Merge master into haskell-updates

maintainers/maintainer-list.nix

@@ -3660,6 +3660,10 @@
     github = "expipiplus1";
     githubId = 857308;
     name = "Ellie Hermaszewska";
+    keys = [{
+      longkeyid = "rsa4096/0xC8116E3A0C1CA76A";
+      fingerprint = "FC1D 3E4F CBCA 80DF E870  6397 C811 6E3A 0C1C A76A";
+    }];
   };
   extends = {
     email = "sharosari@gmail.com";

nixos/doc/manual/from_md/release-notes/rl-2111.section.xml

@@ -479,6 +479,16 @@
           RandomX benchmark.
         </para>
       </listitem>
+      <listitem>
+        <para>
+          Auto nice daemons
+          <link xlink:href="https://github.com/Nefelim4ag/Ananicy">ananicy</link>
+          and
+          <link xlink:href="https://gitlab.com/ananicy-cpp/ananicy-cpp/">ananicy-cpp</link>.
+          Available as
+          <link linkend="opt-services.ananicy.enable">services.ananicy</link>.
+        </para>
+      </listitem>
     </itemizedlist>
   </section>
   <section xml:id="sec-release-21.11-incompatibilities">

nixos/doc/manual/release-notes/rl-2111.section.md

@@ -139,6 +139,8 @@ In addition to numerous new and upgraded packages, this release has the followin
 
 - [xmrig](https://github.com/xmrig/xmrig), a high performance, open source, cross platform RandomX, KawPow, CryptoNight and AstroBWT unified CPU/GPU miner and RandomX benchmark.
 
+- Auto nice daemons [ananicy](https://github.com/Nefelim4ag/Ananicy) and [ananicy-cpp](https://gitlab.com/ananicy-cpp/ananicy-cpp/). Available as [services.ananicy](#opt-services.ananicy.enable).
+
 ## Backward Incompatibilities {#sec-release-21.11-incompatibilities}
 
 - The NixOS VM test framework, `pkgs.nixosTest`/`make-test-python.nix`, now requires detaching commands such as `succeed("foo &")` and `succeed("foo | xclip -i")` to close stdout.

nixos/modules/module-list.nix

@@ -485,6 +485,7 @@
   ./services/mail/roundcube.nix
   ./services/mail/sympa.nix
   ./services/mail/nullmailer.nix
+  ./services/misc/ananicy.nix
   ./services/misc/airsonic.nix
   ./services/misc/ankisyncd.nix
   ./services/misc/apache-kafka.nix

nixos/modules/services/mail/postfix.nix

@@ -294,7 +294,7 @@ in
       };
 
       submissionOptions = mkOption {
-        type = types.attrs;
+        type = with types; attrsOf str;
         default = {
           smtpd_tls_security_level = "encrypt";
           smtpd_sasl_auth_enable = "yes";
@@ -312,7 +312,7 @@ in
       };
 
       submissionsOptions = mkOption {
-        type = types.attrs;
+        type = with types; attrsOf str;
         default = {
           smtpd_sasl_auth_enable = "yes";
           smtpd_client_restrictions = "permit_sasl_authenticated,reject";

nixos/modules/services/misc/ananicy.nix

@@ -0,0 +1,107 @@
+{ config, lib, pkgs, ... }:
+
+with lib;
+
+let
+  cfg = config.services.ananicy;
+  configFile = pkgs.writeText "ananicy.conf" (generators.toKeyValue { } cfg.settings);
+  extraRules = pkgs.writeText "extraRules" cfg.extraRules;
+  servicename = if ((lib.getName cfg.package) == (lib.getName pkgs.ananicy-cpp)) then "ananicy-cpp" else "ananicy";
+in
+{
+  options = {
+    services.ananicy = {
+      enable = mkEnableOption "Ananicy, an auto nice daemon";
+
+      package = mkOption {
+        type = types.package;
+        default = pkgs.ananicy;
+        defaultText = literalExpression "pkgs.ananicy";
+        example = literalExpression "pkgs.ananicy-cpp";
+        description = ''
+          Which ananicy package to use.
+        '';
+      };
+
+      settings = mkOption {
+        type = with types; attrsOf (oneOf [ int bool str ]);
+        default = { };
+        example = {
+          apply_nice = false;
+        };
+        description = ''
+          See <link xlink:href="https://github.com/Nefelim4ag/Ananicy/blob/master/ananicy.d/ananicy.conf"/>
+        '';
+      };
+
+      extraRules = mkOption {
+        type = types.str;
+        default = "";
+        description = ''
+          Extra rules in json format on separate lines. See:
+          <link xlink:href="https://github.com/Nefelim4ag/Ananicy#configuration"/>
+          <link xlink:href="https://gitlab.com/ananicy-cpp/ananicy-cpp/#global-configuration"/>
+        '';
+        example = literalExpression ''
+          '''
+            { "name": "eog", "type": "Image-View" }
+            { "name": "fdupes", "type": "BG_CPUIO" }
+          '''
+        '';
+
+      };
+    };
+  };
+
+  config = mkIf cfg.enable {
+    environment = {
+      systemPackages = [ cfg.package ];
+      etc."ananicy.d".source = pkgs.runCommandLocal "ananicyfiles" { } ''
+        mkdir -p $out
+        # ananicy-cpp does not include rules or settings on purpose
+        cp -r ${pkgs.ananicy}/etc/ananicy.d/* $out
+        rm $out/ananicy.conf
+        cp ${configFile} $out/ananicy.conf
+        ${optionalString (cfg.extraRules != "") "cp ${extraRules} $out/nixRules.rules"}
+      '';
+    };
+
+    # ananicy and ananicy-cpp have different default settings
+    services.ananicy.settings =
+      let
+        mkOD = mkOptionDefault;
+      in
+      {
+        cgroup_load = mkOD true;
+        type_load = mkOD true;
+        rule_load = mkOD true;
+        apply_nice = mkOD true;
+        apply_ioclass = mkOD true;
+        apply_ionice = mkOD true;
+        apply_sched = mkOD true;
+        apply_oom_score_adj = mkOD true;
+        apply_cgroup = mkOD true;
+      } // (if ((lib.getName cfg.package) == (lib.getName pkgs.ananicy-cpp)) then {
+        # https://gitlab.com/ananicy-cpp/ananicy-cpp/-/blob/master/src/config.cpp#L12
+        loglevel = mkOD "warn"; # default is info but its spammy
+        cgroup_realtime_workaround = mkOD true;
+      } else {
+        # https://github.com/Nefelim4ag/Ananicy/blob/master/ananicy.d/ananicy.conf
+        check_disks_schedulers = mkOD true;
+        check_freq = mkOD 5;
+      });
+
+    systemd = {
+      # https://gitlab.com/ananicy-cpp/ananicy-cpp/#cgroups applies to both ananicy and -cpp
+      enableUnifiedCgroupHierarchy = mkDefault false;
+      packages = [ cfg.package ];
+      services."${servicename}" = {
+        wantedBy = [ "default.target" ];
+      };
+    };
+  };
+
+  meta = {
+    maintainers = with maintainers; [ artturin ];
+  };
+}

nixos/modules/services/x11/clight.nix

@@ -71,6 +71,14 @@ in {
   };
 
   config = mkIf cfg.enable {
+    assertions = let
+      inRange = v: l: r: v >= l && v <= r;
+    in [
+      { assertion = config.location.provider == "manual" ->
+          inRange config.location.latitude (-90) 90 && inRange config.location.longitude (-180) 180;
+        message = "You must specify a valid latitude and longitude if manually providing location"; }
+    ];
+
     boot.kernelModules = [ "i2c_dev" ];
     environment.systemPackages = with pkgs; [ clight clightd ];
     services.dbus.packages = with pkgs; [ clight clightd ];

nixos/modules/services/x11/display-managers/lightdm.nix

@@ -146,7 +146,7 @@ in
       };
 
       background = mkOption {
-        type = types.path;
+        type = types.either types.path (types.strMatching "^#[0-9]\{6\}$");
         # Manual cannot depend on packages, we are actually setting the default in config below.
         defaultText = literalExpression "pkgs.nixos-artwork.wallpapers.simple-dark-gray-bottom.gnomeFilePath";
         description = ''

nixos/tests/all-tests.nix

@@ -403,6 +403,7 @@ in
   samba-wsdd = handleTest ./samba-wsdd.nix {};
   sanoid = handleTest ./sanoid.nix {};
   sddm = handleTest ./sddm.nix {};
+  seafile = handleTest ./seafile.nix {};
   searx = handleTest ./searx.nix {};
   service-runner = handleTest ./service-runner.nix {};
   shadow = handleTest ./shadow.nix {};

pkgs/applications/audio/snapcast/default.nix

@@ -1,7 +1,10 @@
 { stdenv, lib, fetchFromGitHub, cmake, pkg-config
 , alsa-lib, asio, avahi, boost17x, flac, libogg, libvorbis, soxr
+, pulseaudioSupport ? false, libpulseaudio
 , nixosTests }:
 
+assert pulseaudioSupport -> libpulseaudio != null;
+
 let
 
   dependency = { name, version, sha256 }:
@@ -50,7 +53,7 @@ stdenv.mkDerivation rec {
     boost17x
     alsa-lib asio avahi flac libogg libvorbis
     aixlog popl soxr
-  ];
+  ] ++ lib.optional pulseaudioSupport libpulseaudio;
 
   # Upstream systemd unit files are pretty awful, so we provide our own in a
   # NixOS module. It might make sense to get that upstreamed...

pkgs/applications/blockchains/bitcoin/default.nix

@@ -5,6 +5,7 @@
 , pkg-config
 , util-linux
 , hexdump
+, autoSignDarwinBinariesHook
 , wrapQtAppsHook ? null
 , boost
 , libevent
@@ -47,6 +48,7 @@ stdenv.mkDerivation rec {
     [ autoreconfHook pkg-config ]
     ++ optionals stdenv.isLinux [ util-linux ]
     ++ optionals stdenv.isDarwin [ hexdump ]
+    ++ optionals (stdenv.isDarwin && stdenv.isAarch64) [ autoSignDarwinBinariesHook ]
     ++ optionals withGui [ wrapQtAppsHook ];
 
   buildInputs = [ boost libevent miniupnpc zeromq zlib ]

pkgs/applications/editors/vscode/vscode.nix

@@ -14,17 +14,17 @@ let
   archive_fmt = if stdenv.isDarwin then "zip" else "tar.gz";
 
   sha256 = {
-    x86_64-linux = "10p815dv86775ky90m96l11026xkhjwvrrhvviqw6g6hsayjqhia";
+    x86_64-linux = "0dwpczbxqy3rsqprdiakmqv6s3jzcg2wqxnf1znarx2qffb4ii9x";
-    x86_64-darwin = "1b8d7iw9v172viczdbcdxhf51dyshmx2665prv2pm0ygsy8yii3p";
+    x86_64-darwin = "0si76v80r0vhl76gbdwbykk6acifhifz8sb8wiyiiywkinlxs19w";
-    aarch64-linux = "155sbsmnapnzhkzkaggm80bkarh4l7dbqyhgy40mmdgqpyp3gx1v";
+    aarch64-linux = "0nwgdvvsblh2r72ys2ng5b084wizkdjd00mm73506mgbs8pzcky4";
-    aarch64-darwin = "1pnqjih37r4xqfjfrf8mhsbvmn62358rmf50rackqh5as50siwa2";
+    aarch64-darwin = "0qivq4077g5a4gwkskvvzxaa60w1gpgl67pmdyqn81rina04rdqs";
-    armv7l-linux = "00k2fmivbsp8fyh9cy6vr6sq031f6marz4sbj1nrlzdl40wd30bi";
+    armv7l-linux = "0myf96s1vdpllnw0vz0rpmyv2pfirv3p8pqgxxnpw860s2c26f2f";
   }.${system};
 in
   callPackage ./generic.nix rec {
     # Please backport all compatible updates to the stable release.
     # This is important for the extension ecosystem.
-    version = "1.62.1";
+    version = "1.62.2";
     pname = "vscode";
 
     executableName = "code" + lib.optionalString isInsiders "-insiders";

pkgs/applications/editors/vscode/vscodium.nix

@@ -13,10 +13,10 @@ let
   archive_fmt = if system == "x86_64-darwin" then "zip" else "tar.gz";
 
   sha256 = {
-    x86_64-linux = "1xblrp4xyw2pcifmzjmlbnmk7lhmlj002sfk28kyf1k5wdp54yv9";
+    x86_64-linux = "19r4883qa73b23xw0fz21bnp9vcvsbn1q77n6pcm1achwpxscrg6";
-    x86_64-darwin = "0ivvdxc4hmv9sh8ap0qy8yciz9pjkm1p1j60dh57y4ll6fdzbbrd";
+    x86_64-darwin = "0gv4208vcr75wyp6vji1cg6644f5yfwgkgkiav37218v1wjzb4r0";
-    aarch64-linux = "0ssm27i12d7gkq31d1zma4zx5n5mgg0a8pj3sdk9jjjsa68b3pyr";
+    aarch64-linux = "00jzjapyj96bqqq6pz4mdlihwa5g1izkqcp4lqml7hqvmcqrjyrs";
-    armv7l-linux = "029shxcwnap28ys6lxml3yiiavw4lhnizf35f0a664vdzy1x5dpv";
+    armv7l-linux = "0daji52lfbgz0by11idai55ip0m859s35vbyvgv655s21aakrs50";
   }.${system};
 
   sourceRoot = {
@@ -31,7 +31,7 @@ in
 
     # Please backport all compatible updates to the stable release.
     # This is important for the extension ecosystem.
-    version = "1.62.1";
+    version = "1.62.2";
     pname = "vscodium";
 
     executableName = "codium";

pkgs/applications/gis/qmapshack/default.nix

@@ -1,5 +1,5 @@
-{ mkDerivation, lib, fetchFromGitHub, cmake
+{ mkDerivation, lib, fetchFromGitHub, cmake, substituteAll
-, qtscript, qtwebengine, gdal, proj, routino, quazip }:
+, qtscript, qttranslations, qtwebengine, gdal, proj, routino, quazip }:
 
 mkDerivation rec {
   pname = "qmapshack";
@@ -12,6 +12,14 @@ mkDerivation rec {
     sha256 = "1yzgkdjxwyg8ggbxyjwr0zjrx99ckrbz2p2524iii9i7qqn8wfsx";
   };
 
+  patches = [
+    # See https://github.com/NixOS/nixpkgs/issues/86054
+    (substituteAll {
+      src = ./fix-qttranslations-path.patch;
+      inherit qttranslations;
+    })
+  ];
+
   nativeBuildInputs = [ cmake ];
 
   buildInputs = [ qtscript qtwebengine gdal proj routino quazip ];

pkgs/applications/gis/qmapshack/fix-qttranslations-path.patch

@@ -0,0 +1,74 @@
+diff --git i/src/qmapshack/setup/CAppSetupLinux.cpp w/src/qmapshack/setup/CAppSetupLinux.cpp
+index 63ea06c0..3a03b816 100644
+--- i/src/qmapshack/setup/CAppSetupLinux.cpp
++++ w/src/qmapshack/setup/CAppSetupLinux.cpp
+@@ -30,7 +30,7 @@ void CAppSetupLinux::initQMapShack()
+     prepareGdal("", "");
+ 
+     // setup translators
+-    QString resourceDir = QLibraryInfo::location(QLibraryInfo::TranslationsPath);
++    QLatin1String resourceDir = QLatin1String("@qttranslations@/translations");
+     QString translationPath = QCoreApplication::applicationDirPath();
+     translationPath.replace(QRegExp("bin$"), "share/qmapshack/translations");
+     prepareTranslator(resourceDir, "qt_");
+diff --git i/src/qmapshack/setup/CAppSetupMac.cpp w/src/qmapshack/setup/CAppSetupMac.cpp
+index ad9b21e9..9dca8a1e 100644
+--- i/src/qmapshack/setup/CAppSetupMac.cpp
++++ w/src/qmapshack/setup/CAppSetupMac.cpp
+@@ -63,7 +63,7 @@ void CAppSetupMac::initQMapShack()
+ 
+     // setup translators
+     QString translationPath = getApplicationDir(relTranslationDir).absolutePath();
+-    prepareTranslator(translationPath, "qt_");
++    prepareTranslator(QLatin1String("@qttranslations@/translations"), "qt_");
+     prepareTranslator(translationPath, "qmapshack_");
+ 
+     // load and apply style sheet
+diff --git i/src/qmaptool/setup/CAppSetupLinux.cpp w/src/qmaptool/setup/CAppSetupLinux.cpp
+index dea1c4f3..8da95574 100644
+--- i/src/qmaptool/setup/CAppSetupLinux.cpp
++++ w/src/qmaptool/setup/CAppSetupLinux.cpp
+@@ -29,7 +29,7 @@ void CAppSetupLinux::initQMapTool()
+     prepareGdal("", "");
+ 
+     // setup translators
+-    QString resourceDir = QLibraryInfo::location(QLibraryInfo::TranslationsPath);
++    QLatin1String resourceDir = QLatin1String("@qttranslations@/translations");
+     QString translationPath = QCoreApplication::applicationDirPath();
+     translationPath.replace(QRegExp("bin$"), "share/qmaptool/translations");
+     prepareTranslator(resourceDir, "qt_");
+diff --git i/src/qmaptool/setup/CAppSetupMac.cpp w/src/qmaptool/setup/CAppSetupMac.cpp
+index 02b27e07..fae27748 100644
+--- i/src/qmaptool/setup/CAppSetupMac.cpp
++++ w/src/qmaptool/setup/CAppSetupMac.cpp
+@@ -64,7 +64,7 @@ void CAppSetupMac::initQMapTool()
+ 
+     // setup translators
+     QString translationPath = getApplicationDir(relTranslationDir).absolutePath();
+-    prepareTranslator(translationPath, "qt_");
++    prepareTranslator(QLatin1String("@qttranslations@/translations"), "qt_");
+     prepareTranslator(translationPath, "qmaptool_");
+ 
+     migrateDirContent(defaultCachePath());
+diff --git i/src/qmt_rgb2pct/main.cpp w/src/qmt_rgb2pct/main.cpp
+index 21267d03..d539cec8 100644
+--- i/src/qmt_rgb2pct/main.cpp
++++ w/src/qmt_rgb2pct/main.cpp
+@@ -50,7 +50,7 @@ static void prepareTranslator(QString translationPath, QString translationPrefix
+ static void loadTranslations()
+ {
+ #if defined(Q_OS_LINUX) || defined(Q_OS_FREEBSD) || defined(__FreeBSD_kernel__) || defined(__GNU__) || defined(Q_OS_CYGWIN)
+-    QString resourceDir = QLibraryInfo::location(QLibraryInfo::TranslationsPath);
++    QLatin1String resourceDir = QLatin1String("@qttranslations@/translations");
+     QString translationPath = QCoreApplication::applicationDirPath();
+     translationPath.replace(QRegExp("bin$"), "share/" APP_STR "/translations");
+     prepareTranslator(resourceDir, "qt_");
+@@ -61,7 +61,7 @@ static void loadTranslations()
+     // os x
+     static QString relTranslationDir = "Resources/translations"; // app
+     QString translationPath = getApplicationDir(relTranslationDir).absolutePath();
+-    prepareTranslator(translationPath, "qt_");
++    prepareTranslator(QLatin1String("@qttranslations@/translations"), "qt_");
+     prepareTranslator(translationPath, APP_STR "_");
+ #endif
+ 

pkgs/applications/misc/calibre/default.nix

@@ -27,21 +27,20 @@
 
 mkDerivation rec {
   pname = "calibre";
-  version = "5.30.0";
+  version = "5.31.1";
 
   src = fetchurl {
     url = "https://download.calibre-ebook.com/${version}/${pname}-${version}.tar.xz";
-    sha256 = "058dqqxhc3pl4is1idlnc3pz80k4r681d5aj4a26v9acp8j7zy4f";
+    sha256 = "sha256-3LGEWuHms54ji9GWSyLl8cFWIRBqHY1Jf/CNPJOywrU=";
   };
 
-  # https://sources.debian.org/patches/calibre/5.30.0+dfsg-1
+  # https://sources.debian.org/patches/calibre/5.31.1+dfsg-1
   patches = [
     #  allow for plugin update check, but no calibre version check
     (fetchpatch {
-      name = "0001_only_plugin_update.patch";
+      name = "0001-only-plugin-update.patch";
-      url =
+      url = "https://raw.githubusercontent.com/debian-calibre/calibre/debian/${version}%2Bdfsg-1/debian/patches/0001-only-plugin-update.patch";
-        "https://sources.debian.org/data/main/c/calibre/${version}%2Bdfsg-1/debian/patches/0001-only-plugin-update.patch";
+      sha256 = "sha256-dLzO1TWP7Q4nw2a3oN7qlhGCmcA0NKJrZidUnD6hUMA=";
-      sha256 = "sha256-aGT8rJ/eQKAkmyHBWdY0ouZuWvDwtLVJU5xY6d3hY3k=";
     })
   ]
   ++ lib.optional (!unrarSupport) ./dont_build_unrar_plugin.patch;

pkgs/applications/misc/pass-secret-service/default.nix

@@ -19,9 +19,8 @@ python3.pkgs.buildPythonApplication rec {
   # /etc/ in check phase.
   postPatch = ''
     substituteInPlace Makefile \
-      --replace \
+      --replace "dbus-run-session" "dbus-run-session --config-file=${dbus}/share/dbus-1/session.conf" \
-        "dbus-run-session" \
+      --replace '-p $(relpassstore)' '-p $(PASSWORD_STORE_DIR)'
-        "dbus-run-session --config-file=${dbus}/share/dbus-1/session.conf"
   '';
 
   propagatedBuildInputs = with python3.pkgs; [

pkgs/applications/misc/sfm/default.nix

@@ -15,6 +15,8 @@ stdenv.mkDerivation rec {
 
   postPatch = lib.optionalString (conf!=null) "cp ${configFile} config.def.h";
 
+  makeFlags = [ "CC:=$(CC)" ];
+
   installFlags = [ "PREFIX=$(out)" ];
 
   meta = with lib; {

pkgs/applications/networking/browsers/chromium/upstream-info.json

@@ -18,9 +18,9 @@
     }
   },
   "beta": {
-    "version": "96.0.4664.35",
+    "version": "96.0.4664.45",
-    "sha256": "047zc1hl5iwhrgnypl7r5ga2cx1yz26lf1x5cnvdqmarmmkq380m",
+    "sha256": "01q4fsf2cbx6g9nnaihvc5jj3ap8jq2gf16pnhf7ixzbhgcnm328",
-    "sha256bin64": "1cw89fafxxhr85x4vzhxv3jkmqfnxjisc7gj9v8y2ixqpn190hjl",
+    "sha256bin64": "1vaazcrlx0999xd9yp25i9kzb8y8g0yqd28xssw7jqwrhz033wgr",
     "deps": {
       "gn": {
         "version": "2021-09-24",

pkgs/applications/networking/browsers/gmni/default.nix

@@ -1,24 +1,24 @@
-{ stdenv, lib, fetchFromSourcehut, pkg-config, bearssl, scdoc }:
+{ stdenv, lib, fetchFromSourcehut, bearssl, scdoc }:
 
 stdenv.mkDerivation rec {
   pname = "gmni";
-  version = "unstable-2021-03-26";
+  version = "1.0";
 
   src = fetchFromSourcehut {
     owner = "~sircmpwn";
     repo = "gmni";
-    rev = "77b73efbcd3ea7ed9e3e4c0aa19d9247e21d3c87";
+    rev = version;
-    sha256 = "1wvnzyv7vyddcd39y6q5aflpnnsdl4k4y5aj5ssb7vgkld0h1b7r";
+    sha256 = "sha256-3MFNAI/SfFigNfitfFs3o9kkz7JeEflMHiH7iJpLfi4=";
   };
 
-  nativeBuildInputs = [ pkg-config ];
+  nativeBuildInputs = [ scdoc ];
-  buildInputs = [ bearssl scdoc ];
+  buildInputs = [ bearssl ];
 
   meta = with lib; {
     description = "A Gemini client";
     homepage = "https://git.sr.ht/~sircmpwn/gmni";
     license = licenses.gpl3Only;
     maintainers = with maintainers; [ bsima jb55 ];
-    platforms = platforms.all;
+    platforms = platforms.linux;
   };
 }

pkgs/applications/networking/cluster/argocd/default.nix

@@ -69,6 +69,6 @@ buildGoModule rec {
     downloadPage = "https://github.com/argoproj/argo-cd";
     homepage = "https://argo-cd.readthedocs.io/en/stable/";
     license = licenses.asl20;
-    maintainers = with maintainers; [ shahrukh330 ];
+    maintainers = with maintainers; [ shahrukh330 bryanasdev000 ];
   };
 }

pkgs/applications/networking/cluster/terranix/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, lib, fetchFromGitHub, jq, nix, ... }:
+{ stdenv, lib, fetchFromGitHub, jq, nix, makeWrapper }:
 
 stdenv.mkDerivation rec {
   pname = "terranix";
@@ -11,29 +11,21 @@ stdenv.mkDerivation rec {
     sha256 = "sha256-HDiyJGgyDUoLnpL8N+wDm3cM/vEfYYc/p4N1kKH/kLk=";
   };
 
+  nativeBuildInputs = [ makeWrapper ];
+
   installPhase = ''
     mkdir -p $out/{bin,core,modules,lib}
     mv bin core modules lib $out/
 
-    mv $out/bin/terranix-doc-json $out/bin/.wrapper_terranix-doc-json
+    wrapProgram $out/bin/terranix-doc-json \
-
+      --prefix PATH : ${lib.makeBinPath [ jq nix ]}
-    # manual wrapper because makeWrapper expectes executables
-    wrapper=$out/bin/terranix-doc-json
-    cat <<EOF>$wrapper
-    #!/usr/bin/env bash
-    export PATH=$PATH:${jq}/bin:${nix}/bin
-    $out/bin/.wrapper_terranix-doc-json "\$@"
-    EOF
-    chmod +x $wrapper
   '';
 
   meta = with lib; {
     description = "A NixOS like terraform-json generator";
     homepage = "https://terranix.org";
     license = licenses.gpl3;
-    platforms = platforms.linux ++ platforms.darwin;
+    platforms = platforms.unix;
     maintainers = with maintainers; [ mrVanDalo ];
   };
-
 }
-

pkgs/applications/networking/cluster/tilt/default.nix

@@ -5,13 +5,13 @@ buildGoModule rec {
   /* Do not use "dev" as a version. If you do, Tilt will consider itself
     running in development environment and try to serve assets from the
     source tree, which is not there once build completes.  */
-  version = "0.22.9";
+  version = "0.22.15";
 
   src = fetchFromGitHub {
     owner  = "tilt-dev";
     repo   = pname;
     rev    = "v${version}";
-    sha256 = "sha256-h19Cj4ztgypT/j1gB+PbvgDJ7jlJ3CYPEbK62tJeMss=";
+    sha256 = "sha256-Aim80bg1vGRkiIlVqDa4qOFQ+mwSOL75HOPYQYovYlE=";
   };
   vendorSha256 = null;
 

pkgs/applications/networking/instant-messengers/ferdi/default.nix

@@ -17,10 +17,10 @@ in
 mkFranzDerivation' rec {
   pname = "ferdi";
   name = "Ferdi";
-  version = "5.6.2";
+  version = "5.6.3";
   src = fetchurl {
     url = "https://github.com/getferdi/ferdi/releases/download/v${version}/ferdi_${version}_amd64.deb";
-    sha256 = "sha256-8rB7SnaIaeCXAaKELNO1CnxpV8TyeKRCVamwpATeia4=";
+    sha256 = "sha256-cfX3x0ZRxT6sxMm20uL8lKhMbrI/yiCHVrBTPKIlDSE=";
   };
   extraBuildInputs = [ xorg.libxshmfence ];
   meta = with lib; {

pkgs/applications/networking/instant-messengers/pidgin/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, makeWrapper, pkg-config, gtk2, gtk2-x11, gtkspell2, aspell
+{ callPackage, stdenv, fetchurl, makeWrapper, pkg-config, gtk2, gtk2-x11, gtkspell2, aspell
 , gst_all_1, libstartup_notification, gettext, perlPackages, libxml2, nss
 , nspr, farstream, libXScrnSaver, avahi, dbus, dbus-glib, intltool, libidn
 , lib, python3, libICE, libXext, libSM, libgnt, ncurses, cyrus_sasl, openssl
@@ -93,7 +93,7 @@ let unwrapped = stdenv.mkDerivation rec {
 };
 
 in if plugins == [] then unwrapped
-    else import ./wrapper.nix {
+    else callPackage ./wrapper.nix {
-      inherit makeWrapper symlinkJoin plugins;
+      inherit plugins;
       pidgin = unwrapped;
     }

pkgs/applications/networking/instant-messengers/pidgin/wrapper.nix

@@ -1,4 +1,4 @@
-{ symlinkJoin, pidgin, makeWrapper, plugins }:
+{ lib, symlinkJoin, pidgin, makeWrapper, plugins }:
 
 let
 extraArgs = map (x: x.wrapArgs or "") plugins;
@@ -11,10 +11,10 @@ in symlinkJoin {
 
   postBuild = ''
     wrapProgram $out/bin/pidgin \
-      --suffix-each PURPLE_PLUGIN_PATH ':' "$out/lib/purple-${pidgin.majorVersion} $out/lib/pidgin" \
+      --suffix-each PURPLE_PLUGIN_PATH ':' "$out/lib/purple-${lib.versions.major pidgin.version} $out/lib/pidgin" \
       ${toString extraArgs}
     wrapProgram $out/bin/finch \
-      --suffix-each PURPLE_PLUGIN_PATH ':' "$out/lib/purple-${pidgin.majorVersion}" \
+      --suffix-each PURPLE_PLUGIN_PATH ':' "$out/lib/purple-${lib.versions.major pidgin.version}" \
       ${toString extraArgs}
   '';
 }

pkgs/applications/networking/instant-messengers/whatsapp-for-linux/default.nix

@@ -1,25 +1,26 @@
 { fetchFromGitHub
 , lib
 , stdenv
-, gtkmm3
-, webkitgtk
 , cmake
-, pkg-config
+, glib-networking
-, libappindicator-gtk3
 , gst_all_1
+, gtkmm3
+, libappindicator-gtk3
 , pcre
+, pkg-config
+, webkitgtk
 , wrapGAppsHook
 }:
 
 stdenv.mkDerivation rec {
   pname = "whatsapp-for-linux";
-  version = "1.2.1";
+  version = "1.3.0";
 
   src = fetchFromGitHub {
     owner = "eneshecan";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-dEJRufOqlY+DnJdUaG5WP9hR1qO7KxR6MjKWq1SJB8A=";
+    sha256 = "sha256-VdkCjzmZqP/ZVY1H9FxBGe5rN0nZEPZbMp3MVKL6WLc=";
   };
 
   nativeBuildInputs = [
@@ -29,14 +30,15 @@ stdenv.mkDerivation rec {
   ];
 
   buildInputs = [
-    gtkmm3
+    glib-networking
-    webkitgtk
+    gst_all_1.gst-libav
-    libappindicator-gtk3
+    gst_all_1.gst-plugins-bad
     gst_all_1.gst-plugins-base
     gst_all_1.gst-plugins-good
-    gst_all_1.gst-plugins-bad
+    gtkmm3
-    gst_all_1.gst-libav
+    libappindicator-gtk3
     pcre
+    webkitgtk
   ];
 
   meta = with lib; {

pkgs/applications/science/chemistry/octopus/default.nix

@@ -11,13 +11,13 @@ assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation rec {
   pname = "octopus";
-  version = "10.5";
+  version = "11.2";
 
   src = fetchFromGitLab {
     owner = "octopus-code";
     repo = "octopus";
     rev = version;
-    sha256 = "1bgdkmsp6pwq3b6nxxkimrdmz71wqr8qi25gdzwpcv9wmcf1q27v";
+    sha256 = "sha256-leEcUSjpiP13l65K9WKN2GXTtTa8vvK/MFxR2zH6Xno=";
   };
 
   nativeBuildInputs = [

pkgs/applications/science/chemistry/openmolcas/default.nix

@@ -5,9 +5,9 @@
 } :
 
 let
-  version = "21.06";
+  version = "21.10";
   # The tag keeps moving, fix a hash instead
-  gitLabRev = "dd982ad4bc94dec8ac1e3e99cb6a7dd249ff71de";
+  gitLabRev = "117305462bac932106e8e3a0347238b768bcb058";
 
   python = python3.withPackages (ps : with ps; [ six pyparsing ]);
 
@@ -19,7 +19,7 @@ in stdenv.mkDerivation {
     owner = "Molcas";
     repo = "OpenMolcas";
     rev = gitLabRev;
-    sha256 = "07dm73n0s7ckif561yb3s9yqxsv39a73kb9qwny4yp39wdvv52hz";
+    sha256 = "sha256-GMi2dsNBog+TmpmP6fhQcp6Z5Bh2LelV//MqLnvRP5c=";
   };
 
   patches = [
@@ -56,7 +56,9 @@ in stdenv.mkDerivation {
     "-DOPENBLASROOT=${openblas.dev}"
   ];
 
-  GAROOT=globalarrays;
+  preConfigure = ''
+    export GAROOT=${globalarrays};
+  '';
 
   postConfigure = ''
     # The Makefile will install pymolcas during the build grrr.

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

@@ -1,22 +1,35 @@
 { lib
-, python3Packages
+, fetchFromGitHub
+, git
+, nodejs
+, python3
 }:
 
-python3Packages.buildPythonApplication rec {
+python3.pkgs.buildPythonApplication rec {
   pname = "cwltool";
-  version = "3.1.20210628163208";
+  version = "3.1.20211104071347";
+  format = "setuptools";
 
-  src = python3Packages.fetchPypi {
+  disabled = python3.pythonOlder "3.6";
-    inherit pname version;
+
-    sha256 = "21b885f725420413d2f87eadc5e81c08a9c91beceda89b35d1a702ec4df47e52";
+  src = fetchFromGitHub {
+    owner = "common-workflow-language";
+    repo = pname;
+    rev = version;
+    sha256 = "sha256-tp4SdilW2PKav7b3/BchXYl33W9U0aQH6FPdOhHSvIQ=";
   };
 
   postPatch = ''
     substituteInPlace setup.py \
-      --replace 'prov == 1.5.1' 'prov'
+      --replace 'prov == 1.5.1' 'prov' \
+      --replace "setup_requires=PYTEST_RUNNER," ""
   '';
 
-  propagatedBuildInputs = with python3Packages; [
+  nativeBuildInputs = [
+    git
+  ];
+
+  propagatedBuildInputs = with python3.pkgs; [
     argcomplete
     bagit
     coloredlogs
@@ -24,18 +37,41 @@ python3Packages.buildPythonApplication rec {
     prov
     psutil
     pydot
+    rdflib
+    requests
+    ruamel-yaml
     schema-salad
     shellescape
     typing-extensions
   ];
 
-  doCheck = false; # hard to setup
+  checkInputs = with python3.pkgs; [
-  pythonImportsCheck = [ "cwltool" ];
+    mock
+    nodejs
+    pytest-mock
+    pytest-xdist
+    pytestCheckHook
+  ];
+
+  disabledTests = [
+    "test_content_types"
+    "test_env_filtering"
+    "test_http_path_mapping"
+  ];
+
+  disabledTestPaths = [
+    "tests/test_udocker.py"
+    "tests/test_provenance.py"
+  ];
+
+  pythonImportsCheck = [
+    "cwltool"
+  ];
 
   meta = with lib; {
+    description = "Common Workflow Language reference implementation";
     homepage = "https://www.commonwl.org";
     license = with licenses; [ asl20 ];
-    description = "Common Workflow Language reference implementation";
     maintainers = with maintainers; [ veprbl ];
   };
 }

pkgs/applications/version-management/git-and-tools/git-big-picture/default.nix

@@ -21,7 +21,6 @@ python3Packages.buildPythonApplication rec {
     description = "Tool for visualization of Git repositories";
     homepage = "https://github.com/git-big-picture/git-big-picture";
     license = lib.licenses.gpl3Plus;
-    platforms = lib.platforms.linux;
     maintainers = [ lib.maintainers.nthorne ];
   };
 }

pkgs/applications/version-management/git-and-tools/glitter/default.nix

@@ -2,22 +2,25 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "glitter";
-  version = "1.4.10";
+  version = "1.5.1";
 
   src = fetchFromGitHub {
     owner = "milo123459";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-5yv0RZfGLS/cxOxettHQHSPldcq+xa+TNj6dDIAmzOM=";
+    sha256 = "sha256-AVHMDDvrSLg0OwoG4I5/W2ttWgBwzOG7553gr9bCDFs=";
   };
 
-  cargoSha256 = "sha256-xG7aic7NCcltz9YmQ4V40/h3OR8Vt5IgApp4yoDbPuc=";
+  cargoSha256 = "sha256-vBzy4gnlJMQwvVieuWuiVOm/HAr6rHkHcLmzY7eklT4=";
 
   # tests require it to be in a git repository
   preCheck = ''
     git init
   '';
 
+  # error: Found argument '--test-threads' which wasn't expected, or isn't valid in this context
+  checkFlags = [ "--skip" "runs_correctly" ];
+
   meta = with lib; {
     description = "A git wrapper that allows you to compress multiple commands into one";
     homepage = "https://github.com/milo123459/glitter";

pkgs/applications/version-management/gitlab/data.json

@@ -1,14 +1,14 @@
 {
-  "version": "14.4.1",
+  "version": "14.4.2",
-  "repo_hash": "0sm44iyn32frc7njg6ypgbcip77mj5c3agn3cihk3lz7z5kr48lm",
+  "repo_hash": "0zhac96b6p7p9vpj083ajfsj5a2fwkv602zxv79cjvpd924c5ws2",
   "yarn_hash": "0l0lgcgxaira980a1y550pfsm4f2pw97gi8s5pghyfil2v2lyxyw",
   "owner": "gitlab-org",
   "repo": "gitlab",
-  "rev": "v14.4.1-ee",
+  "rev": "v14.4.2-ee",
   "passthru": {
-    "GITALY_SERVER_VERSION": "14.4.1",
+    "GITALY_SERVER_VERSION": "14.4.2",
     "GITLAB_PAGES_VERSION": "1.46.0",
     "GITLAB_SHELL_VERSION": "13.21.1",
-    "GITLAB_WORKHORSE_VERSION": "14.4.1"
+    "GITLAB_WORKHORSE_VERSION": "14.4.2"
   }
 }

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

@@ -198,7 +198,7 @@ stdenv.mkDerivation {
   meta = with lib; {
     homepage = "http://www.gitlab.com/";
     platforms = platforms.linux;
-    maintainers = with maintainers; [ fpletz globin krav talyz yuka ];
+    maintainers = with maintainers; [ fpletz globin krav talyz yayayayaka yuka ];
   } // (if gitlabEnterprise then
     {
       license = licenses.unfreeRedistributable; # https://gitlab.com/gitlab-org/gitlab-ee/raw/master/LICENSE

pkgs/applications/version-management/gitlab/gitaly/default.nix

@@ -21,7 +21,7 @@ let
       };
   };
 
-  version = "14.4.1";
+  version = "14.4.2";
   gitaly_package = "gitlab.com/gitlab-org/gitaly/v${lib.versions.major version}";
 in
 
@@ -33,7 +33,7 @@ buildGoModule {
     owner = "gitlab-org";
     repo = "gitaly";
     rev = "v${version}";
-    sha256 = "sha256-bATqaB7q3MlyacEiBXdcEDs+xsJUbULVnYTSpEznxFg=";
+    sha256 = "sha256-MzYUSoG+HjW9o2zn6Q9Pd5NfI7hZkw1xFXOXHbbxJvo=";
   };
 
   vendorSha256 = "sha256-9RhPQosen70E9t1iAoc2SeKs9pYMMpMqgXLekWfKNf8=";

pkgs/applications/version-management/gitlab/gitlab-workhorse/default.nix

@@ -5,7 +5,7 @@ in
 buildGoModule rec {
   pname = "gitlab-workhorse";
 
-  version = "14.4.1";
+  version = "14.4.2";
 
   src = fetchFromGitLab {
     owner = data.owner;

pkgs/build-support/build-dotnet-package/default.nix

@@ -3,7 +3,7 @@
 attrsOrig @
 { baseName
 , version
-, buildInputs ? []
+, nativeBuildInputs ? []
 , xBuildFiles ? [ ]
 , xBuildFlags ? [ "/p:Configuration=Release" ]
 , outputFiles ? [ "bin/Release/*" ]
@@ -19,12 +19,12 @@ attrsOrig @
     attrs = {
       name = "${baseName}-${version}";
 
-      nativeBuildInputs = [ pkg-config ];
+      nativeBuildInputs = [
-      buildInputs = [
+        pkg-config
-        mono
-        dotnetbuildhelpers
         makeWrapper
-      ] ++ buildInputs;
+        dotnetbuildhelpers
+        mono
+      ] ++ nativeBuildInputs;
 
       configurePhase = ''
         runHook preConfigure
@@ -87,7 +87,7 @@ attrsOrig @
             then
               echo "$dll already exported by a buildInputs, not re-exporting"
             else
-              ${dotnetbuildhelpers}/bin/create-pkg-config-for-dll.sh "$out/lib/pkgconfig" "$dll"
+              create-pkg-config-for-dll.sh "$out/lib/pkgconfig" "$dll"
             fi
           done
         done
@@ -113,4 +113,4 @@ attrsOrig @
       '';
     };
   in
-    stdenv.mkDerivation (attrs // (builtins.removeAttrs attrsOrig [ "buildInputs" ] ))
+    stdenv.mkDerivation (attrs // (builtins.removeAttrs attrsOrig [ "nativeBuildInputs" ] ))

pkgs/data/fonts/noto-fonts/tools.nix

@@ -7,7 +7,7 @@
 
 buildPythonPackage rec {
   pname = "nototools";
-  version = "0.2.13";
+  version = "0.2.16";
 
   disabled = pythonOlder "3.6";
 
@@ -15,7 +15,7 @@ buildPythonPackage rec {
     owner = "googlefonts";
     repo = "nototools";
     rev = "v${version}";
-    sha256 = "0ggp65xgkf9y7jamncm65lkm84wapsa47abf133pcb702875v8jz";
+    sha256 = "14rrdamkmhrykff8ln07fq9cm8zwj3k113lzwjcy0lgz23g51jyl";
   };
 
   postPatch = ''

pkgs/data/misc/wireless-regdb/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "wireless-regdb";
-  version = "2021.07.14";
+  version = "2021.08.28";
 
   src = fetchurl {
     url = "https://www.kernel.org/pub/software/network/${pname}/${pname}-${version}.tar.xz";
-    sha256 = "sha256-Li3SFqXxoxC4SXdK9j5jCdlMIgfDR3GlNMR64YsWJ0I=";
+    sha256 = "sha256-z/NwxBDR5tMWrgp/qKxieP3x78pdPWZKynz9Kq+lREY=";
   };
 
   dontBuild = true;

pkgs/development/compilers/binaryen/default.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "binaryen";
-  version = "101";
+  version = "102";
 
   src = fetchFromGitHub {
     owner = "WebAssembly";
     repo = "binaryen";
     rev = "version_${version}";
-    sha256 = "sha256-rNiZQIQqNbc1P2A6UTn0dRHeT3BS+nv1o81aPaJy+5U=";
+    sha256 = "sha256-UlktpY9tyjYNkmiBZM42QGg67kcPo7VDy2B4Ty1YIew=";
   };
 
   nativeBuildInputs = [ cmake python3 ];

pkgs/development/dhall-modules/dhall-grafana.nix

@@ -4,8 +4,8 @@ buildDhallGitHubPackage {
   name = "grafana";
   owner = "weeezes";
   repo = "dhall-grafana";
-  # 2021-11-06
+  # 2021-11-12
-  rev = "9ee0bb643f01db6d9935cf7df1914c32a92730b4";
+  rev = "d5630dc55deacf5100a99802a4df1d9680b263b3";
-  sha256 = "0a123r5a33p8kaqs68rx2ycjr72xvxcpcmvpqxgb2jb05mnjj540";
+  sha256 = "01320hpqgr5r4grsydmdl9yznmly1ssnlc9gcwa8rj1ah0a8xlgz";
   dependencies = [ dhallPackages.Prelude ];
 }

pkgs/development/libraries/libdeltachat/default.nix

@@ -15,13 +15,13 @@
 
 stdenv.mkDerivation rec {
   pname = "libdeltachat";
-  version = "1.63.0";
+  version = "1.64.0";
 
   src = fetchFromGitHub {
     owner = "deltachat";
     repo = "deltachat-core-rust";
     rev = version;
-    sha256 = "1511jh38h7nmn4dpyi1vfxvhybcacc6gavwfifxvb5npirphziga";
+    sha256 = "04a1ncikapx53jjrx0ac1qi907wlj6javylz4aksg4nfbph6y9j4";
   };
 
   patches = [
@@ -33,7 +33,7 @@ stdenv.mkDerivation rec {
   cargoDeps = rustPlatform.fetchCargoTarball {
     inherit src;
     name = "${pname}-${version}";
-    sha256 = "0hfp2k84mvq11h7q96hkcj3k6f3sxw8wx89acg4hy6lbh8xpy6ai";
+    sha256 = "0skrzxn99c1gqil7z0dv0xhg883k98v6mh96nycf7whl2d25965x";
   };
 
   nativeBuildInputs = [

pkgs/development/libraries/lucene++/default.nix

@@ -1,28 +1,36 @@
-{ lib, stdenv, fetchFromGitHub, cmake, boost, gtest }:
+{ lib, stdenv, fetchFromGitHub, cmake, boost, gtest, zlib }:
 
 stdenv.mkDerivation rec {
   pname = "lucene++";
-  version = "3.0.7";
+  version = "3.0.8";
 
   src = fetchFromGitHub {
     owner = "luceneplusplus";
     repo = "LucenePlusPlus";
     rev = "rel_${version}";
-    sha256 = "06b37fly6l27zc6kbm93f6khfsv61w792j8xihfagpcm9cfz2zi1";
+    sha256 = "12v7r62f7pqh5h210pb74sfx6h70lj4pgfpva8ya2d55fn0qxrr2";
   };
 
-  postPatch = ''
-    sed -i -e '/Subversion *REQUIRED/d' \
-           -e '/include.*CMakeExternal/d' \
-           CMakeLists.txt
-  '';
-
-  cmakeFlags = [ "-DGTEST_INCLUDE_DIR=${gtest}/include" ];
   nativeBuildInputs = [ cmake ];
-  buildInputs = [ boost gtest ];
+  buildInputs = [ boost gtest zlib ];
 
   doCheck = true;
-  checkTarget = "test";
+
+  postPatch = ''
+     substituteInPlace src/test/CMakeLists.txt \
+            --replace "add_subdirectory(gtest)" ""
+  '';
+
+  checkPhase = ''
+    runHook preCheck
+    LD_LIBRARY_PATH=$PWD/src/contrib:$PWD/src/core \
+            src/test/lucene++-tester
+    runHook postCheck
+  '';
+
+  postInstall = ''
+    mv $out/include/pkgconfig $out/lib/
+  '';
 
   meta = {
     description = "C++ port of the popular Java Lucene search engine";

pkgs/development/libraries/pcre/default.nix

@@ -17,7 +17,7 @@ in stdenv.mkDerivation {
   name = "${pname}-${version}";
 
   src = fetchurl {
-    url = "https://ftp.pcre.org/pub/pcre/pcre-${version}.tar.bz2";
+    url = "mirror://sourceforge/project/pcre/pcre/${version}/pcre-${version}.tar.bz2";
     sha256 = "0v9nk51wh55pcbnf2jr36yarz8ayajn6d7ywiq2wagivn9c8c40r";
   };
 

pkgs/development/libraries/pixman/default.nix

@@ -9,7 +9,7 @@ stdenv.mkDerivation rec {
     sha256 = "0l0m48lnmdlmnaxn2021qi5cj366d9fzfjxkqgcj9bs14pxbgaw4";
   };
 
-  separateDebugInfo = true;
+  separateDebugInfo = !stdenv.hostPlatform.isStatic;
 
   nativeBuildInputs = [ pkg-config ];
 

pkgs/development/libraries/science/math/p4est-sc/default.nix

@@ -22,11 +22,12 @@ stdenv.mkDerivation {
     sha256 = "14vm0b162jh8399pgpsikbwq4z5lkrw9vfzy3drqykw09n6nc53z";
   };
 
+  strictDeps = true;
   nativeBuildInputs = [ autoreconfHook pkg-config ];
-  propagatedBuildInputs = [ zlib ]
+  propagatedNativeBuildInputs = lib.optional mpiSupport mpi
-    ++ lib.optional mpiSupport mpi
     ++ lib.optional isOpenmpi openssh
   ;
+  propagatedBuildInputs = [ zlib ];
   inherit debugEnable mpiSupport;
 
   postPatch = ''

pkgs/development/libraries/science/math/p4est/default.nix

@@ -21,6 +21,7 @@ stdenv.mkDerivation {
     sha256 = "0vffnf48rzw6d0as4c3x1f31b4kapmdzr1hfj5rz5ngah72gqrph";
   };
 
+  strictDeps = true;
   nativeBuildInputs = [ autoreconfHook pkg-config ];
   propagatedBuildInputs = [ p4est-sc ];
   buildInputs = lib.optional withMetis metis;

pkgs/development/libraries/science/math/petsc/default.nix

@@ -28,10 +28,12 @@ stdenv.mkDerivation rec {
   mpiSupport = !withp4est || p4est.mpiSupport;
   withp4est = petsc-withp4est;
 
-  nativeBuildInputs = [ python3 gfortran ];
+  strictDeps = true;
-  buildInputs = [ blas lapack ]
+  nativeBuildInputs = [ python3 gfortran ]
     ++ lib.optional mpiSupport mpi
     ++ lib.optional (mpiSupport && mpi.pname == "openmpi") openssh
+  ;
+  buildInputs = [ blas lapack ]
     ++ lib.optional withp4est p4est
   ;
 

pkgs/development/libraries/xdg-desktop-portal/default.nix

@@ -1,6 +1,7 @@
 { stdenv
 , lib
 , fetchFromGitHub
+, fetchpatch
 , nixosTests
 , substituteAll
 , autoreconfHook
@@ -38,6 +39,12 @@ stdenv.mkDerivation rec {
       src = ./fix-paths.patch;
       inherit flatpak;
     })
+    # Fixes the issue in https://github.com/flatpak/xdg-desktop-portal/issues/636
+    # Remove it when the next stable release arrives
+    (fetchpatch {
+      url = "https://github.com/flatpak/xdg-desktop-portal/commit/d7622e15ff8fef114a6759dde564826d04215a9f.patch";
+      sha256 = "sha256-vmfxK4ddG6Xon//rpiz6OiBsDLtT0VG5XyBJG3E4PPs=";
+    })
   ];
 
   nativeBuildInputs = [

pkgs/development/misc/resholve/source.nix

@@ -3,7 +3,7 @@
 }:
 
 rec {
-  version = "0.6.6";
+  version = "0.6.8";
   rSrc =
     # local build -> `make ci`; `make clean` to restore
     # return to remote source
@@ -14,6 +14,6 @@ rec {
         owner = "abathur";
         repo = "resholve";
         rev = "v${version}";
-        hash = "sha256-bupf3c9tNPAEMzFEDcvg483bSiwZFuB3ZqveG89dgkE=";
+        hash = "sha256-1bb22GcOIzmQ31ULZuNNCJ8Vcz4Y0+qAhsJ9PhbqnDM=";
       };
 }

pkgs/development/misc/resholve/test.nix

@@ -21,10 +21,17 @@
 , rSrc
 , runDemo ? false
 , binlore
+, sqlite
+, util-linux
+, gawk
+, rlwrap
+, gnutar
+, bc
 }:
 
 let
-
+  default_packages = [ bash file findutils gettext ];
+  parsed_packages = [ coreutils sqlite util-linux gnused gawk findutils rlwrap gnutar bc ];
 in
 rec {
   re_shunit2 = with shunit2;
@@ -56,9 +63,6 @@ rec {
             "/usr/bin/od" = true;
           };
           keep = {
-            # dynamically defined in shunit2:_shunit_mktempFunc
-            eval = [ "shunit_condition_" "_shunit_test_" "_shunit_prepForSourcing" ];
-
             # variables invoked as commands; long-term goal is to
             # resolve the *variable*, but that is complexish, so
             # this is where we are...
@@ -166,13 +170,14 @@ rec {
     # LOGLEVEL="DEBUG";
 
     # default path
-    RESHOLVE_PATH = "${lib.makeBinPath [ bash file findutils gettext ]}";
+    RESHOLVE_PATH = "${lib.makeBinPath default_packages}";
     # but separate packages for combining as needed
     PKG_FILE = "${lib.makeBinPath [ file ]}";
     PKG_FINDUTILS = "${lib.makeBinPath [ findutils ]}";
     PKG_GETTEXT = "${lib.makeBinPath [ gettext ]}";
     PKG_COREUTILS = "${lib.makeBinPath [ coreutils ]}";
-    RESHOLVE_LORE = "${binlore.collect { drvs = [ bash file findutils gettext coreutils ]; } }";
+    RESHOLVE_LORE = "${binlore.collect { drvs = default_packages ++ [ coreutils ] ++ parsed_packages; } }";
+    PKG_PARSED = "${lib.makeBinPath parsed_packages}";
 
     # explicit interpreter for demo suite; maybe some better way...
     INTERP = "${bash}/bin/bash";

pkgs/development/nim-packages/python/default.nix

@@ -0,0 +1,25 @@
+{ lib, buildNimPackage, fetchFromGitHub, python27 }:
+
+buildNimPackage rec {
+  pname = "python";
+  version = "1.2";
+  src = fetchFromGitHub {
+    owner = "nim-lang";
+    repo = pname;
+    rev = "b7c3b2c447a69fdb0a974ba149062e52182fda08";
+    hash = "sha256-Wl4on0rf4zbNxmwmq/ZkNiPIFCZY+1BdokPQoba2EVI=";
+  };
+  postPatch = let pythonLib = "${python27}/lib/libpython2.7.so";
+  in ''
+    substituteInPlace src/python.nim \
+      --replace 'items(LibNames)' "[\"${pythonLib}\"]" \
+      --replace 'dynlib: dllname' 'dynlib: "${pythonLib}"'
+  '';
+  doCheck = true;
+  meta = with lib;
+    src.meta // {
+      description = "Nim wrapper for the Python 2 programming language";
+      license = [ licenses.mit ];
+      maintainers = [ maintainers.ehmry ];
+    };
+}

pkgs/development/nim-packages/rocksdb/default.nix

@@ -0,0 +1,20 @@
+{ lib, buildNimPackage, fetchFromGitHub, rocksdb, stew, tempfile }:
+
+buildNimPackage rec {
+  pname = "rocksdb";
+  version = "0.2.0";
+  src = fetchFromGitHub {
+    owner = "status-im";
+    repo = "nim-${pname}";
+    rev = "5b1307cb1f4c85bb72ff781d810fb8c0148b1183";
+    hash = "sha256-gjMCB9kpWVi9Qv73/jhoAYw857OmQpry//bDQCtyJo0=";
+  };
+  buildInputs = [ stew tempfile ];
+  propagatedBuildInputs = [ rocksdb ];
+  doCheck = false;
+  meta = with lib;
+    src.meta // {
+      description = "Nim wrapper for RocksDB";
+      maintainers = [ maintainers.ehmry ];
+    };
+}

pkgs/development/nim-packages/snappy/config.patch

@@ -0,0 +1,7 @@
+diff --git a/tests/config.nims b/tests/config.nims
+index 46348f1..fbe9f5e 100644
+--- a/tests/config.nims
++++ b/tests/config.nims
+@@ -1 +1,2 @@
+ switch("path", "..")
++switch("passL", "-lsnappy")

pkgs/development/nim-packages/snappy/default.nix

@@ -0,0 +1,25 @@
+{ lib, buildNimPackage, fetchFromGitHub, snappy }:
+
+buildNimPackage rec {
+  pname = "snappy";
+  version = "0.1.0";
+  src = fetchFromGitHub {
+    owner = "jangko";
+    repo = pname;
+    rev = "d13e2ccb2acaa4e8dedce4f25e8dbf28e19278a6";
+    hash = "sha256-18CFRuDK+E701MHrCixx22QSVmglTc0EJwrMCsKwayM=";
+  };
+  propagatedBuildInputs = [ snappy ];
+  patches = [ ./config.patch ];
+  doCheck = true;
+  preCheck = ''
+    mkdir $NIX_BUILD_TOP/nimcache/
+    mv -v tests/data $NIX_BUILD_TOP/nimcache/data
+  ''; # test standards, please
+  meta = with lib;
+    src.meta // {
+      description = "Nim implementation of snappy compression algorithm";
+      license = [ lib.licenses.mit ];
+      maintainers = [ maintainers.ehmry ];
+    };
+}

pkgs/development/nim-packages/spry/default.nix

@@ -0,0 +1,23 @@
+{ lib, buildNimPackage, fetchFromGitHub, python, rocksdb, snappy, spryvm, stew
+, tempfile, ui }:
+
+buildNimPackage rec {
+  pname = "spry";
+  version = "0.9.0";
+  src = fetchFromGitHub {
+    owner = "gokr";
+    repo = pname;
+    rev = "098da7bb34a9113d5db5402fecfc76b1c3fa3b36";
+    hash = "sha256-PfWBrG2Z16tLgcN8JYpHaNMysBbbYX812Lkgk0ItMwE=";
+  };
+  buildInputs = [ python rocksdb snappy spryvm stew tempfile ui ];
+  patches = [ ./nil.patch ];
+  doCheck = true;
+  meta = with lib;
+    src.meta // {
+      description =
+        "A Smalltalk and Rebol inspired language implemented as an AST interpreter in Nim";
+      license = [ licenses.mit ];
+      maintainers = [ maintainers.ehmry ];
+    };
+}

pkgs/development/nim-packages/spry/nil.patch

@@ -0,0 +1,35 @@
+diff --git a/src/ispry.nim b/src/ispry.nim
+index 23ad6c3..dc38a9d 100644
+--- a/src/ispry.nim
++++ b/src/ispry.nim
+@@ -134,8 +134,8 @@ proc main() =
+       #discard spry.setBinding(newEvalWord("@"), result)
+       var output = $result
+       # Print any result
+-      if output.isNil:
+-        output = if suspended: "nil" else: ""
++      if output == "" and suspended:
++        output = "nil"
+       stdout.write(output & "\n")
+ #      except:
+  #       echo "Oops, sorry about that: " & getCurrentExceptionMsg() & "\n"
+diff --git a/src/spry.nim b/src/spry.nim
+index 670a280..d81bb4c 100644
+--- a/src/spry.nim
++++ b/src/spry.nim
+@@ -87,13 +87,13 @@ for kind, key, val in getopt():
+   of cmdEnd: assert(false) # cannot happen
+ 
+ if eval:
+-  if filename == nil:
++  if filename == "":
+     writeHelp()
+   else:
+     code = filename
+ else:
+   code =
+-    if filename == nil:
++    if filename == "":
+       # no filename has been given, so we use stdin
+       readAll stdin
+     else:

pkgs/development/nim-packages/spryvm/default.nix

@@ -0,0 +1,21 @@
+{ lib, buildNimPackage, fetchFromGitHub, sqlite }:
+
+buildNimPackage rec {
+  pname = "spryvm";
+  version = "0.9.3";
+  src = fetchFromGitHub {
+    owner = "gokr";
+    repo = pname;
+    rev = "36c2b56bb194902d33de7bcf70d3041703e107ab";
+    hash = "sha256-OxB49ef6qPvSXLsyVl5g2ic/P9MMbF3jRYDWrxNJ0Iw=";
+  };
+  propagatedBuildInputs = [ sqlite ];
+  patches = [ ./nil.patch ];
+  doCheck = true;
+  meta = with lib;
+    src.meta // {
+      description = "Spry virtual machine";
+      license = [ licenses.mit ];
+      maintainers = [ maintainers.ehmry ];
+    };
+}

pkgs/development/nim-packages/spryvm/nil.patch

@@ -0,0 +1,21 @@
+diff --git a/spryvm/spryui.nim b/spryvm/spryui.nim
+index 37f5329..50440e9 100644
+--- a/spryvm/spryui.nim
++++ b/spryvm/spryui.nim
+@@ -140,14 +140,14 @@ proc addUI*(spry: Interpreter) =
+   nimMeth("openFile"):
+     var win = WindowNode(evalArgInfix(spry))
+     var path = openFile(Window(win.widget))
+-    if path.isNil:
++    if path == "":
+       spry.nilVal
+     else:
+       newValue($path)
+   nimMeth("saveFile"):
+     var win = WindowNode(evalArgInfix(spry))
+     var path = saveFile(Window(win.widget))
+-    if path.isNil:
++    if path == "":
+       spry.nilVal
+     else:
+       newValue($path)

pkgs/development/nim-packages/stew/default.nix

@@ -0,0 +1,20 @@
+{ lib, buildNimPackage, fetchFromGitHub, snappy }:
+
+buildNimPackage rec {
+  pname = "stew";
+  version = "0.1.0";
+  src = fetchFromGitHub {
+    owner = "status-im";
+    repo = "nim-${pname}";
+    rev = "478cc6efdefaabadf0666a3351fb959b78009bcc";
+    hash = "sha256-txlTF0zNV5kV4KfE744oB3aVLCfWS9BdoKxUmTQTTRY=";
+  };
+  doCheck = false;
+  meta = with lib;
+    src.meta // {
+      description =
+        "Backports, standard library candidates and small utilities that don't yet deserve their own repository";
+      license = [ lib.licenses.asl20 ];
+      maintainers = [ maintainers.ehmry ];
+    };
+}

pkgs/development/nim-packages/tempfile/default.nix

@@ -0,0 +1,19 @@
+{ lib, buildNimPackage, fetchFromGitHub }:
+
+buildNimPackage rec {
+  pname = "tempfile";
+  version = "0.1.7";
+  src = fetchFromGitHub {
+    owner = "OpenSystemsLab";
+    repo = "${pname}.nim";
+    rev = version;
+    hash = "sha256-08vvHXVxL1mAcpMzosaHd2FupTJrKJP5JaVcgxN4oYE=";
+  };
+  doCheck = false; # impure
+  meta = with lib;
+    src.meta // {
+      description = "Temporary files and folders";
+      license = [ lib.licenses.mit ];
+      maintainers = [ maintainers.ehmry ];
+    };
+}

pkgs/development/nim-packages/ui/default.nix

@@ -0,0 +1,24 @@
+{ lib, buildNimPackage, fetchFromGitHub, libui, pkg-config }:
+
+buildNimPackage rec {
+  pname = "ui";
+  version = "0.9.4";
+  src = fetchFromGitHub {
+    owner = "nim-lang";
+    repo = pname;
+    rev = "547e1cea8e9fb68c138c422b77af0a3152e50210";
+    hash = "sha256-rcvC0TO1r2zU7WEYfcsi/qX+nRITwKj7Fkqd4fHgTwU=";
+  };
+  propagatedBuildInputs = [ libui ];
+  propagatedNativeBuildInputs = [ pkg-config ];
+  postPatch = ''
+    echo {.passL: r\"$(pkg-config --libs libui)\".} >> ui/rawui.nim
+  '';
+  doCheck = true;
+  meta = with lib;
+    src.meta // {
+      description = "Nim bindings to libui";
+      license = [ licenses.mit ];
+      maintainers = [ maintainers.ehmry ];
+    };
+}

pkgs/development/node-packages/node-packages.json

@@ -151,7 +151,7 @@
 , "insect"
 , "intelephense"
 , "ionic"
-, {"iosevka": "https://github.com/be5invis/Iosevka/archive/v10.3.1.tar.gz"}
+, {"iosevka": "https://github.com/be5invis/Iosevka/archive/v11.0.1.tar.gz"}
 , "jake"
 , "javascript-typescript-langserver"
 , "joplin"

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

@@ -1,30 +1,50 @@
-{ lib, buildDunePackage, fetchFromGitHub, ppx_deriving
+{ lib
-, alcotest, angstrom-unix, biocaml, gnuplot, gsl, lacaml, menhir, owl, printbox }:
+, buildDunePackage
+, fetchurl
+, ppx_deriving
+, bppsuite
+, alcotest
+, angstrom-unix
+, biocaml
+, core
+, gsl
+, lacaml
+, menhir
+, menhirLib
+, printbox
+}:
 
 buildDunePackage rec {
   pname = "phylogenetics";
-  version = "unstable-2020-11-23";
+  version = "0.0.0";
 
   useDune2 = true;
 
-  src = fetchFromGitHub {
+  src = fetchurl {
-    owner  = "biocaml";
+    url = "https://github.com/biocaml/phylogenetics/releases/download/v${version}/${pname}-${version}.tbz";
-    repo   = pname;
+    sha256 = "sha256:0knfh2s0jfnsc0vsq5yw5xla7m7i98xd0qv512dyh3jhkh7m00l9";
-    rev    = "e6e10efa0a3a8fd61bf4ab69e91a09549cc1ded6";
-    sha256 = "0pmypzp0rvlpzm8zpbcfkphwnhrpyfwfv44kshvx2f8nslmksh8c";
   };
 
-  minimumOCamlVersion = "4.08";  # e.g., uses Float.min
+  minimalOCamlVersion = "4.08";
 
-  checkInputs = [ alcotest ];
+  checkInputs = [ alcotest bppsuite ];
   buildInputs = [ menhir ];
-  propagatedBuildInputs = [ angstrom-unix biocaml gnuplot gsl lacaml owl ppx_deriving printbox ];
+  propagatedBuildInputs = [
+    angstrom-unix
+    biocaml
+    core
+    gsl
+    lacaml
+    menhirLib
+    ppx_deriving
+    printbox
+  ];
 
-  doCheck = false;  # many tests require bppsuite
+  doCheck = true;
 
   meta = with lib; {
-    inherit (src.meta) homepage;
+    homepage = "https://github.com/biocaml/phylogenetics";
-    description = "Bioinformatics library for Ocaml";
+    description = "Algorithms and datastructures for phylogenetics";
     maintainers = [ maintainers.bcdarwin ];
     license = licenses.cecill-b;
   };

pkgs/development/python-modules/adafruit-platformdetect/default.nix

@@ -6,19 +6,25 @@
 
 buildPythonPackage rec {
   pname = "adafruit-platformdetect";
-  version = "3.17.1";
+  version = "3.17.2";
+  format = "setuptools";
 
   src = fetchPypi {
     pname = "Adafruit-PlatformDetect";
     inherit version;
-    sha256 = "sha256-M+0q1u/ZcAg2Pii/B2n0v+rw/zIAjeVej/VThi9NLwI=";
+    sha256 = "sha256-IA846zNFmBqSUc0oXJ0eA5wj6PzQ28jxO22z5WNOT24=";
   };
 
-  nativeBuildInputs = [ setuptools-scm ];
+  nativeBuildInputs = [
+    setuptools-scm
+  ];
 
   # Project has not published tests yet
   doCheck = false;
-  pythonImportsCheck = [ "adafruit_platformdetect" ];
+
+  pythonImportsCheck = [
+    "adafruit_platformdetect"
+  ];
 
   meta = with lib; {
     description = "Platform detection for use by Adafruit libraries";

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

@@ -8,14 +8,16 @@
 
 buildPythonPackage rec {
   pname = "adax";
-  version = "0.1.1";
+  version = "0.2.0";
+  format = "setuptools";
+
   disabled = pythonOlder "3.5";
 
   src = fetchFromGitHub {
     owner = "Danielhiversen";
     repo = "pyadax";
     rev = version;
-    sha256 = "sha256-ekpI5GTLbKjlbWH9GSmpp/3URurc7UN+agxMfyGxrVA=";
+    sha256 = "sha256-EMSX2acklwWOYiEeLHYG5mwdiGnWAUo5dGMiHCmZrko=";
   };
 
   propagatedBuildInputs = [

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

@@ -1,12 +1,21 @@
-{ lib, isPy3k, fetchFromGitHub, buildPythonPackage
+{ lib
-, attrs, atpublic }:
+, atpublic
+, attrs
+, buildPythonPackage
+, fetchFromGitHub
+, pytest-mock
+, pytestCheckHook
+, pythonOlder
+, typing-extensions
+}:
 
 buildPythonPackage rec {
   pname = "aiosmtpd";
   version = "1.4.2";
-  disabled = !isPy3k;
+  format = "setuptools";
+
+  disabled = pythonOlder "3.6";
 
-  # Release not published to Pypi
   src = fetchFromGitHub {
     owner = "aio-libs";
     repo = pname;
@@ -15,19 +24,34 @@ buildPythonPackage rec {
   };
 
   propagatedBuildInputs = [
-    atpublic attrs
+    atpublic
+    attrs
+  ] ++ lib.optionals (pythonOlder "3.8") [
+    typing-extensions
   ];
 
-  # Tests need network access
+  checkInputs = [
-  doCheck = false;
+    pytest-mock
+    pytestCheckHook
+  ];
+
+  disabledTests = [
+    # Requires git
+    "test_ge_master"
+    # Seems to be a sandbox issue
+    "test_byclient"
+  ];
+
+  pythonImportsCheck = [
+    "aiosmtpd"
+  ];
 
   meta = with lib; {
-    homepage = "https://aiosmtpd.readthedocs.io/en/latest/";
     description = "Asyncio based SMTP server";
+    homepage = "https://aiosmtpd.readthedocs.io/";
     longDescription = ''
       This is a server for SMTP and related protocols, similar in utility to the
-      standard library's smtpd.py module, but rewritten to be based on asyncio for
+      standard library's smtpd.py module.
-      Python 3.
     '';
     license = licenses.asl20;
     maintainers = with maintainers; [ eadwu ];

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

@@ -1,27 +1,36 @@
-{ lib, fetchFromGitHub, buildPythonPackage, pytestCheckHook }:
+{ lib
+, fetchFromGitHub
+, buildPythonPackage
+, pytestCheckHook
+}:
 
 buildPythonPackage rec {
   pname = "anybadge";
-  version = "1.7.0";
+  version = "1.8.0";
+  format = "setuptools";
 
   src = fetchFromGitHub {
     owner = "jongracecox";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1d02fnig04zlrhfqqcf4505vy4p51whl2ifilnx3mkhis9lcwrmr";
+    sha256 = "sha256-xKHIoV/8qsNMcU5fd92Jjh7d7jTeYN5xakMEjR6qPX8=";
   };
 
   # setup.py reads its version from the TRAVIS_TAG environment variable
   TRAVIS_TAG = "v${version}";
 
-  pythonImportsCheck = [ "anybadge" ];
+  checkInputs = [
+    pytestCheckHook
+  ];
 
-  checkInputs = [ pytestCheckHook ];
+  pythonImportsCheck = [
+    "anybadge"
+  ];
 
   meta = with lib; {
-    description = "A Python project for generating badges for your projects, with a focus on simplicity and flexibility";
+    description = "Python tool for generating badges for your projects";
-    license = licenses.mit;
     homepage = "https://github.com/jongracecox/anybadge";
-    maintainers = [ maintainers.fabiangd ];
+    license = licenses.mit;
+    maintainers = with maintainers; [ fabiangd ];
   };
 }

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

@@ -19,7 +19,7 @@
 
 buildPythonPackage rec {
   pname = "anyio";
-  version = "3.3.1";
+  version = "3.3.2";
   format = "pyproject";
   disabled = pythonOlder "3.7";
 
@@ -27,7 +27,7 @@ buildPythonPackage rec {
     owner = "agronholm";
     repo = pname;
     rev = version;
-    sha256 = "sha256-JQf+OWHV2Vok5FmP7mlzeqbKUlxB+FC1c3ruX2aQEEs=";
+    sha256 = "sha256-XBIrFb/XDneaOf/TeHxyeEfyQ7qQcWO7LJF0k1f4Ark=";
   };
 
   preBuild = ''

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

@@ -1,6 +1,8 @@
-{ lib, isPy3k, pythonOlder, fetchPypi, buildPythonPackage
+{ lib
-, pytest
+, buildPythonPackage
-, pytest-cov
+, fetchPypi
+, pytestCheckHook
+, pythonOlder
 , sybil
 , typing-extensions
 }:
@@ -8,7 +10,9 @@
 buildPythonPackage rec {
   pname = "atpublic";
   version = "2.3";
-  disabled = !isPy3k;
+  format = "setuptools";
+
+  disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
@@ -20,25 +24,25 @@ buildPythonPackage rec {
   ];
 
   checkInputs = [
-    pytest pytest-cov sybil
+    pytestCheckHook
+    sybil
   ];
 
-  checkPhase = ''
+  postPatch = ''
-    pytest
+    substituteInPlace setup.cfg \
+      --replace "--cov=public" ""
   '';
 
+  pythonImportsCheck = [
+    "public"
+  ];
+
   meta = with lib; {
-    homepage = "https://public.readthedocs.io/en/latest/";
+    description = "Python decorator and function which populates a module's __all__ and globals";
-    description = "A decorator and function which populates a module's __all__ and globals";
+    homepage = "https://public.readthedocs.io/";
     longDescription = ''
       This is a very simple decorator and function which populates a module's
       __all__ and optionally the module globals.
-
-      This provides both a pure-Python implementation and a C implementation. It is
-      proposed that the C implementation be added to builtins_ for Python 3.6.
-
-      This proposal seems to have been rejected, for more information see
-      https://bugs.python.org/issue26632.
     '';
     license = licenses.asl20;
     maintainers = with maintainers; [ eadwu ];

pkgs/development/python-modules/bimmer-connected/default.nix

@@ -9,7 +9,8 @@
 
 buildPythonPackage rec {
   pname = "bimmer-connected";
-  version = "0.7.21";
+  version = "0.7.22";
+  format = "setuptools";
 
   disabled = pythonOlder "3.5";
 
@@ -17,7 +18,7 @@ buildPythonPackage rec {
     owner = "bimmerconnected";
     repo = "bimmer_connected";
     rev = version;
-    sha256 = "sha256-98K7FRB//WyCu6NPG0x4ViA8UdMuiANDXshLjx/Yehg=";
+    sha256 = "sha256-tAkgOZvf9nyrAfFRxGkp7O/2oIAdBx+hNZbK9den+5c=";
   };
 
   nativeBuildInputs = [

pkgs/development/python-modules/boost-histogram/default.nix

@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "boost-histogram";
-  version = "1.1.0";
+  version = "1.2.1";
   disabled = !isPy3k;
 
   src = fetchPypi {
     pname = "boost_histogram";
     inherit version;
-    sha256 = "370e8e44a0bac4ebbedb7e62570be3a75a7a3807a297d6e82a94301b4681fc22";
+    sha256 = "a27842b2f1cfecc509382da2b25b03056354696482b38ec3c0220af0fc9b7579";
   };
 
   buildInputs = [ boost ];

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

@@ -6,19 +6,22 @@
 , mock
 , msgpack
 , pytestCheckHook
+, pythonOlder
 , requests
 }:
 
 buildPythonPackage rec {
   pname = "cachecontrol";
-  version = "0.12.8";
+  version = "0.12.10";
   format = "setuptools";
 
+  disabled = pythonOlder "3.6";
+
   src = fetchFromGitHub {
     owner = "ionrock";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0y15xbaqw2lxidwbyrgpy42v3cxgv4ys63fx2586h1szlrd4f3p4";
+    sha256 = "sha256-mgvL0q10UbPHY1H3tJprke5p8qNl3HNYoeLAERZTcTs=";
   };
 
   propagatedBuildInputs = [

pkgs/development/python-modules/crownstone-core/default.nix

@@ -8,7 +8,7 @@
 
 buildPythonPackage rec {
   pname = "crownstone-core";
-  version = "3.0.1";
+  version = "3.1.0";
   format = "setuptools";
 
   disabled = pythonOlder "3.8";
@@ -17,7 +17,7 @@ buildPythonPackage rec {
     owner = "crownstone";
     repo = "crownstone-lib-python-core";
     rev = version;
-    sha256 = "138lignv7c8kkqbqfkdcfpg39gm9x44h7r2j403m4ib7gq420hsn";
+    sha256 = "sha256-ujS4ho9io7KcoK5w1SCn7UPFg1ho3dgW0HS5HfsYsuU=";
   };
 
   propagatedBuildInputs = [

pkgs/development/python-modules/crownstone-uart/default.nix

@@ -8,7 +8,7 @@
 
 buildPythonPackage rec {
   pname = "crownstone-uart";
-  version = "2.1.0";
+  version = "2.2.0";
   format = "setuptools";
 
   disabled = pythonOlder "3.8";
@@ -17,7 +17,7 @@ buildPythonPackage rec {
     owner = "crownstone";
     repo = "crownstone-lib-python-uart";
     rev = version;
-    sha256 = "0sdz131vmrfp6hrm9iwqw8mj9qazsxg7b85yadib1122w9f3b1zc";
+    sha256 = "sha256-5K7NzJ7fKOW4Uh1XIlicVkRZuM84qTM5RQc/DfP9OEc=";
   };
 
   propagatedBuildInputs = [

pkgs/development/python-modules/cyclonedx-python-lib/default.nix

@@ -16,7 +16,7 @@
 
 buildPythonPackage rec {
   pname = "cyclonedx-python-lib";
-  version = "0.11.0";
+  version = "0.11.1";
   format = "pyproject";
 
   disabled = pythonOlder "3.6";
@@ -25,7 +25,7 @@ buildPythonPackage rec {
     owner = "CycloneDX";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-FNEtVTcmVyhAri55GjlzQbg21YByAJjmKQvWaYh3xRw=";
+    sha256 = "sha256-+Gu9WaGC2R5TC8XSqDNSJ3t7aMS69IeeKTzytYFcHvE=";
   };
 
   nativeBuildInputs = [

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

@@ -1,26 +1,28 @@
 { lib
-, buildPythonPackage
-, pythonOlder
-, fetchFromGitHub
 , aiohttp
-, poetry-core
-, yarl
 , aresponses
+, buildPythonPackage
+, fetchFromGitHub
+, poetry-core
+, pydantic
 , pytest-asyncio
 , pytestCheckHook
+, pythonOlder
+, yarl
 }:
 
 buildPythonPackage rec {
   pname = "elgato";
-  version = "2.1.1";
+  version = "2.2.0";
-  disabled = pythonOlder "3.8";
   format = "pyproject";
 
+  disabled = pythonOlder "3.8";
+
   src = fetchFromGitHub {
     owner = "frenck";
     repo = "python-elgato";
     rev = "v${version}";
-    sha256 = "19z568jjyww7vi8s44anrb66qjz5l22nz4jqcz49ybhf22warmff";
+    sha256 = "sha256-xsIglJSnvtd3NKqwoRAonPRN+C9KWyar0mrYcC3hPpw=";
   };
 
   nativeBuildInputs = [
@@ -29,6 +31,7 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [
     aiohttp
+    pydantic
     yarl
   ];
 
@@ -45,7 +48,9 @@ buildPythonPackage rec {
       --replace "--cov" ""
   '';
 
-  pythonImportsCheck = [ "elgato" ];
+  pythonImportsCheck = [
+    "elgato"
+  ];
 
   meta = with lib; {
     description = "Python client for Elgato Key Lights";

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

@@ -4,6 +4,7 @@
 , fetchFromGitHub
 , substituteAll
 , graphviz
+, xdg-utils
 , makeFontsConf
 , freefont_ttf
 , mock
@@ -13,7 +14,7 @@
 
 buildPythonPackage rec {
   pname = "graphviz";
-  version = "0.17";
+  version = "0.18";
 
   disabled = pythonOlder "3.6";
 
@@ -22,13 +23,14 @@ buildPythonPackage rec {
     owner = "xflr6";
     repo = "graphviz";
     rev = version;
-    sha256 = "sha256-K6z2C7hQH2A9bqgRR4MRqxVAH/k2NQBEelb2/6KDUr0=";
+    sha256 = "sha256-K98CwG+V+EFwzyawVjRwVhbX2FVfoX7dCAD5PXAWTq8=";
   };
 
   patches = [
     (substituteAll {
-      src = ./hardcode-graphviz-path.patch;
+      src = ./paths.patch;
       inherit graphviz;
+      xdgutils = xdg-utils;
     })
   ];
 

pkgs/development/python-modules/graphviz/hardcode-graphviz-path.patch

@@ -1,98 +0,0 @@
-diff --git a/graphviz/backend.py b/graphviz/backend.py
-index b66e616..3da4ef0 100644
---- a/graphviz/backend.py
-+++ b/graphviz/backend.py
-@@ -124,7 +124,7 @@ def command(engine: str, format_: str, filepath=None,
-         raise ValueError(f'unknown formatter: {formatter!r}')
- 
-     output_format = [f for f in (format_, renderer, formatter) if f is not None]
--    cmd = ['dot', '-K%s' % engine, '-T%s' % ':'.join(output_format)]
-+    cmd = ['@graphviz@/bin/dot', '-K%s' % engine, '-T%s' % ':'.join(output_format)]
- 
-     if filepath is None:
-         rendered = None
-@@ -297,7 +297,7 @@ def unflatten(source: str,
-     if fanout and stagger is None:
-         raise RequiredArgumentError('fanout given without stagger')
- 
--    cmd = ['unflatten']
-+    cmd = ['@graphviz@/bin/unflatten']
-     if stagger is not None:
-         cmd += ['-l', str(stagger)]
-     if fanout:
-@@ -332,7 +332,7 @@ def version() -> typing.Tuple[int, ...]:
-         Graphviz Release version entry format:
-         https://gitlab.com/graphviz/graphviz/-/blob/f94e91ba819cef51a4b9dcb2d76153684d06a913/gen_version.py#L17-20
-     """
--    cmd = ['dot', '-V']
-+    cmd = ['@graphviz@/bin/dot', '-V']
-     out, _ = run(cmd, check=True, encoding='ascii',
-                  stdout=subprocess.PIPE,
-                  stderr=subprocess.STDOUT)
-diff --git a/tests/test_backend.py b/tests/test_backend.py
-index e0a0e1c..681f178 100644
---- a/tests/test_backend.py
-+++ b/tests/test_backend.py
-@@ -54,7 +54,7 @@ def test_run_encoding_mocked(mocker, Popen, input='sp\xe4m', encoding='utf-8'):
-         m.decode.assert_called_once_with(encoding)
- 
- 
--@pytest.mark.exe
-+@pytest.mark.skip(reason='empty $PATH has no effect')
- @pytest.mark.usefixtures('empty_path')
- @pytest.mark.parametrize('func, args', [
-     (render, ['dot', 'pdf', 'nonfilepath']),
-@@ -148,7 +148,7 @@ def test_render_mocked(capsys, mocker, Popen, quiet):  # noqa: N803
- 
-     assert render('dot', 'pdf', 'nonfilepath', quiet=quiet) == 'nonfilepath.pdf'
- 
--    Popen.assert_called_once_with(['dot', '-Kdot', '-Tpdf', '-O', 'nonfilepath'],
-+    Popen.assert_called_once_with(['@graphviz@/bin/dot', '-Kdot', '-Tpdf', '-O', 'nonfilepath'],
-                                   stdout=subprocess.PIPE,
-                                   stderr=subprocess.PIPE,
-                                   cwd=None, startupinfo=mocker.ANY)
-@@ -211,7 +211,7 @@ def test_pipe_pipe_invalid_data_mocked(mocker, Popen, quiet):  # noqa: N803
-     assert e.value.stdout is out
-     e.value.stdout = mocker.sentinel.new_stdout
-     assert e.value.stdout is mocker.sentinel.new_stdout
--    Popen.assert_called_once_with(['dot', '-Kdot', '-Tpng'],
-+    Popen.assert_called_once_with(['@graphviz@/bin/dot', '-Kdot', '-Tpng'],
-                                   stdin=subprocess.PIPE,
-                                   stdout=subprocess.PIPE,
-                                   stderr=subprocess.PIPE,
-@@ -231,7 +231,7 @@ def test_pipe_mocked(capsys, mocker, Popen, quiet):  # noqa: N803
- 
-     assert pipe('dot', 'png', b'nongraph', quiet=quiet) == b'stdout'
- 
--    Popen.assert_called_once_with(['dot', '-Kdot', '-Tpng'],
-+    Popen.assert_called_once_with(['@graphviz@/bin/dot', '-Kdot', '-Tpng'],
-                                   stdin=subprocess.PIPE,
-                                   stdout=subprocess.PIPE,
-                                   stderr=subprocess.PIPE,
-@@ -259,7 +259,7 @@ def test_unflatten_mocked(capsys, mocker, Popen):
-     proc.communicate.return_value = (b'nonresult', b'')
- 
-     assert unflatten('nonsource') == 'nonresult'
--    Popen.assert_called_once_with(['unflatten'],
-+    Popen.assert_called_once_with(['@graphviz@/bin/unflatten'],
-                                   stdin=subprocess.PIPE,
-                                   stdout=subprocess.PIPE,
-                                   stderr=subprocess.PIPE,
-@@ -290,7 +290,7 @@ def test_version_parsefail_mocked(mocker, Popen):  # noqa: N803
-     with pytest.raises(RuntimeError, match=r'nonversioninfo'):
-         version()
- 
--    Popen.assert_called_once_with(['dot', '-V'],
-+    Popen.assert_called_once_with(['@graphviz@/bin/dot', '-V'],
-                                   stdout=subprocess.PIPE,
-                                   stderr=subprocess.STDOUT,
-                                   startupinfo=mocker.ANY)
-@@ -312,7 +312,7 @@ def test_version_mocked(mocker, Popen, stdout, expected):  # noqa: N803
- 
-     assert version() == expected
- 
--    Popen.assert_called_once_with(['dot', '-V'],
-+    Popen.assert_called_once_with(['@graphviz@/bin/dot', '-V'],
-                                   stdout=subprocess.PIPE,
-                                   stderr=subprocess.STDOUT,
-                                   startupinfo=mocker.ANY)

pkgs/development/python-modules/graphviz/paths.patch

@@ -0,0 +1,89 @@
+diff --git a/graphviz/backend/dot_command.py b/graphviz/backend/dot_command.py
+index d1903e6..6470d11 100644
+--- a/graphviz/backend/dot_command.py
++++ b/graphviz/backend/dot_command.py
+@@ -10,7 +10,7 @@ from . import parameters
+ __all__ = ['command']
+ 
+ #: :class:`pathlib.Path` of layout command (``Path('dot')``).
+-DOT_BINARY = pathlib.Path('dot')
++DOT_BINARY = pathlib.Path('@graphviz@/bin/dot')
+ 
+ 
+ def command(engine: str, format_: str, *,
+diff --git a/graphviz/backend/unflattening.py b/graphviz/backend/unflattening.py
+index 5ed25d6..8d2faf8 100644
+--- a/graphviz/backend/unflattening.py
++++ b/graphviz/backend/unflattening.py
+@@ -11,7 +11,7 @@ from . import execute
+ __all__ = ['unflatten']
+ 
+ #: :class:`pathlib.Path` of unflatten command (``Path('unflatten')``).
+-UNFLATTEN_BINARY = pathlib.Path('unflatten')
++UNFLATTEN_BINARY = pathlib.Path('@graphviz@/bin/unflatten')
+ 
+ 
+ def unflatten(source: str,
+diff --git a/graphviz/backend/viewing.py b/graphviz/backend/viewing.py
+index 6d4a4d1..2cc6cd8 100644
+--- a/graphviz/backend/viewing.py
++++ b/graphviz/backend/viewing.py
+@@ -54,7 +54,7 @@ def view_darwin(filepath, *, quiet: bool) -> None:
+ @tools.attach(view, 'freebsd')
+ def view_unixoid(filepath, *, quiet: bool) -> None:
+     """Open filepath in the user's preferred application (linux, freebsd)."""
+-    cmd = ['xdg-open', filepath]
++    cmd = ['@xdgutils@/bin/xdg-open', filepath]
+     log.debug('view: %r', cmd)
+     kwargs = {'stderr': subprocess.DEVNULL} if quiet else {}
+     subprocess.Popen(cmd, **kwargs)
+diff --git a/tests/_common.py b/tests/_common.py
+index ab93461..7eaca89 100644
+--- a/tests/_common.py
++++ b/tests/_common.py
+@@ -10,7 +10,7 @@ __all__ = ['EXPECTED_DOT_BINARY', 'EXPECTED_DEFAULT_ENCODING',
+            'as_cwd',
+            'check_startupinfo', 'StartupinfoMatcher']
+ 
+-EXPECTED_DOT_BINARY = pathlib.Path('dot')
++EXPECTED_DOT_BINARY = pathlib.Path('@graphviz@/bin/dot')
+ 
+ EXPECTED_DEFAULT_ENCODING = 'utf-8'
+ 
+diff --git a/tests/backend/test_execute.py b/tests/backend/test_execute.py
+index 05d6525..78484cb 100644
+--- a/tests/backend/test_execute.py
++++ b/tests/backend/test_execute.py
+@@ -57,6 +57,7 @@ def test_run_check_input_lines_mocked(mocker, sentinel, mock_popen,
+     mock_sys_stderr.flush.assert_called_once_with()
+ 
+ 
++@pytest.mark.skip(reason='empty $PATH has no effect')
+ @pytest.mark.usefixtures('empty_path')
+ @pytest.mark.parametrize(
+     'func, args',
+diff --git a/tests/backend/test_unflattening.py b/tests/backend/test_unflattening.py
+index 033a4d2..7d52689 100644
+--- a/tests/backend/test_unflattening.py
++++ b/tests/backend/test_unflattening.py
+@@ -8,7 +8,7 @@ import graphviz
+ 
+ import _common
+ 
+-EXPECTED_UNFLATTEN_BINARY = pathlib.Path('unflatten')
++EXPECTED_UNFLATTEN_BINARY = pathlib.Path('@graphviz@/bin/unflatten')
+ 
+ 
+ @pytest.mark.exe
+diff --git a/tests/backend/test_viewing.py b/tests/backend/test_viewing.py
+index f5acddb..6b34884 100644
+--- a/tests/backend/test_viewing.py
++++ b/tests/backend/test_viewing.py
+@@ -25,6 +25,6 @@ def test_view(mocker, mock_platform, mock_popen, mock_startfile, quiet):
+     if mock_platform == 'darwin':
+         mock_popen.assert_called_once_with(['open', 'nonfilepath'], **kwargs)
+     elif mock_platform in ('linux', 'freebsd'):
+-        mock_popen.assert_called_once_with(['xdg-open', 'nonfilepath'], **kwargs)
++        mock_popen.assert_called_once_with(['@xdgutils@/bin/xdg-open', 'nonfilepath'], **kwargs)
+     else:
+         raise RuntimeError

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

@@ -47,6 +47,7 @@ buildPythonPackage rec {
     description = "A Python framework that makes developing APIs as simple as possible, but no simpler";
     homepage = "https://github.com/hugapi/hug";
     license = licenses.mit;
+    # Missing support for later falcon releases
+    broken = true;
   };
-
 }

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

@@ -59,6 +59,9 @@ buildPythonPackage rec {
     "test_alpha_is_080"
     "test_face_and_lines_at_half_visibility"
     "test_polygon_fully_inside_image__no_rectangular_shape"
+    # flaky due to timing-based assertions
+    "test_imap_batches_output_buffer_size"
+    "test_imap_batches_unordered_output_buffer_size"
   ];
 
   disabledTestPaths = [

pkgs/development/python-modules/jupyter-repo2docker/default.nix

@@ -1,9 +1,16 @@
-{ lib, buildPythonPackage, fetchPypi, pythonOlder
+{ lib
+, bash
+, buildPythonPackage
+, chardet
 , docker
+, entrypoints
 , escapism
+, fetchFromGitHub
+, iso8601
 , jinja2
 , pkgs-docker
 , python-json-logger
+, pythonOlder
 , pyyaml
 , ruamel_yaml
 , semver
@@ -12,18 +19,24 @@
 }:
 
 buildPythonPackage rec {
-  version = "2021.8.0";
+  version = "2021.08.0";
   pname = "jupyter-repo2docker";
-  disabled = pythonOlder "3.4";
+  format = "setuptools";
 
-  src = fetchPypi {
+  disabled = pythonOlder "3.6";
-    inherit pname version;
+
-    sha256 = "9d1b3c3ec7944ea6b0a234d6fa77293a2d1ed1c080eba8466aba94f811b3465d";
+  src = fetchFromGitHub {
+    owner = "jupyterhub";
+    repo = "repo2docker";
+    rev = version;
+    sha256 = "10hcdag7ivyqyiqrmr9c48zynp8d81ic3px1ffgnaysih7lvkwb6";
   };
 
   propagatedBuildInputs = [
     docker
+    entrypoints
     escapism
+    iso8601
     jinja2
     pkgs-docker
     python-json-logger
@@ -33,7 +46,7 @@ buildPythonPackage rec {
     traitlets
   ];
 
-  # tests not packaged with pypi release
+  # Tests require a running Docker instance
   doCheck = false;
 
   pythonImportsCheck = [
@@ -44,9 +57,9 @@ buildPythonPackage rec {
   ];
 
   meta = with lib; {
-    homepage = "https://repo2docker.readthedocs.io/en/latest/";
+    description = "Turn code repositories into Jupyter enabled Docker Images";
-    description = "Repo2docker: Turn code repositories into Jupyter enabled Docker Images";
+    homepage = "https://repo2docker.readthedocs.io/";
     license = licenses.bsdOriginal;
-    maintainers = [ maintainers.costrouc ];
+    maintainers = with maintainers; [ costrouc ];
   };
 }

pkgs/development/python-modules/mailman-hyperkitty/default.nix

@@ -5,6 +5,7 @@
 , mock
 , nose2
 , python
+, pythonOlder
 , requests
 , zope_interface
 }:
@@ -14,6 +15,8 @@ buildPythonPackage rec {
   version = "1.1.0";
   format = "setuptools";
 
+  disabled = pythonOlder "3.9";
+
   src = fetchPypi {
     inherit pname version;
     sha256 = "1lfqa9admhvdv71f528jmz2wl0i5cv77v6l64px2pm4zqr9ckkjx";

pkgs/development/python-modules/mill-local/default.nix

@@ -0,0 +1,41 @@
+{ lib
+, aiohttp
+, async-timeout
+, buildPythonPackage
+, fetchFromGitHub
+, pythonOlder
+}:
+
+buildPythonPackage rec {
+  pname = "mill-local";
+  version = "0.1.0";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.8";
+
+  src = fetchFromGitHub {
+    owner = "Danielhiversen";
+    repo = "pyMillLocal";
+    rev = version;
+    sha256 = "0q0frwj9yxdmqi5axl7gxirfflgn8xh1932c6lhp9my2v1d0gdrk";
+  };
+
+  propagatedBuildInputs = [
+    aiohttp
+    async-timeout
+  ];
+
+  # Project has no tests
+  doCheck = false;
+
+  pythonImportsCheck = [
+    "mill_local"
+  ];
+
+  meta = with lib; {
+    description = "Python module to communicate locally with Mill heaters";
+    homepage = "https://github.com/Danielhiversen/pyMillLocal";
+    license = with licenses; [ mit ];
+    maintainers = with maintainers; [ fab ];
+  };
+}

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

@@ -6,12 +6,12 @@
 
 buildPythonPackage rec {
   pname = "nbclient";
-  version = "0.5.4";
+  version = "0.5.8";
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "6c8ad36a28edad4562580847f9f1636fe5316a51a323ed85a24a4ad37d4aefce";
+    sha256 = "sha256-NPUsycuDGl2MzXAxU341THXcYaJEh/mYcS0Sid4yCiU=";
   };
 
   inherit doCheck;
@@ -22,5 +22,6 @@ buildPythonPackage rec {
     homepage = "https://github.com/jupyter/nbclient";
     description = "A client library for executing notebooks";
     license = licenses.bsd3;
+    maintainers = [ maintainers.erictapen ];
   };
 }

pkgs/development/python-modules/nettigo-air-monitor/default.nix

@@ -12,14 +12,16 @@
 
 buildPythonPackage rec {
   pname = "nettigo-air-monitor";
-  version = "1.1.1";
+  version = "1.2.0";
-  disabled = pythonOlder "3.6";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.8";
 
   src = fetchFromGitHub {
     owner = "bieniu";
     repo = pname;
     rev = version;
-    sha256 = "sha256-OIB1d6XtstUr5P0q/dmyJS7+UbtkFQIiuSnzwcdP1mE=";
+    sha256 = "sha256-KPgBbYGbKpKEPMxywgRvJcSCEYSUQkiPEFqj+bB0g1s=";
   };
 
   propagatedBuildInputs = [
@@ -41,7 +43,9 @@ buildPythonPackage rec {
       --replace "--cov --cov-report term-missing " ""
   '';
 
-  pythonImportsCheck = [ "nettigo_air_monitor" ];
+  pythonImportsCheck = [
+    "nettigo_air_monitor"
+  ];
 
   meta = with lib; {
     description = "Python module to get air quality data from Nettigo Air Monitor devices";

pkgs/development/python-modules/open-garage/default.nix

@@ -8,15 +8,16 @@
 
 buildPythonPackage rec {
   pname = "open-garage";
-  version = "0.1.6";
+  version = "0.2.0";
+  format = "setuptools";
 
-  disabled = pythonOlder "3.5";
+  disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "Danielhiversen";
     repo = "pyOpenGarage";
     rev = version;
-    sha256 = "sha256-vm51Fjej0OQ7LftisS/tsnxZxa5c/j7eGIROMsEcXNE=";
+    sha256 = "sha256-iJ7HcJhpTceFpHTUdNZOYDuxUWZGWPmZ9lxD3CyGvk8=";
   };
 
   propagatedBuildInputs = [

pkgs/development/python-modules/pg8000/default.nix

@@ -8,12 +8,14 @@
 
 buildPythonPackage rec {
   pname = "pg8000";
-  version = "1.22.0";
+  version = "1.22.1";
+  format = "setuptools";
+
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "c5172252fc92142ec104cd5e7231be4580a1a0a814403707bafbf7bb8383a29a";
+    sha256 = "sha256-/WmtWvJ4HllgjLP02WayNNlhxi8JPt0xlKxF32W40dQ=";
   };
 
   propagatedBuildInputs = [
@@ -23,7 +25,10 @@ buildPythonPackage rec {
 
   # Tests require a running PostgreSQL instance
   doCheck = false;
-  pythonImportsCheck = [ "pg8000" ];
+
+  pythonImportsCheck = [
+    "pg8000"
+  ];
 
   meta = with lib; {
     description = "Python driver for PostgreSQL";

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

@@ -0,0 +1,34 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pythonOlder
+}:
+
+buildPythonPackage rec {
+  pname = "pybalboa";
+  version = "0.13";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.8";
+
+  src = fetchFromGitHub {
+    owner = "garbled1";
+    repo = pname;
+    rev = version;
+    sha256 = "0aw5jxpsvzyx05y1mg8d63lxx1i607yb6x19n9jil5wfis95m8pd";
+  };
+
+  # Project has no tests
+  doCheck = false;
+
+  pythonImportsCheck = [
+    "pybalboa"
+  ];
+
+  meta = with lib; {
+    description = " Python module to interface with a Balboa Spa";
+    homepage = "https://github.com/garbled1/pybalboa";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ fab ];
+  };
+}

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

@@ -0,0 +1,52 @@
+{ lib
+, aiohttp
+, aresponses
+, buildPythonPackage
+, fetchFromGitHub
+, pytestCheckHook
+, pytest-asyncio
+, pythonOlder
+}:
+
+buildPythonPackage rec {
+  pname = "pylaunches";
+  version = "1.2.0";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.8";
+
+  src = fetchFromGitHub {
+    owner = "ludeeus";
+    repo = pname;
+    rev = version;
+    sha256 = "0mczxkwczyh9kva4xzpmnawy0hjha1fdrwj6igip9w5z1q48zs49";
+  };
+
+  propagatedBuildInputs = [
+    aiohttp
+  ];
+
+  checkInputs = [
+    aresponses
+    pytestCheckHook
+    pytest-asyncio
+  ];
+
+  postPatch = ''
+    # Upstream doesn't set version in the repo
+    substituteInPlace setup.py \
+      --replace 'version="main",' 'version="${version}",' \
+      --replace ', "pytest-runner"' ""
+  '';
+
+  pythonImportsCheck = [
+    "pylaunches"
+  ];
+
+  meta = with lib; {
+    description = "Python module to get information about upcoming space launches";
+    homepage = "https://github.com/ludeeus/pylaunches";
+    license = licenses.mit;
+    maintainers = with maintainers; [ fab ];
+  };
+}

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

@@ -9,14 +9,14 @@
 
 buildPythonPackage rec {
   pname = "pymetno";
-  version = "0.8.3";
+  version = "0.9.0";
   format = "setuptools";
 
   src = fetchFromGitHub {
     owner = "Danielhiversen";
     repo = "PyMetno";
     rev = version;
-    sha256 = "sha256-dvZz+wv9B07yKM4E4fQ9VQOgeil9KxZxcGk6D0kWY4g=";
+    sha256 = "sha256-2LNDFQObGqxrzswnqbmvCGLxEI0j+cIdv8o+RZM/7sM=";
   };
 
   propagatedBuildInputs = [
@@ -30,7 +30,7 @@ buildPythonPackage rec {
     "metno"
   ];
 
-  # no tests
+  # Project has no tests
   doCheck = false;
 
   meta = with lib; {

pkgs/development/python-modules/python3-saml/default.nix

@@ -1,36 +1,18 @@
-{ lib, fetchpatch, fetchFromGitHub, buildPythonPackage, isPy3k,
+{ lib, fetchFromGitHub, buildPythonPackage, isPy3k,
 isodate, lxml, xmlsec, freezegun }:
 
 buildPythonPackage rec {
   pname = "python3-saml";
-  version = "1.10.1";
+  version = "1.12.0";
   disabled = !isPy3k;
 
   src = fetchFromGitHub {
     owner = "onelogin";
     repo = "python3-saml";
     rev = "v${version}";
-    sha256 = "1yk02xq90bm7p6k091av6gapb5h2ccxzgrbm03sj2x8h0wff9s8k";
+    sha256 = "sha256-VPUsjuo4FIes8ti0tkR0kT3J3RdUt1wtl4QEahVsc2c=";
   };
 
-  # Remove both patches on update
-  patches = [
-    # Remove the dependency on defusedxml
-    #
-    # This patch is already merged upstream and does not introduce any
-    # functionality changes.
-    (fetchpatch {
-      url = "https://github.com/onelogin/python3-saml/commit/4b6c4b1f2ed3f6eab70ff4391e595b808ace168c.patch";
-      sha256 = "sha256-KHyAoX3our3Rz2z4xo0lTBB1XOGuC3Pe+lUDCzK5WQI=";
-    })
-
-    # Update expiry dates for test response XMLs
-    (fetchpatch {
-      url = "https://github.com/onelogin/python3-saml/commit/05611bbf6d7d8313adb9c77ff88a9210333ccc38.patch";
-      sha256 = "sha256-62TwgCXDFYsZIAeqAysJRziMvhUVhGzta/C2wS3v4HY=";
-    })
-  ];
-
   propagatedBuildInputs = [
     isodate lxml xmlsec
   ];

pkgs/development/python-modules/schema-salad/default.nix

@@ -1,4 +1,5 @@
 { lib
+, black
 , buildPythonPackage
 , fetchPypi
 , cachecontrol
@@ -8,15 +9,19 @@
 , rdflib-jsonld
 , ruamel_yaml
 , pytestCheckHook
+, pythonOlder
 }:
 
 buildPythonPackage rec {
   pname = "schema-salad";
-  version = "8.2.20210918131710";
+  version = "8.2.20211104054942";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "464180407f49a3533cd5a5bc7db9254769bc77595ea00562bbe4a50493f7f445";
+    sha256 = "sha256-1crKyAON8iZBYxP6bhj0MxV3fSpnCh3Lqp8x91KLBT8=";
   };
 
   propagatedBuildInputs = [
@@ -28,13 +33,20 @@ buildPythonPackage rec {
     ruamel_yaml
   ];
 
-  checkInputs = [ pytestCheckHook ];
+  checkInputs = [
+    black
+    pytestCheckHook
+  ];
+
   disabledTests = [
     # setup for these tests requires network access
     "test_secondaryFiles"
     "test_outputBinding"
   ];
-  pythonImportsCheck = [ "schema_salad" ];
+
+  pythonImportsCheck = [
+    "schema_salad"
+  ];
 
   meta = with lib; {
     description = "Semantic Annotations for Linked Avro Data";

pkgs/development/python-modules/scikit-image/add-testing-data.patch

@@ -0,0 +1,17 @@
+diff --git a/skimage/data/setup.py b/skimage/data/setup.py
+index 528e9c284ce..ba0e155559c 100644
+--- a/skimage/data/setup.py
++++ b/skimage/data/setup.py
+@@ -11,7 +11,11 @@ def configuration(parent_package='', top_path=None):
+     # further notice.
+     # Testing data and additional datasets should only
+     # be made available via pooch
+-    config.add_data_files(*legacy_datasets)
++    # Nix patch: add ALL images to facilitate testing of a fully-built package
++    from pathlib import Path
++    config.add_data_files(
++        *(path.name for path in Path(__file__).parent.glob("*") if path.suffix != ".py")
++    )
+     # It seems hard to create a consistent hash for README.txt since
+     # the line endings keep getting converted
+     config.add_data_files('README.txt')

pkgs/development/python-modules/scikit-image/default.nix

@@ -1,6 +1,7 @@
 { lib
-, fetchPypi
+, fetchFromGitHub
 , buildPythonPackage
+, python
 , cython
 , numpy
 , scipy
@@ -11,20 +12,26 @@
 , pywavelets
 , dask
 , cloudpickle
-, pytest
 , imageio
 , tifffile
+, pytestCheckHook
 }:
 
-buildPythonPackage rec {
+let
+  installedPackageRoot = "${builtins.placeholder "out"}/${python.sitePackages}";
+in buildPythonPackage rec {
   pname = "scikit-image";
   version = "0.18.3";
 
-  src = fetchPypi {
+  src = fetchFromGitHub {
-    inherit pname version;
+    owner = pname;
-    sha256 = "ecae99f93f4c5e9b1bf34959f4dc596c41f2f6b2fc407d9d9ddf85aebd3137ca";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "0a2h3bw5rkk23k4r04qc9maccg00nddssd7lfsps8nhp5agk1vyh";
   };
 
+  patches = [ ./add-testing-data.patch ];
+
   nativeBuildInputs = [ cython ];
 
   propagatedBuildInputs = [
@@ -41,14 +48,51 @@ buildPythonPackage rec {
     tifffile
   ];
 
-  checkInputs = [ pytest ];
+  checkInputs = [ pytestCheckHook ];
 
-  # No tests in archive
+  # (1) The package has cythonized modules, whose .so libs will appear only in the wheel, i.e. in nix store;
-  doCheck = false;
+  # (2) To stop Python from importing the wrong directory, i.e. the one in the build dir, not the one in nix store, `skimage` dir should be removed or renamed;
+  # (3) Therefore, tests should be run on the installed package in nix store.
+
+  # See e.g. https://discourse.nixos.org/t/cant-import-cythonized-modules-at-checkphase/14207 on why the following is needed.
+  preCheck = ''
+    rm -r skimage
+  '';
+
+  disabledTestPaths = [
+    # Requires network access (actually some data is loaded via `skimage._shared.testing.fetch` in the global scope, which calls `pytest.skip` when a network is unaccessible, leading to a pytest collection error).
+    "${installedPackageRoot}/skimage/filters/rank/tests/test_rank.py"
+  ];
+  pytestFlagsArray = [ "${installedPackageRoot}" "--pyargs" "skimage" ] ++ builtins.map (testid: "--deselect=" + testid) [
+    # These tests require network access
+    "skimage/data/test_data.py::test_skin"
+    "skimage/data/tests/test_data.py::test_skin"
+    "skimage/io/tests/test_io.py::test_imread_http_url"
+    "skimage/restoration/tests/test_rolling_ball.py::test_ndim"
+  ];
+
+  # Check cythonized modules
+  pythonImportsCheck = [
+    "skimage"
+    "skimage._shared"
+    "skimage.draw"
+    "skimage.feature"
+    "skimage.restoration"
+    "skimage.filters"
+    "skimage.future.graph"
+    "skimage.graph"
+    "skimage.io"
+    "skimage.measure"
+    "skimage.morphology"
+    "skimage.transform"
+    "skimage.util"
+    "skimage.segmentation"
+  ];
 
   meta = {
     description = "Image processing routines for SciPy";
     homepage = "https://scikit-image.org";
     license = lib.licenses.bsd3;
+    maintainers = with lib.maintainers; [ yl3dy ];
   };
 }

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

@@ -7,13 +7,14 @@
 
 buildPythonPackage rec {
   pname = "twitterapi";
-  version = "2.7.5";
+  version = "2.7.7";
+  format = "setuptools";
 
   src = fetchFromGitHub {
     owner = "geduldig";
     repo = "TwitterAPI";
     rev = "v${version}";
-    sha256 = "1s5q3gzd69syk8khlyy7ap8gpymvhgqrlv3vp6vdmwnaafjvvyy3";
+    sha256 = "sha256-KEJ0lAg6Zi2vps+ZPTkT6ts87qnIBL9pFe1tPEzviCI=";
   };
 
   propagatedBuildInputs = [
@@ -23,7 +24,10 @@ buildPythonPackage rec {
 
   # Tests are interacting with the Twitter API
   doCheck = false;
-  pythonImportsCheck = [ "TwitterAPI" ];
+
+  pythonImportsCheck = [
+    "TwitterAPI"
+  ];
 
   meta = with lib; {
     description = "Python wrapper for Twitter's REST and Streaming APIs";

pkgs/development/tools/analysis/checkov/default.nix

@@ -56,13 +56,13 @@ with py.pkgs;
 
 buildPythonApplication rec {
   pname = "checkov";
-  version = "2.0.566";
+  version = "2.0.568";
 
   src = fetchFromGitHub {
     owner = "bridgecrewio";
     repo = pname;
     rev = version;
-    sha256 = "sha256-Eah4dK23jdHK7s0VF8FLd6KJzHP5YpdLGcM7IXgB880=";
+    sha256 = "sha256-V1YHD0+gXx5wLfhrfze6kAgF1egxXbjf4c2zEc/oT1A=";
   };
 
   nativeBuildInputs = with py.pkgs; [

pkgs/development/tools/analysis/valgrind/default.nix

@@ -87,6 +87,6 @@ stdenv.mkDerivation rec {
       "riscv32-linux" "riscv64-linux"
       "alpha-linux"
     ];
-    broken = stdenv.isDarwin; # https://hydra.nixos.org/build/128521440/nixlog/2
+    broken = stdenv.isDarwin || stdenv.hostPlatform.isStatic; # https://hydra.nixos.org/build/128521440/nixlog/2
   };
 }