Merge master into staging-next

30 files changed, 464 insertions, 109 deletions

diff --git a/pkgs/development/compilers/binaryen/default.nix b/pkgs/development/compilers/binaryen/default.nix
index 8ebed6f4b5bd..77f051156d1e 100644
--- a/pkgs/development/compilers/binaryen/default.nix
+++ b/pkgs/development/compilers/binaryen/default.nix
@@ -1,11 +1,11 @@
 { stdenv, cmake, python, fetchFromGitHub, emscriptenRev ? null }:
 
 let
-  defaultVersion = "84";
+  defaultVersion = "86";
 
   # Map from git revs to SHA256 hashes
   sha256s = {
-    "version_84" = "189zqc5gp8fm7clsgby9h2s758ijil7ma4liwbf81wnwkb4kqxc0";
+    "version_86" = "12h5018rdwg7vjni0mz91vkpdwyqw0nfacig3vg9dvyn4fnfm76z";
     "1.38.28" = "172s7y5f38736ic8ri3mnbdqcrkadd40a26cxcfwbscc53phl11v";
   };
 in
diff --git a/pkgs/development/interpreters/guile/default.nix b/pkgs/development/interpreters/guile/default.nix
index 49715bf256bb..fce94ecc846f 100644
--- a/pkgs/development/interpreters/guile/default.nix
+++ b/pkgs/development/interpreters/guile/default.nix
@@ -12,11 +12,11 @@
 
 (rec {
   name = "guile-${version}";
-  version = "2.2.4";
+  version = "2.2.6";
 
   src = fetchurl {
     url = "mirror://gnu/guile/${name}.tar.xz";
-    sha256 = "07p3g0v2ba2vlfbfidqzlgbhnzdx46wh2rgc5gszq1mjyx5bks6r";
+    sha256 = "1269ymxm56j1z1lvq1y42rm961f2n7rinm3k6l00p9k52hrpcddk";
   };
 
   outputs = [ "out" "dev" "info" ];
diff --git a/pkgs/development/interpreters/mujs/default.nix b/pkgs/development/interpreters/mujs/default.nix
index f071aab94c78..ceea3932063a 100644
--- a/pkgs/development/interpreters/mujs/default.nix
+++ b/pkgs/development/interpreters/mujs/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "mujs-${version}";
-  version = "1.0.5";
+  version = "1.0.6";
 
   src = fetchurl {
     url = "https://mujs.com/downloads/mujs-${version}.tar.xz";
-    sha256 = "02cqrfnww2s3ylcvqin1951f2c5nzpby8gxb207p2hbrivbg8f0l";
+    sha256 = "1q9w2dcspfp580pzx7sw7x9gbn8j0ak6dvj75wd1ml3f3q3i43df";
   };
 
   buildInputs = [ readline ];
diff --git a/pkgs/development/interpreters/picolisp/default.nix b/pkgs/development/interpreters/picolisp/default.nix
index 01cffe93024f..5adf41a0f3b6 100644
--- a/pkgs/development/interpreters/picolisp/default.nix
+++ b/pkgs/development/interpreters/picolisp/default.nix
@@ -3,10 +3,10 @@ with stdenv.lib;
 
 stdenv.mkDerivation rec {
   name = "picoLisp-${version}";
-  version = "18.12";
+  version = "19.6";
   src = fetchurl {
     url = "https://www.software-lab.de/${name}.tgz";
-    sha256 = "0hvgq2vc03bki528jqn95xmvv7mw8xx832spfczhxc16wwbrnrhk";
+    sha256 = "1ixxl6m5glhwqa4q3fb90pciv7jhhvn9pkh316d4wcv0m13l04gq";
   };
   buildInputs = [makeWrapper openssl] ++ optional stdenv.is64bit jdk;
   patchPhase = ''
diff --git a/pkgs/development/libraries/gdal/001.3_0_1.darwin.patch b/pkgs/development/libraries/gdal/001.3_0_1.darwin.patch
new file mode 100644
index 000000000000..3d34f689120f
--- /dev/null
+++ b/pkgs/development/libraries/gdal/001.3_0_1.darwin.patch
@@ -0,0 +1,29 @@
+diff a/swig/python/setup.py b/swig/python/setup.py
+--- a/swig/python/setup.py
++++ b/swig/python/setup.py
+@@ -268,17 +268,17 @@ class gdal_ext(build_ext):
+                     if ext.name != 'osgeo._gdalconst':
+                         ext.extra_compile_args += [cxx11_flag]
+ 
+-        # Adding arch flags here if OS X and compiler is clang
+-        if sys.platform == 'darwin' and [int(x) for x in os.uname()[2].split('.')] >= [11, 0, 0]:
+-            # since MacOS X 10.9, clang no longer accepts -mno-fused-madd
+-            # extra_compile_args.append('-Qunused-arguments')
+-            clang_flag = '-Wno-error=unused-command-line-argument-hard-error-in-future'
+-            if has_flag(self.compiler, clang_flag): 
+-                ext.extra_compile_args += [clang_flag]
+-            else:
+-                clang_flag = '-Wno-error=unused-command-line-argument'
+-                if has_flag(self.compiler, clang_flag):
+-                    ext.extra_compile_args += [clang_flag]
++                    # Adding arch flags here if OS X and compiler is clang
++                    if sys.platform == 'darwin' and [int(x) for x in os.uname()[2].split('.')] >= [11, 0, 0]:
++                        # since MacOS X 10.9, clang no longer accepts -mno-fused-madd
++                        # extra_compile_args.append('-Qunused-arguments')
++                        clang_flag = '-Wno-error=unused-command-line-argument-hard-error-in-future'
++                        if has_flag(self.compiler, clang_flag): 
++                            ext.extra_compile_args += [clang_flag]
++                        else:
++                            clang_flag = '-Wno-error=unused-command-line-argument'
++                            if has_flag(self.compiler, clang_flag):
++                                ext.extra_compile_args += [clang_flag]
diff --git a/pkgs/development/libraries/gdal/2.4.0.nix b/pkgs/development/libraries/gdal/2.4.0.nix
new file mode 100644
index 000000000000..14113d8b87eb
--- /dev/null
+++ b/pkgs/development/libraries/gdal/2.4.0.nix
@@ -0,0 +1,95 @@
+{ stdenv, fetchurl, fetchpatch, unzip, libjpeg, libtiff, zlib
+, postgresql, mysql, libgeotiff, pythonPackages, proj, geos, openssl
+, libpng, sqlite, libspatialite, poppler, hdf4, qhull, giflib, expat
+, libiconv, libxml2
+, netcdfSupport ? true, netcdf, hdf5, curl
+}:
+
+with stdenv.lib;
+
+stdenv.mkDerivation rec {
+  name = "gdal-${version}";
+  version = "2.4.0";
+
+  src = fetchurl {
+    url = "https://download.osgeo.org/gdal/${version}/${name}.tar.xz";
+    sha256 = "09qgy36z0jc9w05373m4n0vm4j54almdzql6z9p9zr9pdp61syf3";
+  };
+
+  buildInputs = [ unzip libjpeg libtiff libgeotiff libpng proj openssl sqlite
+    libspatialite poppler hdf4 qhull giflib expat libxml2 proj ]
+  ++ (with pythonPackages; [ python numpy wrapPython ])
+  ++ stdenv.lib.optional stdenv.isDarwin libiconv
+  ++ stdenv.lib.optionals netcdfSupport [ netcdf hdf5 curl ];
+
+  configureFlags = [
+    "--with-expat=${expat.dev}"
+    "--with-jpeg=${libjpeg.dev}"
+    "--with-libtiff=${libtiff.dev}" # optional (without largetiff support)
+    "--with-png=${libpng.dev}"      # optional
+    "--with-poppler=${poppler.dev}" # optional
+    "--with-libz=${zlib.dev}"       # optional
+    "--with-pg=${postgresql}/bin/pg_config"
+    "--with-mysql=${mysql.connector-c or mysql}/bin/mysql_config"
+    "--with-geotiff=${libgeotiff.dev}"
+    "--with-sqlite3=${sqlite.dev}"
+    "--with-spatialite=${libspatialite}"
+    "--with-python"               # optional
+    "--with-proj=${proj.dev}" # optional
+    "--with-geos=${geos}/bin/geos-config"# optional
+    "--with-hdf4=${hdf4.dev}" # optional
+    "--with-xml2=${libxml2.dev}/bin/xml2-config" # optional
+    (if netcdfSupport then "--with-netcdf=${netcdf}" else "")
+  ];
+
+  hardeningDisable = [ "format" ];
+
+  CXXFLAGS = "-fpermissive";
+
+  postPatch = ''
+    sed -i '/ifdef bool/i\
+      #ifdef swap\
+      #undef swap\
+      #endif' ogr/ogrsf_frmts/mysql/ogr_mysql.h
+    # poppler 0.73.0 support
+    patch -lp2 <${
+      fetchpatch {
+        url = "https://github.com/OSGeo/gdal/commit/29f4dfbcac2de718043f862166cd639ab578b552.diff";
+        sha256 = "1h2rsjjrgwqfgqzppmzv5jgjs1dbbg8pvfmay0j9y0618qp3r734";
+      }
+    } || true
+    patch -p2 <${
+      fetchpatch {
+        url = "https://github.com/OSGeo/gdal/commit/19967e682738977e11e1d0336e0178882c39cad2.diff";
+        sha256 = "12yqd77226i6xvzgqmxiac5ghdinixh8k2crg1r2gnhc0xlc3arj";
+      }
+    }
+  '';
+
+  # - Unset CC and CXX as they confuse libtool.
+  # - teach gdal that libdf is the legacy name for libhdf
+  preConfigure = ''
+      unset CC CXX
+      substituteInPlace configure \
+      --replace "-lmfhdf -ldf" "-lmfhdf -lhdf"
+    '';
+
+  preBuild = ''
+    substituteInPlace swig/python/GNUmakefile \
+      --replace "ifeq (\$(STD_UNIX_LAYOUT),\"TRUE\")" "ifeq (1,1)"
+  '';
+
+  postInstall = ''
+    wrapPythonPrograms
+  '';
+
+  enableParallelBuilding = true;
+
+  meta = {
+    description = "Translator library for raster geospatial data formats";
+    homepage = https://www.gdal.org/;
+    license = stdenv.lib.licenses.mit;
+    maintainers = [ stdenv.lib.maintainers.marcweber ];
+    platforms = with stdenv.lib.platforms; linux ++ darwin;
+  };
+}
diff --git a/pkgs/development/libraries/gdal/default.nix b/pkgs/development/libraries/gdal/default.nix
index e7ffdde6cb1c..0db16e2efe3a 100644
--- a/pkgs/development/libraries/gdal/default.nix
+++ b/pkgs/development/libraries/gdal/default.nix
@@ -1,7 +1,7 @@
-{ stdenv, fetchurl, fetchpatch, unzip, libjpeg, libtiff, zlib
+{ stdenv, fetchFromGitHub, fetchpatch, unzip, libjpeg, libtiff, zlib
 , postgresql, mysql, libgeotiff, pythonPackages, proj, geos, openssl
 , libpng, sqlite, libspatialite, poppler, hdf4, qhull, giflib, expat
-, libiconv, libxml2
+, libiconv, libxml2, autoreconfHook
 , netcdfSupport ? true, netcdf, hdf5, curl
 }:
 
@@ -9,15 +9,23 @@ with stdenv.lib;
 
 stdenv.mkDerivation rec {
   name = "gdal-${version}";
-  version = "2.4.0";
+  version = "3.0.1";
 
-  src = fetchurl {
-    url = "https://download.osgeo.org/gdal/${version}/${name}.tar.xz";
-    sha256 = "09qgy36z0jc9w05373m4n0vm4j54almdzql6z9p9zr9pdp61syf3";
+  src = fetchFromGitHub {
+    owner = "OSGeo";
+    repo = "gdal";
+    rev = "v${version}";
+    sha256 = "04rraqhygv8b8fy87qvdhkgx87whby9n98p3gxqr7kdrfymwnh8l";
   };
 
+  sourceRoot = "source/gdal";
+
+  patches = [ ./001.3_0_1.darwin.patch ];
+
+  nativeBuildInputs = [ autoreconfHook ];
+
   buildInputs = [ unzip libjpeg libtiff libpng proj openssl sqlite
-    libspatialite poppler hdf4 qhull giflib expat libxml2 ]
+    libspatialite libgeotiff poppler hdf4 qhull giflib expat libxml2 ]
   ++ (with pythonPackages; [ python numpy wrapPython ])
   ++ stdenv.lib.optional stdenv.isDarwin libiconv
   ++ stdenv.lib.optionals netcdfSupport [ netcdf hdf5 curl ];
@@ -35,7 +43,7 @@ stdenv.mkDerivation rec {
     "--with-sqlite3=${sqlite.dev}"
     "--with-spatialite=${libspatialite}"
     "--with-python"               # optional
-    "--with-proj=${proj}" # optional
+    "--with-proj=${proj.dev}" # optional
     "--with-geos=${geos}/bin/geos-config"# optional
     "--with-hdf4=${hdf4.dev}" # optional
     "--with-xml2=${libxml2.dev}/bin/xml2-config" # optional
@@ -46,31 +54,9 @@ stdenv.mkDerivation rec {
 
   CXXFLAGS = "-fpermissive";
 
-  postPatch = ''
-    sed -i '/ifdef bool/i\
-      #ifdef swap\
-      #undef swap\
-      #endif' ogr/ogrsf_frmts/mysql/ogr_mysql.h
-
-    # poppler 0.73.0 support
-    patch -lp2 <${
-      fetchpatch {
-        url = "https://github.com/OSGeo/gdal/commit/29f4dfbcac2de718043f862166cd639ab578b552.diff";
-        sha256 = "1h2rsjjrgwqfgqzppmzv5jgjs1dbbg8pvfmay0j9y0618qp3r734";
-      }
-    } || true
-    patch -p2 <${
-      fetchpatch {
-        url = "https://github.com/OSGeo/gdal/commit/19967e682738977e11e1d0336e0178882c39cad2.diff";
-        sha256 = "12yqd77226i6xvzgqmxiac5ghdinixh8k2crg1r2gnhc0xlc3arj";
-      }
-    }
-  '';
-
   # - Unset CC and CXX as they confuse libtool.
   # - teach gdal that libdf is the legacy name for libhdf
   preConfigure = ''
-      unset CC CXX
       substituteInPlace configure \
       --replace "-lmfhdf -ldf" "-lmfhdf -lhdf"
     '';
diff --git a/pkgs/development/libraries/gdal/gdal-1_11.nix b/pkgs/development/libraries/gdal/gdal-1_11.nix
index 32101221e64c..40308a957915 100644
--- a/pkgs/development/libraries/gdal/gdal-1_11.nix
+++ b/pkgs/development/libraries/gdal/gdal-1_11.nix
@@ -11,7 +11,7 @@ stdenv.mkDerivation rec {
     sha256 = "0hphxzvy23v3vqxx1y22hhhg4cypihrb8555y12nb4mrhzlw7zfl";
   };
 
-  buildInputs = [ unzip libjpeg libtiff libpng python pythonPackages.numpy proj openssl ];
+  buildInputs = [ unzip libjpeg libtiff libgeotiff libpng python pythonPackages.numpy proj openssl ];
 
   patches = [
     # This ensures that the python package is installed into gdal's prefix,
@@ -33,12 +33,17 @@ stdenv.mkDerivation rec {
 
     "--with-pg=${postgresql}/bin/pg_config"
     "--with-mysql=${mysql57.connector-c}/bin/mysql_config"
-    "--with-geotiff=${libgeotiff}"
+    "--with-geotiff=${libgeotiff.dev}"
     "--with-python"               # optional
     "--with-static-proj4=${proj}" # optional
     "--with-geos=${geos}/bin/geos-config"# optional
   ];
 
+  # Allow use of old proj_api.h
+  NIX_CFLAGS_COMPILE = [
+    "-DACCEPT_USE_OF_DEPRECATED_PROJ_API_H=1"
+  ];
+
   # Prevent this:
   #
   #   Checking .pth file support in /nix/store/xkrmb8xnvqxzjwsdmasqmsdh1a5y2y99-gdal-1.11.2/lib/python2.7/site-packages/
diff --git a/pkgs/development/libraries/java/commons/lang/default.nix b/pkgs/development/libraries/java/commons/lang/default.nix
index e46f22fadfb9..322cb486e93e 100644
--- a/pkgs/development/libraries/java/commons/lang/default.nix
+++ b/pkgs/development/libraries/java/commons/lang/default.nix
@@ -1,12 +1,12 @@
 { stdenv, fetchurl }:
 
 stdenv.mkDerivation rec {
-  version = "3.6";
+  version = "3.9";
   name    = "commons-lang-${version}";
 
   src = fetchurl {
     url    = "mirror://apache/commons/lang/binaries/commons-lang3-${version}-bin.tar.gz";
-    sha256 = "0r1wdjw48k2mk2wzyq5c3cx2zmark4q9psw52ma6v2i0sh6a9il0";
+    sha256 = "0l0q1hnicvpbjmxl81ig3rwc212x5sdfnlg3cniwbmnx8fxjgbki";
   };
 
   installPhase = ''
diff --git a/pkgs/development/libraries/libgeotiff/default.nix b/pkgs/development/libraries/libgeotiff/default.nix
index 33b9e7830e71..51520eb0fe38 100644
--- a/pkgs/development/libraries/libgeotiff/default.nix
+++ b/pkgs/development/libraries/libgeotiff/default.nix
@@ -1,18 +1,27 @@
-{ stdenv, fetchurl, libtiff, libjpeg, proj, zlib}:
+{ stdenv, fetchFromGitHub, libtiff, libjpeg, proj, zlib, autoreconfHook }:
 
 stdenv.mkDerivation rec {
-  version = "1.4.3";
+  version = "1.5.1";
   name = "libgeotiff-${version}";
 
-  src = fetchurl {
-    url = "https://download.osgeo.org/geotiff/libgeotiff/${name}.tar.gz";
-    sha256 = "0rbjqixi4c8yz19larlzq6jda0px2gpmpp9c52cyhplbjsdhsldq";
+  src = fetchFromGitHub {
+    owner = "OSGeo";
+    repo = "libgeotiff";
+    rev = version;
+    sha256 = "081ag23pn2n5y4fkb2rnh4hmcnq92siqiqv0s20jmx0j3s2nvfxy";
   };
 
+  outputs = [ "out" "dev" ];
+
+  sourceRoot = "source/libgeotiff";
+
   configureFlags = [
     "--with-jpeg=${libjpeg.dev}"
     "--with-zlib=${zlib.dev}"
   ];
+
+  nativeBuildInputs = [ autoreconfHook ];
+
   buildInputs = [ libtiff proj ];
 
   hardeningDisable = [ "format" ];
diff --git a/pkgs/development/libraries/libspatialite/default.nix b/pkgs/development/libraries/libspatialite/default.nix
index 8e7b539527e1..7bd22248d876 100644
--- a/pkgs/development/libraries/libspatialite/default.nix
+++ b/pkgs/development/libraries/libspatialite/default.nix
@@ -11,12 +11,15 @@ stdenv.mkDerivation rec {
   };
 
   nativeBuildInputs = [ pkgconfig ];
+
   buildInputs = [ libxml2 sqlite zlib proj geos libiconv ];
 
   configureFlags = [ "--disable-freexl" ];
 
   enableParallelBuilding = true;
 
+  CFLAGS = "-DACCEPT_USE_OF_DEPRECATED_PROJ_API_H=1";
+
   postInstall = "" + optionalString stdenv.isDarwin ''
     ln -s $out/lib/mod_spatialite.{so,dylib}
   '';
diff --git a/pkgs/development/libraries/proj-datumgrid/default.nix b/pkgs/development/libraries/proj-datumgrid/default.nix
new file mode 100644
index 000000000000..f1c13e93aecd
--- /dev/null
+++ b/pkgs/development/libraries/proj-datumgrid/default.nix
@@ -0,0 +1,32 @@
+{ stdenv, fetchFromGitHub }:
+
+stdenv.mkDerivation rec {
+  name = "proj-datumgrid";
+  version = "world-1.0";
+
+  src = fetchFromGitHub {
+    owner = "OSGeo";
+    repo = "proj-datumgrid";
+    rev = version;
+    sha256 = "132wp77fszx33wann0fjkmi1isxvsb0v9iw0gd9sxapa9h6hf3am";
+  };
+
+  sourceRoot = "source/scripts";
+
+  buildPhase = ''
+    $CC nad2bin.c -o nad2bin
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp nad2bin $out/bin/
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Repository for proj datum grids";
+    homepage = https://proj4.org;
+    license = licenses.mit;
+    platforms = platforms.linux ++ platforms.darwin;
+    maintainers = with maintainers; [ ];
+  };
+}
diff --git a/pkgs/development/libraries/proj/5.2.nix b/pkgs/development/libraries/proj/5.2.nix
new file mode 100644
index 000000000000..8fb4515e70da
--- /dev/null
+++ b/pkgs/development/libraries/proj/5.2.nix
@@ -0,0 +1,20 @@
+{ stdenv, fetchurl }:
+
+stdenv.mkDerivation {
+  name = "proj-5.2.0";
+
+  src = fetchurl {
+    url = https://download.osgeo.org/proj/proj-5.2.0.tar.gz;
+    sha256 = "0q3ydh2j8qhwlxmnac72pg69rw2znbi5b6k5wama8qmwzycr94gg";
+  };
+
+  doCheck = stdenv.is64bit;
+
+  meta = with stdenv.lib; {
+    description = "Cartographic Projections Library";
+    homepage = https://proj4.org;
+    license = licenses.mit;
+    platforms = platforms.linux ++ platforms.darwin;
+    maintainers = with maintainers; [ vbgl ];
+  };
+}
diff --git a/pkgs/development/libraries/proj/default.nix b/pkgs/development/libraries/proj/default.nix
index 8fb4515e70da..ea89dbee0f61 100644
--- a/pkgs/development/libraries/proj/default.nix
+++ b/pkgs/development/libraries/proj/default.nix
@@ -1,13 +1,22 @@
-{ stdenv, fetchurl }:
+{ stdenv, fetchFromGitHub, pkg-config, sqlite, autoreconfHook }:
 
-stdenv.mkDerivation {
-  name = "proj-5.2.0";
+stdenv.mkDerivation rec {
+  name = "proj";
+  version = "6.1.1";
 
-  src = fetchurl {
-    url = https://download.osgeo.org/proj/proj-5.2.0.tar.gz;
-    sha256 = "0q3ydh2j8qhwlxmnac72pg69rw2znbi5b6k5wama8qmwzycr94gg";
+  src = fetchFromGitHub {
+    owner = "OSGeo";
+    repo = "PROJ";
+    rev = version;
+    sha256 = "0w2v2l22kv0xzq5hwl7n8ki6an8vfsr0lg0cdbkwcl4xv889ysma";
   };
 
+  outputs = [ "out" "dev"];
+
+  nativeBuildInputs = [ pkg-config autoreconfHook ];
+
+  buildInputs = [ sqlite ];
+
   doCheck = stdenv.is64bit;
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/libraries/tdlib/default.nix b/pkgs/development/libraries/tdlib/default.nix
new file mode 100644
index 000000000000..716f3d313b42
--- /dev/null
+++ b/pkgs/development/libraries/tdlib/default.nix
@@ -0,0 +1,24 @@
+{ fetchFromGitHub, gperf, openssl, readline, zlib, cmake, stdenv }:
+
+stdenv.mkDerivation rec {
+  version = "1.4.0";
+  pname = "tdlib";
+
+  src = fetchFromGitHub {
+    owner = "tdlib";
+    repo = "td";
+    rev = "v${version}";
+    sha256 = "1ijyn14rjb87rqm39hg7md8ab33yiy8cgzw3p0m37scn58gabpp7";
+  };
+
+  buildInputs = [ gperf openssl readline zlib ];
+  nativeBuildInputs = [ cmake ];
+
+  meta = with stdenv.lib; {
+    description = "Cross-platform library for building Telegram clients";
+    homepage = "https://core.telegram.org/tdlib/";
+    license = [ licenses.boost ];
+    platforms = platforms.linux;
+    maintainers = [ maintainers.vyorkin ];
+  };
+}
diff --git a/pkgs/development/lisp-modules/asdf/default.nix b/pkgs/development/lisp-modules/asdf/default.nix
index c9d8d52b0682..8d316d06fbbf 100644
--- a/pkgs/development/lisp-modules/asdf/default.nix
+++ b/pkgs/development/lisp-modules/asdf/default.nix
@@ -3,11 +3,11 @@ let
   s = # Generated upstream information
   rec {
     baseName="asdf";
-    version="3.3.2";
+    version="3.3.3";
     name="${baseName}-${version}";
-    hash="1bdrybn97qhny5192ifis8fp8m79djql2k4h9r9q2wnwxf9q2d4x";
-    url="http://common-lisp.net/project/asdf/archives/asdf-3.3.2.tar.gz";
-    sha256="1bdrybn97qhny5192ifis8fp8m79djql2k4h9r9q2wnwxf9q2d4x";
+    hash="1167445kmb0dbixc5l2r58cswg5s6jays0l1zxrk3aij0490bkgg";
+    url="http://common-lisp.net/project/asdf/archives/asdf-3.3.3.tar.gz";
+    sha256="1167445kmb0dbixc5l2r58cswg5s6jays0l1zxrk3aij0490bkgg";
   };
   buildInputs = [
     texinfo texLive perl
diff --git a/pkgs/development/python-modules/acme-tiny/default.nix b/pkgs/development/python-modules/acme-tiny/default.nix
index e212e83c2708..51b4b15cd183 100644
--- a/pkgs/development/python-modules/acme-tiny/default.nix
+++ b/pkgs/development/python-modules/acme-tiny/default.nix
@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "acme-tiny";
-  version = "4.0.4";
+  version = "4.1.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0vqlmvk34jgvgx3qdsh50q7m4aiy02786jyjjcq45dcws7a4f9f1";
+    sha256 = "0jmg525n4n98hwy3hf303jbnq23z79sqwgliji9j7qcnph47gkgq";
   };
 
   patchPhase = ''
diff --git a/pkgs/development/python-modules/cartopy/default.nix b/pkgs/development/python-modules/cartopy/default.nix
index e54136a50276..117b6fed5971 100644
--- a/pkgs/development/python-modules/cartopy/default.nix
+++ b/pkgs/development/python-modules/cartopy/default.nix
@@ -1,9 +1,10 @@
 { buildPythonPackage, lib, fetchPypi
 , pytest, filelock, mock, pep8
 , cython, isPy27
-, six, pyshp, shapely, geos, proj, numpy
+, six, pyshp, shapely, geos, numpy
 , gdal, pillow, matplotlib, pyepsg, pykdtree, scipy, owslib, fiona
 , xvfb_run
+, proj_5 # see https://github.com/SciTools/cartopy/pull/1252 for status on proj 6 support
 }:
 
 buildPythonPackage rec {
@@ -27,17 +28,17 @@ buildPythonPackage rec {
     export HOME=$(mktemp -d)
     ${maybeXvfbRun} pytest --pyargs cartopy \
       -m "not network and not natural_earth" \
-      -k "not test_nightshade_image"
+      -k "not test_nightshade_image and not background_img"
   '';
 
   nativeBuildInputs = [
     cython
     geos # for geos-config
-    proj
+    proj_5
   ];
 
   buildInputs = [
-    geos proj
+    geos proj_5
   ];
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/fiona/default.nix b/pkgs/development/python-modules/fiona/default.nix
index ebd100037b25..6dd74742741e 100644
--- a/pkgs/development/python-modules/fiona/default.nix
+++ b/pkgs/development/python-modules/fiona/default.nix
@@ -1,7 +1,7 @@
 { stdenv, buildPythonPackage, fetchPypi, isPy3k, pythonOlder
 , attrs, click, cligj, click-plugins, six, munch, enum34
 , pytest, boto3, mock
-, gdal
+, gdal_2 # can't bump to 3 yet, https://github.com/Toblerity/Fiona/issues/745
 }:
 
 buildPythonPackage rec {
@@ -16,11 +16,11 @@ buildPythonPackage rec {
   CXXFLAGS = stdenv.lib.optionalString stdenv.cc.isClang "-std=c++11";
 
   nativeBuildInputs = [
-    gdal # for gdal-config
+    gdal_2 # for gdal-config
   ];
 
   buildInputs = [
-    gdal
+    gdal_2
   ];
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/pyproj/001.proj.patch b/pkgs/development/python-modules/pyproj/001.proj.patch
new file mode 100644
index 000000000000..b024c28156c1
--- /dev/null
+++ b/pkgs/development/python-modules/pyproj/001.proj.patch
@@ -0,0 +1,47 @@
+diff a/pyproj/datadir.py b/pyproj/datadir.py
+--- a/pyproj/datadir.py
++++ b/pyproj/datadir.py
+@@ -52,6 +52,7 @@ def get_data_dir():
+     str: The valid data directory.
+
+     """
++    return "@proj@/share/proj"
+     # to avoid re-validating
+     global _VALIDATED_PROJ_DATA
+     if _VALIDATED_PROJ_DATA is not None:
+diff a/setup.py b/setup.py
+--- a/setup.py
++++ b/setup.py
+@@ -16,7 +16,7 @@ INTERNAL_PROJ_DIR = os.path.join(CURRENT_FILE_PATH, "pyproj", BASE_INTERNAL_PROJ
+
+ def check_proj_version(proj_dir):
+     """checks that the PROJ library meets the minimum version"""
+-    proj = os.path.join(proj_dir, "bin", "proj")
++    proj = "@proj@/bin/proj"
+     proj_ver_bytes = subprocess.check_output(proj, stderr=subprocess.STDOUT)
+     proj_ver_bytes = (proj_ver_bytes.decode("ascii").split()[1]).strip(",")
+     proj_version = parse_version(proj_ver_bytes)
+@@ -33,6 +33,7 @@ def get_proj_dir():
+     """
+     This function finds the base PROJ directory.
+     """
++    return "@proj@"
+     proj_dir = os.environ.get("PROJ_DIR")
+     if proj_dir is None and os.path.exists(INTERNAL_PROJ_DIR):
+         proj_dir = INTERNAL_PROJ_DIR
+@@ -56,6 +57,7 @@ def get_proj_libdirs(proj_dir):
+     """
+     This function finds the library directories
+     """
++    return ["@proj@/lib"]
+     proj_libdir = os.environ.get("PROJ_LIBDIR")
+     libdirs = []
+     if proj_libdir is None:
+@@ -77,6 +79,7 @@ def get_proj_incdirs(proj_dir):
+     """
+     This function finds the include directories
+     """
++    return ["@proj@/include"]
+     proj_incdir = os.environ.get("PROJ_INCDIR")
+     incdirs = []
+     if proj_incdir is None:
diff --git a/pkgs/development/python-modules/pyproj/default.nix b/pkgs/development/python-modules/pyproj/default.nix
index f08625f62b6d..ddfecbe8ec51 100644
--- a/pkgs/development/python-modules/pyproj/default.nix
+++ b/pkgs/development/python-modules/pyproj/default.nix
@@ -1,38 +1,49 @@
-{ lib
-, buildPythonPackage
-, fetchFromGitHub
-, python
-, nose2
+{ lib, buildPythonPackage, fetchPypi, python, pkgs, pythonOlder, substituteAll
+, aenum
 , cython
-, proj ? null
+, pytest
+, mock
+, numpy
 }:
 
-buildPythonPackage (rec {
+buildPythonPackage rec {
   pname = "pyproj";
-  version = "unstable-2018-11-13";
+  version = "2.2.1";
 
-  src = fetchFromGitHub {
-    owner = "jswhit";
-    repo = pname;
-    rev = "78540f5ff40da92160f80860416c91ee74b7643c";
-    sha256 = "1vq5smxmpdjxialxxglsfh48wx8kaq9sc5mqqxn4fgv1r5n1m3n9";
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0yigcxwmx5cczipf2mpmy2gq1dnl0635yjvjq86ay47j1j5fd2gc";
   };
 
-  buildInputs = [ cython ];
+  # force pyproj to use ${pkgs.proj}
+  patches = [
+    (substituteAll {
+      src = ./001.proj.patch;
+      proj = pkgs.proj;
+    })
+  ];
 
-  checkInputs = [ nose2 ];
+  buildInputs = [ cython pkgs.proj ];
 
+  propagatedBuildInputs = [
+    numpy
+  ] ++ lib.optional (pythonOlder "3.6") aenum;
+
+  checkInputs = [ pytest mock ];
+
+  # ignore rounding errors, and impure docgen
+  # datadir is ignored because it does the proj look up logic, which isn't relevant
   checkPhase = ''
-    runHook preCheck
-    pushd unittest  # changing directory should ensure we're importing the global pyproj
-    ${python.interpreter} test.py && ${python.interpreter} -c "import doctest, pyproj, sys; sys.exit(doctest.testmod(pyproj)[0])"
-    popd
-    runHook postCheck
+    pytest . -k 'not alternative_grid_name \
+                 and not transform_wgs84_to_alaska \
+                 and not repr' \
+            --ignore=test/test_doctest_wrapper.py \
+            --ignore=test/test_datadir.py
   '';
 
   meta = {
     description = "Python interface to PROJ.4 library";
-    homepage = https://github.com/jswhit/pyproj;
+    homepage = "https://github.com/jswhit/pyproj";
     license = with lib.licenses; [ isc ];
   };
-} // (if proj == null then {} else { PROJ_DIR = proj; }))
+}
diff --git a/pkgs/development/python-modules/sklearn-deap/default.nix b/pkgs/development/python-modules/sklearn-deap/default.nix
index 63a048abdb2a..c54997a21fe8 100644
--- a/pkgs/development/python-modules/sklearn-deap/default.nix
+++ b/pkgs/development/python-modules/sklearn-deap/default.nix
@@ -1,17 +1,25 @@
-{ stdenv, buildPythonPackage, fetchFromGitHub, numpy, scipy, deap, scikitlearn, python, isPy3k }:
+{ stdenv, buildPythonPackage, fetchFromGitHub, fetchpatch, numpy, scipy, deap, scikitlearn, python }:
 
 buildPythonPackage rec {
   pname = "sklearn-deap";
-  version = "0.2.2";
+  version = "0.2.3";
 
   # No tests in Pypi
   src = fetchFromGitHub {
     owner = "rsteca";
     repo = pname;
     rev = "${version}";
-    sha256 = "01ynmzxg181xhv2d7bs53zjvk9x2qpxix32sspq54mpigxh13ava";
+    sha256 = "1yqnmy8h08i2y6bb2s0a5nx9cwvyg45293whqh420c195gpzg1x3";
   };
 
+  patches = [
+    # Fix for newer versions of scikit-learn. See: https://github.com/rsteca/sklearn-deap/pull/62
+    (fetchpatch {
+      url = "https://github.com/rsteca/sklearn-deap/commit/3ae62990fc87f36b59382e7c4db3c74cf99ec3bf.patch";
+      sha256 = "1na6wf4v0dcmyz3pz8aiqkmv76d1iz3hi4iyfq9kfnycgzpv1kxk";
+    })
+  ];
+
   propagatedBuildInputs = [ numpy scipy deap scikitlearn ];
 
   checkPhase = ''
@@ -23,7 +31,6 @@ buildPythonPackage rec {
     homepage = https://github.com/rsteca/sklearn-deap;
     license = licenses.lgpl3;
     maintainers = with maintainers; [ psyanticy ];
-    broken = isPy3k; # https://github.com/rsteca/sklearn-deap/issues/65
   };
 }
 
diff --git a/pkgs/development/python-modules/vsts/default.nix b/pkgs/development/python-modules/vsts/default.nix
new file mode 100644
index 000000000000..0f49ffd05c60
--- /dev/null
+++ b/pkgs/development/python-modules/vsts/default.nix
@@ -0,0 +1,30 @@
+{ buildPythonPackage
+, lib
+, python
+, fetchPypi
+, msrest
+}:
+
+buildPythonPackage rec {
+  version = "0.1.25";
+  pname = "vsts";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "15sgwqa72ynpahj101r2kc15s3dnsafg5gqx0sz3hnqz29h925ys";
+  };
+
+  propagatedBuildInputs = [ msrest ];
+
+  # Tests are highly impure
+  checkPhase = ''
+    ${python.interpreter} -c 'import vsts.version; print(vsts.version.VERSION)'
+  '';
+
+  meta = with lib; {
+    description = "Python APIs for interacting with and managing Azure DevOps";
+    homepage = https://github.com/microsoft/azure-devops-python-api;
+    license = licenses.mit;
+    maintainers = with maintainers; [ jonringer ];
+  };
+}
diff --git a/pkgs/development/tools/ammonite/default.nix b/pkgs/development/tools/ammonite/default.nix
index d4edbf44a798..4bd95a8d745a 100644
--- a/pkgs/development/tools/ammonite/default.nix
+++ b/pkgs/development/tools/ammonite/default.nix
@@ -5,12 +5,12 @@
 with stdenv.lib;
 stdenv.mkDerivation rec {
   name = "ammonite-${version}";
-  version = "1.6.8";
+  version = "1.6.9";
   scalaVersion = "2.12";
 
   src = fetchurl {
     url = "https://github.com/lihaoyi/Ammonite/releases/download/${version}/${scalaVersion}-${version}";
-    sha256 = "1lqc071v5f8dy1da669l0bfw9p8l6yavzlizzig9m441zcrmbj5d";
+    sha256 = "1fi5j0kcndq00x72d8bkx6qiy9nh2i6c6m29gzfqql52qgbq1fd0";
   };
 
   propagatedBuildInputs = [ jre ] ;
diff --git a/pkgs/development/tools/continuous-integration/fly/default.nix b/pkgs/development/tools/continuous-integration/fly/default.nix
new file mode 100644
index 000000000000..47af70b37029
--- /dev/null
+++ b/pkgs/development/tools/continuous-integration/fly/default.nix
@@ -0,0 +1,37 @@
+{ buildGoModule, fetchFromGitHub, lib, writeText }:
+
+buildGoModule rec {
+  pname = "fly";
+  version = "5.3.0";
+
+  src = fetchFromGitHub {
+    owner = "concourse";
+    repo = "concourse";
+    rev = "v${version}";
+    sha256 = "06ns98k47nafhkkj7gkmxp7msn4ssypyss6ll0fm6380vq2cavnj";
+  };
+
+  modSha256 = "11rnlmn5hp9nsgkmd716dsjmkr273035j9gzfhjxjsfpiax60i0a";
+
+  subPackages = [ "fly" ];
+
+  buildFlagsArray = ''
+    -ldflags=
+      -X github.com/concourse/concourse.Version=${version}
+  '';
+
+  # The fly.bash file included with this derivation can be replaced by a
+  # call to `fly completion bash` once the `completion` subcommand has
+  # made it into a release. Similarly, `fly completion zsh` will provide
+  # zsh completions. https://github.com/concourse/concourse/pull/4012
+  postInstall = ''
+    install -D -m 444 ${./fly.bash} $out/share/bash-completion/completions/fly
+  '';
+
+  meta = with lib; {
+    description = "A command line interface to Concourse CI";
+    homepage = https://concourse-ci.org;
+    license = licenses.asl20;
+    maintainers = with maintainers; [ ivanbrennan ];
+  };
+}
diff --git a/pkgs/development/tools/continuous-integration/fly/fly.bash b/pkgs/development/tools/continuous-integration/fly/fly.bash
new file mode 100644
index 000000000000..a9acc5f70a40
--- /dev/null
+++ b/pkgs/development/tools/continuous-integration/fly/fly.bash
@@ -0,0 +1,10 @@
+# credits:
+# https://godoc.org/github.com/jessevdk/go-flags#hdr-Completion
+# https://github.com/concourse/concourse/issues/1309#issuecomment-452893900
+_fly_compl() {
+    args=("${COMP_WORDS[@]:1:$COMP_CWORD}")
+    local IFS=$'\n'
+    COMPREPLY=($(GO_FLAGS_COMPLETION=1 ${COMP_WORDS[0]} "${args[@]}"))
+    return 0
+}
+complete -F _fly_compl fly
diff --git a/pkgs/development/tools/misc/babeltrace/default.nix b/pkgs/development/tools/misc/babeltrace/default.nix
index cb00111b2b46..19ed711f1f4c 100644
--- a/pkgs/development/tools/misc/babeltrace/default.nix
+++ b/pkgs/development/tools/misc/babeltrace/default.nix
@@ -1,11 +1,11 @@
 { stdenv, fetchurl, pkgconfig, glib, libuuid, popt, elfutils }:
 
 stdenv.mkDerivation rec {
-  name = "babeltrace-1.5.6";
+  name = "babeltrace-1.5.7";
 
   src = fetchurl {
     url = "https://www.efficios.com/files/babeltrace/${name}.tar.bz2";
-    sha256 = "1dxv2pwyqx2p7kzhcfansij40m9kanl85x2r68dmgp98g0hvq22k";
+    sha256 = "0yw05cnk5w8b5nbznycglyn4h3hq56a1n8rlb9k9rlzz4ph32lr1";
   };
 
   nativeBuildInputs = [ pkgconfig ];
diff --git a/pkgs/development/tools/ocaml/merlin/default.nix b/pkgs/development/tools/ocaml/merlin/default.nix
index 3b176541f517..67acf874baff 100644
--- a/pkgs/development/tools/ocaml/merlin/default.nix
+++ b/pkgs/development/tools/ocaml/merlin/default.nix
@@ -2,7 +2,7 @@
 
 buildDunePackage rec {
   pname = "merlin";
-  version = "3.3.1";
+  version = "3.3.2";
 
   minimumOCamlVersion = "4.02.1";
 
@@ -10,7 +10,7 @@ buildDunePackage rec {
     owner = "ocaml";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1z2m6jykgn3nylh4bfirhxlb0bwamifv4fgml6j34ggk1drs8xrl";
+    sha256 = "1z9mcxflraj15sbz6q7f84n31n9fsialw7z8bi3r1biz68nypva9";
   };
 
   buildInputs = [ yojson ];
diff --git a/pkgs/development/tools/ocaml/opam/default.nix b/pkgs/development/tools/ocaml/opam/default.nix
index f844b369eb32..452f162b2356 100644
--- a/pkgs/development/tools/ocaml/opam/default.nix
+++ b/pkgs/development/tools/ocaml/opam/default.nix
@@ -7,7 +7,7 @@ assert lib.versionAtLeast ocaml.version "4.02.3";
 let
   srcs = {
     cmdliner = fetchurl {
-      url = "https://erratique.ch/software/cmdliner/releases/cmdliner-1.0.2.tbz";
+      url = "http://erratique.ch/software/cmdliner/releases/cmdliner-1.0.2.tbz";
       sha256 = "18jqphjiifljlh9jg8zpl6310p3iwyaqphdkmf89acyaix0s4kj1";
     };
     cppo = fetchurl {
@@ -23,16 +23,16 @@ let
       sha256 = "00yvyfm4j423zqndvgc1ycnmiffaa2l9ab40cyg23pf51qmzk2jm";
     };
     dune-local = fetchurl {
-      url = "https://github.com/ocaml/dune/releases/download/1.2.1/dune-1.2.1.tbz";
-      sha256 = "00c5dbm4hkdapc2i7pg07b2lj8sv6ly38qr7zid58cdmbmzq21z9";
+      url = "https://github.com/ocaml/dune/releases/download/1.6.3/dune-1.6.3.tbz";
+      sha256 = "0dmf0wbfmgdy5plz1bjiisc2hjgblvxsnrqjmw2c8y45v1h23mdz";
     };
     extlib = fetchurl {
       url = "http://ygrek.org.ua/p/release/ocaml-extlib/extlib-1.7.5.tar.gz";
       sha256 = "19slqf5bdj0rrph2w41giwmn6df2qm07942jn058pjkjrnk30d4s";
     };
     mccs = fetchurl {
-      url = "https://github.com/AltGr/ocaml-mccs/archive/1.1+9.tar.gz";
-      sha256 = "0gf86c65jdxxcwd96kcmrqxrmnnzc0570gb9ad6c57rl3fyy8yhv";
+      url = "https://github.com/AltGr/ocaml-mccs/archive/1.1+10.tar.gz";
+      sha256 = "003kam22plnh88liyxi4d1065j2rys1mpdla20rxps53ah1xwmxg";
     };
     ocamlgraph = fetchurl {
       url = "http://ocamlgraph.lri.fr/download/ocamlgraph-1.8.8.tar.gz";
@@ -55,13 +55,13 @@ let
       sha256 = "02lb2d9i12bxrz2ba5wygk2bycan316skqlyri0597q7j9210g8r";
     };
     opam = fetchurl {
-      url = "https://github.com/ocaml/opam/archive/2.0.4.zip";
-      sha256 = "1312nc9s4h0vksiimz7jsv3zw17fa05p6mdx23s5sii0qspvnx8c";
+      url = "https://github.com/ocaml/opam/archive/2.0.5.zip";
+      sha256 = "0arv5zaikvcqbicdk47jpfgvjrqhqm71yq2zmj7pp6zf7bm0js6s";
     };
   };
 in stdenv.mkDerivation rec {
   name = "opam-${version}";
-  version = "2.0.4";
+  version = "2.0.5";
 
   buildInputs = [ unzip curl ncurses ocaml makeWrapper getconf ] ++ lib.optional stdenv.isLinux bubblewrap;
 
@@ -117,4 +117,4 @@ in stdenv.mkDerivation rec {
     platforms = platforms.all;
   };
 }
-# Generated by: ./opam.nix.pl -v 2.0.4 -p opam-shebangs.patch
+# Generated by: ./opam.nix.pl -v 2.0.5 -p opam-shebangs.patch
diff --git a/pkgs/development/web/grails/default.nix b/pkgs/development/web/grails/default.nix
index 018c7f969697..24f567891983 100644
--- a/pkgs/development/web/grails/default.nix
+++ b/pkgs/development/web/grails/default.nix
@@ -11,11 +11,11 @@ let
 in
 stdenv.mkDerivation rec {
   name = "grails-${version}";
-  version = "3.3.10";
+  version = "4.0.0";
 
   src = fetchurl {
     url = "https://github.com/grails/grails-core/releases/download/v${version}/grails-${version}.zip";
-    sha256 = "1lykawfi47c2k6lq4vrnghlz8gcnmqsslxsnaq4d2n78g0y3yyr2";
+    sha256 = "13y0q3gcdpfwib3ahrgh36rhr4smbrq2g4xgvnk8c0a6wvmz85sx";
   };
 
   buildInputs = [ unzip ];