Merge master into staging-next

maintainers/maintainer-list.nix

@@ -8923,7 +8923,7 @@
     name = "pasqui23";
   };
   patryk27 = {
-    email = "wychowaniec.patryk@gmail.com";
+    email = "pwychowaniec@pm.me";
     github = "Patryk27";
     githubId = 3395477;
     name = "Patryk Wychowaniec";

pkgs/applications/graphics/hydrus/default.nix

@@ -10,14 +10,14 @@
 
 python3Packages.buildPythonPackage rec {
   pname = "hydrus";
-  version = "463";
+  version = "464";
   format = "other";
 
   src = fetchFromGitHub {
     owner = "hydrusnetwork";
     repo = "hydrus";
     rev = "v${version}";
-    sha256 = "sha256-GT5aIMskOVn4eAd4612YYA8uAQC8tuJzpEHNhc7pMuc=";
+    sha256 = "sha256-ZAndODbl6cH0H1rA3Bhn3AlfIuba0LjxWxusGPDYvlA=";
   };
 
   nativeBuildInputs = [

pkgs/applications/graphics/pinta/default.nix

@@ -11,7 +11,7 @@ let
 in
 buildDotnetPackage rec {
   baseName = "Pinta";
-  version = "1.6";
+  version = "1.7.1";
 
   outputFiles = [ "bin/*" ];
   buildInputs = [ gtksharp mono-addins gettext ];
@@ -21,7 +21,7 @@ buildDotnetPackage rec {
     owner = "PintaProject";
     repo = "Pinta";
     rev = version;
-    sha256 = "0vgswy981c7ys4q7js5k85sky7bz8v32wsfq3br4j41vg92pw97d";
+    sha256 = "sha256-yRp/dpJ9T4DieqHTj3vhyuASPGe4vjHw0rSXFrTNZVc=";
   };
 
   # Remove version information from nodes <Reference Include="... Version=... ">
@@ -74,6 +74,8 @@ buildDotnetPackage rec {
       --replace _Comment Comment \
       --replace _GenericName GenericName \
       --replace _X-GNOME-FullName X-GNOME-FullName
+    substitute xdg/pinta.appdata.xml.in xdg/pinta.appdata.xml \
+      --replace _p p
 
     xbuild /target:CompileTranslations Pinta.Install.proj
     xbuild /target:Install Pinta.Install.proj

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

@@ -8,13 +8,13 @@
 
 stdenv.mkDerivation rec {
   pname = "fastp";
-  version = "0.23.1";
+  version = "0.23.2";
 
   src = fetchFromGitHub {
     owner = "OpenGene";
     repo = "fastp";
     rev = "v${version}";
-    sha256 = "sha256-vRJlNtg2JabBAUaX91Y04z8MdyxEnreBAlIHn7VB+u4=";
+    sha256 = "sha256-W1mXTfxD7/gHJhao6qqbNcyM3t2cfrUYiBYPJi/O1RI=";
   };
 
   buildInputs = [ zlib libdeflate isa-l ];

pkgs/data/themes/materia-theme/default.nix

@@ -1,4 +1,5 @@
-{ lib, stdenv
+{ lib
+, stdenv
 , fetchFromGitHub
 , meson
 , ninja
@@ -11,30 +12,20 @@
 
 stdenv.mkDerivation rec {
   pname = "materia-theme";
-  version = "20200916";
+  version = "20210322";
 
   src = fetchFromGitHub {
     owner = "nana-4";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0qaxxafsn5zd2ysgr0jyv5j73360mfdmxyd55askswlsfphssn74";
+    sha256 = "1fsicmcni70jkl4jb3fvh7yv0v9jhb8nwjzdq8vfwn256qyk0xvl";
   };
 
-  nativeBuildInputs = [
-    meson
-    ninja
-    sassc
-  ];
+  nativeBuildInputs = [ meson ninja sassc ];
 
-  buildInputs = [
-    gnome.gnome-themes-extra
-    gdk-pixbuf
-    librsvg
-  ];
+  buildInputs = [ gnome.gnome-themes-extra gdk-pixbuf librsvg ];
 
-  propagatedUserEnvPkgs = [
-    gtk-engine-murrine
-  ];
+  propagatedUserEnvPkgs = [ gtk-engine-murrine ];
 
   dontBuild = true;
 

pkgs/development/compilers/julia/1.6-bin.nix

@@ -61,7 +61,7 @@ stdenv.mkDerivation rec {
   '';
 
   meta = {
-    description = "High-level, high-performance dynamic language for technical computing.";
+    description = "High-level, high-performance, dynamic language for technical computing";
     homepage = "https://julialang.org";
     # Bundled and linked with various GPL code, although Julia itself is MIT.
     license = lib.licenses.gpl2Plus;

pkgs/development/compilers/julia/1.7-bin.nix

@@ -1,43 +1,43 @@
-{ autoPatchelfHook, fetchurl, lib, makeWrapper, openssl, stdenv }:
+{ autoPatchelfHook, fetchurl, lib, stdenv }:
 
 stdenv.mkDerivation rec {
   pname = "julia-bin";
-  version = "1.0.5";
+  version = "1.7.0";
 
   src = {
     x86_64-linux = fetchurl {
       url = "https://julialang-s3.julialang.org/bin/linux/x64/${lib.versions.majorMinor version}/julia-${version}-linux-x86_64.tar.gz";
-      sha256 = "00vbszpjmz47nqy19v83xa463ajhzwanjyg5mvcfp9kvfw9xdvcx";
+      sha256 = "0h0d9kfg00vglg2qmcx0k8c2gzn445i0xbsfw6wy1idf72kg76bj";
     };
   }.${stdenv.hostPlatform.system} or (throw "Unsupported system: ${stdenv.hostPlatform.system}");
 
   # Julia’s source files are in different locations for source and binary
-  # releases. Thus we temporarily create symlinks to allow us to share patches
+  # releases. Thus we temporarily create a symlink to allow us to share patches
   # with source releases.
   prePatch = ''
-    ln -s share/julia/stdlib/v${lib.versions.majorMinor version} stdlib
     ln -s share/julia/test
   '';
   patches = [
     # Source release Nix patch(es) relevant for binary releases as well.
-    ./patches/1.0-bin/0002-nix-Skip-tests-that-require-network-access.patch
+    ./patches/1.7-bin/0005-nix-Enable-parallel-unit-tests-for-sandbox.patch
   ];
   postPatch = ''
     # Revert symlink hack.
-    rm stdlib test
+    rm test
+
+    # Julia fails to pick up our Certification Authority root certificates, but
+    # it provides its own so we can simply disable the test. Patching in the
+    # dynamic path to ours require us to rebuild the Julia system image.
+    substituteInPlace share/julia/stdlib/v${lib.versions.majorMinor version}/NetworkOptions/test/runtests.jl \
+      --replace '@test ca_roots_path() != bundled_ca_roots()' \
+        '@test_skip ca_roots_path() != bundled_ca_roots()'
   '';
 
-  buildInputs = [ makeWrapper ];
   nativeBuildInputs = [ autoPatchelfHook ];
 
   installPhase = ''
     runHook preInstall
     cp -r . $out
-    # Setting `LD_LIBRARY_PATH` resolves `Libdl` failures. Not sure why this is
-    # only necessary on v1.0.x and a cleaner solution is welcome, but after
-    # staring at `strace` for a few hours this is as clean as I could make it.
-    wrapProgram $out/bin/julia \
-      --suffix LD_LIBRARY_PATH : $out/lib
     runHook postInstall
   '';
 
@@ -45,7 +45,6 @@ stdenv.mkDerivation rec {
   dontStrip = true;
 
   doInstallCheck = true;
-  installCheckInputs = [ openssl ];
   preInstallCheck = ''
     # Some tests require read/write access to $HOME.
     export HOME="$TMPDIR"
@@ -62,19 +61,11 @@ stdenv.mkDerivation rec {
   '';
 
   meta = {
-    description = "High-level, high-performance dynamic language for technical computing";
+    description = "High-level, high-performance, dynamic language for technical computing";
     homepage = "https://julialang.org";
     # Bundled and linked with various GPL code, although Julia itself is MIT.
     license = lib.licenses.gpl2Plus;
     maintainers = with lib.maintainers; [ ninjin raskin ];
     platforms = [ "x86_64-linux" ];
-    knownVulnerabilities = [
-      # Built with libgit2 v0.27.2:
-      #   https://github.com/JuliaLang/julia/blob/e0837d1e64a9e4d17534a9f981e9a2a3f221356f/deps/libgit2.version
-      # https://nvd.nist.gov/vuln/detail/CVE-2020-12278
-      "CVE-2020-12278"
-      # https://nvd.nist.gov/vuln/detail/CVE-2020-12279
-      "CVE-2020-12279"
-    ];
   };
 }

pkgs/development/compilers/julia/patches/1.0-bin/0002-nix-Skip-tests-that-require-network-access.patch

@@ -1,87 +0,0 @@
-From 4954b99efae367da49412edd31a7bd832ec62c69 Mon Sep 17 00:00:00 2001
-From: Pontus Stenetorp <pontus@stenetorp.se>
-Date: Mon, 15 Mar 2021 05:55:18 +0000
-Subject: [PATCH 2/3] nix: Skip tests that require network access
-
-Necessary as the Nix build sandbox does not permit network access.
----
- stdlib/Sockets/test/runtests.jl | 40 ++++++++++++++++-----------------
- test/file.jl                    |  4 ++--
- 2 files changed, 22 insertions(+), 22 deletions(-)
-
-diff --git a/stdlib/Sockets/test/runtests.jl b/stdlib/Sockets/test/runtests.jl
-index 6145f87616..9cc7a001e5 100644
---- a/stdlib/Sockets/test/runtests.jl
-+++ b/stdlib/Sockets/test/runtests.jl
-@@ -151,33 +151,33 @@ defaultport = rand(2000:4000)
- end
- 
- @testset "getnameinfo on some unroutable IP addresses (RFC 5737)" begin
--    @test getnameinfo(ip"192.0.2.1") == "192.0.2.1"
--    @test getnameinfo(ip"198.51.100.1") == "198.51.100.1"
--    @test getnameinfo(ip"203.0.113.1") == "203.0.113.1"
--    @test getnameinfo(ip"0.1.1.1") == "0.1.1.1"
--    @test getnameinfo(ip"::ffff:0.1.1.1") == "::ffff:0.1.1.1"
--    @test getnameinfo(ip"::ffff:192.0.2.1") == "::ffff:192.0.2.1"
--    @test getnameinfo(ip"2001:db8::1") == "2001:db8::1"
-+    @test_skip getnameinfo(ip"192.0.2.1") == "192.0.2.1"
-+    @test_skip getnameinfo(ip"198.51.100.1") == "198.51.100.1"
-+    @test_skip getnameinfo(ip"203.0.113.1") == "203.0.113.1"
-+    @test_skip getnameinfo(ip"0.1.1.1") == "0.1.1.1"
-+    @test_skip getnameinfo(ip"::ffff:0.1.1.1") == "::ffff:0.1.1.1"
-+    @test_skip getnameinfo(ip"::ffff:192.0.2.1") == "::ffff:192.0.2.1"
-+    @test_skip getnameinfo(ip"2001:db8::1") == "2001:db8::1"
- end
- 
- @testset "getnameinfo on some valid IP addresses" begin
-     @test !isempty(getnameinfo(ip"::")::String)
--    @test !isempty(getnameinfo(ip"0.0.0.0")::String)
--    @test !isempty(getnameinfo(ip"10.1.0.0")::String)
--    @test !isempty(getnameinfo(ip"10.1.0.255")::String)
--    @test !isempty(getnameinfo(ip"10.1.255.1")::String)
--    @test !isempty(getnameinfo(ip"255.255.255.255")::String)
--    @test !isempty(getnameinfo(ip"255.255.255.0")::String)
--    @test !isempty(getnameinfo(ip"192.168.0.1")::String)
--    @test !isempty(getnameinfo(ip"::1")::String)
-+    @test_skip !isempty(getnameinfo(ip"0.0.0.0")::String)
-+    @test_skip !isempty(getnameinfo(ip"10.1.0.0")::String)
-+    @test_skip !isempty(getnameinfo(ip"10.1.0.255")::String)
-+    @test_skip !isempty(getnameinfo(ip"10.1.255.1")::String)
-+    @test_skip !isempty(getnameinfo(ip"255.255.255.255")::String)
-+    @test_skip !isempty(getnameinfo(ip"255.255.255.0")::String)
-+    @test_skip !isempty(getnameinfo(ip"192.168.0.1")::String)
-+    @test_skip !isempty(getnameinfo(ip"::1")::String)
- end
- 
- @testset "getaddrinfo" begin
--    let localhost = getnameinfo(ip"127.0.0.1")::String
--        @test !isempty(localhost) && localhost != "127.0.0.1"
--        @test !isempty(getalladdrinfo(localhost)::Vector{IPAddr})
--        @test getaddrinfo(localhost, IPv4)::IPv4 != ip"0.0.0.0"
--        @test try
-+    let localhost = getnameinfo(ip"::")::String
-+        @test_skip !isempty(localhost) && localhost != "127.0.0.1"
-+        @test_skip !isempty(getalladdrinfo(localhost)::Vector{IPAddr})
-+        @test_skip getaddrinfo(localhost, IPv4)::IPv4 != ip"0.0.0.0"
-+        @test_skip try
-             getaddrinfo(localhost, IPv6)::IPv6 != ip"::"
-         catch ex
-             isa(ex, Sockets.DNSError) && ex.code == Base.UV_EAI_NONAME && ex.host == localhost
-diff --git a/test/file.jl b/test/file.jl
-index e86476f975..579276f82c 100644
---- a/test/file.jl
-+++ b/test/file.jl
-@@ -874,8 +874,8 @@ if !Sys.iswindows() || (Sys.windows_version() >= Sys.WINDOWS_VISTA_VER)
- else
-     @test_throws ErrorException symlink(file, "ba\0d")
- end
--@test_throws ArgumentError download("good", "ba\0d")
--@test_throws ArgumentError download("ba\0d", "good")
-+@test_skip @test_throws ArgumentError download("good", "ba\0d")
-+@test_skip @test_throws ArgumentError download("ba\0d", "good")
- 
- ###################
- #     walkdir     #
--- 
-2.29.3
-

pkgs/development/compilers/julia/patches/1.7-bin/0005-nix-Enable-parallel-unit-tests-for-sandbox.patch

@@ -0,0 +1,30 @@
+From 44c2c979c4f2222567ce65f506cf47fb87482348 Mon Sep 17 00:00:00 2001
+From: Pontus Stenetorp <pontus@stenetorp.se>
+Date: Thu, 8 Apr 2021 04:37:44 +0000
+Subject: [PATCH 5/6] nix: Enable parallel unit tests for sandbox
+
+Disabled by default due to lack of networking in the Nix sandbox. This
+greatly speeds up the build process on a multi-core system.
+---
+ test/runtests.jl | 5 +++--
+ 1 file changed, 3 insertions(+), 2 deletions(-)
+
+diff --git a/test/runtests.jl b/test/runtests.jl
+index 2f9cd058bb..2f8c19fa32 100644
+--- a/test/runtests.jl
++++ b/test/runtests.jl
+@@ -83,8 +83,9 @@ prepend!(tests, linalg_tests)
+ import LinearAlgebra
+ cd(@__DIR__) do
+     n = 1
+-    if net_on
+-        n = min(Sys.CPU_THREADS, length(tests))
++    if net_on || haskey(ENV, "NIX_BUILD_CORES")
++        x = haskey(ENV, "NIX_BUILD_CORES") ? parse(Int, ENV["NIX_BUILD_CORES"]) : Sys.CPU_THREADS
++        n = min(x, Sys.CPU_THREADS, length(tests))
+         n > 1 && addprocs_with_testenv(n)
+         LinearAlgebra.BLAS.set_num_threads(1)
+     end
+-- 
+2.29.3
+

pkgs/development/libraries/libxc/default.nix

@@ -20,6 +20,8 @@ stdenv.mkDerivation rec {
   cmakeFlags = [
     "-DENABLE_FORTRAN=ON"
     "-DBUILD_SHARED_LIBS=ON"
+    # needed for tests to link
+    "-DCMAKE_SKIP_BUILD_RPATH=OFF"
     # Force compilation of higher derivatives
     "-DDISABLE_VXC=0"
     "-DDISABLE_FXC=0"
@@ -27,10 +29,6 @@ stdenv.mkDerivation rec {
     "-DDISABLE_LXC=0"
   ];
 
-  preCheck = ''
-    export LD_LIBRARY_PATH=$(pwd)
-  '';
-
   doCheck = true;
 
   meta = with lib; {

pkgs/development/libraries/nss/default.nix

@@ -27,7 +27,7 @@ let
   #       It will rebuild itself using the version of this package (NSS) and if
   #       an update is required do the required changes to the expression.
   #       Example: nix-shell ./maintainers/scripts/update.nix --argstr package cacert
-  version = "3.72";
+  version = "3.73";
 
 in
 stdenv.mkDerivation rec {
@@ -36,7 +36,7 @@ stdenv.mkDerivation rec {
 
   src = fetchurl {
     url = "mirror://mozilla/security/nss/releases/NSS_${lib.replaceStrings [ "." ] [ "_" ] version}_RTM/src/${pname}-${version}.tar.gz";
-    sha256 = "bqYKn/ET5JPqKrJfQep1qfvRCveQPyb3A9rIaAcy0C4=";
+    sha256 = "1rfqjq02rfv0ycdmvic51pi093rg33zb8kpqkvddf44vv9l3lvan";
   };
 
   depsBuildBuild = [ buildPackages.stdenv.cc ];

pkgs/development/tools/clang-tools/default.nix

@@ -34,6 +34,6 @@ in stdenv.mkDerivation {
 
   meta = unwrapped.meta // {
     description = "Standalone command line tools for C++ development";
-    maintainers = with lib.maintainers; [ aherrmann ];
+    maintainers = with lib.maintainers; [ patryk27 ];
   };
 }

pkgs/top-level/aliases.nix

@@ -394,6 +394,7 @@ mapAliases ({
   julia_1 = throw "julia_1 has been deprecated in favor of julia_10 as it was ambiguous"; # added 2021-03-13
   julia_11 = throw "julia_11 has been deprecated in favor of the latest stable version"; # added 2020-09-15
   julia_13 = throw "julia_13 has been deprecated in favor of the latest stable version"; # added 2021-03-13
+  julia_10-bin = throw "julia_10-bin has been deprecated in favor of the latest LTS version"; # added 2021-12-02
   kbdKeymaps = throw "kbdKeymaps is not needed anymore since dvp and neo are now part of kbd"; # added 2021-04-11
   kdeconnect = plasma5Packages.kdeconnect-kde; # added 2020-10-28
   kdiff3-qt5 = kdiff3; # added 2017-02-18

pkgs/top-level/all-packages.nix

@@ -12438,11 +12438,11 @@ with pkgs;
   julia-stable = julia_15;
   julia = julia-stable;
 
-  julia_10-bin = callPackage ../development/compilers/julia/1.0-bin.nix { };
   julia_16-bin = callPackage ../development/compilers/julia/1.6-bin.nix { };
+  julia_17-bin = callPackage ../development/compilers/julia/1.7-bin.nix { };
 
-  julia-lts-bin = julia_10-bin;
-  julia-stable-bin = julia_16-bin;
+  julia-lts-bin = julia_16-bin;
+  julia-stable-bin = julia_17-bin;
   julia-bin = julia-stable-bin;
 
   jwasm =  callPackage ../development/compilers/jwasm { };