Merge branch 'staging-next'

The failure diff seems good-enough on Hydra now.

3 files changed, 126 insertions, 163 deletions

diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index f3679f497d5e..c21a0c41eba8 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -4491,6 +4491,8 @@ with pkgs;
 
   padthv1 = callPackage ../applications/audio/padthv1 { };
 
+  pagmo2 = callPackage ../development/libraries/pagmo2 { };
+
   pakcs = callPackage ../development/compilers/pakcs {};
 
   pal = callPackage ../tools/misc/pal { };
@@ -8831,7 +8833,7 @@ with pkgs;
 
   grabserial = callPackage ../development/tools/grabserial { };
 
-  mypy = python3Packages.mypy;
+  mypy = with python3Packages; toPythonApplication mypy;
 
   ### DEVELOPMENT / LIBRARIES
 
diff --git a/pkgs/top-level/perl-packages.nix b/pkgs/top-level/perl-packages.nix
index 3623e7511238..51d1a1c2215e 100644
--- a/pkgs/top-level/perl-packages.nix
+++ b/pkgs/top-level/perl-packages.nix
@@ -133,7 +133,7 @@ let
       url = "mirror://cpan/authors/id/M/MD/MDOOTSON/${name}.tar.gz";
       sha256 = "0jg2dmkzhj03f6b0vmv597yryfw9cclsdn9ynvvlrzzgpd5lw8jk";
     };
-    propagatedBuildInputs = [ pkgs.pkgconfig pkgs.gtk2 pkgs.wxGTK ModulePluggable ];
+    propagatedBuildInputs = [ pkgs.pkgconfig pkgs.gtk2 pkgs.wxGTK30 ModulePluggable ];
     buildInputs = [ LWPProtocolHttps ];
   };
 
@@ -215,7 +215,7 @@ let
       url = "mirror://cpan/authors/id/M/MS/MSCHOUT/${name}.tar.gz";
       sha256 = "58daeb3e44c681ff88f8fb00e4aabaa7a40cbee73dbdb84fcf6c285b15d357bd";
     };
-    buildInputs = [ ApacheTest URI ];
+    buildInputs = [ ApacheTest ];
     propagatedBuildInputs = [ ClassLoad HTTPBody HashMultiValue WWWFormUrlEncoded ];
 
     # Fails because /etc/protocols is not available in sandbox and make
@@ -526,10 +526,10 @@ let
   };
 
   ArchiveZip = buildPerlPackage {
-    name = "Archive-Zip-1.60";
+    name = "Archive-Zip-1.62";
     src = fetchurl {
-      url = mirror://cpan/authors/id/P/PH/PHRED/Archive-Zip-1.60.tar.gz;
-      sha256 = "02y2ylq83hy9kgj57sc0239x65br9sm98c0chsm61s08yc2mpiza";
+      url = mirror://cpan/authors/id/P/PH/PHRED/Archive-Zip-1.62.tar.gz;
+      sha256 = "1jax173w7nm5r6k7ymfcskvs1rw590lyscbqrnfbkjj4cxc65wrb";
     };
     buildInputs = [ TestMockModule ];
     meta = {
@@ -1094,10 +1094,10 @@ let
   };
 
   CarpAlways = buildPerlPackage rec {
-    name = "Carp-Always-0.13";
+    name = "Carp-Always-0.16";
     src = fetchurl {
       url = "mirror://cpan/authors/id/F/FE/FERREIRA/${name}.tar.gz";
-      sha256 = "0i2rifkr7ybfcdsqana52487z7vxp2l5qdra0f6ik0ddhn6rzii1";
+      sha256 = "1wb6b0qjga7kvn4p8df6k4g1pl2yzaqiln1713xidh3i454i3alq";
     };
     meta = {
       description = "Warns and dies noisily with stack backtraces";
@@ -1742,10 +1742,10 @@ let
   };
 
   CGI = buildPerlPackage rec {
-    name = "CGI-4.38";
+    name = "CGI-4.40";
     src = fetchurl {
       url = "mirror://cpan/authors/id/L/LE/LEEJO/${name}.tar.gz";
-      sha256 = "8c58f4a529bb92a914b22b7e64c5e31185c9854a4070a6dfad44fe5cc248e7d4";
+      sha256 = "10efff3061b3c31a33b3cc59f955aef9c88d57d12dbac46389758cef92f24f56";
     };
     buildInputs = [ TestDeep TestNoWarnings TestWarn ];
     propagatedBuildInputs = [ HTMLParser ];
@@ -1854,10 +1854,10 @@ let
   };
 
   CGISimple = buildPerlModule rec {
-    name = "CGI-Simple-1.15";
+    name = "CGI-Simple-1.16";
     src = fetchurl {
-      url = mirror://cpan/authors/id/M/MA/MANWAR/CGI-Simple-1.15.tar.gz;
-      sha256 = "013dcy9k4sj9alkksk5aqz65ryxw0rxgg71c7w666y941gd8n46q";
+      url = mirror://cpan/authors/id/M/MA/MANWAR/CGI-Simple-1.16.tar.gz;
+      sha256 = "1j07qy22a9k4g1xasxma7yzfmwwn3iy50rkxdhz8hz9f09hiym0f";
     };
     propagatedBuildInputs = [ IOStringy ];
     meta = {
@@ -2741,10 +2741,10 @@ let
   };
 
   Coro = buildPerlPackage rec {
-     name = "Coro-6.514";
+     name = "Coro-6.52";
      src = fetchurl {
-       url = mirror://cpan/authors/id/M/ML/MLEHMANN/Coro-6.514.tar.gz;
-       sha256 = "0qndvq74knyra9r98pyllsxz0s80dzc1ljx10arjv9whja1l6cyq";
+       url = mirror://cpan/authors/id/M/ML/MLEHMANN/Coro-6.52.tar.gz;
+       sha256 = "1q744smw6m676v8n0ww8jvmh1zg1iw7f7clzblwbfgmhy03h5ja9";
      };
      propagatedBuildInputs = [ AnyEvent Guard commonsense ];
      buildInputs = [ CanaryStability ];
@@ -2781,10 +2781,10 @@ let
   };
 
   CpanelJSONXS = buildPerlPackage rec {
-    name = "Cpanel-JSON-XS-4.04";
+    name = "Cpanel-JSON-XS-4.05";
     src = fetchurl {
       url = "mirror://cpan/authors/id/R/RU/RURBAN/${name}.tar.gz";
-      sha256 = "e128702a266b9a690bd3d380f726c229f9d6d795e8e206b9d32309d06825b2cd";
+      sha256 = "dd2b69265604ac6f18b47131565f712d55ed8df3b85f8f58f0c98cad17383663";
     };
     meta = {
       description = "CPanel fork of JSON::XS, fast and correct serializing";
@@ -2871,10 +2871,10 @@ let
   };
 
   CPANPerlReleases = buildPerlPackage rec {
-    name = "CPAN-Perl-Releases-3.70";
+    name = "CPAN-Perl-Releases-3.74";
     src = fetchurl {
       url = "mirror://cpan/authors/id/B/BI/BINGOS/${name}.tar.gz";
-      sha256 = "1yv9gq3rzhccskmpd9nn2n8v8zc6r9rlq5x47l0yva29yfgqb16r";
+      sha256 = "0qdh79fl38cyq9kp2g2s934gl1nn5jd88rgmqarqcmja8xhpfcp3";
     };
     meta = {
       homepage = https://github.com/bingos/cpan-perl-releases;
@@ -3657,10 +3657,10 @@ let
   };
 
   DateTime = buildPerlPackage rec {
-    name = "DateTime-1.49";
+    name = "DateTime-1.50";
     src = fetchurl {
       url = "mirror://cpan/authors/id/D/DR/DROLSKY/${name}.tar.gz";
-      sha256 = "0hbw4zq1562slnz7g7hyhfhyq98dzkk3i5g21x3xra5cvfix93kh";
+      sha256 = "165iqk1xvhs5j0kzsipa7aqycx3h37wqsl2r4jl104yqvmqhqszd";
     };
     buildInputs = [ CPANMetaCheck TestFatal TestWarnings ];
     propagatedBuildInputs = [ DateTimeLocale DateTimeTimeZone ];
@@ -5950,10 +5950,10 @@ let
   };
 
   FileMimeInfo = buildPerlPackage rec {
-    name = "File-MimeInfo-0.28";
+    name = "File-MimeInfo-0.29";
     src = fetchurl {
-      url = mirror://cpan/authors/id/M/MI/MICHIELB/File-MimeInfo-0.28.tar.gz;
-      sha256 = "1ipbh63bkh1r2gy5g7q4bzhki8j29mm1jkhbv60p9vwsdys5s91a";
+      url = mirror://cpan/authors/id/M/MI/MICHIELB/File-MimeInfo-0.29.tar.gz;
+      sha256 = "1sh8r6vczyz08zm8vfsjmkg6a165wch54akjdrd1vbifcmwjg5pi";
     };
     doCheck = false; # Failed test 'desktop file is the right one'
     buildInputs = [ FileBaseDir FileDesktopEntry ];
@@ -6269,10 +6269,10 @@ let
   };
 
   Filter = buildPerlPackage {
-    name = "Filter-1.58";
+    name = "Filter-1.59";
     src = fetchurl {
-      url = mirror://cpan/authors/id/R/RU/RURBAN/Filter-1.58.tar.gz;
-      sha256 = "6de91cb4cbfe08d0ccffbca39aed57f9237be602b8183f13fd163fc8cb657f3d";
+      url = mirror://cpan/authors/id/R/RU/RURBAN/Filter-1.59.tar.gz;
+      sha256 = "b4babfad4e0566a9a61199735f6e622a60d3274122752304f18f623412bf4e5a";
     };
     meta = {
       description = "Source Filters";
@@ -6367,10 +6367,10 @@ let
   };
 
   GamesSolitaireVerify = buildPerlModule {
-    name = "Games-Solitaire-Verify-0.1800";
+    name = "Games-Solitaire-Verify-0.1900";
     src = fetchurl {
-      url = mirror://cpan/authors/id/S/SH/SHLOMIF/Games-Solitaire-Verify-0.1800.tar.gz;
-      sha256 = "935ba997c49437a095adb39fd18233d5e378941aa9974df46e56aa6234f1fced";
+      url = mirror://cpan/authors/id/S/SH/SHLOMIF/Games-Solitaire-Verify-0.1900.tar.gz;
+      sha256 = "6b17847bd69da05ee089562cf40f2aac15e64c113175eca4fb501d4e86b48181";
     };
     buildInputs = [ TestDifferences ];
     propagatedBuildInputs = [ ClassXSAccessor ExceptionClass ListMoreUtils ];
@@ -6465,10 +6465,10 @@ let
   };
 
   GetoptLongDescriptive = buildPerlPackage rec {
-    name = "Getopt-Long-Descriptive-0.102";
+    name = "Getopt-Long-Descriptive-0.103";
     src = fetchurl {
       url = "mirror://cpan/authors/id/R/RJ/RJBS/${name}.tar.gz";
-      sha256 = "9ad4b98f294aa0515cc3150a1ae878d39e470762b78d8bd9df055eba9dea2846";
+      sha256 = "70e1bae7404a9dfb638b5d12e5bd4ea97e3bee743a4555909307d68e0111f4b2";
     };
     buildInputs = [ CPANMetaCheck TestFatal TestWarnings ];
     propagatedBuildInputs = [ ParamsValidate SubExporter ];
@@ -7795,10 +7795,10 @@ let
   };
 
   IOSocketSSL = buildPerlPackage rec {
-    name = "IO-Socket-SSL-2.058";
+    name = "IO-Socket-SSL-2.059";
     src = fetchurl {
       url = "mirror://cpan/authors/id/S/SU/SULLR/${name}.tar.gz";
-      sha256 = "746cd17c292cfc206b394497a060b0582d0b06a1040e6bb27e6530d56786e40b";
+      sha256 = "217debbe0a79f0b7c5669978b4d733271998df4497f4718f78456e5f54d64849";
     };
     propagatedBuildInputs = [ NetSSLeay ];
     # Fix path to default certificate store.
@@ -8774,10 +8774,10 @@ let
   };
 
   LogAny = buildPerlPackage rec {
-    name = "Log-Any-1.706";
+    name = "Log-Any-1.707";
     src = fetchurl {
       url = "mirror://cpan/authors/id/P/PR/PREACTION/${name}.tar.gz";
-      sha256 = "3ed0e5a4b7d490ab00624b7f905421239261f1dc976192aad2c0d1509bec08be";
+      sha256 = "74510f8cbee12637462e7c6020c8943d447a1e8e149a256f8168ee47562c65f1";
     };
     # Syslog test fails.
     preCheck = "rm t/syslog.t";
@@ -9555,7 +9555,7 @@ let
     };
   };
 
-  MLDBM = buildPerlPackage rec {
+  MLDBM = buildPerlModule rec {
     name = "MLDBM-2.05";
     src = fetchurl {
       url = "mirror://cpan/authors/id/C/CH/CHORNY/${name}.tar.gz";
@@ -9729,10 +9729,10 @@ let
   };
 
   ModuleCoreList = buildPerlPackage {
-    name = "Module-CoreList-5.20180720";
+    name = "Module-CoreList-5.20180820";
     src = fetchurl {
-      url = mirror://cpan/authors/id/B/BI/BINGOS/Module-CoreList-5.20180720.tar.gz;
-      sha256 = "0l6dyj4m4qgv2yzq3pp0bkvg1j9nh9mcm1p4x3g3j93gkba7whws";
+      url = mirror://cpan/authors/id/B/BI/BINGOS/Module-CoreList-5.20180820.tar.gz;
+      sha256 = "1ccs5mqcfxjv8bax2nfsg11b2vc3sqyapfapxyzrjhaa2fmdn54l";
     };
     meta = {
       homepage = http://dev.perl.org/;
@@ -9952,11 +9952,11 @@ let
     };
   };
 
-  ModuleScanDeps = let version = "1.24"; in buildPerlPackage {
+  ModuleScanDeps = let version = "1.25"; in buildPerlPackage {
     name = "Module-ScanDeps-${version}";
     src = fetchurl {
       url = "mirror://cpan/authors/id/R/RS/RSCHUPP/Module-ScanDeps-${version}.tar.gz";
-      sha256 = "0s6cj90ckhy351gql52ksh4ms1x8piv26iadl09fcpzkx7j0srw9";
+      sha256 = "13280nq0d6zc58mcz3kvs2m85a741czq0fabk69ks1nr4j1w2nl4";
     };
     buildInputs = [ TestRequires ];
     meta = {
@@ -10031,10 +10031,10 @@ let
     };
   };
   Mojolicious = buildPerlPackage rec {
-    name = "Mojolicious-7.88";
+    name = "Mojolicious-7.93";
     src = fetchurl {
       url = "mirror://cpan/authors/id/S/SR/SRI/${name}.tar.gz";
-      sha256 = "4c4c9c05131fcd175cd6370e15d2586baec1a3ec882cb6971e1f5f52b5e0d785";
+      sha256 = "00c30fc566fee0823af0a75bdf4f170531655df14beca6d51f0e453a43aaad5d";
     };
     meta = {
       homepage = https://mojolicious.org/;
@@ -10057,10 +10057,10 @@ let
   };
 
   MonitoringPlugin = buildPerlPackage rec {
-    name = "Monitoring-Plugin-0.39";
+    name = "Monitoring-Plugin-0.40";
     src = fetchurl {
       url = "mirror://cpan/authors/id/N/NI/NIERLEIN/${name}.tar.gz";
-      sha256 = "030cw86j8712z8rn66k935gbilb5rcj3lnk4n53vh1b2phrszvjw";
+      sha256 = "0vr3wwdn3zs246qwi04bqk8jir6l88j5m59jk97hmfyj4xz6pfpq";
     };
     propagatedBuildInputs = [ ClassAccessor ConfigTiny MathCalcUnits ParamsValidate ];
     meta = {
@@ -10493,12 +10493,12 @@ let
   };
 
   MooseXGetopt = buildPerlModule rec {
-    name = "MooseX-Getopt-0.71";
+    name = "MooseX-Getopt-0.72";
     src = fetchurl {
       url = "mirror://cpan/authors/id/E/ET/ETHER/${name}.tar.gz";
-      sha256 = "de18f8ea0a5650cbbdebecb8f4c028f5f951fc5698332f7b8e20c7874902c259";
+      sha256 = "a378411a061ed239554d2b7f86b2b82bf55f600901243a6ec3fd29557d171b2e";
     };
-    buildInputs = [ ModuleBuildTiny MooseXStrictConstructor PathTiny TestDeep TestFatal TestRequires TestTrap TestWarnings ];
+    buildInputs = [ ModuleBuildTiny MooseXStrictConstructor PathTiny TestDeep TestFatal TestNeeds TestTrap TestWarnings ];
     propagatedBuildInputs = [ GetoptLongDescriptive MooseXRoleParameterized ];
     meta = {
       homepage = https://github.com/moose/MooseX-Getopt;
@@ -10923,10 +10923,10 @@ let
   };
 
   Mouse = buildPerlModule rec {
-    name = "Mouse-2.5.4";
+    name = "Mouse-2.5.6";
     src = fetchurl {
-      url = mirror://cpan/authors/id/S/SK/SKAJI/Mouse-v2.5.4.tar.gz;
-      sha256 = "041nm46bxxyi1fd8w69r45k434b6m43va2s06pr3bys6igxic79d";
+      url = mirror://cpan/authors/id/S/SK/SKAJI/Mouse-v2.5.6.tar.gz;
+      sha256 = "1j3048ip691j91rdig6wrlg6i4jdzhszxmz5pi2g7n355rl2w00l";
     };
     buildInputs = [ DevelPPPort ModuleBuildXSUtil TestException TestFatal TestLeakTrace TestOutput TestRequires TryTiny self.version ];
     NIX_CFLAGS_COMPILE = stdenv.lib.optionalString stdenv.isi686 "-fno-stack-protector";
@@ -11208,7 +11208,7 @@ let
       sha256 = "8391696db9e96c374b72984c0bad9c7d1c9f3b4efe68f9ddf429a77548e0e269";
     };
     nativeBuildInputs = [ pkgs.pkgconfig ];
-    buildInputs = [ TestPod TestPodCoverage pkgs.dbus ];
+    buildInputs = [ pkgs.dbus TestPod TestPodCoverage ];
     propagatedBuildInputs = [ XMLTwig ];
     meta = {
       homepage = http://www.freedesktop.org/wiki/Software/dbus;
@@ -11218,10 +11218,10 @@ let
   };
 
   NetDNS = buildPerlPackage rec {
-    name = "Net-DNS-1.16";
+    name = "Net-DNS-1.17";
     src = fetchurl {
       url = "mirror://cpan/authors/id/N/NL/NLNETLABS/${name}.tar.gz";
-      sha256 = "8163eebaf46d1a870b6f596684f345da7c3a7461d7dba2b85f23e02d8982ea37";
+      sha256 = "9a79fd8fea1a708726c18d193ae4437479206ccb20ffa7f0971371e172e2c2e0";
     };
     propagatedBuildInputs = [ DigestHMAC IOSocketIP ];
     makeMakerFlags = "--noonline-tests";
@@ -11348,10 +11348,10 @@ let
   };
 
   NetPing = buildPerlPackage {
-    name = "Net-Ping-2.68";
+    name = "Net-Ping-2.70";
     src = fetchurl {
-      url = mirror://cpan/authors/id/R/RU/RURBAN/Net-Ping-2.68.tar.gz;
-      sha256 = "d01ac2fcdf684c4a23a07104fbb147cfbdbda47fd5b660912124258f29afd7e3";
+      url = mirror://cpan/authors/id/R/RU/RURBAN/Net-Ping-2.70.tar.gz;
+      sha256 = "41400089736f528cfa1196083905d4bbd313c4653a03fab8578cebd5b5b6aa5a";
     };
     meta = {
       description = "Check a remote host for reachability";
@@ -11848,10 +11848,10 @@ let
   };
 
   ParamsValidationCompiler = buildPerlPackage rec {
-     name = "Params-ValidationCompiler-0.27";
+     name = "Params-ValidationCompiler-0.30";
      src = fetchurl {
-       url = mirror://cpan/authors/id/D/DR/DROLSKY/Params-ValidationCompiler-0.27.tar.gz;
-       sha256 = "1cpr188c2xm0kkmdir6slcsgv7v6ibqff4lax8s0whwx6ml9kaah";
+       url = mirror://cpan/authors/id/D/DR/DROLSKY/Params-ValidationCompiler-0.30.tar.gz;
+       sha256 = "1jqn1l4m4i341g14kmjsf3a1kn7vv6z89cix0xjjgr1v70iywnyw";
      };
      propagatedBuildInputs = [ EvalClosure ExceptionClass ];
      buildInputs = [ Specio Test2PluginNoWarnings Test2Suite TestSimple13 TestWithoutModule ];
@@ -11862,10 +11862,10 @@ let
   };
 
   Paranoid = buildPerlPackage rec {
-    name = "Paranoid-2.05";
+    name = "Paranoid-2.06";
     src = fetchurl {
       url = "mirror://cpan/authors/id/C/CO/CORLISS/Paranoid/${name}.tar.gz";
-      sha256 = "583dfa0279733531f360795ad1cf4aa652d537b2b0bbd3c6925d0c8d75cbb3df";
+      sha256 = "48763ec19d0a4194ecf613bd63e46325510228da9100c2e796615dc778612d3c";
     };
     patches = [ ../development/perl-modules/Paranoid-blessed-path.patch ];
     preConfigure = ''
@@ -12000,10 +12000,10 @@ let
   };
 
   PathTiny = buildPerlPackage {
-    name = "Path-Tiny-0.106";
+    name = "Path-Tiny-0.108";
     src = fetchurl {
-      url = mirror://cpan/authors/id/D/DA/DAGOLDEN/Path-Tiny-0.106.tar.gz;
-      sha256 = "308e39087b626013569a15783b896d61916fd1e67d06017f40cff567af36464d";
+      url = mirror://cpan/authors/id/D/DA/DAGOLDEN/Path-Tiny-0.108.tar.gz;
+      sha256 = "3c49482be2b3eb7ddd7e73a5b90cff648393f5d5de334ff126ce7a3632723ff5";
     };
     meta = {
       description = "File path utility";
@@ -12256,10 +12256,10 @@ let
   };
 
   PkgConfig = buildPerlPackage rec {
-    name = "PkgConfig-0.19026";
+    name = "PkgConfig-0.21026";
     src = fetchurl {
       url = "mirror://cpan/authors/id/P/PL/PLICEASE/${name}.tar.gz";
-      sha256 = "5cb6e934d29dd93e04c2fa779f4b7e51361edaf56957b47a232017a4bb7e922c";
+      sha256 = "018f8d3c74e661df66046b26e57f4c5991adafe202af7ea2d1c6f6bcafde584b";
     };
     meta = {
       description = "Pure-Perl Core-Only replacement for pkg-config";
@@ -12566,10 +12566,10 @@ let
   };
 
   PPIxRegexp = buildPerlModule rec {
-    name = "PPIx-Regexp-0.061";
+    name = "PPIx-Regexp-0.062";
     src = fetchurl {
       url = "mirror://cpan/authors/id/W/WY/WYANT/${name}.tar.gz";
-      sha256 = "e2d63a4102024e15994c685672d30c6d708272a1600abcd6241e6f2c1b3b7c92";
+      sha256 = "1218fe4c94b3cb9d894c6cd8a69bb4172eac54ce083b70f7a8bf13868a5a0733";
     };
     propagatedBuildInputs = [ PPI ];
     meta = {
@@ -12678,11 +12678,11 @@ let
   };
 
   ProtocolHTTP2 = buildPerlModule rec {
-    name = "Protocol-HTTP2-1.08";
+    name = "Protocol-HTTP2-1.09";
 
     src = fetchurl {
       url = "mirror://cpan/authors/id/C/CR/CRUX/${name}.tar.gz";
-      sha256 = "06y1djgzbn340hixav85728dvp8mj2mx2qf5fzkqxh145g5q860g";
+      sha256 = "1bc0ybkqhv81dscgzlbr62w4zqjsidcikmkbjanzn83g2b6ia9nc";
     };
     buildInputs = [ AnyEvent ModuleBuildTiny NetSSLeay TestLeakTrace TestSharedFork TestTCP ];
   };
@@ -12946,10 +12946,10 @@ let
   };
 
   PodMarkdown = buildPerlPackage {
-    name = "Pod-Markdown-3.005";
+    name = "Pod-Markdown-3.101";
     src = fetchurl {
-      url = mirror://cpan/authors/id/R/RW/RWSTAUNER/Pod-Markdown-3.005.tar.gz;
-      sha256 = "00s3745kl4vbxqyi2lx149q5ghyfazc4fd00kcpl84bb87jfgdzq";
+      url = mirror://cpan/authors/id/R/RW/RWSTAUNER/Pod-Markdown-3.101.tar.gz;
+      sha256 = "0h7hx4k1c3k00cfnlf226bkxnxaz01705m10vxm9cxh52xn6pzz8";
     };
     buildInputs = [ TestDifferences ];
     meta = {
@@ -13230,7 +13230,7 @@ let
       url = "mirror://cpan/authors/id/K/KK/KKANE/${name}.tar.gz";
       sha256 = "a8652a2214308faff2c68be5ce64c904dcccc5e86be7f32376c1590869d01844";
     };
-    propagatedBuildInputs = [ LWP LWPProtocolhttps URI ];
+    propagatedBuildInputs = [ LWPProtocolHttps ];
     meta = {
       description = "A simple client for interacting with RESTful http/https resources";
       license = with stdenv.lib.licenses; [ artistic1 gpl1Plus ];
@@ -14273,7 +14273,7 @@ let
       url = "mirror://cpan/authors/id/C/CL/CLKAO/${name}.tar.gz";
       sha256 = "1ysgi38zx236cxz539k6d6rw5z0vc70rrglsaf5fk6rnwilw2g6n";
     };
-    propagatedBuildInputs = [ pkgs.subversionClient ];
+    propagatedBuildInputs = [ (pkgs.subversionClient.override { inherit perl; }) ];
   };
 
   Swim = buildPerlPackage rec {
@@ -15851,10 +15851,10 @@ let
   };
 
   TestSimple13 = buildPerlPackage rec {
-    name = "Test-Simple-1.302138";
+    name = "Test-Simple-1.302140";
     src = fetchurl {
-      url = mirror://cpan/authors/id/E/EX/EXODIST/Test-Simple-1.302138.tar.gz;
-      sha256 = "568615a551075d3657cb0cbca55cf3672734c954f0306e9823ecd002aa911655";
+      url = mirror://cpan/authors/id/E/EX/EXODIST/Test-Simple-1.302140.tar.gz;
+      sha256 = "73f5440c7ae55e13706e9ebeaa7247df973226470f028344ea3cd21e1642bd1d";
     };
     meta = {
       description = "Basic utilities for writing tests";
@@ -16203,10 +16203,10 @@ let
   };
 
   TextCSV = buildPerlPackage rec {
-    name = "Text-CSV-1.95";
+    name = "Text-CSV-1.97";
     src = fetchurl {
-      url = mirror://cpan/authors/id/I/IS/ISHIGAKI/Text-CSV-1.95.tar.gz;
-      sha256 = "7e0a11d9c1129a55b68a26aa4b37c894279df255aa63ec8341d514ab848dbf61";
+      url = mirror://cpan/authors/id/I/IS/ISHIGAKI/Text-CSV-1.97.tar.gz;
+      sha256 = "cc350462efa8d39d5c8a1da5f205bc31620cd52d9865a769c8e3ed1b41640fd5";
     };
     meta = {
       description = "Comma-separated values manipulator (using XS or PurePerl)";
@@ -16404,10 +16404,10 @@ let
   };
 
   TextQuoted = buildPerlPackage {
-    name = "Text-Quoted-2.09";
+    name = "Text-Quoted-2.10";
     src = fetchurl {
-      url = mirror://cpan/authors/id/A/AL/ALEXMV/Text-Quoted-2.09.tar.gz;
-      sha256 = "446c3e8da7e65f7988cd36e9da1159614eb0b337d6c4c0dec8f6df7673b96c5f";
+      url = mirror://cpan/authors/id/B/BP/BPS/Text-Quoted-2.10.tar.gz;
+      sha256 = "081bf95ec9220af26cec89161e61bf73f9fbcbfeee1d9af15139e5d7b708f445";
     };
     propagatedBuildInputs = [ TextAutoformat ];
     meta = {
@@ -16456,10 +16456,10 @@ let
   };
 
   TextSimpleTable = buildPerlPackage {
-    name = "Text-SimpleTable-2.05";
+    name = "Text-SimpleTable-2.07";
     src = fetchurl {
-      url = mirror://cpan/authors/id/M/MR/MRAMBERG/Text-SimpleTable-2.05.tar.gz;
-      sha256 = "1akcv3iq4y6mjc88p0j9yvv6g0g5cnc9nvzxnmsswnx5si7v5am5";
+      url = mirror://cpan/authors/id/M/MR/MRAMBERG/Text-SimpleTable-2.07.tar.gz;
+      sha256 = "1v8r8qpzg283p2pqqr8dqrak2bxray1b2jmib0qk75jffqw3yv95";
     };
     meta = {
       description = "Simple eyecandy ASCII tables";
@@ -16997,10 +16997,10 @@ let
   };
 
   TypeTiny = buildPerlPackage {
-    name = "Type-Tiny-1.002002";
+    name = "Type-Tiny-1.004002";
     src = fetchurl {
-      url = mirror://cpan/authors/id/T/TO/TOBYINK/Type-Tiny-1.002002.tar.gz;
-      sha256 = "a85b0c8f99b5c9b5558f0bcc8893b44299fcccf3c264ff924940d09d91d8882c";
+      url = mirror://cpan/authors/id/T/TO/TOBYINK/Type-Tiny-1.004002.tar.gz;
+      sha256 = "e52c7e9593052aed157a15d473b5c25a1dbb3454bf3cd6913df94cc9bb2be707";
     };
     propagatedBuildInputs = [ ExporterTiny ];
     meta = {
@@ -17703,10 +17703,10 @@ let
   };
 
   XMLParserLite = buildPerlPackage {
-    name = "XML-Parser-Lite-0.721";
+    name = "XML-Parser-Lite-0.722";
     src = fetchurl {
-      url = mirror://cpan/authors/id/P/PH/PHRED/XML-Parser-Lite-0.721.tar.gz;
-      sha256 = "1fh8g77nkfv9n07ivilnfxdapx6jx13whf8q0anrmnxrr9pa6qjq";
+      url = mirror://cpan/authors/id/P/PH/PHRED/XML-Parser-Lite-0.722.tar.gz;
+      sha256 = "1vk3jwh1kfcsmc5kvxzqdnb1cllvf0yf27fg0ra0w6jkw4ks143g";
     };
     buildInputs = [ TestRequires ];
     meta = {
@@ -17817,10 +17817,10 @@ let
   };
 
   XMLSemanticDiff = buildPerlModule {
-    name = "XML-SemanticDiff-1.0006";
+    name = "XML-SemanticDiff-1.0007";
     src = fetchurl {
-      url = mirror://cpan/authors/id/S/SH/SHLOMIF/XML-SemanticDiff-1.0006.tar.gz;
-      sha256 = "1z0lkb7xzhw9calz4pbwzry2lqqpy6pw6pvfn2gv70ry1xqycr0k";
+      url = mirror://cpan/authors/id/P/PE/PERIGRIN/XML-SemanticDiff-1.0007.tar.gz;
+      sha256 = "1xd00821y795fy2rag8aizb5wsbbzfxgmdf9qwpvdxn3pgpyzz85";
     };
     propagatedBuildInputs = [ XMLParser ];
     meta = {
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index b1c5368b1888..84472b440a58 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -182,6 +182,8 @@ in {
 
   asana = callPackage ../development/python-modules/asana { };
 
+  ase = callPackage ../development/python-modules/ase { };
+
   asn1crypto = callPackage ../development/python-modules/asn1crypto { };
 
   aspy-yaml = callPackage ../development/python-modules/aspy.yaml { };
@@ -272,6 +274,8 @@ in {
     dbus = pkgs.dbus;
   };
 
+  dftfit = callPackage ../development/python-modules/dftfit { };
+
   discid = callPackage ../development/python-modules/discid { };
 
   discordpy = callPackage ../development/python-modules/discordpy { };
@@ -282,6 +286,8 @@ in {
 
   distorm3 = callPackage ../development/python-modules/distorm3 { };
 
+  docutils = callPackage ../development/python-modules/docutils { };
+
   dogtail = callPackage ../development/python-modules/dogtail { };
 
   diff-match-patch = callPackage ../development/python-modules/diff-match-patch { };
@@ -316,6 +322,10 @@ in {
 
   jira = callPackage ../development/python-modules/jira { };
 
+  lammps-cython = callPackage ../development/python-modules/lammps-cython {
+    mpi = pkgs.openmpi;
+  };
+
   lmtpd = callPackage ../development/python-modules/lmtpd { };
 
   logster = callPackage ../development/python-modules/logster { };
@@ -356,6 +366,8 @@ in {
 
   palettable = callPackage ../development/python-modules/palettable { };
 
+  pathlib = callPackage ../development/python-modules/pathlib { };
+
   pdf2image = callPackage ../development/python-modules/pdf2image { };
 
   pdfminer = callPackage ../development/python-modules/pdfminer_six { };
@@ -400,6 +412,8 @@ in {
 
   PyChromecast = callPackage ../development/python-modules/pychromecast { };
 
+  py-cpuinfo = callPackage ../development/python-modules/py-cpuinfo { };
+
   pydbus = callPackage ../development/python-modules/pydbus { };
 
   pydocstyle = callPackage ../development/python-modules/pydocstyle { };
@@ -416,6 +430,8 @@ in {
 
   pygame_sdl2 = callPackage ../development/python-modules/pygame_sdl2 { };
 
+  pygmo = callPackage ../development/python-modules/pygmo { };
+
   pygobject2 = callPackage ../development/python-modules/pygobject { };
 
   pygobject3 = callPackage ../development/python-modules/pygobject/3.nix { };
@@ -445,6 +461,8 @@ in {
 
   pymatgen = callPackage ../development/python-modules/pymatgen { };
 
+  pymatgen-lammps = callPackage ../development/python-modules/pymatgen-lammps { };
+
   pynisher = callPackage ../development/python-modules/pynisher { };
 
   pyparser = callPackage ../development/python-modules/pyparser { };
@@ -532,6 +550,8 @@ in {
 
   spglib = callPackage ../development/python-modules/spglib { };
 
+  statistics = callPackage ../development/python-modules/statistics { };
+
   sumo = callPackage ../development/python-modules/sumo { };
 
   supervise_api = callPackage ../development/python-modules/supervise_api { };
@@ -1466,7 +1486,7 @@ in {
     '';
   };
 
-  celery = callPackage ../development/python-modules/celery { pytest = self.pytest_32; };
+  celery = callPackage ../development/python-modules/celery { };
 
   cerberus = callPackage ../development/python-modules/cerberus { };
 
@@ -1843,28 +1863,21 @@ in {
     };
   };
 
-  pytest = self.pytest_36;
+  pytest = self.pytest_37;
 
-  pytest_36 = callPackage ../development/python-modules/pytest {
+  pytest_37 = callPackage ../development/python-modules/pytest {
     # hypothesis tests require pytest that causes dependency cycle
     hypothesis = self.hypothesis.override { doCheck = false; };
   };
 
-  # Needed for celery
-  pytest_32 = self.pytest_36.overridePythonAttrs( oldAttrs: rec {
-    version = "3.2.5";
-    src = oldAttrs.src.override {
-      inherit version;
-      sha256 = "6d5bd4f7113b444c55a3bbb5c738a3dd80d43563d063fc42dcb0aaefbdd78b81";
-    };
-  });
-
   pytest-httpbin = callPackage ../development/python-modules/pytest-httpbin { };
 
   pytest-asyncio = callPackage ../development/python-modules/pytest-asyncio { };
 
   pytest-aiohttp = callPackage ../development/python-modules/pytest-aiohttp { };
 
+  pytest-benchmark = callPackage ../development/python-modules/pytest-benchmark { };
+
   pytestcache = callPackage ../development/python-modules/pytestcache { };
 
   pytest-catchlog = callPackage ../development/python-modules/pytest-catchlog { };
@@ -4960,37 +4973,6 @@ in {
     };
   };
 
-
-  docutils = buildPythonPackage rec {
-    name = "docutils-${version}";
-    version = "0.14";
-
-    src = pkgs.fetchurl {
-      url = "mirror://sourceforge/docutils/${name}.tar.gz";
-      sha256 = "0x22fs3pdmr42kvz6c654756wja305qv6cx1zbhwlagvxgr4xrji";
-    };
-
-    checkPhase = if isPy3k then ''
-      ${python.interpreter} test3/alltests.py
-    '' else ''
-      ${python.interpreter} test/alltests.py
-    '';
-
-    # Create symlinks lacking a ".py" suffix, many programs depend on these names
-    postFixup = ''
-      (cd $out/bin && for f in *.py; do
-        ln -s $f $(echo $f | sed -e 's/\.py$//')
-      done)
-    '';
-
-    meta = {
-      description = "An open-source text processing system for processing plaintext documentation into useful formats, such as HTML or LaTeX";
-      homepage = http://docutils.sourceforge.net/;
-      maintainers = with maintainers; [ garbas AndersonTorres ];
-    };
-  };
-
-
   dtopt = buildPythonPackage rec {
     name = "dtopt-0.1";
 
@@ -9415,27 +9397,6 @@ in {
 
   patator = callPackage ../development/python-modules/patator { };
 
-  pathlib = buildPythonPackage rec {
-    name = "pathlib-${version}";
-    version = "1.0.1";
-    disabled = pythonAtLeast "3.4"; # Was added to std library in Python 3.4
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/p/pathlib/${name}.tar.gz";
-      sha256 = "17zajiw4mjbkkv6ahp3xf025qglkj0805m9s41c45zryzj6p2h39";
-    };
-
-    checkPhase = ''
-      ${python.interpreter} -m unittest discover
-    '';
-
-    meta = {
-      description = "Object-oriented filesystem paths";
-      homepage = "https://pathlib.readthedocs.org/";
-      license = licenses.mit;
-    };
-  };
-
   pathlib2 = callPackage ../development/python-modules/pathlib2 { };
 
   pathpy = callPackage ../development/python-modules/path.py { };