM2FiaM++s5Uoe7Wd0v1oLM7HjWKDjIonGE=";
   };
 
   nativeBuildInputs = [ dpkg ];
diff --git a/pkgs/tools/security/saml2aws/default.nix b/pkgs/tools/security/saml2aws/default.nix
index 567d3727a16..8ee2c9a4c4e 100644
--- a/pkgs/tools/security/saml2aws/default.nix
+++ b/pkgs/tools/security/saml2aws/default.nix
@@ -1,4 +1,4 @@
-{ lib, buildGoModule, fetchFromGitHub }:
+{ lib, stdenv, buildGoModule, fetchFromGitHub, AppKit }:
 
 buildGoModule rec {
   pname = "saml2aws";
@@ -14,6 +14,8 @@ buildGoModule rec {
   runVend = true;
   vendorSha256 = "sha256-TieQVPSWtIteU0wTqX7si6GrPdYd4WD2eK4ZlLz0VJ8=";
 
+  buildInputs = lib.optionals stdenv.isDarwin [ AppKit ];
+
   doCheck = false;
 
   subPackages = [ "." "cmd/saml2aws" ];
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 96f72a84d6f..af048e28848 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -8591,7 +8591,9 @@ in
 
   samim-fonts = callPackage ../data/fonts/samim-fonts {};
 
-  saml2aws = callPackage ../tools/security/saml2aws {};
+  saml2aws = callPackage ../tools/security/saml2aws {
+    inherit (darwin.apple_sdk.frameworks) AppKit;
+  };
 
   sammler = callPackage ../tools/security/sammler {};