Merge commit 'e19054ab3cd5b7cc9a01d0efc71c8fe310541065'

55 files changed, 155 insertions, 77 deletions

diff --git a/nixpkgs/pkgs/applications/science/astronomy/gildas/default.nix b/nixpkgs/pkgs/applications/science/astronomy/gildas/default.nix
index 968d8769caa3..a21c9f328f40 100644
--- a/nixpkgs/pkgs/applications/science/astronomy/gildas/default.nix
+++ b/nixpkgs/pkgs/applications/science/astronomy/gildas/default.nix
@@ -1,5 +1,5 @@
 { stdenv, fetchurl, gtk2-x11 , pkgconfig , python27 , gfortran , lesstif
-, cfitsio , getopt , perl , groff , which
+, cfitsio , getopt , perl , groff , which, darwin
 }:
 
 let
@@ -7,8 +7,8 @@ let
 in
 
 stdenv.mkDerivation rec {
-  srcVersion = "jul19a";
-  version = "20190701_a";
+  srcVersion = "sep19a";
+  version = "20190901_a";
   pname = "gildas";
 
   src = fetchurl {
@@ -16,19 +16,22 @@ stdenv.mkDerivation rec {
     # source code of the previous release to a different directory
     urls = [ "http://www.iram.fr/~gildas/dist/gildas-src-${srcVersion}.tar.xz"
       "http://www.iram.fr/~gildas/dist/archive/gildas/gildas-src-${srcVersion}.tar.xz" ];
-    sha256 = "97eaa0d0a0f53f0616462642a9bfaddb0305a8a0948e60531d8a524a13a370b6";
+    sha256 = "0l4jfzzxp1ab70a920qfbxiphgnc06m46wfwv0jlsq2mfk7cxac1";
   };
 
   enableParallelBuilding = true;
 
   nativeBuildInputs = [ pkgconfig groff perl getopt gfortran which ];
 
-  buildInputs = [ gtk2-x11 lesstif cfitsio python27Env ];
+  buildInputs = [ gtk2-x11 lesstif cfitsio python27Env ]
+    ++ stdenv.lib.optionals stdenv.isDarwin (with darwin.apple_sdk.frameworks; [ CoreFoundation ]);
 
   patches = [ ./wrapper.patch ./clang.patch ./aarch64.patch ];
 
   NIX_CFLAGS_COMPILE = stdenv.lib.optionalString stdenv.cc.isClang "-Wno-unused-command-line-argument";
 
+  NIX_LDFLAGS = stdenv.lib.optionalString stdenv.isDarwin (with darwin.apple_sdk.frameworks; "-F${CoreFoundation}/Library/Frameworks");
+
   configurePhase=''
     substituteInPlace admin/wrapper.sh --replace '%%OUT%%' $out
     substituteInPlace admin/wrapper.sh --replace '%%PYTHONHOME%%' ${python27Env}
diff --git a/nixpkgs/pkgs/applications/science/astronomy/gpredict/default.nix b/nixpkgs/pkgs/applications/science/astronomy/gpredict/default.nix
index ff273ab8e95b..f36431beac13 100644
--- a/nixpkgs/pkgs/applications/science/astronomy/gpredict/default.nix
+++ b/nixpkgs/pkgs/applications/science/astronomy/gpredict/default.nix
@@ -21,7 +21,7 @@ in stdenv.mkDerivation {
     description = "Real time satellite tracking and orbit prediction";
     longDescription = ''
       Gpredict is a real time satellite tracking and orbit prediction program
-      written using the Gtk+ widgets. Gpredict is targetted mainly towards ham radio
+      written using the GTK widgets. Gpredict is targetted mainly towards ham radio
       operators but others interested in satellite tracking may find it useful as
       well. Gpredict uses the SGP4/SDP4 algorithms, which are compatible with the
       NORAD Keplerian elements.
diff --git a/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix b/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix
index b5bc3b622b91..4e4c093ad7f7 100644
--- a/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "bedtools";
-  version = "2.28.0";
+  version = "2.29.0";
 
   src = fetchFromGitHub {
     owner = "arq5x";
     repo = "bedtools2";
     rev = "v${version}";
-    sha256 = "1266bcn5hgbvysfi6nr4cqxlbxcx7vn7ng8kb0v3gz37qh2zxxw9";
+    sha256 = "0d6i985qqxp92ddq4n6558m70qi5rqhl724wrfys0hm0p6a9h56x";
   };
 
   buildInputs = [ zlib python bzip2 lzma ];
diff --git a/nixpkgs/pkgs/applications/science/biology/cmtk/default.nix b/nixpkgs/pkgs/applications/science/biology/cmtk/default.nix
index 56de61da1c5a..1ebfa2fca57a 100644
--- a/nixpkgs/pkgs/applications/science/biology/cmtk/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/cmtk/default.nix
@@ -1,6 +1,6 @@
 {stdenv, fetchurl, cmake}:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   name = "cmtk-3.3.1";
 
   src = fetchurl {
diff --git a/nixpkgs/pkgs/applications/science/biology/diamond/default.nix b/nixpkgs/pkgs/applications/science/biology/diamond/default.nix
index 854e91b2fcbb..c1d20a11ca96 100644
--- a/nixpkgs/pkgs/applications/science/biology/diamond/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/diamond/default.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchurl, cmake, zlib }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   name = "diamond-0.8.36";
 
   src = fetchurl {
diff --git a/nixpkgs/pkgs/applications/science/biology/platypus/default.nix b/nixpkgs/pkgs/applications/science/biology/platypus/default.nix
index fc6cfbb158c3..6907c6e3ec82 100644
--- a/nixpkgs/pkgs/applications/science/biology/platypus/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/platypus/default.nix
@@ -2,7 +2,7 @@
 
 let python = python27.withPackages (ps: with ps; [ cython ]);
 
-in stdenv.mkDerivation rec {
+in stdenv.mkDerivation {
   pname = "platypus-unstable";
   version = "2018-07-22";
 
diff --git a/nixpkgs/pkgs/applications/science/biology/xenomapper/default.nix b/nixpkgs/pkgs/applications/science/biology/xenomapper/default.nix
new file mode 100644
index 000000000000..cc235c4ca996
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/xenomapper/default.nix
@@ -0,0 +1,23 @@
+{buildPythonPackage, lib, fetchFromGitHub, statistics}:
+
+buildPythonPackage rec {
+  pname = "xenomapper";
+  version = "1.0.2";
+
+  src = fetchFromGitHub {
+    owner = "genomematt";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "0mnmfzlq5mhih6z8dq5bkx95vb8whjycz9mdlqwbmlqjb3gb3zhr";
+  };
+
+  propagatedBuildInputs = [ statistics ];
+
+  meta = with lib; {
+    homepage = "http://github.com/genomematt/xenomapper";
+    description = "A utility for post processing mapped reads that have been aligned to a primary genome and a secondary genome and binning reads into species specific, multimapping in each species, unmapped and unassigned bins";
+    license = licenses.gpl3;
+    platforms = platforms.all;
+    maintainers = [ maintainers.jbedo ];
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/chemistry/siesta/default.nix b/nixpkgs/pkgs/applications/science/chemistry/siesta/default.nix
index a27355afdc8e..9d7880f57df5 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/siesta/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/siesta/default.nix
@@ -3,7 +3,7 @@
 , mpi ? null, scalapack
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   version = "4.1-b3";
   pname = "siesta";
 
diff --git a/nixpkgs/pkgs/applications/science/electronics/alliance/default.nix b/nixpkgs/pkgs/applications/science/electronics/alliance/default.nix
index b351c892c2cf..c863fe6aea85 100644
--- a/nixpkgs/pkgs/applications/science/electronics/alliance/default.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/alliance/default.nix
@@ -20,7 +20,6 @@ stdenv.mkDerivation rec {
 
   configureFlags = [
     "--prefix=$(out)"
-    "--disable-static"
   ];
 
   preConfigure = ''
diff --git a/nixpkgs/pkgs/applications/science/electronics/bitscope/packages.nix b/nixpkgs/pkgs/applications/science/electronics/bitscope/packages.nix
index 58e01f4f9f49..11e1ed524ed2 100644
--- a/nixpkgs/pkgs/applications/science/electronics/bitscope/packages.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/bitscope/packages.nix
@@ -110,7 +110,7 @@ in {
   proto = let
     toolName = "bitscope-proto";
     version = "0.9.FG13B";
-  in mkBitscope rec {
+  in mkBitscope {
     inherit toolName version;
     # NOTE: this is meant as a demo by BitScope
     # NOTE: clicking on logo produces error
diff --git a/nixpkgs/pkgs/applications/science/electronics/dsview/libsigrok4dsl.nix b/nixpkgs/pkgs/applications/science/electronics/dsview/libsigrok4dsl.nix
index 8aa8275510c9..c2cfc69c50c8 100644
--- a/nixpkgs/pkgs/applications/science/electronics/dsview/libsigrok4dsl.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/dsview/libsigrok4dsl.nix
@@ -3,7 +3,7 @@ glib, libzip, libserialport, check, libusb, libftdi,
 systemd, alsaLib, dsview
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   inherit (dsview) version src;
 
   pname = "libsigrok4dsl";
diff --git a/nixpkgs/pkgs/applications/science/electronics/dsview/libsigrokdecode4dsl.nix b/nixpkgs/pkgs/applications/science/electronics/dsview/libsigrokdecode4dsl.nix
index 12d375cf88aa..b7fe5140864c 100644
--- a/nixpkgs/pkgs/applications/science/electronics/dsview/libsigrokdecode4dsl.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/dsview/libsigrokdecode4dsl.nix
@@ -2,7 +2,7 @@
 glib, check, python3, dsview
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   inherit (dsview) version src;
 
   pname = "libsigrokdecode4dsl";
diff --git a/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix b/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix
index 3168fc19d055..2b28f2c06db5 100644
--- a/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix
@@ -36,9 +36,6 @@ let
         qtbase qtdeclarative qtsvg qtlocation qtwebchannel qtwebengine
       ];
 
-    doConfigure = false;
-    doBuild = false;
-
     installPhase = ''
       # Extract eagle tarball
       mkdir "$out"
diff --git a/nixpkgs/pkgs/applications/science/electronics/fped/default.nix b/nixpkgs/pkgs/applications/science/electronics/fped/default.nix
index a3b2945ac3d9..4eb666ada7ce 100644
--- a/nixpkgs/pkgs/applications/science/electronics/fped/default.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/fped/default.nix
@@ -4,7 +4,7 @@
 }:
 
 with lib;
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "fped";
   version = "unstable-2017-05-11";
 
@@ -16,7 +16,7 @@ stdenv.mkDerivation rec {
 
   # This uses '/bin/bash', '/usr/local' and 'lex' by default
   makeFlags = [
-    "PREFIX=${placeholder ''out''}"
+    "PREFIX=${placeholder "out"}"
     "LEX=flex"
     "RGBDEF=${netpbm}/share/netpbm/misc/rgb.txt"
   ];
diff --git a/nixpkgs/pkgs/applications/science/electronics/geda/default.nix b/nixpkgs/pkgs/applications/science/electronics/geda/default.nix
index 71101d7cd74a..1aaa5496ff37 100644
--- a/nixpkgs/pkgs/applications/science/electronics/geda/default.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/geda/default.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchurl, pkgconfig, guile, gtk2, flex, gawk, perl }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "geda";
   version = "1.8.2-20130925";
 
diff --git a/nixpkgs/pkgs/applications/science/electronics/gerbv/default.nix b/nixpkgs/pkgs/applications/science/electronics/gerbv/default.nix
index 3f61a13eab8c..fa5bdbbebdb6 100644
--- a/nixpkgs/pkgs/applications/science/electronics/gerbv/default.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/gerbv/default.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchgit, pkgconfig, gettext, libtool, automake, autoconf, cairo, gtk2, autoreconfHook }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "gerbv";
   version = "2015-10-08";
 
diff --git a/nixpkgs/pkgs/applications/science/electronics/librepcb/default.nix b/nixpkgs/pkgs/applications/science/electronics/librepcb/default.nix
index 110552d1d645..fb931ec91622 100644
--- a/nixpkgs/pkgs/applications/science/electronics/librepcb/default.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/librepcb/default.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchFromGitHub, qtbase, qttools, qmake }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "librepcb";
   version = "0.1.0";
 
diff --git a/nixpkgs/pkgs/applications/science/logic/abc/default.nix b/nixpkgs/pkgs/applications/science/logic/abc/default.nix
index fd50fc825a06..c832d12627a0 100644
--- a/nixpkgs/pkgs/applications/science/logic/abc/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/abc/default.nix
@@ -1,6 +1,6 @@
 { fetchFromGitHub, stdenv, readline, cmake }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "abc-verifier";
   version = "2018-07-08";
 
diff --git a/nixpkgs/pkgs/applications/science/logic/aspino/default.nix b/nixpkgs/pkgs/applications/science/logic/aspino/default.nix
index bf8d3cf03b83..d6190942efab 100644
--- a/nixpkgs/pkgs/applications/science/logic/aspino/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/aspino/default.nix
@@ -7,7 +7,7 @@ let
   };
 in
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   name = "aspino-unstable-2017-03-09";
 
   src = fetchFromGitHub {
diff --git a/nixpkgs/pkgs/applications/science/logic/avy/default.nix b/nixpkgs/pkgs/applications/science/logic/avy/default.nix
index 668fd9fea72d..9b59828ddab7 100644
--- a/nixpkgs/pkgs/applications/science/logic/avy/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/avy/default.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchgit, cmake, zlib, boost }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "avy";
   version = "2017.10.16";
 
diff --git a/nixpkgs/pkgs/applications/science/logic/btor2tools/default.nix b/nixpkgs/pkgs/applications/science/logic/btor2tools/default.nix
index 9d6c866faea3..2d00e9f30464 100644
--- a/nixpkgs/pkgs/applications/science/logic/btor2tools/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/btor2tools/default.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchFromGitHub }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "btor2tools";
   version = "pre55_8c150b39";
 
diff --git a/nixpkgs/pkgs/applications/science/logic/clprover/clprover.nix b/nixpkgs/pkgs/applications/science/logic/clprover/clprover.nix
index e2f48b340292..0319069660ed 100644
--- a/nixpkgs/pkgs/applications/science/logic/clprover/clprover.nix
+++ b/nixpkgs/pkgs/applications/science/logic/clprover/clprover.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchzip }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "clprover";
   version = "1.0.3";
 
diff --git a/nixpkgs/pkgs/applications/science/logic/coq/default.nix b/nixpkgs/pkgs/applications/science/logic/coq/default.nix
index dfe1277d5ac9..a04ec0bb16ce 100644
--- a/nixpkgs/pkgs/applications/science/logic/coq/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/coq/default.nix
@@ -29,7 +29,7 @@ let
    "8.9.0" = "1dkgdjc4n1m15m1p724hhi5cyxpqbjw6rxc5na6fl3v4qjjfnizh";
    "8.9.1" = "1xrq6mkhpq994bncmnijf8jwmwn961kkpl4mwwlv7j3dgnysrcv2";
    "8.10+beta2" = "0jk7pwydhd17ab7ii69zvi4sgrr630q2lsxhckaj3sz55cpjlhal";
-  }."${version}";
+  }.${version};
   coq-version = stdenv.lib.versions.majorMinor version;
   versionAtLeast = stdenv.lib.versionAtLeast coq-version;
   ideFlags = stdenv.lib.optionalString (buildIde && !versionAtLeast "8.10")
diff --git a/nixpkgs/pkgs/applications/science/logic/drat-trim/default.nix b/nixpkgs/pkgs/applications/science/logic/drat-trim/default.nix
index 50454847baf1..4c4ea0f14ce1 100644
--- a/nixpkgs/pkgs/applications/science/logic/drat-trim/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/drat-trim/default.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchFromGitHub }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   name = "drat-trim-2017-08-31";
 
   src = fetchFromGitHub {
diff --git a/nixpkgs/pkgs/applications/science/logic/elan/default.nix b/nixpkgs/pkgs/applications/science/logic/elan/default.nix
index bc4f526bb3a4..f9a911d82108 100644
--- a/nixpkgs/pkgs/applications/science/logic/elan/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/elan/default.nix
@@ -1,7 +1,7 @@
 { stdenv, pkgconfig, curl, openssl, zlib, fetchFromGitHub, rustPlatform }:
 
 rustPlatform.buildRustPackage rec {
-  name = "elan-${version}";
+  pname = "elan";
   version = "0.7.5";
 
   cargoSha256 = "0lc320m3vw76d6pa5wp6c9jblac6lmyf9qqnxmsnkn4ixdhnghsd";
diff --git a/nixpkgs/pkgs/applications/science/logic/fast-downward/default.nix b/nixpkgs/pkgs/applications/science/logic/fast-downward/default.nix
index 21ce6be3e6c1..ed757e444b7c 100644
--- a/nixpkgs/pkgs/applications/science/logic/fast-downward/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/fast-downward/default.nix
@@ -1,6 +1,6 @@
 { stdenv, lib, fetchhg, cmake, which, python3, osi, cplex }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   name = "fast-downward-2019-05-13";
 
   src = fetchhg {
diff --git a/nixpkgs/pkgs/applications/science/logic/lean2/default.nix b/nixpkgs/pkgs/applications/science/logic/lean2/default.nix
index 22177798647b..8cc50bb5e295 100644
--- a/nixpkgs/pkgs/applications/science/logic/lean2/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/lean2/default.nix
@@ -1,7 +1,7 @@
 { stdenv, fetchFromGitHub, cmake, gmp, mpfr, python
 , gperftools, ninja, makeWrapper }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "lean2";
   version = "2017-07-22";
 
diff --git a/nixpkgs/pkgs/applications/science/logic/lingeling/default.nix b/nixpkgs/pkgs/applications/science/logic/lingeling/default.nix
index dbd34f1da6e6..287dbd36eabf 100644
--- a/nixpkgs/pkgs/applications/science/logic/lingeling/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/lingeling/default.nix
@@ -2,7 +2,7 @@
 , aiger
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "lingeling";
   # This is the version used in satcomp2018, which was
   # relicensed, and also known as version 'bcj'
diff --git a/nixpkgs/pkgs/applications/science/logic/metis-prover/default.nix b/nixpkgs/pkgs/applications/science/logic/metis-prover/default.nix
index 7e46dbeb0743..ed1218c401b3 100644
--- a/nixpkgs/pkgs/applications/science/logic/metis-prover/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/metis-prover/default.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchFromGitHub, perl, mlton }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "metis-prover";
   version = "2.3.20160713";
 
diff --git a/nixpkgs/pkgs/applications/science/logic/minisat/unstable.nix b/nixpkgs/pkgs/applications/science/logic/minisat/unstable.nix
index f1a42f8215e3..ef46c694acb7 100644
--- a/nixpkgs/pkgs/applications/science/logic/minisat/unstable.nix
+++ b/nixpkgs/pkgs/applications/science/logic/minisat/unstable.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchFromGitHub, zlib, cmake }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   name = "minisat-unstable-2013-09-25";
 
   src = fetchFromGitHub {
diff --git a/nixpkgs/pkgs/applications/science/logic/monosat/default.nix b/nixpkgs/pkgs/applications/science/logic/monosat/default.nix
index 54bedc7c5e97..30d47687a3eb 100644
--- a/nixpkgs/pkgs/applications/science/logic/monosat/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/monosat/default.nix
@@ -20,7 +20,7 @@ let
     inherit rev sha256;
   };
 
-  core = stdenv.mkDerivation rec {
+  core = stdenv.mkDerivation {
     name = "${pname}-${version}";
     inherit src;
     buildInputs = [ cmake zlib gmp jdk8 ];
diff --git a/nixpkgs/pkgs/applications/science/logic/open-wbo/default.nix b/nixpkgs/pkgs/applications/science/logic/open-wbo/default.nix
index 48546a86112b..32ce9fde0c31 100644
--- a/nixpkgs/pkgs/applications/science/logic/open-wbo/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/open-wbo/default.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchFromGitHub, zlib, gmp }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   name = "open-wbo-2.0";
 
   src = fetchFromGitHub {
diff --git a/nixpkgs/pkgs/applications/science/logic/petrinizer/default.nix b/nixpkgs/pkgs/applications/science/logic/petrinizer/default.nix
index cb35b9f27d52..d277e0e1521a 100644
--- a/nixpkgs/pkgs/applications/science/logic/petrinizer/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/petrinizer/default.nix
@@ -1,6 +1,12 @@
-{ mkDerivation, async, base, bytestring, containers, fetchFromGitLab, mtl
-, parallel-io, parsec, sbv, stdenv, stm, transformers
+{ mkDerivation, callPackage, buildPackages
+, async, base, bytestring, containers, fetchFromGitLab, mtl
+, parallel-io, parsec, stdenv, stm, transformers
 }:
+let
+  z3 = callPackage ./z3.nix { gomp = null; z3 = buildPackages.z3; };
+in let
+  sbv = callPackage ./sbv-7.13.nix { inherit z3; };
+in
 mkDerivation rec {
   pname = "petrinizer";
   version = "0.9.1.1";
diff --git a/nixpkgs/pkgs/applications/science/logic/petrinizer/sbv-7.13.nix b/nixpkgs/pkgs/applications/science/logic/petrinizer/sbv-7.13.nix
new file mode 100644
index 000000000000..ed10e9f3db19
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/logic/petrinizer/sbv-7.13.nix
@@ -0,0 +1,26 @@
+{ mkDerivation, array, async, base, bytestring, containers
+, crackNum, deepseq, directory, doctest, filepath, generic-deriving
+, ghc, Glob, hlint, mtl, pretty, process, QuickCheck, random
+, stdenv, syb, tasty, tasty-golden, tasty-hunit, tasty-quickcheck
+, template-haskell, time, z3
+}:
+mkDerivation {
+  pname = "sbv";
+  version = "7.13";
+  sha256 = "0bk400swnb4s98c5p71ml1px6jndaiqhf5dj7zmnliyplqcgpfik";
+  enableSeparateDataOutput = true;
+  libraryHaskellDepends = [
+    array async base containers crackNum deepseq directory filepath
+    generic-deriving ghc mtl pretty process QuickCheck random syb
+    template-haskell time
+  ];
+  testHaskellDepends = [
+    base bytestring containers crackNum directory doctest filepath Glob
+    hlint mtl QuickCheck random syb tasty tasty-golden tasty-hunit
+    tasty-quickcheck template-haskell
+  ];
+  testSystemDepends = [ z3 ];
+  homepage = "http://leventerkok.github.com/sbv/";
+  description = "SMT Based Verification: Symbolic Haskell theorem prover using SMT solving";
+  license = stdenv.lib.licenses.bsd3;
+}
diff --git a/nixpkgs/pkgs/applications/science/logic/petrinizer/z3.nix b/nixpkgs/pkgs/applications/science/logic/petrinizer/z3.nix
new file mode 100644
index 000000000000..4d868054c09b
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/logic/petrinizer/z3.nix
@@ -0,0 +1,24 @@
+{ mkDerivation, fetchpatch
+, base, containers, gomp, hspec, QuickCheck, stdenv
+, transformers, z3
+}:
+mkDerivation {
+  pname = "z3";
+  version = "408.0";
+  sha256 = "13qkzy9wc17rm60i24fa9sx15ywbxq4a80g33w20887gvqyc0q53";
+  isLibrary = true;
+  isExecutable = true;
+  libraryHaskellDepends = [ base containers transformers ];
+  librarySystemDepends = [ gomp z3 ];
+  testHaskellDepends = [ base hspec QuickCheck ];
+  homepage = "https://github.com/IagoAbal/haskell-z3";
+  description = "Bindings for the Z3 Theorem Prover";
+  license = stdenv.lib.licenses.bsd3;
+  doCheck = false;
+  patches = [
+    (fetchpatch {
+      url = "https://github.com/IagoAbal/haskell-z3/commit/b10e09b8a809fb5bbbb1ef86aeb62109ece99cae.patch";
+      sha256 = "13fnrs27mg3985r3lwks8fxfxr5inrayy2cyx2867d92pnl3yry4";
+    })
+  ];
+}
diff --git a/nixpkgs/pkgs/applications/science/logic/saw-tools/default.nix b/nixpkgs/pkgs/applications/science/logic/saw-tools/default.nix
index 3f8305ff4030..d357bef2c7a0 100644
--- a/nixpkgs/pkgs/applications/science/logic/saw-tools/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/saw-tools/default.nix
@@ -22,7 +22,7 @@ let
       sha256 = "07gyf319v6ama6n1aj96403as04bixi8mbisfy7f7va689zklflr";
     };
 in
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "saw-tools";
   version = "0.1.1-20150731";
 
diff --git a/nixpkgs/pkgs/applications/science/logic/spass/default.nix b/nixpkgs/pkgs/applications/science/logic/spass/default.nix
index 2645aa102d92..ece6f0b9f6a8 100644
--- a/nixpkgs/pkgs/applications/science/logic/spass/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/spass/default.nix
@@ -8,7 +8,7 @@ let
     + " dfg2ascii dfg2dfg tptp2dfg dimacs2dfg pgen rescmp";
 in
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "spass";
   version = "${baseVersion}.${minorVersion}";
 
diff --git a/nixpkgs/pkgs/applications/science/logic/symbiyosys/default.nix b/nixpkgs/pkgs/applications/science/logic/symbiyosys/default.nix
index 29eb8026366b..ed66c77dcabf 100644
--- a/nixpkgs/pkgs/applications/science/logic/symbiyosys/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/symbiyosys/default.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchFromGitHub, yosys, bash, python3 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "symbiyosys";
   version = "2019.08.13";
 
diff --git a/nixpkgs/pkgs/applications/science/logic/verit/default.nix b/nixpkgs/pkgs/applications/science/logic/verit/default.nix
index a04ab46c669b..2c68191b800e 100644
--- a/nixpkgs/pkgs/applications/science/logic/verit/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/verit/default.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchurl, autoreconfHook, gmp, flex, bison }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "veriT";
   version = "2016";
 
diff --git a/nixpkgs/pkgs/applications/science/logic/why3/default.nix b/nixpkgs/pkgs/applications/science/logic/why3/default.nix
index 3cb14d7da21e..6f338f214783 100644
--- a/nixpkgs/pkgs/applications/science/logic/why3/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/why3/default.nix
@@ -1,7 +1,7 @@
 { callPackage, fetchurl, stdenv
 , ocamlPackages, coqPackages, rubber, hevea, emacs }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "why3";
   version = "1.2.0";
 
diff --git a/nixpkgs/pkgs/applications/science/machine-learning/labelimg/default.nix b/nixpkgs/pkgs/applications/science/machine-learning/labelimg/default.nix
index 340073b016e3..4469e7f06e03 100644
--- a/nixpkgs/pkgs/applications/science/machine-learning/labelimg/default.nix
+++ b/nixpkgs/pkgs/applications/science/machine-learning/labelimg/default.nix
@@ -1,6 +1,6 @@
 { stdenv, python2Packages, fetchurl }:
   python2Packages.buildPythonApplication rec {
-    name = "labelImg-${version}";
+    pname = "labelImg";
     version = "1.6.0";
     src = fetchurl {
       url = "https://github.com/tzutalin/labelImg/archive/v${version}.tar.gz";
diff --git a/nixpkgs/pkgs/applications/science/machine-learning/torch/torch-distro.nix b/nixpkgs/pkgs/applications/science/machine-learning/torch/torch-distro.nix
index 9c4f24021430..73272df99221 100644
--- a/nixpkgs/pkgs/applications/science/machine-learning/torch/torch-distro.nix
+++ b/nixpkgs/pkgs/applications/science/machine-learning/torch/torch-distro.nix
@@ -94,7 +94,7 @@ let
     #   rockspec = "lua-cjson-2.1devel-1.rockspec";
     # };
 
-    lua-cjson = stdenv.mkDerivation rec {
+    lua-cjson = stdenv.mkDerivation {
       name = "lua-cjson";
       src = "${distro_src}/extra/lua-cjson";
 
@@ -179,7 +179,7 @@ let
       rockspec = "rocks/${name}-scm-1.rockspec";
     };
 
-    sys = buildLuaRocks rec {
+    sys = buildLuaRocks {
       name = "sys";
       luadeps = [torch];
       buildInputs = [readline cmake];
@@ -190,14 +190,14 @@ let
       '';
     };
 
-    xlua = buildLuaRocks rec {
+    xlua = buildLuaRocks {
       name = "xlua";
       luadeps = [torch sys];
       src = "${distro_src}/pkg/xlua";
       rockspec = "xlua-1.0-0.rockspec";
     };
 
-    nn = buildLuaRocks rec {
+    nn = buildLuaRocks {
       name = "nn";
       luadeps = [torch luaffifb];
       buildInputs = [cmake];
@@ -208,7 +208,7 @@ let
       '';
     };
 
-    graph = buildLuaRocks rec {
+    graph = buildLuaRocks {
       name = "graph";
       luadeps = [ torch ];
       buildInputs = [cmake];
@@ -219,7 +219,7 @@ let
       '';
     };
 
-    nngraph = buildLuaRocks rec {
+    nngraph = buildLuaRocks {
       name = "nngraph";
       luadeps = [ torch nn graph ];
       buildInputs = [cmake];
@@ -229,7 +229,7 @@ let
       '';
     };
 
-    image = buildLuaRocks rec {
+    image = buildLuaRocks {
       name = "image";
       luadeps = [ torch dok sys xlua ];
       buildInputs = [cmake libjpeg libpng];
@@ -240,7 +240,7 @@ let
       '';
     };
 
-    optim = buildLuaRocks rec {
+    optim = buildLuaRocks {
       name = "optim";
       luadeps = [ torch ];
       buildInputs = [cmake];
@@ -251,7 +251,7 @@ let
       '';
     };
 
-    gnuplot = buildLuaRocks rec {
+    gnuplot = buildLuaRocks {
       name = "gnuplot";
       luadeps = [ torch paths ];
       runtimeDeps = [ pkgs_gnuplot less ];
@@ -259,7 +259,7 @@ let
       rockspec = "rocks/gnuplot-scm-1.rockspec";
     };
 
-    unsup = buildLuaRocks rec {
+    unsup = buildLuaRocks {
       name = "unsup";
       luadeps = [ torch xlua optim ];
       buildInputs = [ cmake ];
@@ -275,7 +275,7 @@ let
       meta.broken = true;
     };
 
-    trepl = buildLuaRocks rec {
+    trepl = buildLuaRocks {
       name = "trepl";
       luadeps = [torch gnuplot paths penlight graph nn nngraph image gnuplot optim sys dok unsup];
       runtimeDeps = [ ncurses readline ];
@@ -285,7 +285,7 @@ let
       };
     };
 
-    lbase64 = buildLuaRocks rec {
+    lbase64 = buildLuaRocks {
       name = "lbase64";
       src = fetchgit {
         url = "https://github.com/LuaDist2/lbase64";
@@ -295,7 +295,7 @@ let
       meta.broken = true; # 2018-04-11
     };
 
-    luuid = stdenv.mkDerivation rec {
+    luuid = stdenv.mkDerivation {
       name = "luuid";
       src = fetchgit {
         url = "https://github.com/LuaDist/luuid";
@@ -314,7 +314,7 @@ let
     };
 
     # Doesn't work due to missing deps (according to luarocs).
-    itorch = buildLuaRocks rec {
+    itorch = buildLuaRocks {
       name = "itorch";
       luadeps = [torch gnuplot paths penlight graph nn nngraph image gnuplot
                   optim sys dok lbase64 lua-cjson luuid];
diff --git a/nixpkgs/pkgs/applications/science/math/LiE/default.nix b/nixpkgs/pkgs/applications/science/math/LiE/default.nix
index 6909cfd8ef65..d59ec57c1a85 100644
--- a/nixpkgs/pkgs/applications/science/math/LiE/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/LiE/default.nix
@@ -1,7 +1,7 @@
 { stdenv, fetchurl
 , bison, readline }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   version = "2.2.2";
      # The current version of LiE is 2.2.2, which is more or less unchanged
      # since about the year 2000. Minor bugfixes do get applied now and then.
diff --git a/nixpkgs/pkgs/applications/science/math/form/default.nix b/nixpkgs/pkgs/applications/science/math/form/default.nix
index eb42315f015b..0dbafebf2c06 100644
--- a/nixpkgs/pkgs/applications/science/math/form/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/form/default.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchurl, gmp, zlib }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   version = "4.2.1";
   pname = "form";
 
diff --git a/nixpkgs/pkgs/applications/science/math/mathematica/9.nix b/nixpkgs/pkgs/applications/science/math/mathematica/9.nix
index 1023e7ca3d5c..aaa1c02ec0a0 100644
--- a/nixpkgs/pkgs/applications/science/math/mathematica/9.nix
+++ b/nixpkgs/pkgs/applications/science/math/mathematica/9.nix
@@ -25,7 +25,7 @@ stdenv.mkDerivation rec {
 
   name = "mathematica-9.0.0";
 
-  src = requireFile rec {
+  src = requireFile {
     name = "Mathematica_9.0.0_LINUX.sh";
     message = '' 
       This nix expression requires that Mathematica_9.0.0_LINUX.sh is
diff --git a/nixpkgs/pkgs/applications/science/math/nauty/default.nix b/nixpkgs/pkgs/applications/science/math/nauty/default.nix
index c86354234e3f..bd116b02e29e 100644
--- a/nixpkgs/pkgs/applications/science/math/nauty/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/nauty/default.nix
@@ -14,10 +14,10 @@ stdenv.mkDerivation rec {
     # Prevent nauty from sniffing some cpu features. While those are very
     # widely available, it can lead to nasty bugs when they are not available:
     # https://groups.google.com/forum/#!topic/sage-packaging/Pe4SRDNYlhA
-    "default"        = [ "--disable-clz" "--disable-popcnt" ];
-    "westmere"       = [ "--disable-clz" ];
-    "sandybridge"    = [ "--disable-clz" ];
-    "ivybridge"      = [ "--disable-clz" ];
+    default        = [ "--disable-clz" "--disable-popcnt" ];
+    westmere       = [ "--disable-clz" ];
+    sandybridge    = [ "--disable-clz" ];
+    ivybridge      = [ "--disable-clz" ];
   }.${stdenv.hostPlatform.platform.gcc.arch or "default"} or [];
   buildInputs = [];
   installPhase = ''
diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-tests.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-tests.nix
index 856d604d7518..93ec1e33cf69 100644
--- a/nixpkgs/pkgs/applications/science/math/sage/sage-tests.nix
+++ b/nixpkgs/pkgs/applications/science/math/sage/sage-tests.nix
@@ -23,7 +23,7 @@ let
   relpathToArg = relpath: lib.escapeShellArg "${src}/${relpath}"; # paths need to be absolute
   testFileList = lib.concatStringsSep " " (map relpathToArg files);
 in
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   version = src.version;
   pname = "sage-tests";
   inherit src;
diff --git a/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix b/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix
index 21ce53e70c51..8e85cece9b28 100644
--- a/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix
@@ -15,7 +15,7 @@ let
     else
       badArch;
 in
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   inherit name;
 
   src = fetchurl {
diff --git a/nixpkgs/pkgs/applications/science/misc/gephi/default.nix b/nixpkgs/pkgs/applications/science/misc/gephi/default.nix
index 17b2fe27f297..577c8ecfa058 100644
--- a/nixpkgs/pkgs/applications/science/misc/gephi/default.nix
+++ b/nixpkgs/pkgs/applications/science/misc/gephi/default.nix
@@ -27,7 +27,7 @@ let
     outputHash = "1p7yf97dn0nvr005cbs6vdk3i341s8fya4kfccj8qqad2qgxflif";
   };
 in
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "gephi";
   inherit version;
 
diff --git a/nixpkgs/pkgs/applications/science/misc/megam/default.nix b/nixpkgs/pkgs/applications/science/misc/megam/default.nix
index 59f5afb2f437..f86bed854a2b 100644
--- a/nixpkgs/pkgs/applications/science/misc/megam/default.nix
+++ b/nixpkgs/pkgs/applications/science/misc/megam/default.nix
@@ -1,7 +1,7 @@
 { fetchurl, stdenv, ocaml, makeWrapper, ncurses }:
 
 let version = "0.92"; in
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "megam";
   inherit version;
 
diff --git a/nixpkgs/pkgs/applications/science/misc/openmvs/default.nix b/nixpkgs/pkgs/applications/science/misc/openmvs/default.nix
index 43d57feab71b..bb067fbca7a9 100644
--- a/nixpkgs/pkgs/applications/science/misc/openmvs/default.nix
+++ b/nixpkgs/pkgs/applications/science/misc/openmvs/default.nix
@@ -2,7 +2,7 @@
 , eigen, opencv, ceres-solver, cgal, boost, vcg
 , gmp, mpfr, glog, gflags, libjpeg_turbo }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   name = "openmvs-unstable-2018-05-26";
 
   src = fetchFromGitHub {
diff --git a/nixpkgs/pkgs/applications/science/misc/rink/default.nix b/nixpkgs/pkgs/applications/science/misc/rink/default.nix
index daa8b4943227..0dfcbfda0024 100644
--- a/nixpkgs/pkgs/applications/science/misc/rink/default.nix
+++ b/nixpkgs/pkgs/applications/science/misc/rink/default.nix
@@ -2,7 +2,7 @@
 
 rustPlatform.buildRustPackage rec {
   version = "0.4.4";
-  name = "rink-${version}";
+  pname = "rink";
 
   src = fetchFromGitHub {
     owner = "tiffany352";
diff --git a/nixpkgs/pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix b/nixpkgs/pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix
index c7692dde13aa..b0ed5e946379 100644
--- a/nixpkgs/pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix
+++ b/nixpkgs/pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix
@@ -2,7 +2,7 @@
 , gfortran, mpi
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   version = "1.10";
   pname = "DL_POLY_Classic";
 
diff --git a/nixpkgs/pkgs/applications/science/physics/sacrifice/default.nix b/nixpkgs/pkgs/applications/science/physics/sacrifice/default.nix
index dd092a2ce9a9..80417f0fcc18 100644
--- a/nixpkgs/pkgs/applications/science/physics/sacrifice/default.nix
+++ b/nixpkgs/pkgs/applications/science/physics/sacrifice/default.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchurl, boost, hepmc2, lhapdf, pythia, makeWrapper }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "sacrifice";
   version = "1.0.0";
 
diff --git a/nixpkgs/pkgs/applications/science/robotics/gazebo/6.nix b/nixpkgs/pkgs/applications/science/robotics/gazebo/6.nix
index 0d1aa4a9085f..80c52b49e47f 100644
--- a/nixpkgs/pkgs/applications/science/robotics/gazebo/6.nix
+++ b/nixpkgs/pkgs/applications/science/robotics/gazebo/6.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchurl, callPackage, ignition, gazeboSimulator, ... } @ args:
 
-callPackage ./default.nix (args // rec {
+callPackage ./default.nix (args // {
   version = "6.5.1";
   src-sha256 = "96260aa23f1a1f24bc116f8e359d31f3bc65011033977cb7fb2c64d574321908";
   sdformat = gazeboSimulator.sdformat3;