Merge staging-next into staging

2022-07-21 00:03:40 +00:00 · 2022-07-21 00:03:40 +00:00 · f09c360345
parent e84301980d bc970e700d
commit f09c360345
27 changed files with 251 additions and 98 deletions
--- a/nixos/modules/services/monitoring/prometheus/exporters/mail.nix
+++ b/nixos/modules/services/monitoring/prometheus/exporters/mail.nix
@ -5,6 +5,8 @@ with lib;
 let
  cfg = config.services.prometheus.exporters.mail;

+  configFile = if cfg.configuration != null then configurationFile else (escapeShellArg cfg.configFile);
+
  configurationFile = pkgs.writeText "prometheus-mail-exporter.conf" (builtins.toJSON (
    # removes the _module attribute, null values and converts attrNames to lowercase
    mapAttrs' (name: value:
@ -137,6 +139,13 @@ in
 {
  port = 9225;
  extraOpts = {
+    environmentFile = mkOption {
+      type = types.nullOr types.str;
+      default = null;
+      description = ''
+        File containing env-vars to be substituted into the exporter's config.
+      '';
+    };
    configFile = mkOption {
      type = types.nullOr types.path;
      default = null;
@ -162,13 +171,19 @@ in
  serviceOpts = {
    serviceConfig = {
      DynamicUser = false;
+      EnvironmentFile = mkIf (cfg.environmentFile != null) [ cfg.environmentFile ];
+      RuntimeDirectory = "prometheus-mail-exporter";
+      ExecStartPre = [
+        "${pkgs.writeShellScript "subst-secrets-mail-exporter" ''
+          umask 0077
+          ${pkgs.envsubst}/bin/envsubst -i ${configFile} -o ''${RUNTIME_DIRECTORY}/mail-exporter.json
+        ''}"
+      ];
      ExecStart = ''
        ${pkgs.prometheus-mail-exporter}/bin/mailexporter \
          --web.listen-address ${cfg.listenAddress}:${toString cfg.port} \
          --web.telemetry-path ${cfg.telemetryPath} \
-          --config.file ${
-            if cfg.configuration != null then configurationFile else (escapeShellArg cfg.configFile)
-          } \
+          --config.file ''${RUNTIME_DIRECTORY}/mail-exporter.json \
          ${concatStringsSep " \\\n  " cfg.extraFlags}
      '';
    };
--- a/nixos/modules/services/networking/mxisd.nix
+++ b/nixos/modules/services/networking/mxisd.nix
@ -130,6 +130,7 @@ in {
        EnvironmentFile = mkIf (cfg.environmentFile != null) [ cfg.environmentFile ];
        ExecStart = "${cfg.package}/bin/${executable} -c ${cfg.dataDir}/mxisd-config.yaml";
        ExecStartPre = "${pkgs.writeShellScript "mxisd-substitute-secrets" ''
+          umask 0077
          ${pkgs.envsubst}/bin/envsubst -o ${cfg.dataDir}/mxisd-config.yaml \
            -i ${configFile}
        ''}";
--- a/nixos/modules/services/security/privacyidea.nix
+++ b/nixos/modules/services/security/privacyidea.nix
@ -332,6 +332,7 @@ in
            [ cfg.ldap-proxy.environmentFile ];
          ExecStartPre =
            "${pkgs.writeShellScript "substitute-secrets-ldap-proxy" ''
+              umask 0077
              ${pkgs.envsubst}/bin/envsubst \
                -i ${ldapProxyConfig} \
                -o $STATE_DIRECTORY/ldap-proxy.ini
--- a/nixos/tests/prometheus-exporters.nix
+++ b/nixos/tests/prometheus-exporters.nix
@ -557,10 +557,12 @@ let
        systemd.services.prometheus-mail-exporter = {
          after = [ "postfix.service" ];
          requires = [ "postfix.service" ];
-          preStart = ''
-            mkdir -p -m 0700 mail-exporter/new
-          '';
          serviceConfig = {
+            ExecStartPre = [
+              "${pkgs.writeShellScript "create-maildir" ''
+                mkdir -p -m 0700 mail-exporter/new
+              ''}"
+            ];
            ProtectHome = true;
            ReadOnlyPaths = "/";
            ReadWritePaths = "/var/spool/mail";
--- a/pkgs/applications/editors/vscode/extensions/default.nix
+++ b/pkgs/applications/editors/vscode/extensions/default.nix
@ -1201,8 +1201,8 @@ let
        mktplcRef = {
          name = "haskell";
          publisher = "haskell";
-          version = "1.8.0";
-          sha256 = "sha256-+k8XT2COe9Z8HvZvcrzfVuocRcxXBrVoNHDT/uKK7Hs=";
+          version = "2.2.0";
+          sha256 = "sha256-YGPytmI4PgH6GQuWaRF5quiKGoOabkv7On+WVupI92E=";
        };
        meta = with lib; {
          license = licenses.mit;
@ -1415,8 +1415,8 @@ let
        mktplcRef = {
          name = "language-haskell";
          publisher = "justusadam";
-          version = "3.4.0";
-          sha256 = "0ab7m5jzxakjxaiwmg0jcck53vnn183589bbxh3iiylkpicrv67y";
+          version = "3.6.0";
+          sha256 = "sha256-rZXRzPmu7IYmyRWANtpJp3wp0r/RwB7eGHEJa7hBvoQ=";
        };
        meta = {
          license = lib.licenses.bsd3;
@ -2028,6 +2028,26 @@ let
        };
      };

+      sanaajani.taskrunnercode = buildVscodeMarketplaceExtension {
+        mktplcRef = {
+          name = "taskrunnercode";
+          publisher = "sanaajani";
+          version = "0.3.0";
+          sha256 = "NVGMM9ugmYZNCWhNmclcGuVJPhJ9h4q2G6nNzVUEpes=";
+        };
+        meta = {
+          description = "Extension to view and run tasks from Explorer pane";
+          longDescription = ''
+            This extension adds an additional "Task Runner" view in your Explorer Pane
+            to visualize and individually run the auto-detected or configured tasks
+            in your project.
+          '';
+          homepage = "https://github.com/sana-ajani/taskrunner-code";
+          license = lib.licenses.mit;
+          maintainers = with lib.maintainers; [ pbsds ];
+        };
+      };
+
      scala-lang.scala = buildVscodeMarketplaceExtension {
        mktplcRef = {
          name = "scala";
@ -2077,6 +2097,26 @@ let
        };
      };

+      shd101wyy.markdown-preview-enhanced = buildVscodeMarketplaceExtension {
+        mktplcRef = {
+          publisher = "shd101wyy";
+          name = "markdown-preview-enhanced";
+          version = "0.6.3";
+          sha256 = "dCWERQ5rHnmYLtYl12gJ+dXLnpMu55WnmF1VfdP0x34=";
+        };
+        meta = {
+          description = "Provides a live preview of markdown using either markdown-it or pandoc";
+          longDescription = ''
+            Markdown Preview Enhanced provides you with many useful functionalities
+            such as automatic scroll sync, math typesetting, mermaid, PlantUML,
+            pandoc, PDF export, code chunk, presentation writer, etc.
+          '';
+          homepage = "https://github.com/shd101wyy/vscode-markdown-preview-enhanced";
+          license = lib.licenses.ncsa;
+          maintainers = with lib.maintainers; [ pbsds ];
+        };
+      };
+
      shyykoserhiy.vscode-spotify = buildVscodeMarketplaceExtension {
        mktplcRef = {
          name = "vscode-spotify";
@ -2352,6 +2392,8 @@ let
          sha256 = "1bcj546bp0w4yndd0qxwr8grhiwjd1jvf33jgmpm0j96y34vcszz";
        };
        meta = {
+          description = "Show PDF preview in VSCode";
+          homepage = "https://github.com/tomoki1207/vscode-pdfviewer";
          license = lib.licenses.mit;
        };
      };
--- a/pkgs/applications/editors/vscode/extensions/vscode-utils.nix
+++ b/pkgs/applications/editors/vscode/extensions/vscode-utils.nix
@ -43,7 +43,7 @@ let
  });

  fetchVsixFromVscodeMarketplace = mktplcExtRef:
-    fetchurl((import ./mktplcExtRefToFetchArgs.nix mktplcExtRef));
+    fetchurl (import ./mktplcExtRefToFetchArgs.nix mktplcExtRef);

  buildVscodeMarketplaceExtension = a@{
    name ? "",
@ -65,11 +65,12 @@ let
    "publisher"
    "version"
    "sha256"
+    "arch"
  ];

  mktplcExtRefToExtDrv = ext:
-    buildVscodeMarketplaceExtension ((removeAttrs ext mktplcRefAttrList) // {
-      mktplcRef = ext;
+    buildVscodeMarketplaceExtension (removeAttrs ext mktplcRefAttrList // {
+      mktplcRef = builtins.intersectAttrs (lib.genAttrs mktplcRefAttrList (_: null)) ext;
    });

  extensionFromVscodeMarketplace = mktplcExtRefToExtDrv;
--- a/pkgs/applications/networking/browsers/chromium/upstream-info.json
+++ b/pkgs/applications/networking/browsers/chromium/upstream-info.json
@ -1,8 +1,8 @@
 {
  "stable": {
-    "version": "103.0.5060.114",
-    "sha256": "0rarcd2q1ggl10cw3vwjk7j9aka7i129a0qv8qr7751vy083as3p",
-    "sha256bin64": "1qxbnnnq0miizazprwynvxxvgaaw9dd9y7bssybvmga3g2c00fk9",
+    "version": "103.0.5060.134",
+    "sha256": "0wdmy15602qxrb403p8yyx69k7py85fbawdsgap1l6z4h4j2g2p4",
+    "sha256bin64": "143jc70cyns2bh5cizy32fdsfl6hq22rphx216vywhncdsd96cnw",
    "deps": {
      "gn": {
        "version": "2022-05-11",
@ -12,16 +12,16 @@
      }
    },
    "chromedriver": {
-      "version": "103.0.5060.53",
-      "sha256_linux": "1gpxfrqf2wm2c76701rnw0h5ppmaqzf5ygcrasj1mmwjsfk49v5d",
-      "sha256_darwin": "03ibi0ybr3mmk02mmn6dp7ygjn7c9wwvahbhm2syh0fhxyyxmf0p",
-      "sha256_darwin_aarch64": "13bb2ai32b1q4lvyhcgp5315zzxwbi6609xxb67h7h3i3rb2yhcd"
+      "version": "103.0.5060.134",
+      "sha256_linux": "13ld47n16b9adb6gh9bc7gr0vi3afyz5pn15rq1w983yqab49vwb",
+      "sha256_darwin": "0rpnny902h8il8wvxh4ccrvviqfpds28zgqv1v0vhlbgzgykcw3z",
+      "sha256_darwin_aarch64": "19v7q2wnvp5yfhh8x73p9shayar5yddf22rzqnlvy59saygcc7wa"
    }
  },
  "beta": {
-    "version": "104.0.5112.48",
-    "sha256": "1zk4ywphcy6nrv0yf38yhl2bcq6fk34makglx31aalf2nhhw945i",
-    "sha256bin64": "14cx0m6jak4cma62axli0l4gqzqqh4gs7gam2dfahmwxsgcdwwn7",
+    "version": "104.0.5112.57",
+    "sha256": "1fvcmnxfw65c2dgis2vwhzg671y62irzvcl609vxwxcslhwwqc4r",
+    "sha256bin64": "0nx4ca2v1bgk25yjlfgn8vgdwwplyim6a0ai1hppy4yhm9mhppk7",
    "deps": {
      "gn": {
        "version": "2022-06-08",
@ -45,9 +45,9 @@
    }
  },
  "ungoogled-chromium": {
-    "version": "103.0.5060.114",
-    "sha256": "0rarcd2q1ggl10cw3vwjk7j9aka7i129a0qv8qr7751vy083as3p",
-    "sha256bin64": "1qxbnnnq0miizazprwynvxxvgaaw9dd9y7bssybvmga3g2c00fk9",
+    "version": "103.0.5060.134",
+    "sha256": "0wdmy15602qxrb403p8yyx69k7py85fbawdsgap1l6z4h4j2g2p4",
+    "sha256bin64": "143jc70cyns2bh5cizy32fdsfl6hq22rphx216vywhncdsd96cnw",
    "deps": {
      "gn": {
        "version": "2022-05-11",
@ -56,8 +56,8 @@
        "sha256": "03dqfrdpf5xxl64dby3qmbwpzdq2gsa8g7xl438py3a629rgxg63"
      },
      "ungoogled-patches": {
-        "rev": "103.0.5060.114-1",
-        "sha256": "11i7d480q21vcd9p14rc7rb408xwlg2nkj88dq0sfj2rz60lzy0a"
+        "rev": "103.0.5060.134-1",
+        "sha256": "00mpmyaa8bqxf1f4vhk1waxhjbhcwab8m1x1vf341al64f6bmr1r"
      }
    }
  }
--- a/pkgs/applications/science/electronics/hal-hardware-analyzer/default.nix
+++ b/pkgs/applications/science/electronics/hal-hardware-analyzer/default.nix
@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, cmake, ninja, pkg-config, python3Packages
+{ lib, stdenv, fetchFromGitHub, fetchpatch, cmake, ninja, pkg-config, python3Packages
 , boost, rapidjson, qtbase, qtsvg, igraph, spdlog, wrapQtAppsHook
 , graphviz, llvmPackages, z3
 }:
@ -13,6 +13,18 @@ stdenv.mkDerivation rec {
    rev = "v${version}";
    sha256 = "sha256-uNpELHhSAVRJL/4iypvnl3nX45SqB419r37lthd2WmQ=";
  };
+
+  patches = [
+    (fetchpatch {
+      # Fix build with python 3.10
+      # https://github.com/emsec/hal/pull/463
+      name = "hal-fix-python-3.10.patch";
+      url = "https://github.com/emsec/hal/commit/f695f55cb2209676ef76366185b7c419417fbbc9.patch";
+      sha256 = "sha256-HsCdG3tPllUsLw6kQtGaaEGkEHqZPSC2v9k6ycO2I/8=";
+      includes = [ "plugins/gui/src/python/python_context.cpp" ];
+    })
+  ];
+
  # make sure bundled dependencies don't get in the way - install also otherwise
  # copies them in full to the output, bloating the package
  postPatch = ''
--- a/pkgs/applications/science/misc/root/default.nix
+++ b/pkgs/applications/science/misc/root/default.nix
@ -40,13 +40,27 @@
 , noSplash ? false
 }:

+let
+
+  _llvm_9 = llvm_9.overrideAttrs (prev: {
+    patches = (prev.patches or []) ++ [
+      (fetchpatch {
+        url = "https://github.com/root-project/root/commit/a9c961cf4613ff1f0ea50f188e4a4b0eb749b17d.diff";
+        stripLen = 3;
+        hash = "sha256-LH2RipJICEDWOr7JzX5s0QiUhEwXNMFEJihYKy9qWpo=";
+      })
+    ];
+  });
+
+in
+
 stdenv.mkDerivation rec {
  pname = "root";
-  version = "6.24.06";
+  version = "6.26.04";

  src = fetchurl {
    url = "https://root.cern.ch/download/root_v${version}.source.tar.gz";
-    sha256 = "sha256-kH9p9LrKHk8w7rSXlZjKdZm2qoA8oEboDiW2u6oO9SI=";
+    hash = "sha256-onHPgngtbtLIfqXu9mgYA/LmnhezA2352GNjbpNYQh4=";
  };

  nativeBuildInputs = [ makeWrapper cmake pkg-config git ];
@ -59,7 +73,7 @@ stdenv.mkDerivation rec {
    zstd
    lapack
    libxml2
-    llvm_9
+    _llvm_9
    lz4
    xz
    gsl
@ -80,13 +94,6 @@ stdenv.mkDerivation rec {

  patches = [
    ./sw_vers.patch
-
-    # Fix builtin_llvm=OFF support
-    (fetchpatch {
-      url = "https://github.com/root-project/root/commit/0cddef5d3562a89fe254e0036bb7d5ca8a5d34d2.diff";
-      excludes = [ "interpreter/cling/tools/plugins/clad/CMakeLists.txt" ];
-      sha256 = "sha256-VxWUbxRHB3O6tERFQdbGI7ypDAZD3sjSi+PYfu1OAbM=";
-    })
  ];

  # Fix build against vanilla LLVM 9
--- a/pkgs/applications/virtualization/crun/default.nix
+++ b/pkgs/applications/virtualization/crun/default.nix
@ -39,25 +39,16 @@ let
 in
 stdenv.mkDerivation rec {
  pname = "crun";
-  version = "1.4.5";
+  version = "1.5";

  src = fetchFromGitHub {
    owner = "containers";
    repo = pname;
    rev = version;
-    sha256 = "sha256-YXbyGUY/E8odjljDok+yYyU8yZSyUFc22zumrUuuXXQ=";
+    sha256 = "sha256-eirCENgt25VRPub7c9cxYQ1uFxYbzm75cJ1v4r6O/+k=";
    fetchSubmodules = true;
  };

-  patches = [
-    # Should dropped in next release after 1.4.5
-    (fetchpatch {
-      name = "usrbin-paths.patch";
-      url = "https://github.com/containers/crun/commit/dd29f7f7f713c49784ac30f7cdca33b2ef94d5b8.patch";
-      sha256 = "sha256-kHHix8CUL+c8HbOe5qx4PeF1P19113U4bRZyleMUjqk=";
-    })
-  ];
-
  nativeBuildInputs = [ autoreconfHook go-md2man pkg-config python3 ];

  buildInputs = [ libcap libseccomp systemd yajl ]
--- a/pkgs/development/haskell-modules/configuration-common.nix
+++ b/pkgs/development/haskell-modules/configuration-common.nix
@ -2553,15 +2553,6 @@ self: super: {
  })
  super.polynomial);

-  fast-tags = appendPatches [
-    (fetchpatch {
-      name = "fast-tags-ghc-9.0-fix-test-nondeterminism.patch";
-      url = "https://github.com/elaforge/fast-tags/commit/af861acc2dd239fedd8b169ddc5e3fa694e7af57.patch";
-      sha256 = "0ml678q1n29daqnxsb5p94s5lf7a6dk4lqbbgmiayxrbyxnlbi4f";
-      excludes = [ ".github/**" ];
-    })
-  ] super.fast-tags;
-
  # lucid-htmx has restrictive upper bounds on lucid and servant:
  #
  #   Setup: Encountered missing or private dependencies:
--- a/pkgs/development/haskell-modules/configuration-hackage2nix/broken.yaml
+++ b/pkgs/development/haskell-modules/configuration-hackage2nix/broken.yaml
@ -1424,7 +1424,6 @@ broken-packages:
  - fast-nats
  - fastpbkdf2
  - FastPush
-  - fast-tags
  - FastxPipe
  - fathead-util
  - fb
--- a/pkgs/development/haskell-modules/hackage-packages.nix
+++ b/pkgs/development/haskell-modules/hackage-packages.nix
@ -95044,9 +95044,7 @@ self: {
       ];
       description = "Fast incremental vi and emacs tags";
       license = lib.licenses.bsd3;
-       hydraPlatforms = lib.platforms.none;
       mainProgram = "fast-tags";
-       broken = true;
     }) {};

  "fast-tagsoup" = callPackage
--- a/pkgs/development/libraries/arrow-cpp/default.nix
+++ b/pkgs/development/libraries/arrow-cpp/default.nix
@ -250,7 +250,7 @@ stdenv.mkDerivation rec {

  meta = with lib; {
    description = "A cross-language development platform for in-memory data";
-    homepage = "https://arrow.apache.org/";
+    homepage = "https://arrow.apache.org/docs/cpp/";
    license = licenses.asl20;
    platforms = platforms.unix;
    maintainers = with maintainers; [ tobim veprbl cpcloud ];
--- a/pkgs/development/libraries/arrow-glib/default.nix
+++ b/pkgs/development/libraries/arrow-glib/default.nix
@ -0,0 +1,35 @@
+{ stdenv
+, arrow-cpp
+, fetchurl
+, glib
+, gobject-introspection
+, lib
+, meson
+, ninja
+, pkg-config
+}:
+
+stdenv.mkDerivation rec {
+  pname = "arrow-glib";
+  inherit (arrow-cpp) src version;
+  sourceRoot = "apache-arrow-${version}/c_glib";
+
+  nativeBuildInputs = [
+    meson
+    ninja
+    pkg-config
+  ];
+
+  buildInputs = [
+    arrow-cpp
+    glib
+    gobject-introspection
+  ];
+
+  meta = with lib; {
+    inherit (arrow-cpp.meta) license platforms;
+    description = "GLib bindings for Apache Arrow";
+    homepage = "https://arrow.apache.org/docs/c_glib/";
+    maintainers = with maintainers; [ amarshall ];
+  };
+}
--- a/pkgs/development/libraries/geos/default.nix
+++ b/pkgs/development/libraries/geos/default.nix
@ -6,21 +6,13 @@

 stdenv.mkDerivation rec {
  pname = "geos";
-  version = "3.10.2";
+  version = "3.11.0";

  src = fetchurl {
    url = "https://download.osgeo.org/geos/${pname}-${version}.tar.bz2";
-    sha256 = "sha256-ULvFmaw4a0wrOWLcxBHwBAph8gSq7066ciXs3Qz0VxU=";
+    sha256 = "sha256-eauMq/SqhgTRYVV7UuPk2EV1rNwNCMsJqz96rvpNhYo=";
  };

-  patches = [
-    # Fix paths with absolute CMAKE_INSTALL_*DIR
-    (fetchpatch {
-      url = "https://github.com/libgeos/geos/commit/11faa4db672ed61d64fd8a6f1a59114f5b5f2406.patch";
-      hash = "sha256-oAArwGq91Z93C6hBPQD0AlY8Q4Nnn6tA40HUPoZ5ftc=";
-    })
-  ];
-
  nativeBuildInputs = [ cmake ];

  meta = with lib; {
--- a/pkgs/development/libraries/simdjson/default.nix
+++ b/pkgs/development/libraries/simdjson/default.nix
@ -2,20 +2,20 @@

 stdenv.mkDerivation rec {
  pname = "simdjson";
-  version = "1.0.2";
+  version = "2.2.0";

  src = fetchFromGitHub {
    owner = "simdjson";
    repo = "simdjson";
    rev = "v${version}";
-    sha256 = "sha256-WuqBR1/Iqly+Y8kJxTuZLTVkR3ltXdyr+/6J3zhBNkQ=";
+    sha256 = "sha256-n+W5xvWC3sPSX0SF5x1ArUtWZayoyQRThgWWhRG4Fac=";
  };

  nativeBuildInputs = [ cmake ];

  cmakeFlags = [
-    "-DSIMDJSON_JUST_LIBRARY=ON"
-  ] ++ lib.optional stdenv.hostPlatform.isStatic "-DSIMDJSON_BUILD_STATIC=ON";
+    "-DSIMDJSON_DEVELOPER_MODE=OFF"
+  ] ++ lib.optional stdenv.hostPlatform.isStatic "-DBUILD_SHARED_LIBS=OFF";

  meta = with lib; {
    homepage = "https://simdjson.org/";
--- a/pkgs/development/python-modules/aiobotocore/default.nix
+++ b/pkgs/development/python-modules/aiobotocore/default.nix
@ -10,12 +10,12 @@

 buildPythonPackage rec {
  pname = "aiobotocore";
-  version = "2.3.0";
+  version = "2.3.4";
  disabled = pythonOlder "3.7";

  src = fetchPypi {
    inherit pname version;
-    sha256 = "sha256-/D09YGFBC8GU0J7FReMLRGnV90dw+TespfaqReYqG/4=";
+    sha256 = "sha256-ZVTr6ldk9m9L5USk/KoJU+6A5gDde9gYukiT1yvxK/s=";
  };

  # relax version constraints: aiobotocore works with newer botocore versions
--- a/pkgs/development/python-modules/pygeos/default.nix
+++ b/pkgs/development/python-modules/pygeos/default.nix
@ -17,6 +17,12 @@ buildPythonPackage rec {
    sha256 = "sha256-PEFULvZ8ZgFfRDrj5uaDUDqKIh+cJPsjgPauQq7RYAo=";
  };

+  patches = [
+    # Adapt https://github.com/shapely/shapely/commit/4889bd2d72ff500e51ba70d5b954241878349562,
+    # backporting to pygeos
+    ./fix-for-geos-3-11.patch
+  ];
+
  nativeBuildInputs = [
    geos # for geos-config
    cython
--- a/pkgs/development/python-modules/pygeos/fix-for-geos-3-11.patch
+++ b/pkgs/development/python-modules/pygeos/fix-for-geos-3-11.patch
@ -0,0 +1,29 @@
+From ea82dbefeb573150935eb78a6916813775512e76 Mon Sep 17 00:00:00 2001
+From: Joris Van den Bossche <jorisvandenbossche@gmail.com>
+Date: Tue, 26 Apr 2022 22:17:00 +0200
+Subject: [PATCH] TST: fix tests for GEOS main (#1357) (backported for nixpkgs)
+
+---
+ pygeos/tests/test_constructive.py | 6 +++++-
+ 1 file changed, 5 insertions(+), 1 deletion(-)
+
+diff --git a/pygeos/tests/test_constructive.py b/pygeos/tests/test_constructive.py
+index 87c0a9f..b3459d1 100644
+--- a/pygeos/tests/test_constructive.py
+++ b/pygeos/tests/test_constructive.py
+@@ -48,7 +48,11 @@ def test_no_args_array(geometry, func):
+ @pytest.mark.parametrize("geometry", all_types)
+ @pytest.mark.parametrize("func", CONSTRUCTIVE_FLOAT_ARG)
+ def test_float_arg_array(geometry, func):
+-    if func is pygeos.offset_curve and pygeos.get_type_id(geometry) not in [1, 2]:
+    if (
+        func is pygeos.offset_curve
+        and pygeos.get_type_id(geometry) not in [1, 2]
+        and pygeos.geos_version < (3, 11, 0)
+    ):
+         with pytest.raises(GEOSException, match="only accept linestrings"):
+             func([geometry, geometry], 0.0)
+         return
+-- 
+2.36.1
+
--- a/pkgs/development/python-modules/shapely/default.nix
+++ b/pkgs/development/python-modules/shapely/default.nix
@ -2,6 +2,7 @@
 , stdenv
 , buildPythonPackage
 , fetchPypi
+, fetchpatch
 , substituteAll
 , pythonOlder
 , geos
@ -43,6 +44,12 @@ buildPythonPackage rec {
      libgeos_c = GEOS_LIBRARY_PATH;
      libc = lib.optionalString (!stdenv.isDarwin) "${stdenv.cc.libc}/lib/libc${stdenv.hostPlatform.extensions.sharedLibrary}.6";
    })
+    (fetchpatch {
+      name = "fix-tests-geos-3.11.patch";
+      url = "https://github.com/shapely/shapely/commit/21c8e8a7909e7fb3cce6daa5c5b8284ac927fcb0.patch";
+      includes = [ "tests/test_parallel_offset.py" ];
+      sha256 = "sha256-85c8NlmAzzfCgepe/411ug5Sq+665dFMb3ySaUt9Kew=";
+    })
 ];

  preCheck = ''
--- a/pkgs/servers/atlassian/crowd.nix
+++ b/pkgs/servers/atlassian/crowd.nix
@ -3,11 +3,11 @@

 stdenv.mkDerivation rec {
  pname = "atlassian-crowd";
-  version = "4.4.0";
+  version = "5.0.1";

  src = fetchurl {
    url = "https://www.atlassian.com/software/crowd/downloads/binary/${pname}-${version}.tar.gz";
-    sha256 = "0ipfvdjs8v02y37rmihljy9lkb3ycz5hyc14mcg65ilsscsq3x91";
+    sha256 = "sha256-ccXSNuiXP0+b9WObboikqVd0nKH0Fi2gMVEF3+WAx5M=";
  };

  buildPhase = ''
--- a/pkgs/servers/matrix-synapse/default.nix
+++ b/pkgs/servers/matrix-synapse/default.nix
@ -11,11 +11,11 @@ in
 with python3.pkgs;
 buildPythonApplication rec {
  pname = "matrix-synapse";
-  version = "1.63.0";
+  version = "1.63.1";

  src = fetchPypi {
    inherit pname version;
-    sha256 = "sha256-RiW2D3nkEK4EUiNoYGhkHqtWZfUfXMqFKakTNNmSp3A=";
+    sha256 = "sha256-AjxvZye3bRjGT355eAnwuP2lvTU/RSnOPxxKqaUxN9g=";
  };

  buildInputs = [ openssl ];
--- a/pkgs/servers/mautrix-whatsapp/default.nix
+++ b/pkgs/servers/mautrix-whatsapp/default.nix
@ -2,18 +2,18 @@

 buildGoModule rec {
  pname = "mautrix-whatsapp";
-  version = "0.5.0";
+  version = "0.6.0";

  src = fetchFromGitHub {
    owner = "mautrix";
    repo = "whatsapp";
    rev = "v${version}";
-    sha256 = "xKj1iKKzFQFjzXZGqoCDyuwXs55QNmnPdojgxy0dQTY=";
+    sha256 = "zhFc6BAurjrp0pHa48Eb8Iypww6o6YXPXp2ba2CXB6Q=";
  };

  buildInputs = [ olm ];

-  vendorSha256 = "svpUQQI9dDNQoL+LDoxhEch7dtNd20ojG3YHga1r15c=";
+  vendorSha256 = "EiaQDEsysTiXNHKhbfGVgVdMKgfdUHm48eooGR1rtQg=";

  doCheck = false;

--- a/pkgs/servers/web-apps/sogo/default.nix
+++ b/pkgs/servers/web-apps/sogo/default.nix
@ -1,27 +1,24 @@
 { gnustep, lib, fetchFromGitHub, fetchpatch, makeWrapper, python3, lndir
 , openssl, openldap, sope, libmemcached, curl, libsodium, libytnef, libzip, pkg-config, nixosTests
-, oath-toolkit }:
+, oath-toolkit
+, enableActiveSync ? false
+, libwbxml }:
 gnustep.stdenv.mkDerivation rec {
  pname = "SOGo";
-  version = "5.5.0";
+  version = "5.7.0";

  src = fetchFromGitHub {
    owner = "inverse-inc";
    repo = pname;
    rev = "SOGo-${version}";
-    sha256 = "1kyfn3qw299qsyivbrm487h68va99rrb3gmhpgjpwqd2xdg9aypk";
+    hash = "sha256-3Xy0y1sdixy4gXhzhP9mfWeaDmOVJty+X95xCyxayPE=";
  };

  nativeBuildInputs = [ gnustep.make makeWrapper python3 ];
-  buildInputs = [ gnustep.base sope openssl libmemcached curl libsodium libytnef libzip pkg-config openldap oath-toolkit ];
+  buildInputs = [ gnustep.base sope openssl libmemcached curl libsodium libytnef libzip pkg-config openldap oath-toolkit ]
+    ++ lib.optional enableActiveSync libwbxml;

-  patches = [
-    # TODO: take a closer look at other patches in https://sources.debian.org/patches/sogo/ and https://github.com/Skrupellos/sogo-patches
-    (fetchpatch {
-      url = "https://salsa.debian.org/debian/sogo/-/raw/120ac6390602c811908c7fcb212a79acbc7f7f28/debian/patches/0005-Remove-build-date.patch";
-      sha256 = "151i8504kwdlcirgd0pbif7cxnb1q6jsp5j7dbh9p6zw2xgwkp25";
-    })
-  ];
+  patches = lib.optional enableActiveSync ./enable-activesync.patch;

  postPatch = ''
    # Exclude NIX_ variables
@ -68,6 +65,8 @@ gnustep.stdenv.mkDerivation rec {
    for bin in $out/bin/*; do
      wrapProgram $bin --prefix LD_LIBRARY_PATH : $out/lib/sogo --prefix GNUSTEP_CONFIG_FILE : $out/share/GNUstep/GNUstep.conf
    done
+
+    rmdir $out/nix
  '';

  passthru.tests.sogo = nixosTests.sogo;
--- a/pkgs/servers/web-apps/sogo/enable-activesync.patch
+++ b/pkgs/servers/web-apps/sogo/enable-activesync.patch
@ -0,0 +1,21 @@
+--- a/ActiveSync/NSData+ActiveSync.m
+++ b/ActiveSync/NSData+ActiveSync.m
+@@ -36,7 +36,7 @@ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ #import <NGExtensions/NGBase64Coding.h>
+ #import <NGExtensions/NSObject+Logs.h>
+ 
+-#include <wbxml/wbxml.h>
+#include <libwbxml-1.0/wbxml/wbxml.h>
+ 
+ #define WBXMLDEBUG 0
+ 
+--- a/GNUmakefile
+++ b/GNUmakefile
+@@ -11,6 +11,7 @@ SUBPROJECTS = \
+ 	UI		\
+ 	Tools		\
+ 	Tests/Unit	\
+	ActiveSync	\
+ 
+ 
+ include $(GNUSTEP_MAKEFILES)/aggregate.make
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@ -16115,7 +16115,9 @@ with pkgs;

  kubeaudit = callPackage ../tools/security/kubeaudit { };

-  kubectx = callPackage ../development/tools/kubectx { };
+  kubectx = callPackage ../development/tools/kubectx {
+    buildGoModule = buildGo117Module;
+  };

  kube-linter = callPackage ../development/tools/kube-linter { };

@ -16959,6 +16961,8 @@ with pkgs;

  arrow-cpp = callPackage ../development/libraries/arrow-cpp {};

+  arrow-glib = callPackage ../development/libraries/arrow-glib {};
+
  arsenal = callPackage ../tools/security/arsenal { };

  assimp = callPackage ../development/libraries/assimp { };