Merge master into staging-next

nixos/modules/services/web-servers/nginx/default.nix

@@ -924,7 +924,7 @@ in
         PrivateMounts = true;
         # System Call Filtering
         SystemCallArchitectures = "native";
-        SystemCallFilter = [ "~@cpu-emulation @debug @keyring @mount @obsolete @privileged @setuid @mincore" ] ++ optionals (cfg.package != pkgs.tengine) [ "~@ipc" ];
+        SystemCallFilter = [ "~@cpu-emulation @debug @keyring @mount @obsolete @privileged @setuid" ] ++ optionals (cfg.package != pkgs.tengine) [ "~@ipc" ];
       };
     };
 

pkgs/applications/audio/cozy/default.nix

@@ -22,7 +22,7 @@ python3Packages.buildPythonApplication rec {
   format = "other"; # no setup.py
 
   pname = "cozy";
-  version = "1.1.2";
+  version = "1.2.0";
 
   # Temporary fix
   # See https://github.com/NixOS/nixpkgs/issues/57029
@@ -33,7 +33,7 @@ python3Packages.buildPythonApplication rec {
     owner = "geigi";
     repo = pname;
     rev = version;
-    sha256 = "sha256-QENn8mFMk06/Uj8QJo0mJQ7frJNcv5RVNJwDB+H/LkI=";
+    sha256 = "0igqf9b77i13sxlk4ziw549h379hmz1slrb3vvf8irk94gxabsaw";
   };
 
   nativeBuildInputs = [

pkgs/applications/audio/cyanrip/default.nix

@@ -12,13 +12,13 @@
 }:
 stdenv.mkDerivation rec {
   pname = "cyanrip";
-  version = "0.8.0";
+  version = "0.8.1";
 
   src = fetchFromGitHub {
     owner = "cyanreg";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1aip52bwkq8cb1d8ifyv2m6m5dz7jk6qmbhyb97yyf4nhxv445ky";
+    sha256 = "17bi2xhjv3f3i870whkyqckvjlg32wqkspash87zi0jw7m7jm229";
   };
 
   nativeBuildInputs = [ meson ninja pkg-config ];

pkgs/applications/misc/clight/clightd.nix

@@ -9,13 +9,13 @@
 
 stdenv.mkDerivation rec {
   pname = "clightd";
-  version = "5.4";
+  version = "5.5";
 
   src = fetchFromGitHub {
     owner = "FedeDP";
     repo = "Clightd";
     rev = version;
-    sha256 = "sha256-ppaxfnZB3+aOzvc/wk1f8D2mFYngQspEOl9XArNMdBE=";
+    sha256 = "sha256-uygMc4SPYBk+G+ENp+KsgDhkm+oq9ZMvWX4wF6iohPM=";
   };
 
   # dbus-1.pc has datadir=/etc

pkgs/applications/misc/dbeaver/default.nix

@@ -20,13 +20,13 @@
 
 stdenv.mkDerivation rec {
   pname = "dbeaver";
-  version = "21.3.2"; # When updating also update fetchedMavenDeps.sha256
+  version = "21.3.3"; # When updating also update fetchedMavenDeps.sha256
 
   src = fetchFromGitHub {
     owner = "dbeaver";
     repo = "dbeaver";
     rev = version;
-    sha256 = "SifnnzuETFKtnEwLjJtB7CV2QZaToex3MjKGuiShlwo=";
+    sha256 = "sha256-WycjNxPa4hkxBtT8Pq7ayUu8pNV0DvaJ+29GDKNJNWE=";
   };
 
   fetchedMavenDeps = stdenv.mkDerivation {
@@ -52,7 +52,7 @@ stdenv.mkDerivation rec {
     dontFixup = true;
     outputHashAlgo = "sha256";
     outputHashMode = "recursive";
-    outputHash = "grSFtkohTlLtK8qE4A4wVppC6UHcyaXRQlGnrOmQDC4=";
+    outputHash = "sha256-pfYNHue7tZKYgU16kypZEfr2bXuDoPc4KorIAVjSylo=";
   };
 
   nativeBuildInputs = [

pkgs/applications/misc/neo4j-desktop/default.nix

@@ -1,12 +1,12 @@
 { appimageTools, lib, fetchurl }:
 let
   pname = "neo4j-desktop";
-  version = "1.4.7";
+  version = "1.4.12";
   name = "${pname}-${version}";
 
   src = fetchurl {
     url = "https://s3-eu-west-1.amazonaws.com/dist.neo4j.org/${pname}/linux-offline/${name}-x86_64.AppImage";
-    hash = "sha256-oEcSW7UIeiGY2fCPJQ5EtDBRtd73Q04HaSk+7ObLKJc=";
+    hash = "sha256-CfdXus9Zj6Tx6wAXpV2tRdqvJqowgE+NIL04v3fwtJE=";
   };
 
   appimageContents = appimageTools.extract { inherit name src; };

pkgs/applications/misc/snapmaker-luban/default.nix

@@ -8,11 +8,11 @@
 
 stdenv.mkDerivation rec {
   pname = "snapmaker-luban";
-  version = "4.1.3";
+  version = "4.1.4";
 
   src = fetchurl {
     url = "https://github.com/Snapmaker/Luban/releases/download/v${version}/snapmaker-luban-${version}-linux-x64.tar.gz";
-    sha256 = "sha256-GXpM5dJ3JPf2HgrgTONyeCG6JjK4JhbcGP5ck7v4cqk=";
+    sha256 = "sha256-hbqIwX6YCrUQAjvKKWFAUjHvcZycnIA6v6l6qmAMuUI=";
   };
 
   nativeBuildInputs = [

pkgs/applications/misc/spicetify-cli/default.nix

@@ -2,13 +2,13 @@
 
 buildGoModule rec {
   pname = "spicetify-cli";
-  version = "2.8.4";
+  version = "2.8.5";
 
   src = fetchFromGitHub {
     owner = "khanhas";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-WsNiMlqr9ya06Urvw/m3yPsGLCTOvYFaO0oNHuVKNTs=";
+    sha256 = "sha256-cCIlKTHo+LyhIZkN6ncggBvZMwDBgXqDJVAfGWbUtj8=";
   };
 
   vendorSha256 = "sha256-g0RYIVIq4oMXdRZDBDnVYg7ombN5WEo/6O9hChQvOYs=";

pkgs/applications/misc/todoist-electron/default.nix

@@ -1,12 +1,12 @@
-{ lib, stdenv, fetchurl, appimageTools, makeWrapper, electron, libsecret }:
+{ lib, stdenv, fetchurl, appimageTools, makeWrapper, electron_15, libsecret }:
 
 stdenv.mkDerivation rec {
   pname = "todoist-electron";
-  version = "1.0.1";
+  version = "1.0.3";
 
   src = fetchurl {
     url = "https://electron-dl.todoist.com/linux/Todoist-${version}.AppImage";
-    sha256 = "1c4qmfyfi4hm3fs5bkxjbq1hxs5sgyp531xi5z5vpnzzi5z7dw0k";
+    sha256 = "sha256-bHX/RWDfe+ht66U7xg4HBZxeWlNBu4gYlIVd+9OuMNU=";
   };
 
   appimageContents = appimageTools.extractType2 {
@@ -36,7 +36,7 @@ stdenv.mkDerivation rec {
   '';
 
   postFixup = ''
-    makeWrapper ${electron}/bin/electron $out/bin/${pname} \
+    makeWrapper ${electron_15}/bin/electron $out/bin/${pname} \
       --add-flags $out/share/${pname}/resources/app.asar \
       --prefix LD_LIBRARY_PATH : "${lib.makeLibraryPath [ stdenv.cc.cc libsecret ]}"
   '';

pkgs/applications/misc/xmrig/default.nix

@@ -4,13 +4,13 @@
 
 stdenv.mkDerivation rec {
   pname = "xmrig";
-  version = "6.16.2";
+  version = "6.16.3";
 
   src = fetchFromGitHub {
     owner = "xmrig";
     repo = "xmrig";
     rev = "v${version}";
-    sha256 = "sha256-RbpvEPjRwwGbjt4+A4tbnvEdLc+hH1VszE36xXnIxPE=";
+    sha256 = "sha256-YR/8ApkuZtO2vJA/VlZ06JdQnGDbTzQ5fNqHgBpFZjQ=";
   };
 
   nativeBuildInputs = [ cmake ];

pkgs/applications/networking/aether/default.nix

@@ -9,31 +9,27 @@
 
 let
   binaryName = "AetherP2P";
+  aether-app-git = fetchFromGitHub {
+    owner = "aethereans";
+    repo = "aether-app";
+    rev = "53b6c8b2a9253cbf056ea3ebb077e0e08cbc5b1d";
+    sha256 = "1kgkzh7ih2q9dsckdkinh5dbzvr7gdykf8yz6h8pyhvzyjhk1v0r";
+  };
 in
 stdenv.mkDerivation rec {
   pname = "aether";
   version = "2.0.0-dev.15";
 
-  srcs = [
+  src = fetchurl {
-    (fetchurl {
     url = "https://static.getaether.net/Releases/Aether-${version}/2011262249.19338c93/linux/Aether-${version}%2B2011262249.19338c93.tar.gz";
     sha256 = "1hi8w83zal3ciyzg2m62shkbyh6hj7gwsidg3dn88mhfy68himf7";
     # % in the url / canonical filename causes an error
     name = "aether-tarball.tar.gz";
-    })
+  };
-    (fetchFromGitHub {
-      owner = "aethereans";
-      repo = "aether-app";
-      rev = "53b6c8b2a9253cbf056ea3ebb077e0e08cbc5b1d";
-      sha256 = "1kgkzh7ih2q9dsckdkinh5dbzvr7gdykf8yz6h8pyhvzyjhk1v0r";
-    })
-  ];
-
-  sourceRoot = "Aether-${version}+2011262249.19338c93";
 
   # there is no logo in the tarball so we grab it from github and convert it in the build phase
   buildPhase = ''
-    convert ../source/aether-core/aether/client/src/app/ext_dep/images/Linux-Windows-App-Icon.png -resize 512x512 aether.png
+    convert ${aether-app-git}/aether-core/aether/client/src/app/ext_dep/images/Linux-Windows-App-Icon.png -resize 512x512 aether.png
   '';
 
   dontWrapGApps = true;

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

@@ -19,13 +19,13 @@
 
 stdenv.mkDerivation rec {
   pname = "lagrange";
-  version = "1.10.1";
+  version = "1.10.3";
 
   src = fetchFromGitHub {
     owner = "skyjake";
     repo = "lagrange";
     rev = "v${version}";
-    sha256 = "sha256-HwrIdQv4LDVLLuvukzp28AuKKbEMQeHSb0ZW+a9q4ug=";
+    sha256 = "sha256-4Xjm4P4uK0aZxUT0WzcSDdY6rEeh5YFwsMfVtFB14No=";
     fetchSubmodules = true;
   };
 

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

@@ -2,16 +2,16 @@
 
 buildGoModule rec {
   pname = "driftctl";
-  version = "0.18.3";
+  version = "0.18.5";
 
   src = fetchFromGitHub {
     owner = "cloudskiff";
     repo = "driftctl";
     rev = "v${version}";
-    sha256 = "sha256-JD3T0dCRg0UQlG0pWnI8RJZuRrIFfSMVHMoaEIymdWE=";
+    sha256 = "sha256-Qz/yObF1Df62Hqwl6fPHGkWcsifvgO5EfeiyU3aql3Q=";
   };
 
-  vendorSha256 = "sha256-g3+g+mPXEO2ZcVraKuVYZCMBD5zEr1l8ogcYt3r4UjU=";
+  vendorSha256 = "sha256-wOk4IXD9qHG8R4iddlc4TLH39jVSof9bwTDU1kyAmuA=";
 
   postUnpack = ''
     # Without this, tests fail to locate aws/3.19.0.json

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

@@ -2,13 +2,13 @@
 
 buildGoModule rec {
   pname = "starboard";
-  version = "0.14.0";
+  version = "0.14.1";
 
   src = fetchFromGitHub {
     owner = "aquasecurity";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-/k9lQS3oPOYxhaaXuaDwPnai7byDkge4yBu7/9g4RUE=";
+    sha256 = "sha256-sB7C0IKadgpQ2h6HuH4D6ku/GXnFfFS+fGCW/RBSc10=";
     # populate values that require us to use git. By doing this in postFetch we
     # can delete .git afterwards and maintain better reproducibility of the src.
     leaveDotGit = true;
@@ -22,7 +22,7 @@ buildGoModule rec {
       find "$out" -name .git -print0 | xargs -0 rm -rf
     '';
   };
-  vendorSha256 = "sha256-7SVEyyJRE7oYIhuENraZy0aieIAoFFWtq4mrSXxURlQ=";
+  vendorSha256 = "sha256-R7tF724y5WNIByE+9nRoNSZDZzfLtPfK/9tSBkARaN0=";
 
   nativeBuildInputs = [ installShellFiles ];
 

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

@@ -44,11 +44,11 @@ in
 
 stdenv.mkDerivation rec {
   pname = "bluejeans";
-  version = "2.25.0.78";
+  version = "2.26.0.136";
 
   src = fetchurl {
     url = "https://swdl.bluejeans.com/desktop-app/linux/${getFirst 3 version}/BlueJeans_${version}.rpm";
-    sha256 = "sha256-Xk9iU7mNm3YlXKsmf6yPqd1YAklsFOWu+04Llb+2yWQ=";
+    sha256 = "sha256-9QiE7CjCepDXQCzduqGzNUGqUgYS+PWBS71ouzHa83o=";
   };
 
   nativeBuildInputs = [ rpmextract makeWrapper ];

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

@@ -7,11 +7,16 @@ let
     canary = "0.0.132";
   } else {
     stable = "0.0.264";
-    ptb = "0.0.58";
+    ptb = "0.0.59";
     canary = "0.0.280";
   };
   version = versions.${branch};
-  srcs = {
+  srcs = let
+    darwin-ptb = fetchurl {
+      url = "https://dl-ptb.discordapp.net/apps/osx/${version}/DiscordPTB.dmg";
+      sha256 = "sha256-LS7KExVXkOv8O/GrisPMbBxg/pwoDXIOo1dK9wk1yB8=";
+    };
+  in {
     x86_64-linux = {
       stable = fetchurl {
         url =
@@ -34,11 +39,7 @@ let
         url = "https://dl.discordapp.net/apps/osx/${version}/Discord.dmg";
         sha256 = "1jvlxmbfqhslsr16prsgbki77kq7i3ipbkbn67pnwlnis40y9s7p";
       };
-      ptb = fetchurl {
+      ptb = darwin-ptb;
-        url =
-          "https://dl-ptb.discordapp.net/apps/osx/${version}/DiscordPTB.dmg";
-        sha256 = "sha256-GwYUoPBbx9lSaRP1JwzI0UE9gEU+rV4a9BNPVSxHki0=";
-      };
       canary = fetchurl {
         url =
           "https://dl-canary.discordapp.net/apps/osx/${version}/DiscordCanary.dmg";
@@ -46,13 +47,7 @@ let
       };
     };
     # Only PTB bundles a MachO Universal binary with ARM support.
-    aarch64-darwin = {
+    aarch64-darwin = { ptb = darwin-ptb; };
-      ptb = fetchurl {
-        url =
-          "https://dl-ptb.discordapp.net/apps/osx/${version}/DiscordPTB.dmg";
-        sha256 = "sha256-GwYUoPBbx9lSaRP1JwzI0UE9gEU+rV4a9BNPVSxHki0=";
-      };
-    };
   };
   src = srcs.${stdenv.hostPlatform.system}.${branch};
 

pkgs/applications/networking/remote/teamviewer/default.nix

@@ -6,11 +6,11 @@
 
 mkDerivation rec {
   pname = "teamviewer";
-  version = "15.25.5";
+  version = "15.26.4";
 
   src = fetchurl {
     url = "https://dl.tvcdn.de/download/linux/version_15x/teamviewer_${version}_amd64.deb";
-    sha256 = "sha256-LtITPS0bLy85dv/zdOo8JcsEZ0ZgtVmM+CcggaYJxXA=";
+    sha256 = "sha256-2CprtdKHHTLxS8jA4bRVoHvj/8zyVUV0aGPzU7mNxM8=";
   };
 
   unpackPhase = ''

pkgs/applications/office/foliate/default.nix

@@ -4,13 +4,13 @@
 
 stdenv.mkDerivation rec {
   pname = "foliate";
-  version = "2.6.3";
+  version = "2.6.4";
 
   src = fetchFromGitHub {
     owner = "johnfactotum";
     repo = pname;
     rev = version;
-    sha256 = "0ribqaxl8g1i83fxbn288afwbzzls48ni57xqi07d19p9ka892mr";
+    sha256 = "sha256-Pr2YA2MHXD4W7lyCxGAVLKyoZarZ8t92RSkWle3LNuc=";
   };
 
   nativeBuildInputs = [ meson ninja python3 wrapGAppsHook ];

pkgs/applications/office/jabref/default.nix

@@ -2,12 +2,12 @@
 , zlib , libX11, libXext, libXi, libXrender, libXtst, libGL, alsa-lib, cairo, freetype, pango, gdk-pixbuf, glib }:
 
 stdenv.mkDerivation rec {
-  version = "5.1";
+  version = "5.5";
   pname = "jabref";
 
   src = fetchurl {
     url = "https://github.com/JabRef/jabref/releases/download/v${version}/JabRef-${version}-portable_linux.tar.gz";
-    sha256 = "04f612byrq3agzy26byg1sgrjyhcpa8xfj0ssh8dl8d8vnhx9742";
+    sha256 = "sha256-9MHNehyAmu7CiBp1rgb4zTkSqmjXm2tcmiGKFBFapKI=";
   };
 
   preferLocalBuild = true;

pkgs/applications/office/libreoffice/darwin.nix

@@ -0,0 +1,51 @@
+{ stdenv
+, lib
+, fetchurl
+, undmg
+}:
+
+let
+  appName = "LibreOffice.app";
+  version = "7.2.5";
+  dist = {
+    aarch64-darwin = {
+      arch = "aarch64";
+      sha256 = "bdbcb9a98211f866ca089d440aebcd1d313aa99e8ab4104aae4e65ea3cee74ca";
+    };
+
+    x86_64-darwin = {
+      arch = "x86_64";
+      sha256 = "0b7ef18ed08341ac6c15339fe9a161ad17f6b469009d987cfc7d50c628d12a4e";
+    };
+  }."${stdenv.hostPlatform.system}";
+in
+stdenv.mkDerivation {
+  inherit version;
+  pname = "libreoffice";
+  src = fetchurl {
+    url = "https://download.documentfoundation.org/libreoffice/stable/${version}/mac/${dist.arch}/LibreOffice_${version}_MacOS_${dist.arch}.dmg";
+    inherit (dist) sha256;
+  };
+
+  nativeBuildInputs = [ undmg ];
+  sourceRoot = "${appName}";
+  dontPatch = true;
+  dontConfigure = true;
+  dontBuild = true;
+
+  installPhase = ''
+    runHook preInstallPhase
+    mkdir -p $out/{Applications/${appName},bin}
+    cp -R . $out/Applications/${appName}
+    ln -s $out/Applications/${appName}/Contents/MacOS/soffice $out/bin
+    runHook postInstallPhase
+  '';
+
+  meta = with lib; {
+    description = "Comprehensive, professional-quality productivity suite, a variant of openoffice.org";
+    homepage = "https://libreoffice.org/";
+    license = licenses.lgpl3;
+    maintainers = with maintainers; [ tricktron ];
+    platforms = [ "aarch64-darwin" "x86_64-darwin" ];
+  };
+}

pkgs/applications/radio/gnuradio/default.nix

@@ -48,13 +48,13 @@
 , pname ? "gnuradio"
 , versionAttr ? {
   major = "3.10";
-  minor = "0";
+  minor = "1";
   patch = "0";
 }
 }:
 
 let
-  sourceSha256 = "sha256-1K8nlNiirks3MJ+9cH9bkILVFtu5OxhKkNhetGqojn4=";
+  sourceSha256 = "sha256-bU6z7H08G8QIToogAMI2P5tHBtVZezlBDqSbnEsqAjE=";
   featuresInfo = {
     # Needed always
     basic = {

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

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "kallisto";
-  version = "0.46.2";
+  version = "0.48.0";
 
   src = fetchFromGitHub {
     repo = "kallisto";
     owner = "pachterlab";
     rev = "v${version}";
-    sha256 = "0m0r2820ca3rch99md1zzbgkilmlfkhdkpys2lfnb87qxmf1jnmb";
+    sha256 = "sha256-r0cdR0jTRa1wu/LDKW6NdxI3XaKj6wcIVbIlct0fFvI=";
   };
 
   nativeBuildInputs = [ autoconf cmake ];

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

@@ -0,0 +1,27 @@
+{ lib, stdenv, fetchurl }:
+
+stdenv.mkDerivation rec {
+  pname = "repseek";
+  version = "9Sep2014";
+  src = fetchurl {
+    url = "https://bioinfo.mnhn.fr/abi/public/RepSeek/RepSeek.${version}.tgz";
+    sha256 = "1jiknji3ivrv7zmrfbf2mccfpdwhin3lfxfsciaqwf69b3sda8nf";
+  };
+
+  preConfigure = ''
+    mkdir -p $out/bin
+    substituteInPlace Makefile \
+      --replace "INSTALLDIR = \$\$HOME/bin" "INSTALLDIR = $out/bin/" \
+      --replace "CC= gcc" "CC = $CC"
+  '' + lib.optionalString stdenv.isLinux ''
+    substituteInPlace Makefile --replace "MACHINE = MACOSX" "MACHINE = LINUX"
+  '';
+
+  meta = {
+    description = "Tool to retrieve approximate repeats from large DNA sequences";
+    homepage = "https://bioinfo.mnhn.fr/abi/public/RepSeek";
+    maintainers = [ lib.maintainers.bzizou ];
+    license = lib.licenses.lgpl21;
+  };
+
+}

pkgs/applications/science/math/sage/default.nix

@@ -14,13 +14,17 @@ let
       # `sagelib`, i.e. all of sage except some wrappers and runtime dependencies
       sagelib = self.callPackage ./sagelib.nix {
         inherit flint arb;
-        inherit sage-src env-locations pynac singular;
+        inherit sage-src env-locations singular;
         inherit (maxima) lisp-compiler;
         linbox = pkgs.linbox.override { withSage = true; };
         pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config
       };
 
-      sage_docbuild = self.callPackage ./sage_docbuild.nix {
+      sage-docbuild = self.callPackage ./python-modules/sage-docbuild.nix {
+        inherit sage-src;
+      };
+
+      sage-setup = self.callPackage ./python-modules/sage-setup.nix {
         inherit sage-src;
       };
     };
@@ -58,9 +62,9 @@ let
   # the env-locations file.
   sage-env = callPackage ./sage-env.nix {
     sagelib = python3.pkgs.sagelib;
-    sage_docbuild = python3.pkgs.sage_docbuild;
+    sage-docbuild = python3.pkgs.sage-docbuild;
     inherit env-locations;
-    inherit python3 singular palp flint pynac pythonEnv maxima;
+    inherit python3 singular palp flint pythonEnv maxima;
     pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config
   };
 
@@ -74,7 +78,7 @@ let
   sage-with-env = callPackage ./sage-with-env.nix {
     inherit python3 pythonEnv;
     inherit sage-env;
-    inherit pynac singular maxima;
+    inherit singular maxima;
     inherit three;
     pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config
   };
@@ -91,7 +95,7 @@ let
 
   pythonRuntimeDeps = with python3.pkgs; [
     sagelib
-    sage_docbuild
+    sage-docbuild
     cvxopt
     networkx
     service-identity
@@ -132,9 +136,6 @@ let
     };
   };
 
-  # *not* to confuse with the python package "pynac"
-  pynac = pkgs.pynac.override { inherit singular flint; };
-
   # With openblas (64 bit), the tests fail the same way as when sage is build with
   # openblas instead of openblasCompat. Apparently other packages somehow use flints
   # blas when it is available. Alternative would be to override flint to use

pkgs/applications/science/math/sage/patches/Only-test-external-software-when-all-of-sage-is.patch

@@ -0,0 +1,46 @@
+diff --git a/src/sage/doctest/control.py b/src/sage/doctest/control.py
+index 01f32fb8e4..4d83dc7b47 100644
+--- a/src/sage/doctest/control.py
++++ b/src/sage/doctest/control.py
+@@ -1253,6 +1253,7 @@ class DocTestController(SageObject):
+ 
+             self.log("Using --optional=" + self._optional_tags_string())
+             available_software._allow_external = self.options.optional is True or 'external' in self.options.optional
++            available_software._autodetect_safe = self.options.optional is True or 'sage' in self.options.optional
+             self.log("Features to be detected: " + ','.join(available_software.detectable()))
+             self.add_files()
+             self.expand_files_into_sources()
+diff --git a/src/sage/doctest/external.py b/src/sage/doctest/external.py
+index 84dae19ea5..badc61466e 100644
+--- a/src/sage/doctest/external.py
++++ b/src/sage/doctest/external.py
+@@ -409,6 +409,7 @@ class AvailableSoftware(object):
+             []
+         """
+         self._allow_external = True
++        self._autodetect_safe = True
+         # For multiprocessing of doctests, the data self._seen should be
+         # shared among subprocesses. Thus we use Array class from the
+         # multiprocessing module.
+@@ -430,6 +431,8 @@ class AvailableSoftware(object):
+             sage: 'internet' in available_software # random, optional - internet
+             True
+         """
++        if not self._autodetect_safe:
++            return False
+         try:
+             idx = self._indices[item]
+         except KeyError:
+diff --git a/src/sage/features/sagemath.py b/src/sage/features/sagemath.py
+index 433338766d..233623b14a 100644
+--- a/src/sage/features/sagemath.py
++++ b/src/sage/features/sagemath.py
+@@ -12,7 +12,7 @@ class sagemath_doc_html(StaticFile):
+ 
+     EXAMPLES::
+ 
+-        sage: from sage.features.sagemath import sagemath_doc_html
++        sage: from sage.features.sagemath import sagemath_doc_html  # optional - sagemath_doc_html
+         sage: sagemath_doc_html().is_present()  # optional - sagemath_doc_html
+         FeatureTestResult('sagemath_doc_html', True)
+     """

pkgs/applications/science/math/sage/patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch

@@ -1,26 +0,0 @@
-From f5ea42a7aaed7611fb55b65897b9fcf2b7bcf97e Mon Sep 17 00:00:00 2001
-From: Timo Kaufmann <timokau@zoho.com>
-Date: Sun, 21 Oct 2018 17:52:40 +0200
-Subject: [PATCH] Only test py2/py3 optional tests when all of sage is tested
-
----
- src/sage/doctest/control.py | 3 ++-
- 1 file changed, 2 insertions(+), 1 deletion(-)
-
-diff --git a/src/sage/doctest/control.py b/src/sage/doctest/control.py
-index 2d93841e50..6d156e29a1 100644
---- a/src/sage/doctest/control.py
-+++ b/src/sage/doctest/control.py
-@@ -375,7 +375,8 @@ class DocTestController(SageObject):
-                     if not optionaltag_regex.search(o):
-                         raise ValueError('invalid optional tag {!r}'.format(o))
- 
--                options.optional |= auto_optional_tags
-+                if "sage" in options.optional:
-+                    options.optional |= auto_optional_tags
- 
-         self.options = options
- 
--- 
-2.28.0
-

pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch

@@ -1,8 +1,8 @@
 diff --git a/src/sage/env.py b/src/sage/env.py
-index 95980cc2df..37107a30e1 100644
+index c4953cfa65..47b880f9ad 100644
 --- a/src/sage/env.py
 +++ b/src/sage/env.py
-@@ -227,93 +227,12 @@ OPENMP_CXXFLAGS = var("OPENMP_CXXFLAGS", "")
+@@ -244,81 +244,8 @@ os.environ['MPMATH_SAGE'] = '1'
  SAGE_BANNER = var("SAGE_BANNER", "")
  SAGE_IMPORTALL = var("SAGE_IMPORTALL", "yes")
  
@@ -29,20 +29,12 @@ index 95980cc2df..37107a30e1 100644
 -
 -    EXAMPLES::
 -
--        sage: import sys
--        sage: from fnmatch import fnmatch
 -        sage: from sage.env import _get_shared_lib_path
--        sage: lib_filename = _get_shared_lib_path("Singular", "singular-Singular")
+-        sage: "gap" in _get_shared_lib_path("gap")
--        sage: if sys.platform == 'cygwin':
--        ....:     pattern = "*/cygSingular-*.dll"
--        ....: elif sys.platform == 'darwin':
--        ....:     pattern = "*/libSingular-*.dylib"
--        ....: else:
--        ....:     pattern = "*/lib*Singular-*.so"
--        sage: fnmatch(str(lib_filename), pattern)
 -        True
 -        sage: _get_shared_lib_path("an_absurd_lib") is None
 -        True
+-
 -    """
 -
 -    for libname in libnames:
@@ -87,11 +79,6 @@ index 95980cc2df..37107a30e1 100644
 -    # Just return None if no files were found
 -    return None
 -
- # locate singular shared object
- # On Debian it's libsingular-Singular so try that as well
--SINGULAR_SO = var("SINGULAR_SO", _get_shared_lib_path("Singular", "singular-Singular"))
-+SINGULAR_SO = var("SINGULAR_SO", '/default')
- 
  # locate libgap shared object
 -GAP_SO = var("GAP_SO", _get_shared_lib_path("gap", ""))
 +GAP_SO = var("GAP_SO", '/default')

pkgs/applications/science/math/sage/patches/linbox-1.7-upgrade.patch

@@ -0,0 +1,58 @@
+diff --git a/src/sage/libs/linbox/conversion.pxd b/src/sage/libs/linbox/conversion.pxd
+index 7794c9edc3..1753277b1f 100644
+--- a/src/sage/libs/linbox/conversion.pxd
++++ b/src/sage/libs/linbox/conversion.pxd
+@@ -177,9 +177,8 @@ cdef inline Vector_integer_dense new_sage_vector_integer_dense(P, DenseVector_in
+     - v -- linbox vector
+     """
+     cdef Vector_integer_dense res = P()
+-    cdef cppvector[Integer] * vec = &v.refRep()
+     cdef size_t i
+     for i in range(<size_t> res._degree):
+-        mpz_set(res._entries[i], vec[0][i].get_mpz_const())
++        mpz_set(res._entries[i], v.getEntry(i).get_mpz_const())
+ 
+     return res
+diff --git a/src/sage/libs/linbox/linbox.pxd b/src/sage/libs/linbox/linbox.pxd
+index 9112d151f8..dcc482960c 100644
+--- a/src/sage/libs/linbox/linbox.pxd
++++ b/src/sage/libs/linbox/linbox.pxd
+@@ -32,7 +32,7 @@ cdef extern from "linbox/matrix/dense-matrix.h":
+         ctypedef Modular_double Field
+         ctypedef double Element
+         DenseMatrix_Modular_double(Field F, size_t m, size_t n)
+-        DenseMatrix_Modular_double(Field F, Element*, size_t m, size_t n)
++        DenseMatrix_Modular_double(Field F, size_t m, size_t n, Element*)
+         void setEntry(size_t i, size_t j, Element& a)
+         Element &getEntry(size_t i, size_t j)
+ 
+@@ -42,7 +42,7 @@ cdef extern from "linbox/matrix/dense-matrix.h":
+         ctypedef Modular_float Field
+         ctypedef float Element
+         DenseMatrix_Modular_float(Field F, size_t m, size_t n)
+-        DenseMatrix_Modular_float(Field F, Element*, size_t m, size_t n)
++        DenseMatrix_Modular_float(Field F, size_t m, size_t n, Element*)
+         void setEntry(size_t i, size_t j, Element& a)
+         Element &getEntry(size_t i, size_t j)
+ 
+@@ -101,7 +101,6 @@ cdef extern from "linbox/vector/vector.h":
+         DenseVector_integer (Field &F)
+         DenseVector_integer (Field &F, long& m)
+         DenseVector_integer (Field &F, cppvector[Integer]&)
+-        cppvector[Element]& refRep()
+         size_t size()
+         void resize(size_t)
+         void resize(size_t n, const Element&)
+diff --git a/src/sage/matrix/matrix_modn_dense_template.pxi b/src/sage/matrix/matrix_modn_dense_template.pxi
+index 010365d76f..3d60726ff9 100644
+--- a/src/sage/matrix/matrix_modn_dense_template.pxi
++++ b/src/sage/matrix/matrix_modn_dense_template.pxi
+@@ -219,7 +219,7 @@ cdef inline linbox_echelonize_efd(celement modulus, celement* entries, Py_ssize_
+         return 0,[]
+ 
+     cdef ModField *F = new ModField(<long>modulus)
+-    cdef DenseMatrix *A = new DenseMatrix(F[0], <ModField.Element*>entries,<Py_ssize_t>nrows, <Py_ssize_t>ncols)
++    cdef DenseMatrix *A = new DenseMatrix(F[0], <Py_ssize_t>nrows, <Py_ssize_t>ncols, <ModField.Element*>entries)
+     cdef Py_ssize_t r = reducedRowEchelonize(A[0])
+     cdef Py_ssize_t i,j
+     for i in range(nrows):

pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch

@@ -1,8 +1,8 @@
 diff --git a/src/sage_docbuild/__init__.py b/src/sage_docbuild/__init__.py
-index 79005b903a..fbe6fe2595 100644
+index 8a5c1a19d2..21fd192642 100644
 --- a/src/sage_docbuild/__init__.py
 +++ b/src/sage_docbuild/__init__.py
-@@ -85,27 +85,6 @@ def builder_helper(type):
+@@ -89,27 +89,6 @@ def builder_helper(type):
      """
      Returns a function which builds the documentation for
      output type ``type``.
@@ -12,7 +12,7 @@ index 79005b903a..fbe6fe2595 100644
 -    Check that :trac:`25161` has been resolved::
 -
 -        sage: from sage_docbuild import DocBuilder, setup_parser
--        sage: DocBuilder._options = setup_parser().parse_args([])[0] # builder_helper needs _options to be set
+-        sage: DocBuilder._options = setup_parser().parse_args([]) # builder_helper needs _options to be set
 -
 -        sage: import sage_docbuild.sphinxbuild
 -        sage: def raiseBaseException():
@@ -30,7 +30,7 @@ index 79005b903a..fbe6fe2595 100644
      """
      def f(self, *args, **kwds):
          output_dir = self._output_dir(type)
-@@ -127,10 +106,9 @@ def builder_helper(type):
+@@ -131,10 +110,9 @@ def builder_helper(type):
          logger.debug(build_command)
  
          # Run Sphinx with Sage's special logger
@@ -44,10 +44,10 @@ index 79005b903a..fbe6fe2595 100644
              if ABORT_ON_ERROR:
                  raise
 diff --git a/src/sage_docbuild/sphinxbuild.py b/src/sage_docbuild/sphinxbuild.py
-index f58f6c61d7..ef51a55411 100644
+index d917c3e9d4..551cc8028a 100644
 --- a/src/sage_docbuild/sphinxbuild.py
 +++ b/src/sage_docbuild/sphinxbuild.py
-@@ -326,3 +326,8 @@ def runsphinx():
+@@ -327,3 +327,8 @@ def runsphinx():
          sys.stderr = saved_stderr
          sys.stdout.flush()
          sys.stderr.flush()

pkgs/applications/science/math/sage/python-modules/sage-docbuild.nix

@@ -0,0 +1,28 @@
+{ lib
+, buildPythonPackage
+, sage-src
+, sphinx
+}:
+
+buildPythonPackage rec {
+  version = src.version;
+  pname = "sage-docbuild";
+  src = sage-src;
+
+  propagatedBuildInputs = [
+    sphinx
+  ];
+
+  preBuild = ''
+    cd pkgs/sage-docbuild
+  '';
+
+  doCheck = false; # we will run tests in sagedoc.nix
+
+  meta = with lib; {
+    description = "Build system of the Sage documentation";
+    homepage = "https://www.sagemath.org";
+    license = licenses.gpl2Plus;
+    maintainers = teams.sage.members;
+  };
+}

pkgs/applications/science/math/sage/python-modules/sage-setup.nix

@@ -0,0 +1,28 @@
+{ lib
+, buildPythonPackage
+, sage-src
+, pkgconfig # the python module, not the pkg-config alias
+}:
+
+buildPythonPackage rec {
+  version = src.version;
+  pname = "sage-setup";
+  src = sage-src;
+
+  buildInputs = [
+    pkgconfig
+  ];
+
+  preBuild = ''
+    cd pkgs/sage-setup
+  '';
+
+  doCheck = false; # sagelib depends on sage-setup, but sage-setup's tests depend on sagelib
+
+  meta = with lib; {
+    description = "Build system of the Sage library";
+    homepage = "https://www.sagemath.org";
+    license = licenses.gpl2Plus;
+    maintainers = teams.sage.members;
+  };
+}

pkgs/applications/science/math/sage/sage-env.nix

@@ -2,7 +2,7 @@
 , lib
 , writeTextFile
 , sagelib
-, sage_docbuild
+, sage-docbuild
 , env-locations
 , gfortran
 , bash
@@ -45,11 +45,10 @@
 , flint
 , gmp
 , mpfr
-, pynac
 , zlib
 , gsl
 , ntl
-, jdk8
+, jdk
 , less
 }:
 
@@ -60,8 +59,6 @@ assert (!blas.isILP64) && (!lapack.isILP64);
 # dependencies.
 
 let
-  jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
-
   runtimepath = (lib.makeBinPath ([
     "@sage-local@"
     "@sage-local@/build"
@@ -163,7 +160,6 @@ writeTextFile rec {
         gmp
         mpfr
         pari
-        pynac
         zlib
         eclib
         gsl
@@ -179,7 +175,6 @@ writeTextFile rec {
         glpk
         flint
         gap
-        pynac
         mpfr.dev
       ])
     }'
@@ -193,5 +188,5 @@ writeTextFile rec {
   '';
 } // { # equivalent of `passthru`, which `writeTextFile` doesn't support
   lib = sagelib;
-  docbuild = sage_docbuild;
+  docbuild = sage-docbuild;
 }

pkgs/applications/science/math/sage/sage-src.nix

@@ -57,24 +57,29 @@ let
   );
 in
 stdenv.mkDerivation rec {
-  version = "9.4";
+  version = "9.5";
   pname = "sage-src";
 
   src = fetchFromGitHub {
     owner = "sagemath";
     repo = "sage";
     rev = version;
-    sha256 = "sha256-jqkr4meG02KbTCMsGvyr1UbosS4ZuUJhPXU/InuS+9A=";
+    sha256 = "sha256-uOsLpsGpcIGs8Xr82X82MElnTB2E908gytyNJ8WVD5w=";
   };
 
   # Patches needed because of particularities of nix or the way this is packaged.
   # The goal is to upstream all of them and get rid of this list.
   nixPatches = [
-    # Make sure py2/py3 tests are only run when their expected context (all "sage"
+    # Since https://trac.sagemath.org/ticket/32174, some external features are
-    # tests) are also run. That is necessary to test dochtml individually. See
+    # marked as "safe" and get auto-detected, in which case the corresponding
-    # https://trac.sagemath.org/ticket/26110 for an upstream discussion.
+    # optional tests are executed. We disable auto-detection of safe features if
-    # TODO: Determine if it is still necessary.
+    # we are doctesting with an "--optional" argument which does not include
-    ./patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch
+    # "sage", because tests from autodetected features expect context provided
+    # by running basic sage tests. This is necessary to test sagemath_doc_html
+    # separately. See https://trac.sagemath.org/ticket/26110 for a related
+    # upstream discussion (from the time when Sage still had optional py2/py3
+    # tags).
+    ./patches/Only-test-external-software-when-all-of-sage-is.patch
 
     # Fixes a potential race condition which can lead to transient doctest failures.
     ./patches/fix-ecl-race.patch
@@ -117,46 +122,6 @@ stdenv.mkDerivation rec {
     # Let's just assume warnings are expected until we update to 4.27.0.
     ./patches/fonttools-deprecation-warnings.patch
 
-    # https://trac.sagemath.org/ticket/32305
-    (fetchSageDiff {
-      base = "9.4";
-      name = "networkx-2.6-upgrade.patch";
-      rev = "9808325853ba9eb035115e5b056305a1c9d362a0";
-      sha256 = "sha256-gJSqycCtbAVr5qnVEbHFUvIuTOvaxFIeffpzd6nH4DE=";
-    })
-
-    # https://trac.sagemath.org/ticket/32420
-    (fetchSageDiff {
-      base = "9.5.beta2";
-      name = "sympy-1.9-update.patch";
-      rev = "beed4e16aff32e47d0c3b1c58cb1e2f4c38590f8";
-      sha256 = "sha256-3eJPfWfCrCAQ5filIn7FbzjRQeO9QyTIVl/HyRuqFtE=";
-    })
-
-    # https://trac.sagemath.org/ticket/32567
-    (fetchSageDiff {
-      base = "9.5.beta2";
-      name = "arb-2.21.0-update.patch";
-      rev = "eb3304dd521a3d5a9334e747a08e234bbf16b4eb";
-      sha256 = "sha256-XDkaY4VQGyESXI6zuD7nCNzyQOl/fmBFvAESH9+RRvk=";
-    })
-
-    # https://trac.sagemath.org/ticket/32797
-    (fetchSageDiff {
-      base = "9.5.beta7";
-      name = "pari-2.13.3-update.patch";
-      rev = "f5f7a86908daf60b25e66e6a189c51ada7e0a732";
-      sha256 = "sha256-H/caGx3q4KcdsyGe+ojV9bUTQ5y0siqM+QHgDbeEnbw=";
-    })
-
-    # https://trac.sagemath.org/ticket/32909
-    (fetchSageDiff {
-      base = "9.5.beta7";
-      name = "matplotlib-3.5-deprecation-warnings.patch";
-      rev = "a5127dc56fdf5c2e82f6bc781cfe78dbd04e97b7";
-      sha256 = "sha256-p23qUu9mgEUbdbX6cy7ArxZAtpcFjCKbgyxN4jWvj1o=";
-    })
-
     # https://trac.sagemath.org/ticket/32968
     (fetchSageDiff {
       base = "9.5.beta8";
@@ -164,6 +129,11 @@ stdenv.mkDerivation rec {
       rev = "fc84f82f52b6f05f512cb359ec7c100f93cf8841";
       sha256 = "sha256-bBbfdcnw/9LUOlY8rHJRbFJEdMXK4shosqTNaobTS1Q=";
     })
+
+    # Upstream has not upgraded to linbox 1.7 yet because it conflicts with
+    # pre-4.2.1p3 versions of Singular, but we don't have this problem.
+    # https://trac.sagemath.org/ticket/32959
+    ./patches/linbox-1.7-upgrade.patch
   ];
 
   patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;

pkgs/applications/science/math/sage/sage-with-env.nix

@@ -18,7 +18,6 @@
 , eclib
 , ntl
 , ecm
-, pynac
 , pythonEnv
 }:
 
@@ -36,7 +35,6 @@ let
     blas lapack
     singular
     three
-    pynac
     giac
     gap
     pari
@@ -126,6 +124,10 @@ stdenv.mkDerivation rec {
     cp -r src/bin "$out/bin"
     cp -r build/bin "$out/build/bin"
 
+    # sage assumes the existence of sage-src-env-config.in means it's being executed in-tree. in this case, it
+    # adds SAGE_SRC/bin to PATH, breaking our wrappers
+    rm "$out/bin"/*.in "$out/build/bin"/*.in
+
     cp -f '${sage-env}/sage-env' "$out/bin/sage-env"
     substituteInPlace "$out/bin/sage-env" \
       --subst-var-by sage-local "$out"

pkgs/applications/science/math/sage/sage.nix

@@ -62,7 +62,8 @@ stdenv.mkDerivation rec {
 
   meta = with lib; {
     description = "Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab";
-    license = licenses.gpl2;
+    homepage = "https://www.sagemath.org";
+    license = licenses.gpl2Plus;
     maintainers = teams.sage.members;
   };
 }

pkgs/applications/science/math/sage/sage_docbuild.nix

@@ -1,20 +0,0 @@
-{ buildPythonPackage
-, sage-src
-, sphinx
-}:
-
-buildPythonPackage rec {
-  version = src.version;
-  pname = "sage_docbuild";
-  src = sage-src;
-
-  propagatedBuildInputs = [
-    sphinx
-  ];
-
-  preBuild = ''
-    cd build/pkgs/sage_docbuild/src
-  '';
-
-  doCheck = false; # we will run tests in sagedoc.nix
-}

pkgs/applications/science/math/sage/sagedoc.nix

@@ -23,7 +23,7 @@ stdenv.mkDerivation rec {
     jmol
     cddlib
   ] ++ (with python3.pkgs; [
-    sage_docbuild
+    sage-docbuild
     psutil
     future
     sphinx
@@ -83,6 +83,6 @@ stdenv.mkDerivation rec {
 
   doCheck = true;
   checkPhase = ''
-    ${sage-with-env}/bin/sage -t --optional=dochtml --all
+    ${sage-with-env}/bin/sage -t --optional=sagemath_doc_html --all
   '';
 }

pkgs/applications/science/math/sage/sagelib.nix

@@ -2,6 +2,7 @@
 , env-locations
 , perl
 , buildPythonPackage
+, m4
 , arb
 , blas
 , lapack
@@ -37,7 +38,7 @@
 , pkg-config
 , planarity
 , ppl
-, pynac
+, primecountpy
 , python
 , ratpoints
 , readline
@@ -49,11 +50,24 @@
 , singular
 , pip
 , jupyter_core
+, sage-setup
 , libhomfly
 , libbraiding
 , gmpy2
 , pplpy
 , sqlite
+, jupyter-client
+, ipywidgets
+, mpmath
+, rpy2
+, fpylll
+, scipy
+, sympy
+, matplotlib
+, pillow
+, ipykernel
+, networkx
+, sphinx # TODO: this is in setup.cfg, bug should we override it?
 }:
 
 assert (!blas.isILP64) && (!lapack.isILP64);
@@ -73,8 +87,10 @@ buildPythonPackage rec {
     perl
     jupyter_core
     pkg-config
+    sage-setup
     pip # needed to query installed packages
     lisp-compiler
+    m4
   ];
 
   buildInputs = [
@@ -116,7 +132,7 @@ buildPythonPackage rec {
     pari
     planarity
     ppl
-    pynac
+    primecountpy
     rankwidth
     ratpoints
     singular
@@ -130,6 +146,18 @@ buildPythonPackage rec {
     gmpy2
     pplpy
     sqlite
+    mpmath
+    rpy2
+    scipy
+    sympy
+    matplotlib
+    pillow
+    ipykernel
+    fpylll
+    networkx
+    jupyter-client
+    ipywidgets
+    sphinx
   ];
 
   preBuild = ''
@@ -148,8 +176,24 @@ buildPythonPackage rec {
     mkdir -p "$SAGE_SHARE/sage/ext/notebook-ipython"
     mkdir -p "var/lib/sage/installed"
 
-    # src/setup.py should not be used, see https://trac.sagemath.org/ticket/31377#comment:124
+    cd build/pkgs/sagelib
-    cd build/pkgs/sagelib/src
+
+    # some files, like Pipfile, pyproject.toml, requirements.txt and setup.cfg
+    # are generated by the bootstrap script using m4. these can fetch data from
+    # build/pkgs, either directly or via sage-get-system-packages.
+    sed -i 's/==2.1.0rc1/>=2.1.1/' ../gmpy2/install-requires.txt
+    sed -i 's/, <3.4//' ../rpy2/install-requires.txt
+    sed -i 's/, <4.3//' ../sphinx/install-requires.txt
+    sed -i '/sage_conf/d' src/setup.cfg.m4
+    sed -i '/sage_conf/d' src/requirements.txt.m4
+    for infile in src/*.m4; do
+        if [ -f "$infile" ]; then
+            outfile="src/$(basename $infile .m4)"
+            m4 "$infile" > "$outfile"
+        fi
+    done
+
+    cd src
   '';
 
   postInstall = ''

pkgs/applications/science/math/singular/default.nix

@@ -1,7 +1,7 @@
 { stdenv, fetchFromGitHub, gmp, bison, perl, ncurses, readline, coreutils, pkg-config
 , lib
-, fetchpatch
 , autoreconfHook
+, buildPackages
 , sharutils
 , file
 , flint
@@ -11,6 +11,7 @@
 , lrcalc
 , doxygen
 , graphviz
+, latex2html
 # upstream generates docs with texinfo 4. later versions of texinfo
 # use letters instead of numbers for post-appendix chapters, and we
 # want it to match the upstream format because sage depends on it.
@@ -22,66 +23,25 @@
 
 stdenv.mkDerivation rec {
   pname = "singular";
-  version = "4.2.0p2";
+  version = "4.3.0";
 
-  # since the tarball does not contain tests or documentation (and
+  # since the tarball does not contain tests, we fetch from GitHub.
-  # there is no separate tests tarball for 4.2.0), we fetch from
-  # GitHub.
   src = fetchFromGitHub {
     owner = "Singular";
     repo = "Singular";
 
-    # 4.2.0p2 is not tagged, but the tarball matches the commit below.
+    # if a release is tagged (which sometimes does not happen), it will
-    rev = "6f68939ddf612d96e3caaaaa8275f77613ac1da8";
+    # be in the format below.
-    sha256 = "sha256-BJNzYylzDqD/5YjzjxPRb/c96tYiuGy9Y+A7qf3ZSG8=";
+    # rev = "Release-${lib.replaceStrings ["."] ["-"] version}";
-
+    rev = "d895b0f1f543c61eb03adddad20f08655a419d4e";
-    # if a release is tagged it will be in the format below.
+    sha256 = "sha256-c5Qr6VUuPKjfw8fowjJJz3oGAyUwo/K0WeMvU5djzVA=";
-    # rev = "Release${lib.replaceStrings ["."] ["-"] version}";
 
     # the repository's .gitattributes file contains the lines "/Tst/
     # export-ignore" and "/doc/ export-ignore" so some directories are
-    # not included in the tarball downloaded by fetchzip. setting
+    # not included in the tarball downloaded by fetchzip.
-    # fetchSubmodules works around this by using fetchgit instead of
+    forceFetchGit = true;
-    # fetchzip.
-    fetchSubmodules = true;
   };
 
-  patches = [
-    # fix timeouts when docbuilding with >= 64 cpus
-    # https://github.com/Singular/Singular/issues/1117
-    ./vspace-MAX_PROCESS.patch
-
-    # add aarch64 support to cpu-check.m4. copied from redhat.
-    ./redhat-aarch64.patch
-
-    # the newest version of ax-prog-cc-for-build.m4 seems to trigger
-    # linker errors. see
-    # https://github.com/alsa-project/alsa-firmware/issues/3 for a
-    # related issue.
-    ./use-older-ax-prog-cc-for-build.patch
-
-    # https://github.com/Singular/Singular/issues/1086
-    (fetchpatch {
-      name = "schubert-lib-fails-with-too-many-cpus.patch";
-      url = "https://github.com/Singular/Singular/commit/3cda50c00a849455efa2502e56596955491a353a.patch";
-      sha256 = "sha256-fgYd+2vT32w5Ki8kKx6PfZn2e4QSJcYWOwEFXtc+lSA=";
-    })
-  ] ++ lib.optionals enableDocs [
-    # singular supports building without 4ti2, bertini, normaliz or
-    # topcom just fine, but the docbuilding does not skip manual pages
-    # tagged as depending on those binaries (probably a bug in
-    # doc2tex.pl::HandleLib, since it seems to ignore "-exclude"
-    # argumens). skip them manually.
-    ./disable-docs-for-optional-unpackaged-deps.patch
-
-    # fix some non-ascii characters in doc/decodegb.doc
-    (fetchpatch {
-      name = "decodegb-ascii.patch";
-      url = "https://github.com/Singular/Singular/commit/36966d9009de572ee4dbc487f3e5744098fe91be.patch";
-      sha256 = "sha256-9WcEov/oOQRC584ag6WVHFwY2aCjbM75HWyvZoEwppw=";
-    })
-  ];
-
   configureFlags = [
     "--with-ntl=${ntl}"
     "--disable-pyobject-module"
@@ -114,6 +74,7 @@ stdenv.mkDerivation rec {
   ] ++ lib.optionals enableGfanlib [
     cddlib
   ];
+
   nativeBuildInputs = [
     bison
     perl
@@ -123,9 +84,11 @@ stdenv.mkDerivation rec {
   ] ++ lib.optionals enableDocs [
     doxygen
     graphviz
+    latex2html
     texinfo4
     texlive.combined.scheme-small
   ];
+  depsBuildBuild = [ buildPackages.stdenv.cc ];
 
   preAutoreconf = ''
     find . -type f -readable -writable -exec sed \
@@ -137,21 +100,14 @@ stdenv.mkDerivation rec {
 
   hardeningDisable = lib.optional stdenv.isi686 "stackprotector";
 
-  # The Makefile actually defaults to `make install` anyway
-  buildPhase = ''
-    # do nothing
-  '';
-
   doCheck = true; # very basic checks, does not test any libraries
 
   installPhase = ''
-    mkdir -p "$out"
-    cp -r Singular/LIB "$out/lib"
     make install
   '' + lib.optionalString enableDocs ''
-    # Sage uses singular.hlp (which is not in the tarball)
+    # Sage uses singular.info, which is not installed by default
     mkdir -p $out/share/info
-    cp doc/singular.hlp $out/share/info
+    cp doc/singular.info $out/share/info
   '' + ''
     # Make sure patchelf picks up the right libraries
     rm -rf libpolys factory resources omalloc Singular
@@ -211,5 +167,6 @@ stdenv.mkDerivation rec {
     license = licenses.gpl3; # Or GPLv2 at your option - but not GPLv4
     homepage = "http://www.singular.uni-kl.de";
     downloadPage = "http://www.mathematik.uni-kl.de/ftp/pub/Math/Singular/SOURCES/";
+    mainProgram = "Singular";
   };
 }

pkgs/applications/science/math/singular/disable-docs-for-optional-unpackaged-deps.patch

@@ -1,112 +0,0 @@
-commit 9e8b044d982e132cf35a106a1cc0cf7e77b27f7c
-Author: Mauricio Collares <mauricio@collares.org>
-Date:   Thu Apr 15 20:33:21 2021 -0300
-
-    Disable manual sections using optional packages not yet in Nixpkgs
-
-        * normaliz.lib depends on normaliz.
-        * polymake.lib depends on topcom.
-        * recover.lib depends on bertini.
-        * sing4ti2.lib depends on 4ti2.
-        * tateProdCplxNegGrad.lib uses multigrading.lib, which depends on 4ti2.
-
-diff --git a/doc/singular.doc b/doc/singular.doc
-index 64b969d39..e704f95f0 100644
---- a/doc/singular.doc
-+++ b/doc/singular.doc
-@@ -407,7 +407,6 @@ LIB "all.lib";
- * nfmodsyz_lib:: Syzygy modules of submodules of free modules over algebraic number fields
- * noether_lib:: Noether normalization of an ideal
- * normal_lib:: procedure for normalization
--* normaliz_lib:: integral closure, normalization for monomial ideals, toric ideals
- * pointid_lib:: factorized lex GB of the vanishing ideal of a set of points
- * primdec_lib:: procedures for primary decomposition
- * primdecint_lib:: primary decomposition over the integers
-@@ -416,7 +415,6 @@ LIB "all.lib";
- * reesclos_lib:: Rees Algebra and integral closure of an ideal
- * rstandard_lib:: Janet bases and border bases for ideals
- * sagbi_lib:: Subalgebras bases Analogous to Groebner bases for ideals
--* sing4ti2_lib:: interface to program 4ti2
- * symodstd_lib:: Groebner bases for symmetric ideals
- * toric_lib:: toric ideals
- @end menu
-@@ -521,10 +519,6 @@ LIB "all.lib";
- @node normal_lib
- @subsection normal_lib
- @c lib normal.lib
--@c ---------------------------------------------------------
--@node normaliz_lib
--@subsection normaliz_lib
--@c lib normaliz.lib tag:normaliz
- @c ----------------------------------------------------------
- @node pointid_lib
- @subsection pointid_lib
-@@ -558,10 +552,6 @@ LIB "all.lib";
- @subsection sagbi_lib
- @c lib sagbi.lib
- @c ---------------------------------------------------------
--@node sing4ti2_lib
--@subsection sing4ti2_lib
--@c lib sing4ti2.lib tag:sing4ti2
--@c ----------------------------------------------------------
- @node symodstd_lib
- @subsection symodstd_lib
- @c lib symodstd.lib
-@@ -873,7 +863,6 @@ iniD, reslist, sumlist, dividelist, createlist
- * solve_lib:: procedures to solve polynomial systems
- * triang_lib:: procedures for decomposing zero-dimensional ideals
- * ntsolve_lib:: one real solution of polynomial systems (Newton iteration)
--* recover_lib:: Hybrid numerical/symbolical algorithms
- * rootisolation_lib:: real root isolation with intervals
- * signcond_lib:: computing realizable sign conditions
- * zeroset_lib:: procedures for roots and factorization
-@@ -904,10 +893,6 @@ iniD, reslist, sumlist, dividelist, createlist
- @subsection ntsolve_lib
- @c lib ntsolve.lib
- @c ---------------------------------------------------------
--@node recover_lib
--@subsection recover_lib
--@c lib recover.lib tag:bertini
--@c ----------------------------------------------------------
- @node rootisolation_lib
- @subsection rootisolation_lib
- @c lib rootisolation.lib
-@@ -1108,7 +1093,6 @@ but not for serious computations.
- * cimonom_lib:: complete intersection for toric ideals
- * gfan_lib:: A gfanlib interface for Singular
- * gitfan_lib:: Compute GIT-fans
--* polymake_lib:: interface to TOPCOM
- * realizationMatroids_lib:: Realizability for Tropical Fan Curves
- * tropical_lib:: interface to gfan
- * tropicalNewton_lib:: Newton polygons in tropical geometry
-@@ -1125,10 +1109,7 @@ but not for serious computations.
- @node gitfan_lib
- @subsection gitfan_lib
- @c lib gitfan.lib
--@c ----------------------------------------------------------
--@node polymake_lib
--@subsection polymake_lib
--@c lib polymake.lib tag:topcom
-+
- @c ----------------------------------------------------------
- @node realizationMatroids_lib
- @subsection realizationMatroids_lib
-@@ -1219,7 +1200,6 @@ Comments should be send to the author of the library directly.
- * stanleyreisner_lib:: T1 and T2 for a general Stanley-Reiser ring
- * swalk_lib:: Sagbi Walk Conversion Algorithm
- * systhreads_lib:: multi-threaded objects
--* tateProdCplxNegGrad_lib:: sheaf cohomology on product of projective spaces
- * VecField_lib:: vector fields
- @end menu
- @c ----------------------------------------------------------
-@@ -1310,10 +1290,6 @@ Todos/Issues:
- @subsection systhreads_lib
- @c lib systhreads.lib
- @c ---------------------------------------------------------
--@node tateProdCplxNegGrad_lib
--@subsection tateProdCplxNegGrad_lib
--@c lib tateProdCplxNegGrad.lib
--@c ---------------------------------------------------------
- @node VecField_lib
- @subsection VecField_lib
- @c lib VecField.lib

pkgs/applications/science/math/singular/redhat-aarch64.patch

@@ -1,38 +0,0 @@
-diff --git a/m4/cpu-check.m4 b/m4/cpu-check.m4
-index 3cf0a7f08..12bb926ac 100644
---- a/m4/cpu-check.m4
-+++ b/m4/cpu-check.m4
-@@ -37,6 +37,18 @@ if test "$ac_cv_singcpuname" = ppc; then
-   AC_DEFINE(SI_CPU_PPC,1,"PPC")
-   AC_SUBST(SI_CPU_PPC)
- fi
-+if test "$ac_cv_singcpuname" = arm -o "$ac_cv_singcpuname" = armel; then
-+  AC_DEFINE(SI_CPU_ARM,1,"ARM")
-+  AC_SUBST(SI_CPU_ARM)
-+fi
-+if test "$ac_cv_singcpuname" = aarch64; then
-+  AC_DEFINE(SI_CPU_AARCH64,1,"AARCH64")
-+  AC_SUBST(SI_CPU_AARCH64)
-+fi
-+if test "$ac_cv_singcpuname" = s390; then
-+  AC_DEFINE(SI_CPU_S390,1,"S390")
-+  AC_SUBST(SI_CPU_S390)
-+fi
- 
- # UNAME and PATH
- AC_MSG_CHECKING(uname for Singular)
-@@ -65,6 +77,14 @@ dnl testet on: ppc_Linux, 740/750 PowerMac G3, 512k L2 cache
-   [powerpc*|ppc*], [AC_DEFINE(HAVE_GENERIC_MULT,1,multiplication is fast on the cpu: a*b is with mod otherwise using tables of logartihms)],
- dnl the following settings seems to be better on arm processors
-   [arm*], [],
-+dnl FIXME: need to run some tests
-+  [aarch64*], [
-+            AC_DEFINE(HAVE_MULT_MOD,1,multiplication is fast on the cpu: a*b is with mod otherwise using tables of logartihms)
-+            AC_DEFINE(HAVE_GENERIC_ADD,1,use branch for addition in Z/p otherwise it uses a generic add)
-+            AC_DEFINE(HAVE_DIV_MOD,1,division using extend euclidian algorithm otherwise using tables of logartihms)
-+            ],
-+dnl FIXME: need to run some tests
-+  [s390*], [AC_DEFINE(HAVE_GENERIC_ADD,1,use branch for addition in Z/p otherwise it uses a generic add)],
-   []
- )
- 

pkgs/applications/science/math/singular/use-older-ax-prog-cc-for-build.patch

@@ -1,194 +0,0 @@
-diff --git a/m4/ax_prog_cc_for_build.m4 b/m4/ax_prog_cc_for_build.m4
-index f7410d74b..12cb005a5 100644
---- a/m4/ax_prog_cc_for_build.m4
-+++ b/m4/ax_prog_cc_for_build.m4
-@@ -32,35 +32,31 @@
- #   and this notice are preserved. This file is offered as-is, without any
- #   warranty.
- 
--#serial 18
-+#serial 9
- 
- AU_ALIAS([AC_PROG_CC_FOR_BUILD], [AX_PROG_CC_FOR_BUILD])
- AC_DEFUN([AX_PROG_CC_FOR_BUILD], [dnl
- AC_REQUIRE([AC_PROG_CC])dnl
- AC_REQUIRE([AC_PROG_CPP])dnl
--AC_REQUIRE([AC_CANONICAL_BUILD])dnl
-+AC_REQUIRE([AC_EXEEXT])dnl
-+AC_REQUIRE([AC_CANONICAL_HOST])dnl
- 
- dnl Use the standard macros, but make them use other variable names
- dnl
- pushdef([ac_cv_prog_CPP], ac_cv_build_prog_CPP)dnl
--pushdef([ac_cv_prog_cc_c89], ac_cv_build_prog_cc_c89)dnl
- pushdef([ac_cv_prog_gcc], ac_cv_build_prog_gcc)dnl
- pushdef([ac_cv_prog_cc_works], ac_cv_build_prog_cc_works)dnl
- pushdef([ac_cv_prog_cc_cross], ac_cv_build_prog_cc_cross)dnl
- pushdef([ac_cv_prog_cc_g], ac_cv_build_prog_cc_g)dnl
--pushdef([ac_cv_c_compiler_gnu], ac_cv_build_c_compiler_gnu)dnl
- pushdef([ac_cv_exeext], ac_cv_build_exeext)dnl
- pushdef([ac_cv_objext], ac_cv_build_objext)dnl
- pushdef([ac_exeext], ac_build_exeext)dnl
- pushdef([ac_objext], ac_build_objext)dnl
- pushdef([CC], CC_FOR_BUILD)dnl
- pushdef([CPP], CPP_FOR_BUILD)dnl
--pushdef([GCC], GCC_FOR_BUILD)dnl
- pushdef([CFLAGS], CFLAGS_FOR_BUILD)dnl
- pushdef([CPPFLAGS], CPPFLAGS_FOR_BUILD)dnl
--pushdef([EXEEXT], BUILD_EXEEXT)dnl
- pushdef([LDFLAGS], LDFLAGS_FOR_BUILD)dnl
--pushdef([OBJEXT], BUILD_OBJEXT)dnl
- pushdef([host], build)dnl
- pushdef([host_alias], build_alias)dnl
- pushdef([host_cpu], build_cpu)dnl
-@@ -71,29 +67,27 @@ pushdef([ac_cv_host_alias], ac_cv_build_alias)dnl
- pushdef([ac_cv_host_cpu], ac_cv_build_cpu)dnl
- pushdef([ac_cv_host_vendor], ac_cv_build_vendor)dnl
- pushdef([ac_cv_host_os], ac_cv_build_os)dnl
--pushdef([ac_tool_prefix], ac_build_tool_prefix)dnl
--pushdef([am_cv_CC_dependencies_compiler_type], am_cv_build_CC_dependencies_compiler_type)dnl
--pushdef([am_cv_prog_cc_c_o], am_cv_build_prog_cc_c_o)dnl
--pushdef([cross_compiling], cross_compiling_build)dnl
-+pushdef([ac_cpp], ac_build_cpp)dnl
-+pushdef([ac_compile], ac_build_compile)dnl
-+pushdef([ac_link], ac_build_link)dnl
- 
--cross_compiling_build=no
-+save_cross_compiling=$cross_compiling
-+save_ac_tool_prefix=$ac_tool_prefix
-+cross_compiling=no
-+ac_tool_prefix=
- 
--ac_build_tool_prefix=
--AS_IF([test -n "$build"],      [ac_build_tool_prefix="$build-"],
--      [test -n "$build_alias"],[ac_build_tool_prefix="$build_alias-"])
--
--AC_LANG_PUSH([C])
- AC_PROG_CC
--_AC_COMPILER_EXEEXT
--_AC_COMPILER_OBJEXT
- AC_PROG_CPP
-+AC_EXEEXT
-+
-+ac_tool_prefix=$save_ac_tool_prefix
-+cross_compiling=$save_cross_compiling
- 
- dnl Restore the old definitions
- dnl
--popdef([cross_compiling])dnl
--popdef([am_cv_prog_cc_c_o])dnl
--popdef([am_cv_CC_dependencies_compiler_type])dnl
--popdef([ac_tool_prefix])dnl
-+popdef([ac_link])dnl
-+popdef([ac_compile])dnl
-+popdef([ac_cpp])dnl
- popdef([ac_cv_host_os])dnl
- popdef([ac_cv_host_vendor])dnl
- popdef([ac_cv_host_cpu])dnl
-@@ -104,33 +98,25 @@ popdef([host_vendor])dnl
- popdef([host_cpu])dnl
- popdef([host_alias])dnl
- popdef([host])dnl
--popdef([OBJEXT])dnl
- popdef([LDFLAGS])dnl
--popdef([EXEEXT])dnl
- popdef([CPPFLAGS])dnl
- popdef([CFLAGS])dnl
--popdef([GCC])dnl
- popdef([CPP])dnl
- popdef([CC])dnl
- popdef([ac_objext])dnl
- popdef([ac_exeext])dnl
- popdef([ac_cv_objext])dnl
- popdef([ac_cv_exeext])dnl
--popdef([ac_cv_c_compiler_gnu])dnl
- popdef([ac_cv_prog_cc_g])dnl
- popdef([ac_cv_prog_cc_cross])dnl
- popdef([ac_cv_prog_cc_works])dnl
--popdef([ac_cv_prog_cc_c89])dnl
- popdef([ac_cv_prog_gcc])dnl
- popdef([ac_cv_prog_CPP])dnl
- 
--dnl restore global variables ac_ext, ac_cpp, ac_compile,
--dnl ac_link, ac_compiler_gnu (dependant on the current
--dnl language after popping):
--AC_LANG_POP([C])
--
- dnl Finally, set Makefile variables
- dnl
-+BUILD_EXEEXT=$ac_build_exeext
-+BUILD_OBJEXT=$ac_build_objext
- AC_SUBST(BUILD_EXEEXT)dnl
- AC_SUBST(BUILD_OBJEXT)dnl
- AC_SUBST([CFLAGS_FOR_BUILD])dnl
-diff --git a/m4/ax_prog_cxx_for_build.m4 b/m4/ax_prog_cxx_for_build.m4
-index 4d976769f..17c19a89f 100644
---- a/m4/ax_prog_cxx_for_build.m4
-+++ b/m4/ax_prog_cxx_for_build.m4
-@@ -31,7 +31,7 @@
- #   and this notice are preserved. This file is offered as-is, without any
- #   warranty.
- 
--#serial 4
-+#serial 3
- 
- AU_ALIAS([AC_PROG_CXX_FOR_BUILD], [AX_PROG_CXX_FOR_BUILD])
- AC_DEFUN([AX_PROG_CXX_FOR_BUILD], [dnl
-@@ -49,7 +49,6 @@ pushdef([ac_cv_prog_cxx_cross], ac_cv_build_prog_cxx_cross)dnl
- pushdef([ac_cv_prog_cxx_g], ac_cv_build_prog_cxx_g)dnl
- pushdef([CXX], CXX_FOR_BUILD)dnl
- pushdef([CXXCPP], CXXCPP_FOR_BUILD)dnl
--pushdef([GXX], GXX_FOR_BUILD)dnl
- pushdef([CXXFLAGS], CXXFLAGS_FOR_BUILD)dnl
- pushdef([CPPFLAGS], CPPFLAGS_FOR_BUILD)dnl
- pushdef([CXXCPPFLAGS], CXXCPPFLAGS_FOR_BUILD)dnl
-@@ -63,25 +62,26 @@ pushdef([ac_cv_host_alias], ac_cv_build_alias)dnl
- pushdef([ac_cv_host_cpu], ac_cv_build_cpu)dnl
- pushdef([ac_cv_host_vendor], ac_cv_build_vendor)dnl
- pushdef([ac_cv_host_os], ac_cv_build_os)dnl
--pushdef([ac_tool_prefix], ac_build_tool_prefix)dnl
--pushdef([am_cv_CXX_dependencies_compiler_type], am_cv_build_CXX_dependencies_compiler_type)dnl
--pushdef([cross_compiling], cross_compiling_build)dnl
-+pushdef([ac_cxxcpp], ac_build_cxxcpp)dnl
-+pushdef([ac_compile], ac_build_compile)dnl
-+pushdef([ac_link], ac_build_link)dnl
- 
--cross_compiling_build=no
-+save_cross_compiling=$cross_compiling
-+save_ac_tool_prefix=$ac_tool_prefix
-+cross_compiling=no
-+ac_tool_prefix=
- 
--ac_build_tool_prefix=
--AS_IF([test -n "$build"],      [ac_build_tool_prefix="$build-"],
--      [test -n "$build_alias"],[ac_build_tool_prefix="$build_alias-"])
--
--AC_LANG_PUSH([C++])
- AC_PROG_CXX
- AC_PROG_CXXCPP
- 
-+ac_tool_prefix=$save_ac_tool_prefix
-+cross_compiling=$save_cross_compiling
-+
- dnl Restore the old definitions
- dnl
--popdef([cross_compiling])dnl
--popdef([am_cv_CXX_dependencies_compiler_type])dnl
--popdef([ac_tool_prefix])dnl
-+popdef([ac_link])dnl
-+popdef([ac_compile])dnl
-+popdef([ac_cxxcpp])dnl
- popdef([ac_cv_host_os])dnl
- popdef([ac_cv_host_vendor])dnl
- popdef([ac_cv_host_cpu])dnl
-@@ -103,10 +103,6 @@ popdef([ac_cv_prog_cxx_works])dnl
- popdef([ac_cv_prog_gxx])dnl
- popdef([ac_cv_prog_CXXCPP])dnl
- 
--dnl restore global variables (dependant on the current
--dnl language after popping):
--AC_LANG_POP([C++])
--
- dnl Finally, set Makefile variables
- dnl
- AC_SUBST([CXXFLAGS_FOR_BUILD])dnl

pkgs/applications/science/math/singular/vspace-MAX_PROCESS.patch

@@ -1,35 +0,0 @@
-diff --git a/kernel/GBEngine/kChinese.cc b/kernel/GBEngine/kChinese.cc
-index 829a66609..84655caf2 100644
---- a/kernel/GBEngine/kChinese.cc
-+++ b/kernel/GBEngine/kChinese.cc
-@@ -209,6 +209,8 @@ ideal id_ChineseRemainder_0(ideal *xx, number *q, int rl, const ring r)
-     return NULL;
-   }
-   int cpus=(int)(long)feOptValue(FE_OPT_CPUS);
-+  if (cpus>=vspace::internals::MAX_PROCESS)
-+    cpus=vspace::internals::MAX_PROCESS-1;
-   if ((cpus==1) || (2*cpus>=cnt))
-     /* at least 2 polys for each process, or switch to seriell version */
-     return id_ChineseRemainder(xx,q,rl,r);
-@@ -295,6 +297,8 @@ ideal id_Farey_0(ideal x, number N, const ring r)
- {
-   int cnt=IDELEMS(x)*x->nrows;
-   int cpus=(int)(long)feOptValue(FE_OPT_CPUS);
-+  if (cpus>=vspace::internals::MAX_PROCESS)
-+    cpus=vspace::internals::MAX_PROCESS-1;
-   if (2*cpus>=cnt) /* at least 2 polys for each process, 
-                      or switch to seriell version */
-     return id_Farey(x,N,r);
-diff --git a/kernel/GBEngine/kverify.cc b/kernel/GBEngine/kverify.cc
-index 909d84994..aa06d6624 100644
---- a/kernel/GBEngine/kverify.cc
-+++ b/kernel/GBEngine/kverify.cc
-@@ -176,6 +176,8 @@ BOOLEAN kVerify2(ideal F, ideal Q)
-   /*---------------------------------------------------------------------*/
-   BOOLEAN all_okay=TRUE;
-   int cpus=(int)(long)feOptValue(FE_OPT_CPUS);
-+  if (cpus>=vspace::internals::MAX_PROCESS)
-+    cpus=vspace::internals::MAX_PROCESS-1;
-   int parent_pid=getpid();
-   using namespace vspace;
-   vmem_init();

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

@@ -2,16 +2,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "glitter";
-  version = "1.5.12";
+  version = "1.5.13";
 
   src = fetchFromGitHub {
     owner = "milo123459";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-XQ3HLmT3sWjoHTxnOU9FSHbnCwitFH0tOOpT7WwTEPE=";
+    sha256 = "sha256-arHwIQXZYxwnFbyLoKQiv3gYHEN80DxbdaO4dM9ZBs8=";
   };
 
-  cargoSha256 = "sha256-V54Itj7/zUO1bp0y30TjV1mSo/oNJOxEofpSqrYz6xk=";
+  cargoSha256 = "sha256-d+DERHE8Nzre1MXNj4Cp9fcRkLPEC8hzh0SeTpS2C5A=";
 
   # tests require it to be in a git repository
   preCheck = ''

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

@@ -8,16 +8,16 @@ with lib;
 
 buildGoModule rec {
   pname = "gogs";
-  version = "0.12.3";
+  version = "0.12.4";
 
   src = fetchFromGitHub {
     owner = "gogs";
     repo = "gogs";
     rev = "v${version}";
-    sha256 = "0ix3mxy8cpqbx24qffbzyf5z88x7605icm7rk5n54r8bdsr7cckd";
+    sha256 = "sha256-t2aXRYCr54sqXwv6cJHDf1z1z94SqJM0WQRd2ejc7XY=";
   };
 
-  vendorSha256 = "0m0g4dsiq8p2ngsbjxfi3wff7x4xpm67qlhgcgf8b48mqai4d2gc";
+  vendorSha256 = "sha256-3dT5D+oDd0mpJp/cP53TQcRUkmqh6g3sRBWWAUqhaAo=";
 
   subPackages = [ "." ];
 

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

@@ -2,12 +2,12 @@
 
 stdenv.mkDerivation rec {
   pname = "got";
-  version = "0.64";
+  version = "0.66";
 
   src = fetchurl {
     url =
       "https://gameoftrees.org/releases/portable/got-portable-${version}.tar.gz";
-    sha256 = "1qigv8fnmiynrx6qrg28n2981a30n56nh3xbhmlpihl7fqxmg1sq";
+    sha256 = "13xrwndj80jix210fxkadivxyd1f5qavdrhxyl32n68xyv5xmkgg";
   };
 
   nativeBuildInputs = [ pkg-config ];

pkgs/applications/video/plex-media-player/default.nix

@@ -36,12 +36,16 @@ in mkDerivation rec {
 
   cmakeFlags = [ "-DCMAKE_BUILD_TYPE=RelWithDebInfo" "-DQTROOT=${qtbase}" ];
 
+  # plexmediaplayer currently segfaults under wayland
+  qtWrapperArgs = [ "--set" "QT_QPA_PLATFORM" "xcb" ];
+
   passthru.updateScript = ./update.sh;
 
   meta = with lib; {
     description = "Streaming media player for Plex";
     license = licenses.gpl2;
-    maintainers = with maintainers; [ ];
+    maintainers = with maintainers; [ b4dm4n ];
     homepage = "https://plex.tv";
+    mainProgram = "plexmediaplayer";
   };
 }

pkgs/applications/virtualization/cloud-hypervisor/default.nix

@@ -2,19 +2,22 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "cloud-hypervisor";
-  version = "20.2";
+  version = "21.0";
 
   src = fetchFromGitHub {
     owner = "cloud-hypervisor";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-yIp1p8GyBojWKmvFRZ/OeyF2bjlqYsuXUrYTVunYV8Y=";
+    sha256 = "00b0ij9sfv7zsrgwrcj2rzpy1z8bp0m0lmzjp433xzpcgcnzw3w5";
   };
 
   nativeBuildInputs = [ pkg-config ];
   buildInputs = [ openssl ] ++ lib.optional stdenv.isAarch64 dtc;
 
-  cargoSha256 = "sha256-s2u6e2JbukPo3pXYzQJXP5d2G213u1+1ke9gZFnB+5g=";
+  cargoSha256 = "0lf7bb468s2ic9vabx954i46605gf7c6064vvwqvz7djk30z0y0d";
+
+  # Integration tests require root.
+  cargoTestFlags = [ "--bins" ];
 
   meta = with lib; {
     homepage = "https://github.com/cloud-hypervisor/cloud-hypervisor";

pkgs/data/misc/ddccontrol-db/default.nix

@@ -8,13 +8,13 @@
 
 stdenv.mkDerivation rec {
   pname = "ddccontrol-db";
-  version = "20210812";
+  version = "20220119";
 
   src = fetchFromGitHub {
     owner = "ddccontrol";
     repo = "ddccontrol-db";
     rev = version;
-    sha256 = "sha256-dRqyjDC9yNkNOnYQ9fkWPlnyzSqIZ4zxZ2T7t8Bu9FE=";
+    sha256 = "sha256-8JJ6RG7yA1ssoYsvgDYp3/r+h1+rKnOwwoDhRx2brY8=";
   };
 
   preConfigure = ''

pkgs/data/themes/kwin-decorations/kde-rounded-corners/default.nix

@@ -0,0 +1,38 @@
+{ stdenv
+, fetchFromGitHub
+, cmake
+, extra-cmake-modules
+, wrapQtAppsHook
+, kwin
+, kdelibs4support
+, libepoxy
+, libXdmcp
+, lib
+}:
+
+stdenv.mkDerivation rec {
+  pname = "kde-rounded-corners";
+  version = "unstable-2021-11-06";
+
+  src = fetchFromGitHub {
+    owner = "matinlotfali";
+    repo = "KDE-Rounded-Corners";
+    rev = "8ad8f5f5eff9d1625abc57cb24dc484d51f0e1bd";
+    sha256 = "0xbskf7jd03d2invfz1nnfc82klzvc784snw539n4kn6c6rc381p";
+  };
+
+  postConfigure = ''
+    substituteInPlace cmake_install.cmake \
+      --replace "${kdelibs4support}" "$out"
+  '';
+
+  nativeBuildInputs = [ cmake extra-cmake-modules wrapQtAppsHook ];
+  buildInputs = [ kwin kdelibs4support libepoxy libXdmcp ];
+
+  meta = with lib; {
+    description = "Rounds the corners of your windows";
+    homepage = "https://github.com/matinlotfali/KDE-Rounded-Corners";
+    license = licenses.gpl3Only;
+    maintainers = with maintainers; [ flexagoon ];
+  };
+}

pkgs/development/interpreters/lunatic/default.nix

@@ -2,16 +2,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "lunatic";
-  version = "0.7.4";
+  version = "0.7.5";
 
   src = fetchFromGitHub {
     owner = "lunatic-solutions";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-RX8JarGpY6dhPGpvOX1FuUjirEPff0wGqLkGFxOa+bc=";
+    sha256 = "sha256-HqDrGoyYzdx8OTanlRd95L1wAtFeew7Xs2rZ7nK2Zus=";
   };
 
-  cargoSha256 = "sha256-UvrDqxaZSgUJ/a6abigTuiUOfw+C7UolBApt5kVR+yo=";
+  cargoSha256 = "sha256-t3EwVYrKx7dvUcSp0B1iUAklg7WdQDld/T0O1HgHw54=";
 
   nativeBuildInputs = [ cmake ];
 

pkgs/development/libraries/fflas-ffpack/default.nix

@@ -6,13 +6,13 @@ assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation rec {
   pname = "fflas-ffpack";
-  version = "2.4.3";
+  version = "2.5.0";
 
   src = fetchFromGitHub {
     owner = "linbox-team";
     repo = pname;
-    rev = version;
+    rev = "v${version}";
-    sha256 = "1ynbjd72qrwp0b4kpn0p5d7gddpvj8dlb5fwdxajr5pvkvi3if74";
+    sha256 = "sha256-Eztc2jUyKRVUiZkYEh+IFHkDuPIy+Gx3ZW/MsuOVaMc=";
   };
 
   checkInputs = [

pkgs/development/libraries/fplll/default.nix

@@ -1,6 +1,6 @@
 { lib, stdenv
 , fetchFromGitHub
-, fetchpatch
+, pkg-config
 , gettext
 , autoreconfHook
 , gmp
@@ -9,16 +9,17 @@
 
 stdenv.mkDerivation rec {
   pname = "fplll";
-  version = "5.3.2";
+  version = "5.4.1";
 
   src = fetchFromGitHub {
     owner = "fplll";
     repo = "fplll";
     rev = version;
-    sha256 = "00iyz218ywspizjiimrjdcqvdqmrsb2367zyy3vkmypnf9i9l680";
+    sha256 = "sha256-6Zde8/bPOQQ16DqhqrQuGXDrf5HQEn5lwxauvyBr4XQ=";
   };
 
   nativeBuildInputs = [
+    pkg-config
     gettext
     autoreconfHook
   ];

pkgs/development/libraries/givaro/default.nix

@@ -1,12 +1,12 @@
 { lib, stdenv, fetchFromGitHub, automake, autoconf, libtool, autoreconfHook, gmpxx }:
 stdenv.mkDerivation rec {
   pname = "givaro";
-  version = "4.1.1";
+  version = "4.2.0";
   src = fetchFromGitHub {
     owner = "linbox-team";
     repo = pname;
     rev = "v${version}";
-    sha256 = "11wz57q6ijsvfs5r82masxgr319as92syi78lnl9lgdblpc6xigk";
+    sha256 = "sha256-KR0WJc0CSvaBnPRott4hQJhWNBb/Wi6MIhcTExtVobQ=";
   };
 
   enableParallelBuilding = true;

pkgs/development/libraries/leatherman/default.nix

@@ -2,10 +2,10 @@
 
 stdenv.mkDerivation rec {
   pname = "leatherman";
-  version = "1.12.6";
+  version = "1.12.7";
 
   src = fetchFromGitHub {
-    sha256 = "sha256-k5Lt/NCSlBaTGhpR4T3Q4Ih+RR1xKROxz+RNYor7zaQ=";
+    sha256 = "sha256-a79/seKO6Efn6g4RWdqsP83pL5AIBAp1InjnMdOs3Qk=";
     rev = version;
     repo = "leatherman";
     owner = "puppetlabs";

pkgs/development/libraries/libamqpcpp/default.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "libamqpcpp";
-  version = "4.3.15";
+  version = "4.3.16";
 
   src = fetchFromGitHub {
     owner = "CopernicaMarketingSoftware";
     repo = "AMQP-CPP";
     rev = "v${version}";
-    sha256 = "sha256-S2/ecWC78Q4ihVLtDQ6DD8/qX1cDslnTjqd5IkKCjc4=";
+    sha256 = "sha256-aBLNdw9LhHFwnIt70vIYlX1/j2IUTmpm5Ub+ZImF8FI=";
   };
 
   buildInputs = [ openssl ];

pkgs/development/libraries/libtorrent-rasterbar/1.1.nix

@@ -46,5 +46,6 @@ in stdenv.mkDerivation {
     license = licenses.bsd3;
     maintainers = [ ];
     platforms = platforms.unix;
+    broken = stdenv.isDarwin; # never built on Hydra https://hydra.nixos.org/job/nixpkgs/trunk/libtorrent-rasterbar-1_1_x.x86_64-darwin
   };
 }

pkgs/development/libraries/linbox/default.nix

@@ -14,13 +14,13 @@ assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation rec {
   pname = "linbox";
-  version = "1.6.3"; # TODO: Check postPatch script on update
+  version = "1.7.0";
 
   src = fetchFromGitHub {
     owner = "linbox-team";
     repo = pname;
     rev = "v${version}";
-    sha256 = "10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571";
+    sha256 = "sha256-mW84a98KPLqcHMjX3LIYTmVe0ngUdz6RJLpoDaAqKU8=";
   };
 
   nativeBuildInputs = [
@@ -35,20 +35,6 @@ stdenv.mkDerivation rec {
     fflas-ffpack
   ];
 
-  patches = [
-    # Remove inappropriate `const &` qualifiers on data members that can be
-    # modified via member functions.
-    # See also: https://github.com/linbox-team/linbox/pull/256
-    ./patches/linbox-pr256-part2.patch # TODO: Remove on 1.7.0 update
-  ];
-
-  postPatch = ''
-    # Remove @LINBOXSAGE_LIBS@ that is actually undefined.
-    # See also: https://github.com/linbox-team/linbox/pull/249
-    # TODO: Remove on 1.7.0 update
-    find . -type f -exec sed -e 's/@LINBOXSAGE_LIBS@//' -i {} \;
-  '';
-
   configureFlags = [
     "--with-blas-libs=-lblas"
     "--disable-optimization"

pkgs/development/libraries/linbox/patches/linbox-pr256-part2.patch

@@ -1,13 +0,0 @@
---- a/linbox/algorithms/det-rational.h
-+++ b/linbox/algorithms/det-rational.h
-@@ -79,8 +79,8 @@
- 	struct MyRationalModularDet {
- 		const Blackbox &A;
- 		const MyMethod &M;
--		const Integer &mul;//multiplicative prec;
--		const Integer ÷
-+		Integer mul;//multiplicative prec;
-+		Integer div;
- 
- 		MyRationalModularDet(const Blackbox& b, const MyMethod& n,
- 				     const Integer & p1, const Integer & p2) :

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

@@ -1,94 +1,38 @@
 { lib, stdenv
-, fetchurl
+, autoreconfHook
-, fetchpatch
+, gengetopt
+, pkg-config
+, fetchFromGitLab
 , pari
 }:
 
 stdenv.mkDerivation rec {
-  version = "1.23";
+  version = "2.0.5";
   pname = "lcalc";
 
-  src = fetchurl {
+  src = fetchFromGitLab {
-    # original at http://oto.math.uwaterloo.ca/~mrubinst/L_function_public/CODE/L-${version}.tar.gz, no longer available
+    owner = "sagemath";
-    # "newer" version at google code https://code.google.com/archive/p/l-calc/source/default/source
+    repo = pname;
-    url = "mirror://sageupstream/lcalc/lcalc-${version}.tar.bz2";
+    rev = version;
-    sha256 = "1c6dsdshgxhqppjxvxhp8yhpxaqvnz3d1mlh26r571gkq8z2bm43";
+    sha256 = "sha256-RxWZ7T0I9zV7jUVnL6jV/PxEoU32KY7Q1UsOL5Lonuc=";
   };
 
-  preConfigure = "cd src";
+  nativeBuildInputs = [
+    autoreconfHook
+    gengetopt
+    pkg-config
+  ];
 
   buildInputs = [
     pari
   ];
 
-  patches = [
+  configureFlags = [
-    # Port to newer pari
+    "--with-pari"
-    (fetchpatch {
-      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/lcalc/patches/pari-2.7.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
-      sha256 = "1x3aslldm8njjm7p9g9s9w2c91kphnci2vpkxkrcxfihw3ayss6c";
-    })
-
-    # Uncomment the definition of lcalc_to_double(const long double& x).
-    # (Necessary for GCC >= 4.6.0, cf. https://trac.sagemath.org/ticket/10892)
-    (fetchpatch {
-      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/lcalc/patches/Lcommon.h.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
-      sha256 = "0g4ybvsrcv48rmlh1xjnkms19jp25k58azv6ds1f2cm34hxs8fdx";
-    })
-
-    # Include also <time.h> in Lcommandline_numbertheory.h (at least required
-    # on Cygwin, cf. https://trac.sagemath.org/ticket/9845)
-    (fetchpatch {
-      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/lcalc/patches/time.h.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
-      sha256 = "1brf04n11kkc43ylagf8dm32j5r2g9zv51dp5wag1mpm4p04l7cl";
-    })
-
-    # Fix for gcc >4.6
-    (fetchpatch {
-      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/lcalc/patches/lcalc-1.23_default_parameters_1.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
-      sha256 = "0i2yvxm5fx4z0v6m4srgh8rj98kijmlvyirlxf1ky0bp2si6bpka";
-    })
-
-    # gcc 5.1
-    (fetchpatch {
-      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/lcalc/patches/lcalc-1.23_default_parameters_2.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
-      sha256 = "0dqwmxpm9wb53qbypsyfkgsvk2f8nf67sydphd4dkc2vw4yz6vlh";
-    })
-
-    # based on gentoos makefile patch -- fix paths, adhere to flags
-    ./makefile.patch
-
-    # (fetchpatch {
-    #   name = "default-double.patch";
-    #   url = "https://github.com/dimpase/lcalc/pull/1/commits/0500c67b6aa1f492715591669f6647c8f7a3ea59.patch";
-    #   sha256 = "0dqwmxpm9wb53qbypsyfkgsvk2f8nf67sydphd4dkc2vw4yz6vla";
-    # })
-
-    (fetchpatch {
-      name = "c++11.patch";
-      url = "https://raw.githubusercontent.com/archlinux/svntogit-community/3607b97df5a8c231191115b0cb5c62426b339e71/trunk/lcalc-c++11.patch";
-      sha256 = "1ccrl61lv2vvx8ggldq54m5d0n1iy6mym7qz0i8nj6yj0dshnpk3";
-    })
-  ] ++ lib.optional stdenv.isDarwin
-  (fetchpatch {
-    url = "https://git.sagemath.org/sage.git/plain/build/pkgs/lcalc/patches/clang.patch";
-    sha256 = "0bb7656z6cp6i4p2qj745cmq0lhh52v2akl9whi760dynfdxbl18";
-  });
-
-  postPatch = lib.optionalString stdenv.isDarwin ''
-    substituteInPlace src/Makefile --replace g++ c++
-  '';
-
-  installFlags = [
-    "DESTDIR=$(out)"
-  ];
-
-  makeFlags = [
-    "PARI_DEFINE=-DINCLUDE_PARI"
-    "PARI_PREFIX=${pari}"
   ];
 
   meta = with lib; {
-    homepage = "http://oto.math.uwaterloo.ca/~mrubinst/L_function_public/L.html";
+    homepage = "https://gitlab.com/sagemath/lcalc";
     description = "A program for calculating with L-functions";
     license = with licenses; [ gpl2 ];
     maintainers = teams.sage.members;

pkgs/development/libraries/science/math/lcalc/makefile.patch

@@ -1,113 +0,0 @@
-diff --git a/src/Makefile b/src/Makefile
-index 84e4e88..56ca676 100644
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -58,7 +58,7 @@ ifeq ($(G5),TRUE)
-    #MACHINE_SPECIFIC_FLAGS = -mpowerpc -mpowerpc64 -m64
- endif
- 
--CCFLAGS =  -Wa,-W -O3 $(OPENMP_FLAG) -Wno-deprecated $(PREPROCESSOR_DEFINE) $(MACHINE_SPECIFIC_FLAGS) $(EXTRA)
-+CCFLAGS = $(CXXFLAGS) $(OPENMP_FLAG) $(PREPROCESSOR_DEFINE) $(MACHINE_SPECIFIC_FLAGS)
- #CCFLAGS =  -Wa,-W -O3 $(OPENMP_FLAG)  $(PREPROCESSOR_DEFINE) $(MACHINE_SPECIFIC_FLAGS) $(EXTRA)
- #CCFLAGS =  -Wa,-W -O2 -fno-exceptions -Wno-deprecated $(PREPROCESSOR_DEFINE) $(MACHINE_SPECIFIC_FLAGS) $(EXTRA)
- 
-@@ -68,12 +68,12 @@ CCFLAGS =  -Wa,-W -O3 $(OPENMP_FLAG) -Wno-deprecated $(PREPROCESSOR_DEFINE) $(MA
- 
- ifeq ($(PARI_DEFINE),-DINCLUDE_PARI)
-     #location of pari.h.
--    LOCATION_PARI_H = /usr/local/include/pari #usual location
-+    LOCATION_PARI_H = $(PARI_PREFIX)/include/pari #usual location
- 
-     #location of libpari.a or of libpari.so
-     #depending on whether static or dynamic libraries are being used.
-     #On mac os x it's the former, on linux I think usually the latter.
--    LOCATION_PARI_LIBRARY = /usr/local/lib #usual location
-+    LOCATION_PARI_LIBRARY = $(PARI_PREFIX)/lib #usual location
- else
-     #supplied as a dummy so as to avoid more ifeq's below
-     LOCATION_PARI_H = .
-@@ -89,24 +89,24 @@ INCLUDEFILES= -I../include
- 
- ifeq ($(OS_NAME),Darwin)
-     LDFLAGS2 =
--    DYN_OPTION=dynamiclib
-+    DYN_OPTION=-dynamiclib
- else
--    LDFLAGS1 = -Xlinker -export-dynamic #not sure why pari calls these when linking but on the web I found
-+    LDFLAGS1 = #not sure why pari calls these when linking but on the web I found
-     #'Libtool provides the `-export-dynamic' link flag (see section Link mode), which does this declaration.
-     #You need to use this flag if you are linking a shared library that will be dlopened'
-     #see notes below
-     #ifeq ($(PARI_DEFINE),-DINCLUDE_PARI)
--       LDFLAGS2 = $(LDFLAGS1) -Xlinker -rpath -Xlinker $(LOCATION_PARI_LIBRARY)
-+       LDFLAGS2 = $(LDFLAGS)
-     #else
-     #    LDFLAGS2 = $(LDFLAGS1)
-     #endif
--    DYN_OPTION=shared
-+    DYN_OPTION=$(LDFLAGS) -shared -Wl,-soname,libLfunction.so
- endif
- 
- ifeq ($(PARI_DEFINE),-DINCLUDE_PARI)
--    LDFLAGS = $(LDFLAGS2) -L$(LOCATION_PARI_LIBRARY) -lpari
-+    MYLDFLAGS = $(LDFLAGS2) -L$(LOCATION_PARI_LIBRARY) -lpari
- else
--    LDFLAGS = $(LDFLAGS2)
-+    MYLDFLAGS = $(LDFLAGS2)
- endif
- 
- 
-@@ -129,7 +129,8 @@ endif
- #become clear which libraries the computer can find.
- 
- 
--INSTALL_DIR= /usr/local
-+INSTALL_DIR= $(DESTDIR)
-+LIB_DIR ?=lib
- 
- #object files for the libLfunction library
- OBJ_L = Lglobals.o Lgamma.o Lriemannsiegel.o Lriemannsiegel_blfi.o Ldokchitser.o
-@@ -141,9 +142,8 @@ OBJECTS = $(OBJ3)
- 
- all:
- #	make print_vars
--	make libLfunction.so
--	make lcalc
--	make examples
-+	${MAKE} libLfunction.so
-+	${MAKE} lcalc
- #	make find_L
- #	make test
- 
-@@ -151,7 +151,7 @@ print_vars:
- 	@echo OS_NAME = $(OS_NAME)
- 
- lcalc: $(OBJECTS)
--	$(CC) $(CCFLAGS) $(INCLUDEFILES) $(OBJECTS) $(LDFLAGS) -o lcalc $(GMP_FLAGS)
-+	$(CC) $(CCFLAGS) $(INCLUDEFILES) $(OBJECTS) $(MYLDFLAGS) -o lcalc $(GMP_FLAGS)
- 
- examples:
- 	$(CC) $(CCFLAGS) $(INCLUDEFILES) example_programs/example.cc libLfunction.so -o example_programs/example $(GMP_FLAGS)
-@@ -262,15 +262,18 @@ Lcommandline.o: ../include/Lcommandline_values_zeros.h
- 
- 
- libLfunction.so: $(OBJ_L)
--	g++ -$(DYN_OPTION)  -o libLfunction.so $(OBJ_L)
-+	g++ $(DYN_OPTION) -o libLfunction.so $(OBJ_L)
- 
- clean:
- 	rm -f *.o lcalc libLfunction.so example_programs/example
- 
- install:
--	cp -f lcalc $(INSTALL_DIR)/bin/.
--	cp -f libLfunction.so $(INSTALL_DIR)/lib/.
--	cp -rf ../include $(INSTALL_DIR)/include/Lfunction
-+	install -d $(INSTALL_DIR)/bin
-+	install -d $(INSTALL_DIR)/$(LIB_DIR)
-+	install -d $(INSTALL_DIR)/include/Lfunction
-+	install lcalc $(INSTALL_DIR)/bin
-+	install libLfunction.so $(INSTALL_DIR)/$(LIB_DIR)
-+	install -m 644 -t $(INSTALL_DIR)/include/Lfunction ../include/*.h
- 
- 
- SRCS = Lcommandline.cc Lcommandline_elliptic.cc Lcommandline_globals.cc Lcommandline_misc.cc Lcommandline_numbertheory.cc Lcommandline_twist.cc Lcommandline_values_zeros.cc Lgamma.cc Lglobals.cc Lmisc.cc Lriemannsiegel.cc Lriemannsiegel_blfi.cc cmdline.c

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

@@ -15,6 +15,14 @@ stdenv.mkDerivation rec {
     sha256 = "sha256-/Cb/HkD4UQ9gXsRpvRiEuQBoRd0THxNHsBaAAa+CqQo=";
   };
 
+  cmakeFlags = [
+    "-DBUILD_STATIC_LIBS=OFF"
+    "-DBUILD_SHARED_LIBS=ON"
+    "-DBUILD_TESTS=ON"
+    "-DBUILD_PRIMECOUNT=ON"
+    "-DBUILD_LIBPRIMESIEVE=ON"
+  ];
+
   meta = with lib; {
     description = "Fast prime counting function implementations";
     homepage = "https://github.com/kimwalisch/primecount";

pkgs/development/libraries/sofia-sip/default.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "sofia-sip";
-  version = "1.13.6";
+  version = "1.13.7";
 
   src = fetchFromGitHub {
     owner = "freeswitch";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0b1gq499ksgsi16f5nf3dzbj6s8knwkiak5j810jzdfm7vkm0vvm";
+    sha256 = "sha256-gBejwt5YAkCKQh0vzN00J4y1ifcdc4TglA+SqEevaGQ=";
   };
 
   buildInputs = [ glib openssl ] ++ lib.optional stdenv.isDarwin SystemConfiguration;

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

@@ -1,24 +1,44 @@
-{ lib, fetchPypi, buildPythonPackage, docutils, six, sphinx, isPy3k, isPy27 }:
+{ lib
+, buildPythonPackage
+, docutils
+, fetchFromGitHub
+, pytestCheckHook
+, pythonOlder
+, sphinx
+}:
 
 buildPythonPackage rec {
-  version = "4.31.0";
   pname = "breathe";
-  disabled = isPy27;
+  version = "4.32.0";
+  format = "setuptools";
 
-  src = fetchPypi {
+  disabled = pythonOlder "3.7";
-    inherit pname version;
+
-    sha256 = "925eeff96c6640cd857e4ddeae6f75464a1d5e2e08ee56dccce4043583ae2050";
+  src = fetchFromGitHub {
+    owner = "michaeljones";
+    repo = pname;
+    rev = "v${version}";
+    hash = "sha256-U85iLVS6bmA2Ty0AC4z2qODy9u4rWg6Nb42/k2Ix+kk=";
   };
 
-  propagatedBuildInputs = [ docutils six sphinx ];
+  propagatedBuildInputs = [
+    docutils
+    sphinx
+  ];
 
-  doCheck = !isPy3k;
+  checkInputs = [
+    pytestCheckHook
+  ];
 
-  meta = {
+  pythonImportsCheck = [
-    homepage = "https://github.com/michaeljones/breathe";
+    "breathe"
-    license = lib.licenses.bsd3;
+  ];
+
+  meta = with lib; {
     description = "Sphinx Doxygen renderer";
+    homepage = "https://github.com/michaeljones/breathe";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ ];
     inherit (sphinx.meta) platforms;
   };
 }
-

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

@@ -6,11 +6,11 @@
 
 buildPythonPackage rec {
   pname = "django-reversion";
-  version = "4.0.1";
+  version = "4.0.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "6991f16e5d3a972912db3d56e3a714d10b07becd566ab87f85f2e9b671981339";
+    sha256 = "sha256-XTO6lE2/GccDDJ5w43MSSK40Nozyr+3hDg0I+/ieb4w=";
   };
 
   # tests assume the availability of a mysql/postgresql database

pkgs/development/python-modules/flask-paginate/default.nix

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "flask-paginate";
-  version = "2021.12.28";
+  version = "2022.1.8";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "c722a25067d722483e24cde16ed987a822292ca758a213299e445694d2b5b587";
+    sha256 = "a32996ec07ca004c45b768b0d50829728ab8f3986c0650ef538e42852c7aeba2";
   };
 
   propagatedBuildInputs = [ flask ];

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

@@ -1,6 +1,5 @@
 { lib
 , fetchFromGitHub
-, fetchpatch
 , buildPythonPackage
 , pkgconfig
 , gmp
@@ -15,29 +14,15 @@
 
 buildPythonPackage rec {
   pname = "fpylll";
-  version = "0.5.1dev";
+  version = "0.5.6";
 
   src = fetchFromGitHub {
     owner = "fplll";
     repo = "fpylll";
     rev = version;
-    sha256 = "15vdfgx448mr1nf054h7lr2j3dd35fsfhikqzrh9zsng8n12hxa5";
+    sha256 = "sha256-Bxcc0941+pl2Uzam48qe+PFlcBWsJ0rDYZxrxIYQpEA=";
   };
 
-  patches = [
-    # two patches to fix the testsuite on aarch64 (https://github.com/fplll/fpylll/issues/162)
-    (fetchpatch {
-      url = "https://github.com/fplll/fpylll/commit/d5809a8fdb86b2693b1fa94e655bbbe4ad80e286.patch";
-      name = "less-precision-in-tests.patch";
-      sha256 = "0vkvi25nwwvk5r4a4xmkbf060di4hjq32bys75l2hsaysxmk93nz";
-    })
-    (fetchpatch {
-      url = "https://github.com/fplll/fpylll/commit/b5b146a010d50da219a313adc4b6f7deddcc146b.patch";
-      name = "dont-hardcode-precision.patch";
-      sha256 = "1rsbwh90i1j5p2rp6jd5n25v1jzw1n8728fzz1lhb91zmk0hlxc9";
-    })
-  ];
-
   buildInputs = [
     gmp
     pari

pkgs/development/python-modules/httpx-socks/default.nix

@@ -20,7 +20,7 @@
 
 buildPythonPackage rec {
   pname = "httpx-socks";
-  version = "0.7.2";
+  version = "0.7.3";
   format = "setuptools";
 
   disabled = pythonOlder "3.6";
@@ -29,7 +29,7 @@ buildPythonPackage rec {
     owner = "romis2012";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1wigmkhn4ymfr12z9vhdaimjcma9llicwrr29q0cc8xmy23f3445";
+    sha256 = "11wnhx9nfsg5lsnlgh33zngyhc2klichpfrkwajbbyq95fdqj8ri";
   };
 
   propagatedBuildInputs = [

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

@@ -10,14 +10,14 @@
 
 buildPythonPackage rec {
   pname = "jc";
-  version = "1.18.1";
+  version = "1.18.2";
   disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "kellyjonbrazil";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0xzx32fnm39w916z8wm387ry480rbf7n9qppc18bjdv4jjwgf2rw";
+    sha256 = "sha256-5GGY23MDsUbSC2tYGVqwwtFi5vnSldozMR4HuY+h+l4=";
   };
 
   propagatedBuildInputs = [ ruamel-yaml xmltodict pygments ];

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

@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "manimpango";
-  version = "0.4.0.post1";
+  version = "0.4.0.post2";
 
   src = fetchFromGitHub {
     owner = "ManimCommunity";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1in9ibis91rlqmd7apbdp9c8y1mgnpm5bg6ldad8whx62nkkvwa3";
+    sha256 = "sha256-BMRlEdvJJOUbsvKEoZx2qJqHSbL475dhBthUpnsXkn4=";
   };
 
   postPatch = ''

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

@@ -4,11 +4,11 @@
 
 buildPythonPackage rec {
   pname = "mautrix";
-  version = "0.14.6";
+  version = "0.14.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "46a87a8ee9e45e90c72e17ebb75190073e773f0890cfde7b81b0a36e15caec5d";
+    sha256 = "sha256-P4yibI2KQQtIK8G28rkutaaMejiygZY1l/EjTl9Mju8=";
   };
 
   propagatedBuildInputs = [

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

@@ -6,11 +6,11 @@
 
 buildPythonPackage rec {
   pname = "nameparser";
-  version = "1.1.0";
+  version = "1.1.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "bbd4831c72426757ec59674a1aad29c40bf411358a6d6e1cdd68002cbcb90d08";
+    sha256 = "sha256-zoM27XRk+nubh0X0i5xi3qa+2TG5lxXKlHk2BUSZIUM=";
   };
 
   LC_ALL="en_US.UTF-8";

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

@@ -25,11 +25,11 @@
 
 buildPythonPackage rec {
   pname = "papermill";
-  version = "2.3.3";
+  version = "2.3.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "349aecd526c15c39f73a08df836467e2fead877c474d82c7df349f27ad272525";
+    sha256 = "be12d2728989c0ae17b42fcb05b623500004e94b34f56bd153355ccebb84a59a";
   };
 
   propagatedBuildInputs = [

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

@@ -25,7 +25,7 @@
 
 buildPythonPackage rec {
   pname = "pikepdf";
-  version = "4.4.0";
+  version = "4.4.1";
   disabled = ! isPy3k;
 
   src = fetchFromGitHub {
@@ -38,7 +38,7 @@ buildPythonPackage rec {
     extraPostFetch = ''
       rm "$out/.git_archival.txt"
     '';
-    hash = "sha256-AfHqKcb+ejEmY53irbIv9+1fPEczMgd7/VaFt01cNUs=";
+    hash = "sha256-8yYqyXz4ZqZxsk2Ka8S0rDsHaqO4l6cZTyNuVQuHkew=";
   };
 
   patches = [

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

@@ -11,7 +11,7 @@
 
 buildPythonPackage rec {
   pname = "pipx";
-  version = "0.17.0";
+  version = "1.0.0";
 
   disabled = pythonOlder "3.6";
 
@@ -20,7 +20,7 @@ buildPythonPackage rec {
     owner = "pipxproject";
     repo = pname;
     rev = version;
-    sha256 = "sha256-vR/tKV+ZB0nZaxEcB83dwoSI7kBC1rA+6fo30rizroM=";
+    sha256 = "1sgfrlhci2m83k436dfwfmqjpb8hij6yypm03pm3n8drmr2aaa4s";
   };
 
   propagatedBuildInputs = [

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

@@ -0,0 +1,33 @@
+{ lib
+, fetchPypi
+, buildPythonPackage
+, primecount
+, cython
+, cysignals
+}:
+
+buildPythonPackage rec {
+  pname = "primecountpy";
+  version = "0.1.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "78fe7cc32115f0669a45d7c90faaf39f7ce3939e39e2e7e5f14c17fe4bff0676";
+  };
+
+  buildInputs = [ primecount ];
+
+  propagatedBuildInputs = [ cython cysignals ];
+
+  # depends on pytest-cython for "pytest --doctest-cython"
+  doCheck = false;
+
+  pythonImportsCheck = [ "primecountpy" ];
+
+  meta = with lib; {
+    description = "Cython interface for C++ primecount library";
+    homepage = "https://github.com/dimpase/primecountpy/";
+    maintainers = teams.sage.members;
+    license = licenses.gpl3Only;
+  };
+}

pkgs/development/python-modules/pycryptodome-test-vectors/default.nix

@@ -5,12 +5,12 @@
 
 buildPythonPackage rec {
   pname = "pycryptodome-test-vectors";
-  version = "1.0.4";
+  version = "1.0.6";
   format = "setuptools";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-2+ZL8snmaB0tNxGZRbUM6SdfXZf4CM0nh3/wTOu9R50=";
+    hash = "sha256-oNfIVm7wyhgU9pgDhdP6BVJehuEw4d238GDaYMuAYLQ=";
     extension = "zip";
   };
 

pkgs/development/python-modules/python-lsp-black/default.nix

@@ -9,14 +9,14 @@
 
 buildPythonPackage rec {
   pname = "python-lsp-black";
-  version = "1.0.1";
+  version = "1.1.0";
   disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "python-lsp";
     repo = "python-lsp-black";
     rev = "v${version}";
-    sha256 = "03k32m4jfqfzrawj69yxhk9kwzsdcwginip77kxdbra2xwgqfc3w";
+    sha256 = "sha256-WIQf1oz3b1PLIcXfQsu4hQ58nfp7l3J7zkcWNT6RbUY=";
   };
 
   checkInputs = [ pytestCheckHook ];

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

@@ -18,11 +18,11 @@
 
 buildPythonPackage rec {
   pname = "pywlroots";
-  version = "0.15.3";
+  version = "0.15.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sCHeiD6KugHZLtxcVcLggdHC1gqCxStuHy1065TbGiY=";
+    sha256 = "Cyj3B9uK1RoIuStCO+z9/bq7RjTPdjTqVhfc+tCRofo=";
   };
 
   # The XWayland detection uses some hard-coded FHS paths. Since we

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

@@ -13,7 +13,7 @@
 
 buildPythonPackage rec {
   pname = "seatconnect";
-  version = "1.1.3";
+  version = "1.1.4";
   format = "setuptools";
 
   disabled = pythonOlder "3.8";
@@ -22,7 +22,7 @@ buildPythonPackage rec {
     owner = "farfar";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-EOaFZch/C9N4lacZ4IqIJUVSaEn8wOFN/WN6WOL/1mo=";
+    sha256 = "sha256-NA/UiapJ/SyUmrj9hd2xGV5WWy1KhxwQtqGLV73TfHk=";
   };
 
   SETUPTOOLS_SCM_PRETEND_VERSION = version;

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

@@ -13,12 +13,12 @@
 
 buildPythonPackage rec {
   pname = "tablib";
-  version = "3.1.0";
+  version = "3.2.0";
   disabled = isPy27;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "d64c9f6712918a3d90ec5d71b44b8bab1083e3609e4844ad2be80eb633e097ed";
+    sha256 = "12d8686454c721de88d8ca5adf07e1f419ef6dbcecedf65e8950d4a329daf3a0";
   };
 
   nativeBuildInputs = [ setuptools-scm ];

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

@@ -9,13 +9,13 @@
 
 python3Packages.buildPythonPackage rec {
   pname = "timetagger";
-  version = "22.1.3";
+  version = "22.1.4";
 
   src = fetchFromGitHub {
     owner = "almarklein";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1x0hy9wnifi694glwv6irhnjvwh1kgl6wn6qlk5qy4x6z6bkii24";
+    sha256 = "sha256-aOA/2SqvTpXtkURyJ2vf5gGqPpy5reN7/2zUUdaJvyA=";
   };
 
   propagatedBuildInputs = with python3Packages; [

pkgs/development/python-modules/types-setuptools/default.nix

@@ -5,12 +5,12 @@
 
 buildPythonPackage rec {
   pname = "types-setuptools";
-  version = "57.4.7";
+  version = "57.4.8";
   format = "setuptools";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sha256-lnfZabAOwcFFUvW+KytHpvvqTQ7U3g/c7hir2qDMkmc=";
+    sha256 = "sha256-1VRfKrPa0k9cscAbp0way3QHqzGyYY1CMVj8hAhRYPE=";
   };
 
   # Module doesn't have tests

pkgs/development/python-modules/zeroc-ice/default.nix

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "zeroc-ice";
-  version = "3.7.6";
+  version = "3.7.7";
 
   src = fetchPypi {
     inherit version pname;
-    sha256 = "e8d8a7828e4994545bf57059bd0a0d431d387d31cc4af2eb5eeb93ef28c2d827";
+    sha256 = "415f4a673009fe9a5ef67b61c4469ddf14b73857b6d40f02d6b74f02ad935147";
   };
 
   buildInputs = [ openssl bzip2 ];

pkgs/development/tools/air/default.nix

@@ -2,16 +2,16 @@
 
 buildGoModule rec {
   pname = "air";
-  version = "1.27.8";
+  version = "1.27.9";
 
   src = fetchFromGitHub {
     owner = "cosmtrek";
     repo = "air";
     rev = "v${version}";
-    sha256 = "sha256-CVx4TDDAVIrJ3lnD2AIuxhmTV+/sIA0viX20zFkznNc=";
+    sha256 = "sha256-8VuCZoAV54TG8MiF6n5O8ZStGujfJ/7w95BYhe5/7dE=";
   };
 
-  vendorSha256 = "sha256-dloXz1hiKAQUmSQv1rLbE5vYrZpKAcwakC71AFXWZqM=";
+  vendorSha256 = "sha256-gUZPX1ymyzf0IuCpK8Nsq2UKPV5f9SAReJ6YxgpxpqE=";
 
   subPackages = [ "." ];
 

pkgs/development/tools/database/dbmate/default.nix

@@ -2,16 +2,16 @@
 
 buildGoModule rec {
   pname = "dbmate";
-  version = "1.12.1";
+  version = "1.13.0";
 
   src = fetchFromGitHub {
     owner = "amacneil";
     repo = "dbmate";
     rev = "v${version}";
-    sha256 = "sha256-XNxy8CnhO3rQi3VHr7nikFNXvY2eM30jR0ngNc0FV3E=";
+    sha256 = "sha256-j7u8TidiuaA5SbXoD+p23wwTsePi6/hzNdVS5IJMEh0=";
   };
 
-  vendorSha256 = "sha256-Qe3fwyEf/NiGmUSha/zZHRBR1okw2vE97u7tybqiWNI=";
+  vendorSha256 = "sha256-GEJ8n0VN9Qt73dRj7Qjx1DAomSy+hQEH74Dx2h/hv9M=";
 
   doCheck = false;
 

pkgs/development/tools/doctl/default.nix

@@ -2,7 +2,7 @@
 
 buildGoModule rec {
   pname = "doctl";
-  version = "1.68.0";
+  version = "1.69.0";
 
   vendorSha256 = null;
 
@@ -31,7 +31,7 @@ buildGoModule rec {
     owner = "digitalocean";
     repo = "doctl";
     rev = "v${version}";
-    sha256 = "sha256-3W6jDMT4UUtSND9bJJEexQ9LrqxL4oZtpucdcM1McdE=";
+    sha256 = "sha256-Bm6Xrgp/6/NpIndCVRDamKndBbCANnW5j3vOVRVxnE4=";
   };
 
   meta = with lib; {

pkgs/development/tools/earthly/default.nix

@@ -2,16 +2,16 @@
 
 buildGoModule rec {
   pname = "earthly";
-  version = "0.6.2";
+  version = "0.6.4";
 
   src = fetchFromGitHub {
     owner = "earthly";
     repo = "earthly";
     rev = "v${version}";
-    sha256 = "sha256-a2NNpQvbhMY66nbk4RAXFb/o1qR5OXPm93ujzS2cxp4=";
+    sha256 = "sha256-QrlxH9ihWAVzf9lh3CcVCqFPLmn7bM2pNZUqxnHD2WA=";
   };
 
-  vendorSha256 = "sha256-0wyefhY/KR79K9DDI4/8EaA/DFI1rf6wxsBIAZo+rUI=";
+  vendorSha256 = "sha256-pI5aBBUJoAmeJ2Kr0eqP9O/tGhgHCBjINL3406LQ9Dc=";
 
   ldflags = [
     "-s" "-w"

pkgs/development/tools/esbuild/default.nix

@@ -2,13 +2,13 @@
 
 buildGoModule rec {
   pname = "esbuild";
-  version = "0.14.11";
+  version = "0.14.13";
 
   src = fetchFromGitHub {
     owner = "evanw";
     repo = "esbuild";
     rev = "v${version}";
-    sha256 = "sha256-hS+LJfYB+nH5z/UA6RKdqA8qc1jT9Gskt6LufHCiqv8=";
+    sha256 = "sha256-DBu6j8UjbRVMoT0j/WwtVlJ+k3VwVKFbX2tdUs0neDs=";
   };
 
   vendorSha256 = "sha256-QPkBR+FscUc3jOvH7olcGUhM6OW4vxawmNJuRQxPuGs=";

pkgs/development/tools/frugal/default.nix

@@ -2,13 +2,13 @@
 
 buildGoModule rec {
   pname = "frugal";
-  version = "3.14.12";
+  version = "3.14.13";
 
   src = fetchFromGitHub {
     owner = "Workiva";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-2fXefYvcclcxMeX6JtHjoVNRwJTsUAhxet646BDPHic=";
+    sha256 = "sha256-apX4MFzeR7+5gWauw5HXPK0c7N4uTSqkE2vqnYB5LJs=";
   };
 
   subPackages = [ "." ];

pkgs/development/tools/ginkgo/default.nix

@@ -2,13 +2,13 @@
 
 buildGoModule rec {
   pname = "ginkgo";
-  version = "2.0.0";
+  version = "2.1.0";
 
   src = fetchFromGitHub {
     owner = "onsi";
     repo = "ginkgo";
     rev = "v${version}";
-    sha256 = "sha256-a3AZ/7UfB9qjMK9yWHSaBRnDA/5FmIGGxXAvNhcfKCc=";
+    sha256 = "sha256-GF96AOyQcVI01dP6yqMwyPmXMDRVxrScu1UL76jF2qA=";
   };
   vendorSha256 = "sha256-kMQ60HdsorZU27qoOY52DpwFwP+Br2bp8mRx+ZwnQlI=";
   doCheck = false;

pkgs/development/tools/java/visualvm/default.nix

@@ -1,12 +1,12 @@
 { stdenv, fetchzip, lib, makeWrapper, makeDesktopItem, jdk, gawk }:
 
 stdenv.mkDerivation rec {
-  version = "2.1.1";
+  version = "2.1.2";
   pname = "visualvm";
 
   src = fetchzip {
     url = "https://github.com/visualvm/visualvm.src/releases/download/${version}/visualvm_${builtins.replaceStrings ["."] [""]  version}.zip";
-    sha256 = "sha256-LXMPdzIOFPzFUx3uufx+2UeJ6mg/9kJXGews4KU3rrU=";
+    sha256 = "sha256-khbXzdsC0PA10HEu/dIFQ87+QbKpctmTUTt/zEuxV6c=";
   };
 
   desktopItem = makeDesktopItem {

pkgs/development/tools/rust/cargo-make/default.nix

@@ -13,11 +13,11 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "cargo-make";
-  version = "0.35.7";
+  version = "0.35.8";
 
   src = fetchCrate {
     inherit pname version;
-    sha256 = "sha256-rMeaKzCGY9jRrw8GaGtgm1rg3FIdaX/P+bOZRAtAI/s=";
+    sha256 = "sha256-YNPAIdN9FDUHs/5aCYJN+1/12ZYk1YJsUjjB1a09KvA=";
   };
 
   nativeBuildInputs = [ pkg-config ];
@@ -25,7 +25,7 @@ rustPlatform.buildRustPackage rec {
   buildInputs = [ openssl ]
     ++ lib.optionals stdenv.isDarwin [ Security SystemConfiguration libiconv ];
 
-  cargoSha256 = "sha256-ZXQM2ij9Cpa5WCEHhcDc/tThfKZ7s1URmYsmqRg73m0=";
+  cargoSha256 = "sha256-xLFBF8fEbupLgFNdYC1NzM6p7O2gvsv0Utk4Et2oBDc=";
 
   # Some tests fail because they need network access.
   # However, Travis ensures a proper build.

pkgs/development/tools/wasm-bindgen-cli/default.nix

@@ -12,14 +12,14 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "wasm-bindgen-cli";
-  version = "0.2.78";
+  version = "0.2.79";
 
   src = fetchCrate {
     inherit pname version;
-    sha256 = "sha256-5s+HidnVfDV0AXA+/YcXNGVjv/E9JeK0Ttng4mCVX8M=";
+    sha256 = "sha256-3kWhhzYmIo/GFieI0i7XVJIZxIaaJHHuDp38k5xcFmI=";
   };
 
-  cargoSha256 = "sha256-CbtjUFwowP/QqyAMCzmUiSib4EpRhQAmO4ekX00xYGE=";
+  cargoSha256 = "sha256-xKYdvcrx3a9AKiRU8yJ3JNQp1Q2pEufwo+in82yTV6c=";
 
   nativeBuildInputs = [ pkg-config ];
 

pkgs/games/openttd/nml.nix

@@ -2,13 +2,13 @@
 
 python3Packages.buildPythonApplication rec {
   pname = "openttd-nml";
-  version = "0.5.3";
+  version = "0.6.1";
 
   src = fetchFromGitHub {
     owner = "OpenTTD";
     repo = "nml";
     rev = version;
-    sha256 = "0kfnkshff3wrxsj1wpfbbw2mmgww2q80v63p5d2pp1f38x8j33w9";
+    sha256 = "0z0n4lqvnqigfjjhmmz7mvis7iivd4a8d287ya2yscfg5hznnqh2";
   };
 
   propagatedBuildInputs = with python3Packages; [ply pillow];

pkgs/games/osu-lazer/default.nix

@@ -13,13 +13,13 @@
 
 buildDotnetModule rec {
   pname = "osu-lazer";
-  version = "2021.1225.0";
+  version = "2022.118.0";
 
   src = fetchFromGitHub {
     owner = "ppy";
     repo = "osu";
     rev = version;
-    sha256 = "sha256-kN5pR37b0giKGJVnJo/Mce+MWFwZiY+mZAHG/fUt0O4=";
+    sha256 = "sha256-/BzoLiQLiBcWqThzDOVb4Y7s6WhcKnCRRhAzUi5Jstk=";
   };
 
   projectFile = "osu.Desktop/osu.Desktop.csproj";

pkgs/games/osu-lazer/deps.nix

@@ -1,12 +1,12 @@
 { fetchNuGet }: [
-  (fetchNuGet { pname = "AutoMapper"; version = "10.1.1"; sha256 = "1l1p9g7f7finr8laklbm7h2c45k0swl47iq0ik68js5s6pzvd6f8"; })
+  (fetchNuGet { pname = "AutoMapper"; version = "11.0.0"; sha256 = "1ni9mmrqfbspwf7xz6by5415ci5zhg15z3f7596qqpmbn8bqg7wq"; })
   (fetchNuGet { pname = "DeltaCompressionDotNet"; version = "2.0.0.0"; sha256 = "0zhj7m3zaf9wcg51385in9qg1xgkvp8yyzgq3r5k4sagm7y68aqy"; })
   (fetchNuGet { pname = "DiffPlex"; version = "1.7.0"; sha256 = "09a8hkbx99iwikfl8war629945yv7i8llj9480dbc4kyp6qqlr00"; })
   (fetchNuGet { pname = "DiscordRichPresence"; version = "1.0.175"; sha256 = "180sax976327d70qbinv07f65g3w2zbw80n49hckg8wd4rw209vd"; })
   (fetchNuGet { pname = "FFmpeg.AutoGen"; version = "4.3.0.1"; sha256 = "0n6x57mnnvcjnrs8zyvy07h5zm4bcfy9gh4n4bvd9fx5ys4pxkvv"; })
   (fetchNuGet { pname = "Fody"; version = "6.6.0"; sha256 = "0cx708ah61cxmvpaq040mhqwrv937rvlmskwihg1w118729k9yv0"; })
   (fetchNuGet { pname = "HidSharpCore"; version = "1.2.1.1"; sha256 = "1zkndglmz0s8rblfhnqcvv90rkq2i7lf4bc380g7z8h1avf2ikll"; })
-  (fetchNuGet { pname = "HtmlAgilityPack"; version = "1.11.39"; sha256 = "05rlw9h3ps1gx4pwdxjwpx1lajyvj1b35j3536ixfmnnvjx4v2yj"; })
+  (fetchNuGet { pname = "HtmlAgilityPack"; version = "1.11.40"; sha256 = "0k1cpkfgz4v5qigvmmvlk8lv2a731kqkmx6acf3rzr8rlj3cfnc4"; })
   (fetchNuGet { pname = "Humanizer"; version = "2.13.14"; sha256 = "155g2700x6sbym2jd4dshm4rf3jjr8flx6w9xnw28zrrv7r2rdy8"; })
   (fetchNuGet { pname = "Humanizer.Core"; version = "2.13.14"; sha256 = "1ni4mcyhcs46ih9b8c8l3xq3iai56rdlcw0afwhji3hxwbxqbk7i"; })
   (fetchNuGet { pname = "Humanizer.Core"; version = "2.2.0"; sha256 = "08mzg65y9d3zvq16rsmpapcdan71ggq2mpks6k777h3wlm2sh3p5"; })
@@ -156,14 +156,14 @@
   (fetchNuGet { pname = "OpenTabletDriver"; version = "0.5.3.1"; sha256 = "16xw8w943x9gvnnpbryahff5azzy8n26j2igyqgv88m352jd9rb8"; })
   (fetchNuGet { pname = "OpenTabletDriver.Plugin"; version = "0.5.3.1"; sha256 = "17dxsvcz9g8kzydk5xlfz9kfxl62x9wi20609rh76wjd881bg1br"; })
   (fetchNuGet { pname = "ppy.LocalisationAnalyser"; version = "2021.1210.0"; sha256 = "0dn6fc31yllr5nizylvkfl2b603b5m9694nsn5mmkh8w43h0rkbq"; })
-  (fetchNuGet { pname = "ppy.osu.Framework"; version = "2021.1225.0"; sha256 = "1md0zsjwi8zx2az42cch1wgvb5ygscncmpc4ysgz1pl6jn02v3by"; })
+  (fetchNuGet { pname = "ppy.osu.Framework"; version = "2022.118.0"; sha256 = "1c81r8s9zivj9hany0yqsza1y3nhh24zbkwwnjm0m6z4mls04l1y"; })
   (fetchNuGet { pname = "ppy.osu.Framework.NativeLibs"; version = "2021.1221.0"; sha256 = "1ffxp4nsgbqw1f6nypirmc0a3h203qikbmxm2x8w3kgcfga5dx3k"; })
-  (fetchNuGet { pname = "ppy.osu.Game.Resources"; version = "2021.1215.0"; sha256 = "1aarb8wkzz31xa8fa6g5axwmvx89ix66ygbqq7zcyz8k9yy2ilh1"; })
+  (fetchNuGet { pname = "ppy.osu.Game.Resources"; version = "2022.115.0"; sha256 = "0w2hnci93644ayfpgpsyxsifz38yklvn42fkgd860i3mn04lyl2z"; })
   (fetchNuGet { pname = "ppy.osuTK.NS20"; version = "1.0.187"; sha256 = "0ididsxn3005dvs0hvx7bz2xzjsfpa8kmnyfqq4c2ybjxlx15gkw"; })
   (fetchNuGet { pname = "ppy.SDL2-CS"; version = "1.0.486-alpha"; sha256 = "0hp6wfjgpwdgy1ag2bpjkyalw92k6qg9pc5mriij6a5vhxzadhk3"; })
   (fetchNuGet { pname = "ppy.squirrel.windows"; version = "1.9.0.5"; sha256 = "0nmhrg3q6izapfpwdslq80fqkvjj12ad9r94pd0nr2xx1zw0x1zl"; })
-  (fetchNuGet { pname = "Realm"; version = "10.7.1"; sha256 = "058jigmsxvzb7571ll9qkf0hwmgff5zddfq4pqvnzkf87i5kd2kq"; })
+  (fetchNuGet { pname = "Realm"; version = "10.8.0"; sha256 = "1ixpms8x9z5ia9yiqvhmgdlcrjvqrhbqnr8b9z6mlxwcms1z2f45"; })
-  (fetchNuGet { pname = "Realm.Fody"; version = "10.7.1"; sha256 = "1m3cglh39fr84pr3nr7q1hyiq83gqj0m6h8m79wl96g5xxq5v6pa"; })
+  (fetchNuGet { pname = "Realm.Fody"; version = "10.8.0"; sha256 = "0hj3cqan96y01k5qgs0knkqzg3rlr2794az68xqffd2vqphvqvqq"; })
   (fetchNuGet { pname = "Remotion.Linq"; version = "2.2.0"; sha256 = "1y46ni0xswmmiryp8sydjgryafwn458dr91f9xn653w73kdyk4xf"; })
   (fetchNuGet { pname = "runtime.debian.8-x64.runtime.native.System.Security.Cryptography.OpenSsl"; version = "4.3.0"; sha256 = "16rnxzpk5dpbbl1x354yrlsbvwylrq456xzpsha1n9y3glnhyx9d"; })
   (fetchNuGet { pname = "runtime.fedora.23-x64.runtime.native.System.Security.Cryptography.OpenSsl"; version = "4.3.0"; sha256 = "0hkg03sgm2wyq8nqk6dbm9jh5vcq57ry42lkqdmfklrw89lsmr59"; })
@@ -185,7 +185,7 @@
   (fetchNuGet { pname = "runtime.ubuntu.14.04-x64.runtime.native.System.Security.Cryptography.OpenSsl"; version = "4.3.0"; sha256 = "160p68l2c7cqmyqjwxydcvgw7lvl1cr0znkw8fp24d1by9mqc8p3"; })
   (fetchNuGet { pname = "runtime.ubuntu.16.04-x64.runtime.native.System.Security.Cryptography.OpenSsl"; version = "4.3.0"; sha256 = "15zrc8fgd8zx28hdghcj5f5i34wf3l6bq5177075m2bc2j34jrqy"; })
   (fetchNuGet { pname = "runtime.ubuntu.16.10-x64.runtime.native.System.Security.Cryptography.OpenSsl"; version = "4.3.0"; sha256 = "1p4dgxax6p7rlgj4q73k73rslcnz4wdcv8q2flg1s8ygwcm58ld5"; })
-  (fetchNuGet { pname = "Sentry"; version = "3.12.1"; sha256 = "1bqldqc0bnrxdgfxh71w3vjf3cygcn6jyrhxmjvikciirlgcs3cz"; })
+  (fetchNuGet { pname = "Sentry"; version = "3.13.0"; sha256 = "0wnivy7rhzghr94pdczv7kw72y1hv5kp6hw0fkmw1nfgnsh4qjfm"; })
   (fetchNuGet { pname = "SharpCompress"; version = "0.17.1"; sha256 = "1ffiacghbcnr3fkgvdcad7b1nky54nhmmn2sm43sks9zm8grvva4"; })
   (fetchNuGet { pname = "SharpCompress"; version = "0.30.1"; sha256 = "1hib2hxjrlikwsczym1qn2slaapgjw8qzd8gmid8bryaz8hv044h"; })
   (fetchNuGet { pname = "SharpFNT"; version = "2.0.0"; sha256 = "1bgacgh9hbck0qvji6frbb50sdiqfdng2fvvfgfw8b9qaql91mx0"; })
@@ -276,7 +276,6 @@
   (fetchNuGet { pname = "System.Reflection.Emit"; version = "4.0.1"; sha256 = "0ydqcsvh6smi41gyaakglnv252625hf29f7kywy2c70nhii2ylqp"; })
   (fetchNuGet { pname = "System.Reflection.Emit"; version = "4.3.0"; sha256 = "11f8y3qfysfcrscjpjym9msk7lsfxkk4fmz9qq95kn3jd0769f74"; })
   (fetchNuGet { pname = "System.Reflection.Emit"; version = "4.6.0"; sha256 = "18h375q5bn9h7swxnk4krrxym1dxmi9bm26p89xps9ygrj4q6zqw"; })
-  (fetchNuGet { pname = "System.Reflection.Emit"; version = "4.7.0"; sha256 = "121l1z2ypwg02yz84dy6gr82phpys0njk7yask3sihgy214w43qp"; })
   (fetchNuGet { pname = "System.Reflection.Emit.ILGeneration"; version = "4.0.1"; sha256 = "1pcd2ig6bg144y10w7yxgc9d22r7c7ww7qn1frdfwgxr24j9wvv0"; })
   (fetchNuGet { pname = "System.Reflection.Emit.ILGeneration"; version = "4.3.0"; sha256 = "0w1n67glpv8241vnpz1kl14sy7zlnw414aqwj4hcx5nd86f6994q"; })
   (fetchNuGet { pname = "System.Reflection.Emit.Lightweight"; version = "4.0.1"; sha256 = "1s4b043zdbx9k39lfhvsk68msv1nxbidhkq6nbm27q7sf8xcsnxr"; })

pkgs/games/vassal/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "VASSAL";
-  version = "3.6.1";
+  version = "3.6.4";
 
   src = fetchzip {
     url = "https://github.com/vassalengine/vassal/releases/download/${version}/${pname}-${version}-linux.tar.bz2";
-    sha256 = "sha256-elcSwm7KvDpGVBF7Gs6GFreQPyVwWBxYN0NO1N6JWDM=";
+    sha256 = "sha256-WUEpYxzNcH9kJRn4nROoaeXTe1+D4/0VRqTwc7ac1hc=";
   };
 
   nativeBuildInputs = [ makeWrapper ];

pkgs/misc/emulators/vice/default.nix

@@ -25,11 +25,11 @@
 
 stdenv.mkDerivation rec {
   pname = "vice";
-  version = "3.6";
+  version = "3.6.1";
 
   src = fetchurl {
     url = "mirror://sourceforge/vice-emu/vice-${version}.tar.gz";
-    sha256 = "sha256-Zb/lXM5ifbm1oKx4dqkMCH6f6G6fVRfoCURsQGSi0/0=";
+    sha256 = "sha256-IN+EyFGq8vUABRCSf20xsy8mmRbTUUZcNm3Ar8ncFQw=";
   };
 
   nativeBuildInputs = [

pkgs/misc/vscode-extensions/default.nix

@@ -243,8 +243,8 @@ let
         mktplcRef = {
           name = "vscode-pylance";
           publisher = "MS-python";
-          version = "2020.11.2";
+          version = "2022.1.5";
-          sha256 = "0n2dm21vgzir3hx1m3pmx7jq4zy3hdxfsandd2wv5da4fs9b5g50";
+          sha256 = "1b5ihrac9xsq35a39vlq7krr1ffqpdjxdlhv9s056hs033kayazl";
         };
 
         buildInputs = [ nodePackages.pyright ];