Merge master into staging-next

pkgs/development/compilers/chicken/4/default.nix

@@ -0,0 +1,21 @@
+{ newScope } :
+let
+  callPackage = newScope self;
+
+  self = {
+    pkgs = self;
+
+    fetchegg = callPackage ./fetchegg { };
+
+    eggDerivation = callPackage ./eggDerivation.nix { };
+
+    chicken = callPackage ./chicken.nix {
+      bootstrap-chicken = self.chicken.override { bootstrap-chicken = null; };
+    };
+
+    chickenEggs = callPackage ./eggs.nix { };
+
+    egg2nix = callPackage ./egg2nix.nix { };
+  };
+
+in self

pkgs/development/compilers/chicken/4/eggDerivation.nix

@@ -17,9 +17,8 @@ let
 in
 stdenv.mkDerivation ({
   name = "chicken-${name}";
-  propagatedBuildInputs = buildInputs ++ [ chicken ];
-  propagatedUserEnvPkgs = buildInputs ++ [ chicken ];
-  buildInputs = [ makeWrapper ];
+  propagatedBuildInputs = buildInputs;
+  buildInputs = [ makeWrapper chicken ];
 
   CSC_OPTIONS = stdenv.lib.concatStringsSep " " cscOptions;
 

pkgs/development/compilers/chicken/4/fetchegg/builder.sh

@@ -0,0 +1,9 @@
+source $stdenv/setup
+
+header "exporting egg ${eggName} (version $version) into $out"
+
+mkdir -p $out
+chicken-install -r "${eggName}:${version}"
+cp -r ${eggName}/* $out/
+
+stopNest

pkgs/development/compilers/chicken/4/fetchegg/default.nix

@@ -0,0 +1,25 @@
+# Fetches a chicken egg from henrietta using `chicken-install -r'
+# See: http://wiki.call-cc.org/chicken-projects/egg-index-4.html
+
+{ stdenvNoCC, chicken }:
+{ name, version, md5 ? "", sha256 ? "" }:
+
+if md5 != "" then
+  throw "fetchegg does not support md5 anymore, please use sha256"
+else
+stdenvNoCC.mkDerivation {
+  name = "chicken-${name}-export-${version}";
+  builder = ./builder.sh;
+  nativeBuildInputs = [ chicken ];
+
+  outputHashAlgo = "sha256";
+  outputHashMode = "recursive";
+  outputHash = sha256;
+
+  inherit version;
+
+  eggName = name;
+
+  impureEnvVars = stdenvNoCC.lib.fetchers.proxyImpureEnvVars;
+}
+

pkgs/development/compilers/chicken/5/chicken.nix

@@ -0,0 +1,62 @@
+{ stdenv, fetchurl, makeWrapper, bootstrap-chicken ? null }:
+
+let
+  version = "5.0.0";
+  platform = with stdenv;
+    if isDarwin then "macosx"
+    else if isCygwin then "cygwin"
+    else if (isFreeBSD || isOpenBSD) then "bsd"
+    else if isSunOS then "solaris"
+    else "linux"; # Should be a sane default
+  lib = stdenv.lib;
+in
+stdenv.mkDerivation {
+  name = "chicken-${version}";
+
+  binaryVersion = 9;
+
+  src = fetchurl {
+    url = "https://code.call-cc.org/releases/${version}/chicken-${version}.tar.gz";
+    sha256 = "15b5yrzfa8aimzba79x7v6y282f898rxqxfxrr446sjx9jwlpfd8";
+  };
+
+  setupHook = lib.ifEnable (bootstrap-chicken != null) ./setup-hook.sh;
+
+  buildFlags = "PLATFORM=${platform} PREFIX=$(out) VARDIR=$(out)/var/lib";
+  installFlags = "PLATFORM=${platform} PREFIX=$(out) VARDIR=$(out)/var/lib";
+
+  buildInputs = [
+    makeWrapper
+  ] ++ (lib.ifEnable (bootstrap-chicken != null) [
+    bootstrap-chicken
+  ]);
+
+  postInstall = ''
+    for f in $out/bin/*
+    do
+      wrapProgram $f \
+        --prefix PATH : ${stdenv.cc}/bin
+    done
+
+    mv $out/var/lib/chicken $out/lib
+    rmdir $out/var/lib
+    rmdir $out/var
+  '';
+
+  # TODO: Assert csi -R files -p '(pathname-file (repository-path))' == binaryVersion
+
+  meta = {
+    homepage = http://www.call-cc.org/;
+    license = stdenv.lib.licenses.bsd3;
+    maintainers = with stdenv.lib.maintainers; [ the-kenny ];
+    platforms = stdenv.lib.platforms.linux; # Maybe other non-darwin Unix
+    description = "A portable compiler for the Scheme programming language";
+    longDescription = ''
+      CHICKEN is a compiler for the Scheme programming language.
+      CHICKEN produces portable and efficient C, supports almost all
+      of the R5RS Scheme language standard, and includes many
+      enhancements and extensions. CHICKEN runs on Linux, macOS,
+      Windows, and many Unix flavours.
+    '';
+  };
+}

pkgs/development/compilers/chicken/5/default.nix

@@ -0,0 +1,21 @@
+{ newScope } :
+let
+  callPackage = newScope self;
+
+  self = {
+    pkgs = self;
+
+    fetchegg = callPackage ./fetchegg { };
+
+    eggDerivation = callPackage ./eggDerivation.nix { };
+
+    chicken = callPackage ./chicken.nix {
+      bootstrap-chicken = self.chicken.override { bootstrap-chicken = null; };
+    };
+
+    chickenEggs = callPackage ./eggs.nix { };
+
+    egg2nix = callPackage ./egg2nix.nix { };
+  };
+
+in self

pkgs/development/compilers/chicken/5/egg2nix.nix

@@ -0,0 +1,29 @@
+{ stdenv, eggDerivation, fetchFromGitHub, chickenEggs }:
+
+# Note: This mostly reimplements the default.nix already contained in
+# the tarball. Is there a nicer way than duplicating code?
+
+let
+  version = "c5-git";
+in
+eggDerivation {
+  src = fetchFromGitHub {
+    owner = "corngood";
+    repo = "egg2nix";
+    rev = "chicken-5";
+    sha256 = "1vfnhbcnyakywgjafhs0k5kpsdnrinzvdjxpz3fkwas1jsvxq3d1";
+  };
+
+  name = "egg2nix-${version}";
+  buildInputs = with chickenEggs; [
+    args matchable
+  ];
+
+  meta = {
+    description = "Generate nix-expression from CHICKEN scheme eggs";
+    homepage = https://github.com/the-kenny/egg2nix;
+    license = stdenv.lib.licenses.bsd3;
+    platforms = stdenv.lib.platforms.unix;
+    maintainers = [ stdenv.lib.maintainers.the-kenny ];
+  };
+}

pkgs/development/compilers/chicken/5/eggDerivation.nix

@@ -0,0 +1,41 @@
+{ stdenv, chicken, makeWrapper }:
+{ name, src
+, buildInputs ? []
+, chickenInstallFlags ? []
+, cscOptions          ? []
+, ...} @ args:
+
+let
+  overrides = import ./overrides.nix;
+  baseName = (builtins.parseDrvName name).name;
+  override = if builtins.hasAttr baseName overrides
+   then
+     builtins.getAttr baseName overrides
+   else
+     {};
+in
+stdenv.mkDerivation ({
+  name = "chicken-${name}";
+  propagatedBuildInputs = buildInputs;
+  buildInputs = [ makeWrapper chicken ];
+
+  CSC_OPTIONS = stdenv.lib.concatStringsSep " " cscOptions;
+
+  installPhase = ''
+    runHook preInstall
+
+    export CHICKEN_INSTALL_PREFIX=$out
+    export CHICKEN_INSTALL_REPOSITORY=$out/lib/chicken/${toString chicken.binaryVersion}
+    chicken-install ${stdenv.lib.concatStringsSep " " chickenInstallFlags}
+
+    for f in $out/bin/*
+    do
+      wrapProgram $f \
+        --prefix CHICKEN_REPOSITORY_PATH : "$out/lib/chicken/${toString chicken.binaryVersion}/:$CHICKEN_REPOSITORY_PATH" \
+        --prefix CHICKEN_INCLUDE_PATH : "$CHICKEN_INCLUDE_PATH:$out/share/" \
+        --prefix PATH : "$out/bin:${chicken}/bin:$CHICKEN_REPOSITORY_PATH"
+    done
+
+    runHook postInstall
+  '';
+} // (builtins.removeAttrs args ["name" "buildInputs"]) // override)

pkgs/development/compilers/chicken/5/eggs.nix

@@ -0,0 +1,91 @@
+{ pkgs, stdenv }:
+rec {
+  inherit (pkgs) eggDerivation fetchegg;
+
+  args = eggDerivation {
+    name = "args-1.6.0";
+
+    src = fetchegg {
+      name = "args";
+      version = "1.6.0";
+      sha256 = "1y9sznh4kxqxvhd8k44bjx0s7xspp52sx4bn8i8i0f8lwch6r2g4";
+    };
+
+    buildInputs = [
+      srfi-1
+      srfi-13
+      srfi-37
+    ];
+  };
+
+  matchable = eggDerivation {
+    name = "matchable-1.0";
+
+    src = fetchegg {
+      name = "matchable";
+      version = "1.0";
+      sha256 = "01vy2ppq3sq0wirvsvl3dh0bwa5jqs1i6rdjdd7pnwj4nncxd1ga";
+    };
+
+    buildInputs = [
+      
+    ];
+  };
+
+  srfi-1 = eggDerivation {
+    name = "srfi-1-0.5";
+
+    src = fetchegg {
+      name = "srfi-1";
+      version = "0.5";
+      sha256 = "0gh1h406xbxwm5gvc5znc93nxp9xjbhyqf7zzga08k5y6igxrlvk";
+    };
+
+    buildInputs = [
+      
+    ];
+  };
+
+  srfi-13 = eggDerivation {
+    name = "srfi-13-0.2";
+
+    src = fetchegg {
+      name = "srfi-13";
+      version = "0.2";
+      sha256 = "0jazbdnn9bjm7wwxqq7xzqxc9zfvaapq565rf1czj6ayl96yvk3n";
+    };
+
+    buildInputs = [
+      srfi-14
+    ];
+  };
+
+  srfi-14 = eggDerivation {
+    name = "srfi-14-0.2";
+
+    src = fetchegg {
+      name = "srfi-14";
+      version = "0.2";
+      sha256 = "13nm4nn1d52nkvhjizy26z3s6q41x1ml4zm847xzf86x1zwvymni";
+    };
+
+    buildInputs = [
+      
+    ];
+  };
+
+  srfi-37 = eggDerivation {
+    name = "srfi-37-1.4";
+
+    src = fetchegg {
+      name = "srfi-37";
+      version = "1.4";
+      sha256 = "17f593497n70gldkj6iab6ilgryiqar051v6azn1szhnm1lk7dwd";
+    };
+
+    buildInputs = [
+      
+    ];
+  };
+}
+

pkgs/development/compilers/chicken/5/eggs.scm

@@ -0,0 +1,3 @@
+;; Eggs used by egg2nix
+args
+matchable

pkgs/development/compilers/chicken/5/fetchegg/builder.sh

@@ -0,0 +1,10 @@
+source $stdenv/setup
+
+header "exporting egg ${eggName} (version $version) into $out"
+
+mkdir -p $out
+CHICKEN_EGG_CACHE=. chicken-install -r "${eggName}:${version}"
+rm ${eggName}/{STATUS,TIMESTAMP}
+cp -r ${eggName}/* $out/
+
+stopNest

pkgs/development/compilers/chicken/5/fetchegg/default.nix

@@ -0,0 +1,25 @@
+# Fetches a chicken egg from henrietta using `chicken-install -r'
+# See: http://wiki.call-cc.org/chicken-projects/egg-index-5.html
+
+{ stdenvNoCC, chicken }:
+{ name, version, md5 ? "", sha256 ? "" }:
+
+if md5 != "" then
+  throw "fetchegg does not support md5 anymore, please use sha256"
+else
+stdenvNoCC.mkDerivation {
+  name = "chicken-${name}-export";
+  builder = ./builder.sh;
+  nativeBuildInputs = [ chicken ];
+
+  outputHashAlgo = "sha256";
+  outputHashMode = "recursive";
+  outputHash = sha256;
+
+  inherit version;
+
+  eggName = name;
+
+  impureEnvVars = stdenvNoCC.lib.fetchers.proxyImpureEnvVars;
+}
+

pkgs/development/compilers/chicken/5/overrides.nix

@@ -0,0 +1,2 @@
+{
+}

pkgs/development/compilers/chicken/5/setup-hook.sh

@@ -0,0 +1,6 @@
+addChickenRepositoryPath() {
+    addToSearchPathWithCustomDelimiter : CHICKEN_REPOSITORY_PATH "$1/lib/chicken/9/"
+    addToSearchPathWithCustomDelimiter : CHICKEN_INCLUDE_PATH "$1/share/"
+}
+
+addEnvHooks "$targetOffset" addChickenRepositoryPath

pkgs/development/compilers/nextpnr/default.nix

@@ -7,13 +7,13 @@ let
 in
 stdenv.mkDerivation rec {
   name = "nextpnr-${version}";
-  version = "2018.10.17";
+  version = "2018.12.29";
 
   src = fetchFromGitHub {
     owner  = "yosyshq";
     repo   = "nextpnr";
-    rev    = "529a595157a2eef24f8529b0de0c504a40ed503b";
-    sha256 = "06yp89rpvb2s4zc1qkbcp76kqwkk9s8j2ckblqw547dy5ah2cl7h";
+    rev    = "eb456ef476e8342b4709d71cbff6ef22a714d6ec";
+    sha256 = "1gw9r8c6wyfhbzhm3hz1xpbq8ax27qnjwlrimzcykrr9r1cykiik";
   };
 
   nativeBuildInputs = [ cmake ];

pkgs/development/compilers/urn/default.nix

@@ -4,7 +4,7 @@
 }:
 
 let
-  version = "0.7.1";
+  version = "0.7.2";
   # Build a sort of "union package" with all the native dependencies we
   # have: Lua (or LuaJIT), readline, etc. Then, we can depend on this
   # and refer to ${urn-rt} instead of ${lua}, ${readline}, etc.
@@ -27,7 +27,7 @@ stdenv.mkDerivation rec {
     owner = "urn";
     repo = "urn";
     rev = "v${version}";
-    sha256 = "1vw0sljrczbwl7fl5d3frbpklb0larzyp7s7mwwprkb07b027sd5";
+    sha256 = "0nclr3d8ap0y5cg36i7g4ggdqci6m5q27y9f26b57km8p266kcpy";
   };
 
   buildInputs = [ makeWrapper ];

pkgs/development/haskell-modules/configuration-ghc-8.6.x.nix

@@ -87,6 +87,7 @@ self: super: {
   psqueues = dontCheck super.psqueues;    # won't cope with QuickCheck 2.12.x
   system-fileio = dontCheck super.system-fileio;  # avoid dependency on broken "patience"
   unicode-transforms = dontCheck super.unicode-transforms;
+  RSA = dontCheck super.RSA; # https://github.com/GaloisInc/RSA/issues/14 
   monad-par = dontCheck super.monad-par;  # https://github.com/simonmar/monad-par/issues/66
 
   # https://github.com/jgm/skylighting/issues/55

pkgs/development/interpreters/picolisp/default.nix

@@ -1,22 +1,26 @@
-{ stdenv, fetchurl, jdk }:
+{ stdenv, fetchurl, jdk, makeWrapper }:
 with stdenv.lib;
 
 stdenv.mkDerivation rec {
   name = "picoLisp-${version}";
-  version = "16.12";
+  version = "18.12";
   src = fetchurl {
     url = "https://www.software-lab.de/${name}.tgz";
-    sha256 = "1k3x6mvk9b34iiyml142bzh3gf241f25ywjlaagbxzb9vklpws75";
+    sha256 = "0hvgq2vc03bki528jqn95xmvv7mw8xx832spfczhxc16wwbrnrhk";
   };
-  buildInputs = optional stdenv.is64bit jdk;
-  patchPhase = optionalString stdenv.isAarch32 ''
-    sed -i s/-m32//g Makefile
-    cat >>Makefile <<EOF
-    ext.o: ext.c
-    	\$(CC) \$(CFLAGS) -fPIC -D_OS='"\$(OS)"' \$*.c
-    ht.o: ht.c
-    	\$(CC) \$(CFLAGS) -fPIC -D_OS='"\$(OS)"' \$*.c
-    EOF
+  buildInputs = [makeWrapper] ++ optional stdenv.is64bit jdk;
+  patchPhase = ''
+    sed -i "s/which java/command -v java/g" mkAsm
+
+    ${optionalString stdenv.isAarch32 ''
+      sed -i s/-m32//g Makefile
+      cat >>Makefile <<EOF
+      ext.o: ext.c
+        \$(CC) \$(CFLAGS) -fPIC -D_OS='"\$(OS)"' \$*.c
+      ht.o: ht.c
+        \$(CC) \$(CFLAGS) -fPIC -D_OS='"\$(OS)"' \$*.c
+      EOF
+    ''}
   '';
   sourceRoot = ''picoLisp/src${optionalString stdenv.is64bit "64"}'';
   installPhase = ''
@@ -27,11 +31,13 @@ stdenv.mkDerivation rec {
     ln -s "$out/share/picolisp/build-dir" "$out/lib/picolisp"
     ln -s "$out/lib/picolisp/bin/picolisp" "$out/bin/picolisp"
 
-    cat >"$out/bin/pil" <<EOF
-    #! /bin/sh
-    exec $out/bin/picolisp $out/lib/picolisp/lib.l @lib/misc.l @lib/btree.l @lib/db.l @lib/pilog.l
-    EOF
-    chmod +x "$out/bin/pil"
+
+    makeWrapper $out/bin/picolisp $out/bin/pil \
+      --add-flags "$out/lib/picolisp/lib.l" \
+      --add-flags "@lib/misc.l" \
+      --add-flags "@lib/btree.l" \
+      --add-flags "@lib/db.l" \
+      --add-flags "@lib/pilog.l"
 
     mkdir -p "$out/share/emacs"
     ln -s "$out/lib/picolisp/lib/el" "$out/share/emacs/site-lisp"

pkgs/development/libraries/alembic/default.nix

@@ -3,13 +3,13 @@
 stdenv.mkDerivation rec
 {
   name = "alembic-${version}";
-  version = "1.7.9";
+  version = "1.7.10";
 
   src = fetchFromGitHub {
     owner = "alembic";
     repo = "alembic";
     rev = "${version}";
-    sha256 = "0xyclln1m4079akr31vib242912004lln678prda0qwmwvsdrf7z";
+    sha256 = "186wwlbz90gmzr4vsykk4z8bgkd45yhbyfpn8bqwidf9fcimcr2a";
   };
 
   outputs = [ "bin" "dev" "out" "lib" ];

pkgs/development/libraries/allegro/allegro4-mesa-18.2.5.patch

@@ -0,0 +1,26 @@
+--- a/addons/allegrogl/include/alleggl.h
++++ b/addons/allegrogl/include/alleggl.h
+@@ -63,9 +63,11 @@ typedef __int64 INT64;
+ /* HACK: Prevent both Mesa and SGI's broken headers from screwing us */
+ #define __glext_h_
+ #define __glxext_h_
++#define __glx_glxext_h_
+ #include <GL/gl.h>
+ #undef  __glext_h_
+ #undef  __glxext_h_
++#undef  __glx_glxext_h_
+ 
+ #endif /* ALLEGRO_MACOSX */
+ 
+--- a/addons/allegrogl/include/allegrogl/GLext/glx_ext_defs.h
++++ b/addons/allegrogl/include/allegrogl/GLext/glx_ext_defs.h
+@@ -1,7 +1,9 @@
+ /* HACK: Prevent both Mesa and SGI's broken headers from screwing us */
+ #define __glxext_h_
++#define __glx_glxext_h_
+ #include <GL/glx.h>
+ #undef __glxext_h_
++#undef __glx_glxext_h_
+ 
+ #ifndef GLX_VERSION_1_3
+ #define AGLX_VERSION_1_3

pkgs/development/libraries/allegro/default.nix

@@ -13,6 +13,7 @@ stdenv.mkDerivation rec {
   };
 
   patches = [
+    ./allegro4-mesa-18.2.5.patch
     ./nix-unstable-sandbox-fix.patch
   ];
 

pkgs/development/libraries/arrow-cpp/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, symlinkJoin, fetchurl, fetchFromGitHub, boost, brotli, cmake, double-conversion, flatbuffers, gflags, glog, gtest_static, lz4, perl, python, rapidjson, snappy, thrift, which, zlib, zstd }:
+{ stdenv, symlinkJoin, fetchurl, fetchFromGitHub, boost, brotli, cmake, double-conversion, flatbuffers, gflags, glog, gtest, lz4, perl, python, rapidjson, snappy, thrift, which, zlib, zstd }:
 
 let
   parquet-testing = fetchFromGitHub {
@@ -49,7 +49,7 @@ stdenv.mkDerivation rec {
   FLATBUFFERS_HOME = flatbuffers;
   GFLAGS_HOME = gflags;
   GLOG_HOME = glog;
-  GTEST_HOME = symlinkJoin { name="gtest-wrap"; paths = [ gtest_static gtest_static.dev ]; };
+  GTEST_HOME = symlinkJoin { name="gtest-wrap"; paths = [ gtest gtest.dev ]; };
   LZ4_HOME = symlinkJoin { name="lz4-wrap"; paths = [ lz4 lz4.dev ]; };
   RAPIDJSON_HOME = rapidjson;
   SNAPPY_HOME = symlinkJoin { name="snappy-wrap"; paths = [ snappy snappy.dev ]; };

pkgs/development/libraries/aspell/dictionaries.nix

@@ -146,11 +146,11 @@ in rec {
   };
 
   en = buildDict rec {
-    shortName = "en-2016.06.26-0";
+    shortName = "en-2018.04.16-0";
     fullName = "English";
     src = fetchurl {
       url = "mirror://gnu/aspell/dict/en/aspell6-${shortName}.tar.bz2";
-      sha256 = "1clzsfq2cbgp6wvfr2qwfsd2nziipml5m5vqm45r748wczlxihv1";
+      sha256 = "0bxxdzkk9g27plg22y9qzsx9cfjw3aa29w5bmzs561qc9gkp247i";
     };
   };
 

pkgs/development/libraries/capstone/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name    = "capstone-${version}";
-  version = "3.0.5";
+  version = "4.0";
 
   src = fetchurl {
     url    = "https://github.com/aquynh/capstone/archive/${version}.tar.gz";
-    sha256 = "1wbd1g3r32ni6zd9vwrq3kn7fdp9y8qwn9zllrrbk8n5wyaxcgci";
+    sha256 = "0yp6y5m3v674i2pq6s804ikvz43gzgsjwq1maqhmj3b730b4dii6";
   };
 
   configurePhase = '' patchShebangs make.sh '';

pkgs/development/libraries/editline/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, autoreconfHook }:
+{ stdenv, fetchFromGitHub, fetchpatch, autoreconfHook }:
 
 stdenv.mkDerivation rec {
   name = "editline-${version}";
@@ -10,6 +10,15 @@ stdenv.mkDerivation rec {
     sha256 = "0a751dp34mk9hwv59ss447csknpm5i5cgd607m3fqf24rszyhbf2";
   };
 
+  patches = [
+    # will be in 1.17.0
+    (fetchpatch {
+      name = "redisplay-clear-screen.patch";
+      url = "https://github.com/troglobit/editline/commit/a4b67d226829a55bc8501f36708d5e104a52fbe4.patch";
+      sha256 = "0dbgdqxa4x9wgr9kx89ql74np4qq6fzdbph9j9c65ns3gnaanjkw";
+    })
+  ];
+
   nativeBuildInputs = [ autoreconfHook ];
 
   outputs = [ "out" "dev" "man" "doc" ];

pkgs/development/libraries/exiv2/default.nix

@@ -2,38 +2,16 @@
 , autoconf }:
 
 stdenv.mkDerivation rec {
-  name = "exiv2-0.26.2018.06.09";
+  name = "exiv2-0.26.2018.12.30";
 
     #url = "http://www.exiv2.org/builds/${name}-trunk.tar.gz";
   src = fetchFromGitHub rec {
     owner = "exiv2";
     repo  = "exiv2";
-    rev = "4aa57ad";
-    sha256 = "1kblpxbi4wlb0l57xmr7g23zn9adjmfswhs6kcwmd7skwi2yivcd";
+    rev = "f5d0b25"; # https://github.com/Exiv2/exiv2/commits/0.26
+    sha256 = "1blaz3g8dlij881g14nv2nsgr984wy6ypbwgi2pixk978p0gm70i";
   };
 
-  patches = [
-    (fetchurl rec {
-      name = "CVE-2017-9239.patch";
-      url = let patchname = "0006-1296-Fix-submitted.patch";
-          in "https://src.fedoraproject.org/lookaside/pkgs/exiv2/${patchname}"
-          + "/sha512/${sha512}/${patchname}";
-      sha512 = "3f9242dbd4bfa9dcdf8c9820243b13dc14990373a800c4ebb6cf7eac5653cfef"
-             + "e6f2c47a94fbee4ed24f0d8c2842729d721f6100a2b215e0f663c89bfefe9e32";
-    })
-    # Two backports from master, submitted as https://github.com/Exiv2/exiv2/pull/398
-    (fetchpatch {
-      name = "CVE-2018-12264.diff";
-      url = "https://github.com/vcunat/exiv2/commit/fd18e853.diff";
-      sha256 = "0y7ahh45lpaiazjnfllndfaa5pyixh6z4kcn2ywp7qy4ra7qpwdr";
-    })
-    (fetchpatch {
-      name = "CVE-2018-12265.diff";
-      url = "https://github.com/vcunat/exiv2/commit/9ed1671bd4.diff";
-      sha256 = "1cn446pfcgsh1bn9vxikkkcy1cqq7ghz2w291h1094ydqg6w7q6w";
-    })
-  ];
-
   postPatch = "patchShebangs ./src/svn_version.sh";
 
   preConfigure = "make config"; # needed because not using tarball

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

@@ -1,4 +1,5 @@
 { stdenv, fetchFromGitHub, autoreconfHook, givaro, pkgconfig, blas
+, fetchpatch
 , gmpxx
 , optimize ? false # impure
 }:
@@ -14,6 +15,15 @@ stdenv.mkDerivation rec {
     sha256 = "1cqhassj2dny3gx0iywvmnpq8ca0d6m82xl5rz4mb8gaxr2kwddl";
   };
 
+  patches = [
+    # https://github.com/linbox-team/fflas-ffpack/issues/146
+    (fetchpatch {
+      name = "fix-flaky-test-fgemm-check.patch";
+      url = "https://github.com/linbox-team/fflas-ffpack/commit/d8cd67d91a9535417a5cb193cf1540ad6758a3db.patch";
+      sha256 = "1gnfc616fvnlr0smvz6lb2d445vn8fgv6vqcr6pwm3dj4wa6v3b3";
+    })
+  ];
+
   checkInputs = [
     gmpxx
   ];

pkgs/development/libraries/gvfs/default.nix

@@ -2,7 +2,7 @@
 , glib, libgudev, udisks2, libgcrypt, libcap, polkit
 , libgphoto2, avahi, libarchive, fuse, libcdio
 , libxml2, libxslt, docbook_xsl, docbook_xml_dtd_42, samba, libmtp
-, gnomeSupport ? false, gnome, makeWrapper, gcr
+, gnomeSupport ? false, gnome, gcr, wrapGAppsHook
 , libimobiledevice, libbluray, libcdio-paranoia, libnfs, openssh
 , libsecret, libgdata, python3
 }:
@@ -28,7 +28,7 @@ in stdenv.mkDerivation rec {
 
   nativeBuildInputs = [
     meson ninja python3
-    pkgconfig gettext makeWrapper
+    pkgconfig gettext wrapGAppsHook
     libxml2 libxslt docbook_xsl docbook_xml_dtd_42
   ];
 
@@ -40,6 +40,7 @@ in stdenv.mkDerivation rec {
     # ToDo: a ligther version of libsoup to have FTP/HTTP support?
   ] ++ stdenv.lib.optionals gnomeSupport (with gnome; [
     libsoup gcr
+    glib-networking # TLS support
     gnome-online-accounts libsecret libgdata
   ]);
 
@@ -57,14 +58,6 @@ in stdenv.mkDerivation rec {
   doCheck = false; # fails with "ModuleNotFoundError: No module named 'gi'"
   doInstallCheck = doCheck;
 
-  preFixup = ''
-    for f in $out/libexec/*; do
-      wrapProgram $f \
-        ${stdenv.lib.optionalString gnomeSupport "--prefix GIO_EXTRA_MODULES : \"${stdenv.lib.getLib gnome.dconf}/lib/gio/modules\""} \
-        --prefix XDG_DATA_DIRS : "$GSETTINGS_SCHEMAS_PATH"
-    done
-  '';
-
   passthru = {
     updateScript = gnome3.updateScript {
       packageName = pname;

pkgs/development/libraries/libaom/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchgit, yasm, perl, cmake, pkgconfig, python3Packages }:
+{ stdenv, fetchgit, yasm, perl, cmake, pkgconfig, python3, writeText }:
 
 stdenv.mkDerivation rec {
   name = "libaom-${version}";
@@ -10,8 +10,23 @@ stdenv.mkDerivation rec {
     sha256 = "07h2vhdiq7c3fqaz44rl4vja3dgryi6n7kwbwbj1rh485ski4j82";
   };
 
-  buildInputs = [ perl yasm ];
-  nativeBuildInputs = [ cmake pkgconfig python3Packages.python ];
+  nativeBuildInputs = [
+    yasm perl cmake pkgconfig python3
+  ];
+
+  cmakeFlags = [
+    "-DBUILD_SHARED_LIBS=ON"
+  ];
+
+  preConfigure = ''
+    # build uses `git describe` to set the build version
+    cat > $NIX_BUILD_TOP/git << "EOF"
+    #!${stdenv.shell}
+    echo v${version}
+    EOF
+    chmod +x $NIX_BUILD_TOP/git
+    export PATH=$NIX_BUILD_TOP:$PATH
+  '';
 
   meta = with stdenv.lib; {
     description = "AV1 Bitstream and Decoding Library";

pkgs/development/libraries/libmkv/default.nix

@@ -15,6 +15,11 @@ stdenv.mkDerivation rec {
   preConfigure = "sh bootstrap.sh";
 
   meta = {
+    description = "Abandoned library. Alternative lightweight Matroska muxer written for HandBrake";
+    longDescription = ''
+      Library was meant to be an alternative to the official libmatroska library.
+      It is written in plain C, and intended to be very portable.
+    '';
     homepage = https://github.com/saintdev/libmkv;
     license = stdenv.lib.licenses.gpl2;
     maintainers = [ stdenv.lib.maintainers.wmertens ];

pkgs/development/libraries/libogg/default.nix

@@ -11,6 +11,12 @@ stdenv.mkDerivation rec {
   outputs = [ "out" "dev" "doc" ];
 
   meta = with stdenv.lib; {
+    description = "Media container library to manipulate Ogg files";
+    longDescription = ''
+      Library to work with Ogg multimedia container format.
+      Ogg is flexible file storage and streaming format that supports
+      plethora of codecs. Open format free for anyone to use.
+    '';
     homepage = https://xiph.org/ogg/;
     license = licenses.bsd3;
     maintainers = [ maintainers.ehmry ];

pkgs/development/libraries/libs3/default.nix

@@ -1,26 +1,23 @@
 { stdenv, fetchFromGitHub, curl, libxml2 }:
 
 stdenv.mkDerivation {
-  name = "libs3-2017-06-01";
+  name = "libs3-2018-12-03";
 
   src = fetchFromGitHub {
     owner = "bji";
     repo = "libs3";
-    rev = "fd8b149044e429ad30dc4c918f0713cdd40aadd2";
-    sha256 = "0a4c9rsd3wildssvnvph6cd11adn0p3rd4l02z03lvxkjhm20gw3";
+    rev = "111dc30029f64bbf82031f3e160f253a0a63c119";
+    sha256 = "1ahf08hc7ql3fazfmlyj9vrhq7cvarsmgn2v8149y63zr1fl61hs";
   };
 
   buildInputs = [ curl libxml2 ];
 
-  # added to fix build with gcc7, review on update
-  NIX_CFLAGS_COMPILE = [ "-Wno-error=format-truncation" ];
-
-  DESTDIR = "\${out}";
+  makeFlags = [ "DESTDIR=$(out)" ];
 
   meta = with stdenv.lib; {
     homepage = https://github.com/bji/libs3;
     description = "A library for interfacing with amazon s3";
-    license = licenses.lgpl3;
+    license = licenses.lgpl3Plus;
     platforms = platforms.linux;
   };
 }

pkgs/development/libraries/mp4v2/default.nix

@@ -25,8 +25,14 @@ stdenv.mkDerivation rec {
   enableParallelBuilding = true;
 
   meta = {
+    description = "Abandoned library. Provides functions to read, create, and modify mp4 files";
+    longDescription = ''
+      MP4v2 library provides an API to work with mp4 files
+      as defined by ISO-IEC:14496-1:2001 MPEG-4 Systems.
+      This container format is derived from Apple's QuickTime format.
+    '';
     homepage = https://code.google.com/archive/p/mp4v2/;
-    maintainers = [ ];
+    maintainers = [ lib.maintainers.Anton-Latukha ];
     platforms = lib.platforms.unix;
     license = lib.licenses.mpl11;
   };

pkgs/development/libraries/pipewire/default.nix

@@ -4,7 +4,7 @@
 }:
 
 let
-  version = "0.2.3";
+  version = "0.2.5";
 
   fontsConf = makeFontsConf {
     fontDirectories = [ freefont_ttf ];
@@ -16,7 +16,7 @@ in stdenv.mkDerivation rec {
     owner = "PipeWire";
     repo = "pipewire";
     rev = version;
-    sha256 = "1y04brfi5bv4y0hdyqzrcbayr674njf6a5hiwjfv2yi6lazkqv1k";
+    sha256 = "0hxm89ps6p75zm7rndrdr715p4ixx4f521fkjkyi7q2wh0b769s7";
   };
 
   outputs = [ "out" "lib" "dev" "doc" ];
@@ -31,7 +31,7 @@ in stdenv.mkDerivation rec {
 
   mesonFlags = [
     "-Ddocs=true"
-    "-Dgstreamer=true"
+    "-Dgstreamer=enabled"
   ];
 
   PKG_CONFIG_SYSTEMD_SYSTEMDUSERUNITDIR = "${placeholder "out"}/lib/systemd/user";

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

@@ -87,14 +87,37 @@ stdenv.mkDerivation rec {
     cp -r lib $out/
     cp -r include $out/
     cp -r share $out/
+    ''
+    + stdenv.lib.optionalString stdenv.isDarwin ''
+    # The fixDarwinDylibNames in nixpkgs can't seem to fix all the libraries.
+    # We manually fix them up here.
+    fixDarwinDylibNames() {
+        local flags=()
+        local old_id
 
+        for fn in "$@"; do
+            flags+=(-change "$PWD/lib/$(basename "$fn")" "$fn")
+        done
+
+        for fn in "$@"; do
+            if [ -L "$fn" ]; then continue; fi
+            echo "$fn: fixing dylib"
+            install_name_tool -id "$fn" "''${flags[@]}" "$fn"
+        done
+    }
+
+    fixDarwinDylibNames $(find "$out" -name "*.dylib")
+    ''
+    + stdenv.lib.optionalString (!stdenv.isDarwin) ''
     # Fix rpaths
     cd $out
     find -name \*.so\* -type f -exec \
       patchelf --set-rpath "$out/lib:${stdenv.lib.makeLibraryPath buildInputs}" {} \;
-
+    ''
+    +
+    ''
     runHook postInstall
-  '';
+    '';
 
   nativeBuildInputs = [ cmake ]
     ++ stdenv.lib.optional stdenv.isDarwin fixDarwinDylibNames;

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

@@ -4,7 +4,7 @@
 
 buildPythonPackage rec {
   pname = "aioamqp";
-  version = "0.11.0";
+  version = "0.12.0";
 
   meta = {
     homepage = https://github.com/polyconseil/aioamqp;
@@ -14,7 +14,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "7f1eb9e0f1b7c7e21a3a6ca498c3daafdfc3e95b4a1a0633fd8d6ba2dfcab777";
+    sha256 = "17vrl6jajr81bql7kjgq0zkxy225px97z4g9wmbhbbnvzn1p92c0";
   };
 
   buildInputs = lib.optionals isPy33 [ asyncio ];

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

@@ -3,6 +3,13 @@
 , fetchPypi
 , dateutil
 , sigtools
+, six
+, attrs
+, od
+, docutils
+, repeated_test
+, unittest2
+, pygments
 }:
 
 buildPythonPackage rec {
@@ -14,8 +21,20 @@ buildPythonPackage rec {
     sha256 = "dbcfba5571dc30aaf90dc98fc279e2aab69d0f8f3665fc0394fbc10a87a2be60";
   };
 
-  buildInputs = [ dateutil ];
-  propagatedBuildInputs = [ sigtools ];
+  checkInputs = [ 
+    dateutil
+    pygments
+    repeated_test
+    unittest2
+  ];
+  
+  propagatedBuildInputs = [ 
+    attrs
+    docutils
+    od
+    sigtools
+    six
+  ];
 
   meta = with stdenv.lib; {
     description = "Command-line argument parsing for Python";

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

@@ -9,11 +9,11 @@ assert pariSupport -> pari != null;
 
 buildPythonPackage rec {
   pname = "cysignals";
-  version = "1.8.0";
+  version = "1.8.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1yh4lyrinhxxra42p0k4hiyjdrqjmifg4gnmf4bky5wa0mqnyai6";
+    sha256 = "1hnkcrrxgh6g8a197v2yw61xz43iyv81jbl6jpy19ql3k66w81zx";
   };
 
   # explicit check:
@@ -22,9 +22,9 @@ buildPythonPackage rec {
     "fortify"
   ];
 
-  # currently fails, probably because of formatting changes in gdb 8.0
-  # https://trac.sagemath.org/ticket/24692
+  # known failure: https://github.com/sagemath/cysignals/blob/582dbf6a7b0f9ade0abe7a7b8720b7fb32435c3c/testgdb.py#L5
   doCheck = false;
+  checkTarget = "check-install";
 
   preCheck = ''
     # Make sure cysignals-CSI is in PATH

pkgs/development/python-modules/dependency-injector/default.nix

@@ -1,19 +1,26 @@
-{ stdenv, buildPythonPackage, fetchPypi, six, unittest2 }:
+{ stdenv, buildPythonPackage, fetchPypi, isPy3k, six, unittest2 }:
+
+let
+  testPath =
+    if isPy3k
+    then "test_*_py3.py"
+    else "test_*_py2_py3.py";
+in
 
 buildPythonPackage rec {
   pname = "dependency-injector";
-  version = "3.14.2";
+  version = "3.14.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "f478a26e9bf3111ce98bbfb8502af274643947f87a7e12a6481a35eaa693062b";
+    sha256 = "07366palyav9bawyq2b1gi76iamjkq6r5akzzbqv8s930sxq6yim";
   };
 
   propagatedBuildInputs = [ six ];
   checkInputs = [ unittest2 ];
 
   checkPhase = ''
-    unit2 discover tests/unit
+    unit2 discover -s tests/unit -p "${testPath}"
   '';
 
   meta = with stdenv.lib; {

pkgs/development/python-modules/flask-jwt-extended/default.nix

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "Flask-JWT-Extended";
-  version = "3.13.1";
+  version = "3.14.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "10qz3ljr2kpd93al2km6iijxp23z33kvvwd0y5bc840f86b4mra8";
+    sha256 = "133s9js7j1b2m6vv56a2xd9in0rmx5zrdp4r005qwbvr5qxld39s";
   };
 
   propagatedBuildInputs = [ flask pyjwt werkzeug ];

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

@@ -1,39 +1,24 @@
-{ stdenv
-, buildPythonPackage
-, fetchPypi
-, isPy3k
-, oauth2client
-, gdata
-, google_api_python_client
-, simplejson
-, httplib2
-, keyring
-, six
-, rsa
+{ stdenv, buildPythonPackage, fetchPypi, isPy3k
+, google_api_python_client, simplejson, oauth2client
 }:
 
 buildPythonPackage rec {
   pname = "goobook";
-  version = "3.1";
-  disabled = isPy3k;
+  version = "3.3";
+  disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "139a98d646d5c5963670944d5cfcc1a107677ee11fa98329221bd600457fda6d";
+    sha256 = "0sanlki1rcqvhbds7a049v2kzglgpm761i728115mdracw0s6i3h";
   };
 
-  propagatedBuildInputs = [ oauth2client gdata google_api_python_client simplejson httplib2 keyring six rsa ];
-
-  preConfigure = ''
-    sed -i '/distribute/d' setup.py
-  '';
+  propagatedBuildInputs = [ google_api_python_client simplejson oauth2client ];
 
   meta = with stdenv.lib; {
     description = "Search your google contacts from the command-line or mutt";
     homepage    = https://pypi.python.org/pypi/goobook;
     license     = licenses.gpl3;
-    maintainers = with maintainers; [ lovek323 hbunke ];
+    maintainers = with maintainers; [ primeos ];
     platforms   = platforms.unix;
   };
-
 }

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

@@ -2,12 +2,12 @@
 , python, pytest, sortedcontainers }:
 
 buildPythonPackage rec {
-  version = "2.1.0";
+  version = "3.0.2";
   pname = "intervaltree";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "02w191m9zxkcjqr1kv2slxvhymwhj3jnsyy3a28b837pi15q19dc";
+    sha256 = "0wz234g6irlm4hivs2qzmnywk0ss06ckagwh15nflkyb3p462kyb";
   };
 
   buildInputs = [ pytest ];

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

@@ -0,0 +1,23 @@
+{ lib, buildPythonPackage, fetchPypi, unittest2, repeated_test }:
+
+buildPythonPackage rec {
+  pname = "od";
+  version = "1.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1az30snc3w6s4k1pi7mspcv8y0kp3ihf3ly44z517nszmz9lrjfi";
+  };
+
+  checkInputs = [
+    repeated_test
+    unittest2
+  ];
+
+  meta = with lib; {
+    description = "Shorthand syntax for building OrderedDicts";
+    homepage = https://github.com/epsy/od;
+    license = licenses.mit;
+  };
+
+}

pkgs/development/python-modules/opt-einsum/default.nix

@@ -0,0 +1,31 @@
+{ buildPythonPackage, fetchPypi, lib, numpy, pytest, pytestpep8, pytestcov }:
+buildPythonPackage rec {
+  version = "2.3.2";
+  pname = "opt_einsum";
+
+  src = fetchPypi {
+    inherit version pname;
+    sha256 = "0ny3v8x83mzpwmqjdzqhzy2pzwyy4wx01r1h9i29xw3yvas69m6k";
+  };
+
+  checkInputs = [
+    pytest
+    pytestpep8
+    pytestcov
+  ];
+
+  checkPhase = ''
+    pytest
+  '';
+
+  propagatedBuildInputs = [
+    numpy
+  ];
+
+  meta = {
+    description = "Optimizing NumPy's einsum function with order optimization and GPU support.";
+    homepage = http://optimized-einsum.readthedocs.io;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ teh ];
+  };
+}

pkgs/development/python-modules/pyqt/5.x.nix

@@ -1,30 +1,21 @@
 { lib, fetchurl, fetchpatch, pythonPackages, pkgconfig
-, qmake, lndir, qtbase, qtsvg, qtwebkit, qtwebengine, dbus
-, withWebSockets ? false, qtwebsockets
+, qmake, lndir, qtbase, qtsvg, qtwebengine, dbus
 , withConnectivity ? false, qtconnectivity
+, withWebKit ? false, qtwebkit
+, withWebSockets ? false, qtwebsockets
 }:
 
 let
-  pname = "PyQt";
-  version = "5.11.3";
 
   inherit (pythonPackages) buildPythonPackage python isPy3k dbus-python enum34;
 
   sip = pythonPackages.sip.override { sip-module = "PyQt5.sip"; };
 
-in buildPythonPackage {
-  pname = pname;
-  version = version;
+in buildPythonPackage rec {
+  pname = "PyQt";
+  version = "5.11.3";
   format = "other";
 
-  meta = with lib; {
-    description = "Python bindings for Qt5";
-    homepage    = http://www.riverbankcomputing.co.uk;
-    license     = licenses.gpl3;
-    platforms   = platforms.mesaPlatforms;
-    maintainers = with maintainers; [ sander ];
-  };
-
   src = fetchurl {
     url = "mirror://sourceforge/pyqt/PyQt5/PyQt-${version}/PyQt5_gpl-${version}.tar.gz";
     sha256 = "0wqh4srqkcc03rvkwrcshaa028psrq58xkys6npnyhqxc0apvdf9";
@@ -36,9 +27,11 @@ in buildPythonPackage {
 
   buildInputs = [ dbus sip ];
 
-  propagatedBuildInputs = [
-    qtbase qtsvg qtwebkit qtwebengine
-  ] ++ lib.optional (!isPy3k) enum34 ++ lib.optional withWebSockets qtwebsockets ++ lib.optional withConnectivity qtconnectivity;
+  propagatedBuildInputs = [ qtbase qtsvg qtwebengine ]
+    ++ lib.optional (!isPy3k) enum34
+    ++ lib.optional withConnectivity qtconnectivity
+    ++ lib.optional withWebKit qtwebkit
+    ++ lib.optional withWebSockets qtwebsockets;
 
   configurePhase = ''
     runHook preConfigure
@@ -49,10 +42,6 @@ in buildPythonPackage {
 
     export PYTHONPATH=$PYTHONPATH:$out/${python.sitePackages}
 
-    substituteInPlace configure.py \
-      --replace 'install_dir=pydbusmoddir' "install_dir='$out/${python.sitePackages}/dbus/mainloop'" \
-      --replace "ModuleMetadata(qmake_QT=['webkitwidgets'])" "ModuleMetadata(qmake_QT=['webkitwidgets', 'printsupport'])"
-
     ${python.executable} configure.py  -w \
       --confirm-license \
       --dbus=${dbus.dev}/include/dbus-1.0 \
@@ -74,4 +63,12 @@ in buildPythonPackage {
   '';
 
   enableParallelBuilding = true;
+
+  meta = with lib; {
+    description = "Python bindings for Qt5";
+    homepage    = http://www.riverbankcomputing.co.uk;
+    license     = licenses.gpl3;
+    platforms   = platforms.mesaPlatforms;
+    maintainers = with maintainers; [ sander ];
+  };
 }

pkgs/development/python-modules/pyro-ppl/default.nix

@@ -0,0 +1,38 @@
+{ buildPythonPackage, fetchPypi, lib, pytorch, contextlib2
+, graphviz, networkx, six, opt-einsum, tqdm }:
+buildPythonPackage rec {
+  version = "0.3.0";
+  pname = "pyro-ppl";
+
+  src = fetchPypi {
+    inherit version pname;
+    sha256 = "0shsnc5bia9k1fzmqnwwbm1x5qvac3zrq4lvyhg27rjgpcamvb9l";
+  };
+
+  propagatedBuildInputs = [
+    pytorch
+    contextlib2
+    # TODO(tom): graphviz pulls in a lot of dependencies - make
+    # optional when some time to figure out how.
+    graphviz
+    networkx
+    six
+    opt-einsum
+    tqdm
+  ];
+
+  # pyro not shipping tests do simple smoke test instead
+  checkPhase = ''
+    python -c "import pyro"
+    python -c "import pyro.distributions"
+    python -c "import pyro.infer"
+    python -c "import pyro.optim"
+  '';
+
+  meta = {
+    description = "A Python library for probabilistic modeling and inference";
+    homepage = http://pyro.ai;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ teh ];
+  };
+}

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

@@ -31,7 +31,7 @@ buildPythonPackage rec {
     description = "Jupyter Qt console";
     homepage = http://jupyter.org/;
     license = lib.licenses.bsd3;
-    platforms = lib.platforms.linux; # fails on Darwin
+    platforms = lib.platforms.unix;
     maintainers = with lib.maintainers; [ fridh ];
   };
 }

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

@@ -3,11 +3,11 @@
 buildPythonPackage rec {
   pname = "shippai";
   # Please make sure that vdirsyncer still builds if you update this package.
-  version = "0.2.4";
+  version = "0.3.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "87cc9899212d917031853becd7cb14808181289c3c329b1418e9b4b6aae93c80";
+    sha256 = "0r6iwvmay8ygn2m15pyjrk9am4mfpk7rkf0lcbcb15pnabixlyzj";
   };
 
   meta = with stdenv.lib; {

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

@@ -0,0 +1,21 @@
+{ lib, buildPythonPackage, fetchFromGitHub }:
+
+buildPythonPackage rec {
+  pname = "unidiff";
+  version = "0.5.5";
+
+  # PyPI tarball doesn't ship tests
+  src = fetchFromGitHub {
+    owner = "matiasb";
+    repo = "python-unidiff";
+    rev = "v${version}";
+    sha256 = "1nvi7s1nn5p7j6aql1nkn2kiadnfby98yla5m3jq8xwsx0aplwdm";
+  };
+
+  meta = with lib; {
+    description = "Unified diff python parsing/metadata extraction library";
+    homepage = https://github.com/matiasb/python-unidiff;
+    license = licenses.mit;
+    maintainers = [ maintainers.marsam ];
+  };
+}

pkgs/development/python-modules/update-copyright/default.nix

@@ -0,0 +1,22 @@
+{ lib, buildPythonPackage, fetchPypi, isPy3k }:
+
+buildPythonPackage rec {
+  pname = "update-copyright";
+  version = "0.6.2";
+
+  disabled = !isPy3k;
+
+  # Has no tests
+  doCheck = false;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "17ybdgbdc62yqhda4kfy1vcs1yzp78d91qfhj5zbvz1afvmvdk7z";
+  };
+
+  meta = with lib; {
+    description = "An automatic copyright update tool";
+    homepage = http://blog.tremily.us/posts/update-copyright;
+    license = licenses.gpl3;
+  };
+}

pkgs/development/python-modules/x256/default.nix

@@ -0,0 +1,22 @@
+{ stdenv, buildPythonPackage, fetchPypi
+}:
+
+buildPythonPackage rec {
+  pname = "x256";
+  version = "0.0.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "00g02b9a6jsl377xb5fmxvkjff3lalw21n430a4zalqyv76dnmgq";
+  };
+
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "Find the nearest xterm 256 color index for an RGB";
+    homepage = https://github.com/magarcia/python-x256;
+    license = licenses.mit;
+    maintainers = with maintainers; [ Scriptkiddi ];
+  };
+}
+

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

@@ -7,11 +7,11 @@
 
 buildPythonPackage rec {
   pname = "zc.lockfile";
-  version = "1.3.0";
+  version = "1.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "96cb13769e042988ea25d23d44cf09342ea0f887083d0f9736968f3617665853";
+    sha256 = "0lrj2zdr06sff7i151710jbbnnhx4phdc0qpns8jkarpd62f7a4m";
   };
 
   buildInputs = [ mock ];

pkgs/development/tools/build-managers/tup/default.nix

@@ -1,21 +1,22 @@
-{ stdenv, fetchFromGitHub, fuse, pkgconfig }:
+{ stdenv, fetchFromGitHub, fuse, pkgconfig, pcre }:
 
 stdenv.mkDerivation rec {
   name = "tup-${version}";
-  version = "0.7.5";
+  version = "0.7.8";
 
   src = fetchFromGitHub {
     owner = "gittup";
     repo = "tup";
     rev = "v${version}";
-    sha256 = "0jzp1llq6635ldb7j9qb29j2k0x5mblimdqg3179dvva1hv0ia23";
+    sha256 = "07dmz712zbs5kayf98kywp7blssgh0y2gc1623jbsynmqwi77mcb";
   };
 
   nativeBuildInputs = [ pkgconfig ];
-  buildInputs = [ fuse ];
+  buildInputs = [ fuse pcre ];
 
   configurePhase = ''
-    sed -i 's/`git describe`/v${version}/g' Tupfile
+    sed -i 's/`git describe`/v${version}/g' src/tup/link.sh
+    sed -i 's/pcre-confg/pkg-config pcre/g' Tupfile Tuprules.tup
   '';
 
   # Regular tup builds require fusermount to have suid, which nix cannot
@@ -23,6 +24,7 @@ stdenv.mkDerivation rec {
   # generate' instead
   buildPhase = ''
     ./build.sh
+    ./build/tup init
     ./build/tup generate script.sh
     ./script.sh
   '';

pkgs/development/tools/detect-secrets/default.nix

@@ -0,0 +1,34 @@
+{ lib, buildPythonApplication, fetchFromGitHub, isPy27, pyyaml, unidiff, configparser, enum34, future, functools32, mock, pytest }:
+
+buildPythonApplication rec {
+  pname = "detect-secrets";
+  version = "0.11.0";
+
+  # PyPI tarball doesn't ship tests
+  src = fetchFromGitHub {
+    owner = "Yelp";
+    repo = "detect-secrets";
+    rev = "v${version}";
+    sha256 = "11r11q6d8aajqqnhhz4lsa93qf1x745331kl9jd3z4y4w91l4gdz";
+  };
+
+  propagatedBuildInputs = [ pyyaml unidiff ]
+    ++ lib.optionals isPy27 [ configparser enum34 future functools32 ];
+
+  checkInputs = [ mock pytest ];
+
+  # deselect tests which require git setup
+  checkPhase = ''
+    PYTHONPATH=$PWD:$PYTHONPATH pytest \
+      --deselect tests/main_test.py::TestMain \
+      --deselect tests/pre_commit_hook_test.py::TestPreCommitHook \
+      --deselect tests/core/baseline_test.py::TestInitializeBaseline
+  '';
+
+  meta = with lib; {
+    description = "An enterprise friendly way of detecting and preventing secrets in code";
+    homepage = https://github.com/Yelp/detect-secrets;
+    license = licenses.asl20;
+    maintainers = [ maintainers.marsam ];
+  };
+}

pkgs/development/tools/doctl/default.nix

@@ -4,8 +4,8 @@ buildGoPackage rec {
   name = "doctl-${version}";
   version = "${major}.${minor}.${patch}";
   major = "1";
-  minor = "8";
-  patch = "0";
+  minor = "12";
+  patch = "2";
   goPackagePath = "github.com/digitalocean/doctl";
 
   excludedPackages = ''\(doctl-gen-doc\|install-doctl\|release-doctl\)'';
@@ -21,7 +21,7 @@ buildGoPackage rec {
     owner = "digitalocean";
     repo   = "doctl";
     rev    = "v${version}";
-    sha256 = "1h94qagbni8cvzdparmgx3m9qcnbwbk0kjlvy9jzxfd3vcpbg38j";
+    sha256 = "01li9ywzvmzmhqgk9a5li2wkqmdn7jl8pqz2rn7dnay4fr2259fv";
   };
 
   meta = {

pkgs/development/tools/elm2nix/default.nix

@@ -0,0 +1,24 @@
+{ mkDerivation, aeson, ansi-wl-pprint, async, base, binary
+, bytestring, containers, data-default, directory, filepath, here
+, mtl, optparse-applicative, process, req, stdenv, text
+, transformers, unordered-containers
+}:
+mkDerivation {
+  pname = "elm2nix";
+  version = "0.1.0";
+  sha256 = "9ec1f1f694a38b466ebd03aaa1a035bbdb9bdae390be5b9a030611bcbfd91890";
+  isLibrary = true;
+  isExecutable = true;
+  libraryHaskellDepends = [
+    aeson async base binary bytestring containers data-default
+    directory filepath here mtl process req text transformers
+    unordered-containers
+  ];
+  executableHaskellDepends = [
+    ansi-wl-pprint base directory here optparse-applicative
+  ];
+  testHaskellDepends = [ base ];
+  homepage = "https://github.com/domenkozar/elm2nix#readme";
+  description = "Turn your Elm project into buildable Nix project";
+  license = stdenv.lib.licenses.bsd3;
+}

pkgs/development/tools/misc/lit/default.nix

@@ -2,11 +2,11 @@
 
 python2.pkgs.buildPythonApplication rec {
   pname = "lit";
-  version = "0.6.0";
+  version = "0.7.1";
 
   src = python2.pkgs.fetchPypi {
     inherit pname version;
-    sha256 = "1png3jgbhrw8a602gy6rnzvjcrj8w2p2kk6szdg9lz42zr090lgb";
+    sha256 = "ecef2833aef7f411cb923dac109c7c9dcc7dbe7cafce0650c1e8d19c243d955f";
   };
 
   # Non-standard test suite. Needs custom checkPhase.

pkgs/development/tools/misc/strace/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "strace-${version}";
-  version = "4.25";
+  version = "4.26";
 
   src = fetchurl {
     url = "https://strace.io/files/${version}/${name}.tar.xz";
-    sha256 = "00f7zagfh3np5gwi0z7hi7zjd7s5nixcaq7z78n87dvhakkgi1fn";
+    sha256 = "070yz8xii8gnb4psiz628zwm5srh266sfb06f7f1qzagxzz2ykbw";
   };
 
   depsBuildBuild = [ buildPackages.stdenv.cc ];
@@ -23,7 +23,7 @@ stdenv.mkDerivation rec {
   meta = with stdenv.lib; {
     homepage = https://strace.io/;
     description = "A system call tracer for Linux";
-    license = licenses.bsd3;
+    license =  with licenses; [ lgpl21Plus gpl2Plus ]; # gpl2Plus is for the test suite
     platforms = platforms.linux;
     maintainers = with maintainers; [ jgeerds globin ];
   };

pkgs/development/tools/solarus-quest-editor/default.nix

@@ -1,36 +1,23 @@
 { stdenv, fetchFromGitLab, cmake, luajit,
   SDL2, SDL2_image, SDL2_ttf, physfs,
   openal, libmodplug, libvorbis, solarus,
-  qtbase, qttools, fetchpatch }:
+  qtbase, qttools, fetchpatch, glm }:
 
 stdenv.mkDerivation rec {
   name = "solarus-quest-editor-${version}";
-  version = "1.5.3";
+  version = "1.6.0";
     
   src = fetchFromGitLab {
     owner = "solarus-games";
     repo = "solarus-quest-editor";
-    rev = "v1.5.3";
-    sha256 = "1b9mg04yy4pnrl745hbc82rz79k0f8ci3wv7gvsm3a998q8m98si";
+    rev = "v${version}";
+    sha256 = "1a7816kaljfh9ynzy9g36mqzzv2p800nnbrja73q6vjfrsv3vq4c";
   };
   
   buildInputs = [ cmake luajit SDL2
     SDL2_image SDL2_ttf physfs
     openal libmodplug libvorbis
-    solarus qtbase qttools ];
-    
-  patches = [
-    ./patches/fix-install.patch
-
-    # Next two patches should be fine to remove for next release.
-    # This commit fixes issues AND adds features *sighs*
-    ./patches/partial-f285beab62594f73e57190c49848c848487214cf.patch
-
-    (fetchpatch {
-      url = https://gitlab.com/solarus-games/solarus-quest-editor/commit/8f308463030c18cd4f7c8a6052028fff3b7ca35a.patch;
-      sha256 = "1jq48ghhznrp47q9lq2rhh48a1z4aylyy4qaniaqyfyq3vihrchr";
-    })
-  ];
+    solarus qtbase qttools glm ];
 
   meta = with stdenv.lib; {
     description = "The editor for the Zelda-like ARPG game engine, Solarus";

pkgs/development/tools/solarus-quest-editor/patches/fix-install.patch

@@ -1,16 +0,0 @@
-# Description Fix CMakeLists.txt to install binaries. Fixed in 1.5 upstream.
-# Author "Nathan R. Moore <natedevv@gmail.com>"
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -359,6 +359,11 @@
-   "${MODPLUG_LIBRARY}"
- )
- 
-+# Set files to install
-+install(TARGETS solarus-quest-editor
-+    RUNTIME DESTINATION bin
-+)
-+
- # Platform specific.
- 
- # Windows: disable the console.

pkgs/development/tools/solarus-quest-editor/patches/partial-f285beab62594f73e57190c49848c848487214cf.patch

@@ -1,33 +0,0 @@
-From f285beab62594f73e57190c49848c848487214cf Mon Sep 17 00:00:00 2001
-From: stdgregwar <gregoirehirt@gmail.com>
-Date: Sun, 1 Jul 2018 00:00:41 +0200
-Subject: [PATCH] Shader previewer base
-
-
-diff --git a/include/widgets/tileset_view.h b/include/widgets/tileset_view.h
-index 615f432..799a4c6 100644
---- a/include/widgets/tileset_view.h
-+++ b/include/widgets/tileset_view.h
-@@ -23,6 +23,7 @@
- #include "pattern_separation.h"
- #include <QGraphicsView>
- #include <QPointer>
-+#include <QMenu>
- 
- class QAction;
- 
-diff --git a/src/widgets/text_editor.cpp b/src/widgets/text_editor.cpp
-index 4f2ff68..90080a9 100644
---- a/src/widgets/text_editor.cpp
-+++ b/src/widgets/text_editor.cpp
-@@ -26,6 +26,7 @@
- #include <QList>
- #include <QPlainTextEdit>
- #include <QScrollBar>
-+#include <QAction>
- #include <QTextStream>
- #include <QUndoStack>
- 
--- 
-2.18.0
-

pkgs/development/web/nodejs/nodejs.nix

@@ -12,12 +12,16 @@ with stdenv.lib;
 { enableNpm ? true, version, sha256, patches ? [] } @args:
 
 let
-
   inherit (darwin.apple_sdk.frameworks) CoreServices ApplicationServices;
 
+  majorVersion = versions.major version;
+  minorVersion = versions.minor version;
+
   baseName = if enableNpm then "nodejs" else "nodejs-slim";
 
-  sharedLibDeps = { inherit openssl zlib libuv; } // (optionalAttrs (!stdenv.isDarwin) { inherit http-parser; });
+  useSharedHttpParser = !stdenv.isDarwin && versionOlder "${majorVersion}.${minorVersion}" "11.4";
+
+  sharedLibDeps = { inherit openssl zlib libuv; } // (optionalAttrs useSharedHttpParser { inherit http-parser; });
 
   sharedConfigureFlags = concatMap (name: [
     "--shared-${name}"
@@ -102,7 +106,7 @@ in
     passthru.updateScript = import ./update.nix {
       inherit stdenv writeScript coreutils gnugrep jq curl common-updater-scripts gnupg nix;
       inherit (stdenv) lib;
-      majorVersion = with stdenv.lib; elemAt (splitString "." version) 0;
+      inherit majorVersion;
     };
 
     meta = {

pkgs/development/web/nodejs/v11.nix

@@ -0,0 +1,10 @@
+{ stdenv, callPackage, lib, openssl, enableNpm ? true }:
+
+let
+  buildNodejs = callPackage ./nodejs.nix { inherit openssl; };
+in
+  buildNodejs {
+    inherit enableNpm;
+    version = "11.5.0";
+    sha256 = "07fdpl8wzkcdd8iyaiwf2ah1rgishk2hrl0g73i8aggwplrl69fx";
+  }

pkgs/development/web/nodejs/v6.nix

@@ -5,6 +5,6 @@ let
 in
   buildNodejs {
     inherit enableNpm;
-    version = "6.14.4";
-    sha256 = "03zc6jhid6jyi871zlcrkjqffmrpxh01z2xfsl3xp2vzg2czqjws";
+    version = "6.15.1";
+    sha256 = "1hi9h54ni7m1lmhfqvwxdny969j31mixxlxsiyl00l2bj25fbgf3";
   }

pkgs/development/web/nodejs/v8.nix

@@ -5,6 +5,6 @@ let
 in
   buildNodejs {
     inherit enableNpm;
-    version = "8.12.0";
-    sha256 = "16j1rrxkhmvpcw689ndw1raql1gz4jqn7n82z55zn63c05cgz7as";
+    version = "8.14.1";
+    sha256 = "16vb5baw6nk71n7jfbyd9x8qi0kbkzv2bw1rczy7dyyz7n08gpxi";
   }