NixOS · Nov 4, 2018 · Nov 7, 2018 · Nov 7, 2018 · Nov 7, 2018 · Nov 7, 2018
diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix
@@ -39,7 +39,19 @@ stdenv.mkDerivation rec {
     ./patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch
   ];
 
-  packageUpgradePatches = [
+  packageUpgradePatches = let
+    # fetch a diff between base and rev on sage's git server
+    # used to fetch trac tickets by setting the base to the release and the
+    # revision to the last commit that should be included
+    fetchSageDiff = { base, rev, ...}@args: (
+      fetchpatch ({
+        url = "https://git.sagemath.org/sage.git/patch?id2=${base}&id=${rev}";
+        # We don't care about sage's own build system (which builds all its dependencies).
+        # Exclude build system changes to avoid conflicts.
+        excludes = [ "build/*" ];
+      } // builtins.removeAttrs args [ "rev" "base" ])
+    );
+  in [
     # New glpk version has new warnings, filter those out until upstream sage has found a solution
     # https://trac.sagemath.org/ticket/24824
     ./patches/pari-stackwarn.patch # not actually necessary since tha pari upgrade, but necessary for the glpk patch to apply
@@ -65,6 +77,21 @@ stdenv.mkDerivation rec {
       url = "https://git.sagemath.org/sage.git/patch/?id=30cc778d46579bd0c7537ed33e8d7a4f40fd5c31";
       sha256 = "13vc2q799dh745sm59xjjabllfj0sfjzcacf8k59kwj04x755d30";
     })
+
+    # https://trac.sagemath.org/ticket/26326
+    # needs to be split because there is a merge commit in between
+    (fetchSageDiff {
+      name = "networkx-2.2-1.patch";
+      base = "8.4";
+      rev = "68f5ad068184745b38ba6716bf967c8c956c52c5";
+      sha256 = "112b5ywdqgyzgvql2jj5ss8la9i8rgnrzs8vigsfzg4shrcgh9p6";
+    })
+    (fetchSageDiff {
+      name = "networkx-2.2-2.patch";
+      base = "626485bbe5f33bf143d6dfba4de9c242f757f59b~1";
+      rev = "db10d327ade93711da735a599a67580524e6f7b4";
+      sha256 = "09v87id25fa5r9snfn4mv79syhc77jxfawj5aizmdpwdmpgxjk1f";
+    })
   ];
 
   patches = nixPatches ++ packageUpgradePatches ++ [

diff --git a/pkgs/applications/window-managers/i3/default.nix b/pkgs/applications/window-managers/i3/default.nix
@@ -5,11 +5,11 @@
 
 stdenv.mkDerivation rec {
   name = "i3-${version}";
-  version = "4.15";
+  version = "4.16";
 
   src = fetchurl {
     url = "https://i3wm.org/downloads/${name}.tar.bz2";
-    sha256 = "09jk70hsdxab24lqvj2f30ijrkbv3f6q9xi5dcsax1dw3x6m4z91";
+    sha256 = "1d2mnryn7m9c6d69awd7lwzadliapd0ahi5n8d0ppqy533ssaq6c";
   };
 
   nativeBuildInputs = [ which pkgconfig makeWrapper ];

diff --git a/pkgs/development/python-modules/autologging/default.nix b/pkgs/development/python-modules/autologging/default.nix
@@ -0,0 +1,19 @@
+{ stdenv, buildPythonPackage, fetchPypi }:
+
+buildPythonPackage rec {
+  pname = "Autologging";
+  version = "1.2.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "16v2k16m433fxlvl7f0081n67rpxhs2hyn1ivkx1xs5qjxpv5n3k";
+    extension = "zip";
+  };
+
+  meta = with stdenv.lib; {
+    homepage = http://ninthtest.info/python-autologging/;
+    description = "Easier logging and tracing for Python classes";
+    license = licenses.mit;
+    maintainers = with maintainers; [ twey ];
+  };
+}
diff --git a/pkgs/development/python-modules/networkx/default.nix b/pkgs/development/python-modules/networkx/default.nix
@@ -7,12 +7,13 @@
 
 buildPythonPackage rec {
   pname = "networkx";
-  version = "2.1";
+  # upgrade may break sage, please test the sage build or ping @timokau on upgrade
+  version = "2.2";
 
   src = fetchPypi {
     inherit pname version;
     extension = "zip";
-    sha256 = "64272ca418972b70a196cb15d9c85a5a6041f09a2f32e0d30c0255f25d458bb1";
+    sha256 = "12swxb15299v9vqjsq4z8rgh5sdhvpx497xwnhpnb0gynrx6zra5";
   };
 
   checkInputs = [ nose ];

diff --git a/pkgs/development/tools/vagrant/default.nix b/pkgs/development/tools/vagrant/default.nix
@@ -1,11 +1,11 @@
-{ lib, fetchurl, buildRubyGem, bundlerEnv, ruby, libarchive, writeText }:
+{ lib, fetchurl, buildRubyGem, bundlerEnv, ruby, libarchive, writeText, withLibvirt ? true, libvirt, pkgconfig }:
 
 let
   # NOTE: bumping the version and updating the hash is insufficient;
   # you must use bundix to generate a new gemset.nix in the Vagrant source.
-  version = "2.1.2";
+  version = "2.2.0";
   url = "https://github.com/hashicorp/vagrant/archive/v${version}.tar.gz";
-  sha256 = "0fb90v43d30whhyjlgb9mmy93ccbpr01pz97kp5hrg3wfd7703b1";
+  sha256 = "1wa8l3j6hpy0m0snz7wvfcf0wsjikp22c2z29crpk10f7xl7c56b";
 
   deps = bundlerEnv rec {
     name = "${pname}-${version}";
@@ -15,15 +15,15 @@ let
     inherit ruby;
     gemfile = writeText "Gemfile" "";
     lockfile = writeText "Gemfile.lock" "";
-    gemset = lib.recursiveUpdate (import ./gemset.nix) {
+    gemset = lib.recursiveUpdate (import ./gemset.nix) ({
       vagrant = {
         source = {
           type = "url";
           inherit url sha256;
         };
         inherit version;
       };
-    };
+    } // lib.optionalAttrs withLibvirt (import ./gemset_libvirt.nix));
   };
 
 in buildRubyGem rec {
@@ -35,6 +35,8 @@ in buildRubyGem rec {
   dontBuild = false;
   src = fetchurl { inherit url sha256; };
 
+  buildInputs = lib.optional withLibvirt [ libvirt pkgconfig ];
+
   patches = [
     ./unofficial-installation-nowarn.patch
     ./use-system-bundler-version.patch
@@ -45,7 +47,12 @@ in buildRubyGem rec {
   postInstall = ''
     wrapProgram "$out/bin/vagrant" \
       --set GEM_PATH "${deps}/lib/ruby/gems/${ruby.version.libDir}" \
-      --prefix PATH ':' "${lib.getBin libarchive}/bin"
+      --prefix PATH ':' "${lib.getBin libarchive}/bin" \
+      ${lib.optionalString withLibvirt ''
+        --prefix PATH ':' "${pkgconfig}/bin" \
+        --prefix PKG_CONFIG_PATH ':' \
+          "${lib.makeSearchPath "lib/pkgconfig" [ libvirt ]}"
+      ''}
   '';
 
   installCheckPhase = ''

diff --git a/pkgs/development/tools/vagrant/gemset.nix b/pkgs/development/tools/vagrant/gemset.nix
@@ -70,10 +70,10 @@
   ffi = {
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0zw6pbyvmj8wafdc7l5h7w20zkp1vbr2805ql5d941g2b20pk4zr";
+      sha256 = "0jpm2dis1j7zvvy3lg7axz9jml316zrn7s0j59vyq3qr127z0m7q";
       type = "gem";
     };
-    version = "1.9.23";
+    version = "1.9.25";
   };
   gssapi = {
     dependencies = ["ffi"];
@@ -172,18 +172,18 @@
     dependencies = ["mime-types-data"];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0087z9kbnlqhci7fxh9f6il63hj1k02icq2rs0c6cppmqchr753m";
+      sha256 = "0fjxy1jm52ixpnv3vg9ld9pr9f35gy0jp66i1njhqjvmnvq0iwwk";
       type = "gem";
     };
-    version = "3.1";
+    version = "3.2.2";
   };
   mime-types-data = {
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "04my3746hwa4yvbx1ranhfaqkgf6vavi1kyijjnw8w3dy37vqhkm";
+      sha256 = "07wvp0aw2gjm4njibb70as6rh5hi1zzri5vky1q6jx95h8l56idc";
       type = "gem";
     };
-    version = "3.2016.0521";
+    version = "3.2018.0812";
   };
   multi_json = {
     source = {
@@ -214,10 +214,10 @@
   net-ssh = {
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "07c4v97zl1daabmri9zlbzs6yvkl56z1q14bw74d53jdj0c17nhx";
+      sha256 = "0qfanf71yv8w7yl9l9wqcy68i2x1ghvnf8m581yy4pl0anfdhqw8";
       type = "gem";
     };
-    version = "4.2.0";
+    version = "5.0.2";
   };
   netrc = {
     source = {
@@ -238,10 +238,10 @@
   public_suffix = {
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0mvzd9ycjw8ydb9qy3daq3kdzqs2vpqvac4dqss6ckk4rfcjc637";
+      sha256 = "08q64b5br692dd3v0a9wq9q5dvycc6kmiqmjbdxkxbfizggsvx6l";
       type = "gem";
     };
-    version = "3.0.1";
+    version = "3.0.3";
   };
   rake = {
     source = {
@@ -358,10 +358,10 @@
   rubyzip = {
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "06js4gznzgh8ac2ldvmjcmg9v1vg9llm357yckkpylaj6z456zqz";
+      sha256 = "1n1lb2sdwh9h27y244hxzg1lrxxg2m53pk1vq7p33bna003qkyrj";
       type = "gem";
     };
-    version = "1.2.1";
+    version = "1.2.2";
   };
   safe_yaml = {
     source = {
@@ -397,19 +397,28 @@
     version = "0.0.7.5";
   };
   vagrant = {
-    dependencies = ["childprocess" "erubis" "hashicorp-checkpoint" "i18n" "listen" "log4r" "net-scp" "net-sftp" "net-ssh" "rb-kqueue" "rest-client" "ruby_dep" "wdm" "winrm" "winrm-elevated" "winrm-fs"];
+    dependencies = ["childprocess" "erubis" "hashicorp-checkpoint" "i18n" "listen" "log4r" "net-scp" "net-sftp" "net-ssh" "rb-kqueue" "rest-client" "ruby_dep" "rubyzip" "vagrant_cloud" "wdm" "winrm" "winrm-elevated" "winrm-fs"];
   };
   vagrant-spec = {
     dependencies = ["childprocess" "log4r" "rspec" "thor"];
     source = {
       fetchSubmodules = false;
-      rev = "9413ab298407114528766efefd1fb1ff24589636";
-      sha256 = "1z77m3p6x82hipa7y4i71zafy0rdfajw2vhqdxczjmrlwp0pvisl";
+      rev = "abfc34474d122235d56e4c6b6fb5d3e35bedfa90";
+      sha256 = "08xy2c82lrxkwjlvrbx1v32968a6psni3952y3knriqgygv2kzbn";
       type = "git";
       url = "https://github.com/hashicorp/vagrant-spec.git";
     };
     version = "0.0.1";
   };
+  vagrant_cloud = {
+    dependencies = ["rest-client"];
+    source = {
+      remotes = ["https://rubygems.org"];
+      sha256 = "0k325a1cblj3jd2av8a6j3xsjjm36g578gpbmxw7h5dbffp49il1";
+      type = "gem";
+    };
+    version = "2.0.1";
+  };
   wdm = {
     source = {
       remotes = ["https://rubygems.org"];
@@ -431,10 +440,10 @@
     dependencies = ["builder" "erubis" "gssapi" "gyoku" "httpclient" "logging" "nori" "rubyntlm"];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "02lzbixdbjvhmb0byqx9rl9x4xx9pqc8jwm7y6mmp7w7mri72zh6";
+      sha256 = "05c1xji4afwxx4vgim5n4nj62zbyppmm67ci3kwi0jjrqaj9y11q";
       type = "gem";
     };
-    version = "2.2.3";
+    version = "2.3.0";
   };
   winrm-elevated = {
     dependencies = ["winrm" "winrm-fs"];
@@ -449,9 +458,9 @@
     dependencies = ["erubis" "logging" "rubyzip" "winrm"];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1i3w2j2rmhjqj8lynca2m1dm1m5fv1x35xwhk3vyr15dn260z56g";
+      sha256 = "12g9grzp03knh1nxcicnm93pmlf4r264lhvl5yviyri8swmqlbz5";
       type = "gem";
     };
-    version = "1.2.0";
+    version = "1.3.1";
   };
 }
diff --git a/pkgs/development/tools/vagrant/gemset_libvirt.nix b/pkgs/development/tools/vagrant/gemset_libvirt.nix
@@ -0,0 +1,19 @@
+{
+  mini_portile2 = {
+    source = {
+      remotes = ["https://rubygems.org"];
+      sha256 = "0gzfmcywp1da8nzfqsql2zqi648mfnx6qwkig3cv36n9m0yy676y";
+      type = "gem";
+    };
+    version = "2.3.0";
+  };
+  nokogiri = {
+    dependencies = ["mini_portile2"];
+      source = {
+        remotes = ["https://rubygems.org"];
+        sha256 = "0byyxrazkfm29ypcx5q4syrv126nvjnf7z6bqi01sqkv4llsi4qz";
+        type = "gem";
+      };
+    version = "1.8.5";
+  };
+}
diff --git a/pkgs/servers/mail/dovecot/default.nix b/pkgs/servers/mail/dovecot/default.nix
@@ -34,13 +34,6 @@ stdenv.mkDerivation rec {
   postInstall = ''
     cp -r $out/$out/* $out
     rm -rf $out/$(echo "$out" | cut -d "/" -f2)
-  '' + lib.optionalString stdenv.isDarwin ''
-    install_name_tool -change libclucene-shared.1.dylib \
-        ${clucene_core_2}/lib/libclucene-shared.1.dylib \
-        $out/lib/dovecot/lib21_fts_lucene_plugin.so
-    install_name_tool -change libclucene-core.1.dylib \
-        ${clucene_core_2}/lib/libclucene-core.1.dylib \
-        $out/lib/dovecot/lib21_fts_lucene_plugin.so
   '';
 
   patches = [

diff --git a/pkgs/tools/networking/ip2unix/default.nix b/pkgs/tools/networking/ip2unix/default.nix
@@ -4,13 +4,13 @@
 
 stdenv.mkDerivation rec {
   name = "ip2unix-${version}";
-  version = "1.1.0";
+  version = "1.1.1";
 
   src = fetchFromGitHub {
     owner = "nixcloud";
     repo = "ip2unix";
     rev = "v${version}";
-    sha256 = "11scvwbnwivvsp2c9vfwzgmd3gprnhj9y170594bc3iisbdlj69k";
+    sha256 = "0lw4f1p1frfpf5l7faqdd80d6pi9g5sx7g3wpmig9sa50k6pmc0v";
   };
 
   nativeBuildInputs = [

diff --git a/pkgs/tools/security/pcsclite/default.nix b/pkgs/tools/security/pcsclite/default.nix
@@ -3,13 +3,13 @@
 
 stdenv.mkDerivation rec {
   name = "pcsclite-${version}";
-  version = "1.8.23";
+  version = "1.8.24";
 
   outputs = [ "bin" "out" "dev" "doc" "man" ];
 
   src = fetchurl {
     url = "https://pcsclite.apdu.fr/files/pcsc-lite-${version}.tar.bz2";
-    sha256 = "1jc9ws5ra6v3plwraqixin0w0wfxj64drahrbkyrrwzghqjjc9ss";
+    sha256 = "0s3mv6csbi9303vvis0hilm71xsmi6cqkbh2kiipdisydbx6865q";
   };
 
   patches = [ ./no-dropdir-literals.patch ];

diff --git a/pkgs/top-level/haskell-packages.nix b/pkgs/top-level/haskell-packages.nix
@@ -119,11 +119,6 @@ in {
       ghc = bh.compiler.ghc822;
       compilerConfig = callPackage ../development/haskell-modules/configuration-ghc-8.2.x.nix { };
     };
-    ghc843 = callPackage ../development/haskell-modules {
-      buildHaskellPackages = bh.packages.ghc843;
-      ghc = bh.compiler.ghc843;
-      compilerConfig = callPackage ../development/haskell-modules/configuration-ghc-8.4.x.nix { };
-    };
     ghc844 = callPackage ../development/haskell-modules {
       buildHaskellPackages = bh.packages.ghc844;
       ghc = bh.compiler.ghc844;

diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
@@ -202,6 +202,8 @@ in {
 
   autograd = callPackage ../development/python-modules/autograd { };
 
+  autologging = callPackage ../development/python-modules/autologging { };
+
   automat = callPackage ../development/python-modules/automat { };
 
   awkward = callPackage ../development/python-modules/awkward { };

diff --git a/pkgs/top-level/release.nix b/pkgs/top-level/release.nix
@@ -66,7 +66,7 @@ let
               jobs.inkscape.x86_64-darwin
               # jobs.gimp.x86_64-darwin
               jobs.emacs.x86_64-darwin
-              # jobs.wireshark.x86_64-darwin
+              jobs.wireshark.x86_64-darwin
               jobs.transmission-gtk.x86_64-darwin
 
               # Tests