6 files changed, 52 insertions, 31 deletions
diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix
index 4c4278c30faa..d5dae364cc3d 100644
--- a/pkgs/applications/science/chemistry/jmol/default.nix
+++ b/pkgs/applications/science/chemistry/jmol/default.nix
@@ -1,4 +1,5 @@
 { stdenv
+, lib
 , fetchurl
 , unzip
 , makeDesktopItem
@@ -16,15 +17,15 @@ let
   };
 in
 stdenv.mkDerivation rec {
-  version = "${baseVersion}.${patchVersion}";
-  baseVersion = "14.29";
-  patchVersion = "12";
+  version = "14.29.17";
   pname = "jmol";
   name = "${pname}-${version}";
 
-  src = fetchurl {
+  src = let 
+    baseVersion = "${lib.versions.major version}.${lib.versions.minor version}";
+  in fetchurl {
     url = "mirror://sourceforge/jmol/Jmol/Version%20${baseVersion}/Jmol%20${version}/Jmol-${version}-binary.tar.gz";
-    sha256 = "1ndq9am75janshrnk26334z1nmyh3k4bp20napvf2zv0lfp8k3bv";
+    sha256 = "1dnxbvi8ha9z2ldymkjpxydd216afv6k7fdp3j70sql10zgy0isk";
   };
 
   patchPhase = ''
diff --git a/pkgs/applications/science/logic/abc/default.nix b/pkgs/applications/science/logic/abc/default.nix
index bab9b302d7d1..6e7a3cfc88ac 100644
--- a/pkgs/applications/science/logic/abc/default.nix
+++ b/pkgs/applications/science/logic/abc/default.nix
@@ -1,20 +1,21 @@
-{ fetchhg, stdenv, readline }:
+{ fetchFromGitHub, stdenv, readline, cmake }:
 
 stdenv.mkDerivation rec {
   name = "abc-verifier-${version}";
-  version = "20160818";
+  version = "2018-07-08";
 
-  src = fetchhg {
-    url    = "https://bitbucket.org/alanmi/abc";
-    rev    = "a2e5bc66a68a72ccd267949e5c9973dd18f8932a";
-    sha256 = "09yvhj53af91nc54gmy7cbp7yljfcyj68a87494r5xvdfnsj11gy";
+  src = fetchFromGitHub {
+    owner = "berkeley-abc";
+    repo = "abc";
+    rev    = "24407e13db4b8ca16c3996049b2d33ec3722de39";
+    sha256 = "1rckji7nk81n6v1yajz7daqwipxacv7zlafknvmbiwji30j47sq5";
   };
 
+  nativeBuildInputs = [ cmake ];
   buildInputs = [ readline ];
-  preBuild = ''
-    export buildFlags="CC=$CC CXX=$CXX LD=$CXX"
-  '';
+
   enableParallelBuilding = true;
+
   installPhase = ''
     mkdir -p $out/bin
     mv abc $out/bin
@@ -22,7 +23,7 @@ stdenv.mkDerivation rec {
 
   meta = {
     description = "A tool for squential logic synthesis and formal verification";
-    homepage    = "https://people.eecs.berkeley.edu/~alanmi/abc/abc.htm";
+    homepage    = https://people.eecs.berkeley.edu/~alanmi/abc;
     license     = stdenv.lib.licenses.mit;
     platforms   = stdenv.lib.platforms.unix;
     maintainers = [ stdenv.lib.maintainers.thoughtpolice ];
diff --git a/pkgs/applications/science/logic/poly/default.nix b/pkgs/applications/science/logic/poly/default.nix
index 1b401c927b6e..2f765572f9ad 100644
--- a/pkgs/applications/science/logic/poly/default.nix
+++ b/pkgs/applications/science/logic/poly/default.nix
@@ -1,17 +1,20 @@
-{stdenv, fetchurl, gmp, cmake, python}:
+{stdenv, fetchFromGitHub, gmp, cmake, python}:
 
-let version = "0.1.4";
-in
+stdenv.mkDerivation rec {
+  name = "${pname}-${version}";
+  pname = "libpoly";
+  version = "0.1.7";
 
-stdenv.mkDerivation {
-  name = "libpoly-${version}";
-
-  src = fetchurl {
-    url = "https://github.com/SRI-CSL/libpoly/archive/v${version}.tar.gz";
-    sha256 = "16x1pk2a3pcb5a0dzyw28ccjwkhmbsck4hy80ss7kx0dd7qgpi7j";
+  src = fetchFromGitHub {
+    owner = "SRI-CSL";
+    repo = "libpoly";
+    rev = "v${version}";
+    sha256 = "0i5ar4lhs88glk0rvkmag656ii434i6i1q5dspx6d0kyg78fii64";
   };
 
-  buildInputs = [ cmake gmp python ];
+  nativeBuildInputs = [ cmake ];
+
+  buildInputs = [ gmp python ];
 
   meta = with stdenv.lib; {
     homepage = https://github.com/SRI-CSL/libpoly;
diff --git a/pkgs/applications/science/logic/yices/default.nix b/pkgs/applications/science/logic/yices/default.nix
index a607f1066395..3121a83e5b98 100644
--- a/pkgs/applications/science/logic/yices/default.nix
+++ b/pkgs/applications/science/logic/yices/default.nix
@@ -2,12 +2,12 @@
 
 stdenv.mkDerivation rec {
   name    = "yices-${version}";
-  version = "2.5.4";
+  version = "2.6.0";
 
   src = fetchurl {
     url = "https://github.com/SRI-CSL/yices2/archive/Yices-${version}.tar.gz";
     name = "${name}-src.tar.gz";
-    sha256 = "1k8wmlddi3zv5kgg6xbch3a0s0xqsmsfc7y6z8zrgcyhswl36h7p";
+    sha256 = "10ikq7ib8jhx7hlxfm6mp5qg6r8dflqs8242q5zaicn80qixpm12";
   };
 
   nativeBuildInputs = [ autoreconfHook ];
@@ -26,9 +26,11 @@ stdenv.mkDerivation rec {
 
   # Includes a fix for the embedded soname being libyices.so.2.5, but
   # only installing the libyices.so.2.5.x file.
-  installPhase = ''
+  installPhase = let
+    ver_XdotY = builtins.concatStringsSep "." (stdenv.lib.take 2 (stdenv.lib.splitString "." version));
+  in ''
       make install LDCONFIG=true
-      (cd $out/lib && ln -s -f libyices.so.${version} libyices.so.2.5)
+      ln -sfr $out/lib/libyices.so.{${version},${ver_XdotY}}
   '';
 
   meta = with stdenv.lib; {
diff --git a/pkgs/applications/science/logic/z3/default.nix b/pkgs/applications/science/logic/z3/default.nix
index 54c9799a01b8..10a526192764 100644
--- a/pkgs/applications/science/logic/z3/default.nix
+++ b/pkgs/applications/science/logic/z3/default.nix
@@ -20,6 +20,20 @@ stdenv.mkDerivation rec {
     cd build
   '';
 
+  postInstall = ''
+    mkdir -p $dev $lib $python/lib
+
+    mv $out/lib/python*  $python/lib/
+    mv $out/lib          $lib/lib
+    mv $out/include      $dev/include
+
+    # clean up a copy of libz3.so and symlink it instead
+    rm $python/${python.sitePackages}/z3/lib/libz3.so
+    ln -s $lib/lib/libz3.so $python/${python.sitePackages}/z3/lib/libz3.so
+  '';
+
+  outputs = [ "out" "lib" "dev" "python" ];
+
   meta = {
     description = "A high-performance theorem prover and SMT solver";
     homepage    = "https://github.com/Z3Prover/z3";
diff --git a/pkgs/applications/science/math/qalculate-gtk/default.nix b/pkgs/applications/science/math/qalculate-gtk/default.nix
index 28bd31506874..7990088ffbe9 100644
--- a/pkgs/applications/science/math/qalculate-gtk/default.nix
+++ b/pkgs/applications/science/math/qalculate-gtk/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "qalculate-gtk-${version}";
-  version = "2.6.0";
+  version = "2.6.1";
 
   src = fetchFromGitHub {
     owner = "qalculate";
     repo = "qalculate-gtk";
     rev = "v${version}";
-    sha256 = "0b2g9ziypcplczsm14b4i2k7vpiw9ll28qskv1fdhyqb0fij3qcx";
+    sha256 = "19jw1w29x0r1qq5r8gmqrqr00ml2pfi2w433723vjzxpfg2pp70r";
   };
 
   patchPhase = ''