Merge commit 'a1dd419c1ffacea87eba066a2bb332e03cb68f66'

5 files changed, 43 insertions, 79 deletions

diff --git a/nixpkgs/pkgs/applications/science/biology/cd-hit/default.nix b/nixpkgs/pkgs/applications/science/biology/cd-hit/default.nix
new file mode 100644
index 000000000000..1a41a28a19aa
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/cd-hit/default.nix
@@ -0,0 +1,34 @@
+{ stdenv, fetchFromGitHub, makeWrapper, zlib, perl, perlPackages }:
+
+stdenv.mkDerivation rec {
+  version = "4.8.1";
+  pname = "cd-hit";
+
+  src = fetchFromGitHub {
+    owner = "weizhongli";
+    repo = "cdhit";
+    rev = "V${version}";
+    sha256 = "032nva6iiwmw59gjipm1mv0xlcckhxsf45mc2qbnv19lbis0q22i";
+  };
+
+  propagatedBuildInputs = [ perl perlPackages.TextNSP perlPackages.PerlMagick perlPackages.Storable ];
+
+  nativeBuildInputs = [ zlib makeWrapper ];
+
+  makeFlags = [ "PREFIX=$(out)/bin" ];
+
+  preInstall = "mkdir -p $out/bin";
+
+  postFixup = ''
+    wrapProgram $out/bin/FET.pl --prefix PERL5LIB : $PERL5LIB
+    wrapProgram $out/bin/plot_2d.pl --prefix PERL5LIB : $PERL5LIB
+    wrapProgram $out/bin/clstr_list_sort.pl --prefix PERL5LIB : $PERL5LIB
+  '';
+  meta = with stdenv.lib; {
+    description = "Clustering and comparing protein or nucleotide sequences";
+    homepage = http://weizhongli-lab.org/cd-hit/;
+    license = licenses.gpl2;
+    maintainers = [ maintainers.bzizou ];
+    platforms = platforms.unix;
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix b/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix
index 5fc71c9fc6ba..4b580a6cf52e 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix
@@ -3,7 +3,7 @@
 }:
 
 let
-  version = "8.4";
+  version = "9.0";
   fftwAll = symlinkJoin { name ="ftw-dev-out"; paths = [ fftw.dev fftw.out ]; };
 
 in stdenv.mkDerivation {
@@ -11,7 +11,7 @@ in stdenv.mkDerivation {
 
   src = fetchurl {
     url = "http://www.tddft.org/programs/octopus/down.php?file=${version}/octopus-${version}.tar.gz";
-    sha256 = "1fx5ssnf65b9ld7xs9rvvg8i80pblxpyhqkir0a7xshkk1g60z55";
+    sha256 = "0p1gjykjnzm4m93mgjsmnxd0n2j381jk5kn3a7gkzxanixp60ilm";
   };
 
   nativeBuildInputs = [ perl procps fftw.dev ];
diff --git a/nixpkgs/pkgs/applications/science/electronics/pulseview/default.nix b/nixpkgs/pkgs/applications/science/electronics/pulseview/default.nix
index 4e86d1d917f8..c91443bf64a5 100644
--- a/nixpkgs/pkgs/applications/science/electronics/pulseview/default.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/pulseview/default.nix
@@ -4,11 +4,11 @@
 }:
 
 stdenv.mkDerivation rec {
-  name = "pulseview-0.4.0";
+  name = "pulseview-0.4.1";
 
   src = fetchurl {
     url = "https://sigrok.org/download/source/pulseview/${name}.tar.gz";
-    sha256 = "1f8f2342d5yam98mmcb8f9g2vslcwv486bmi4x45pxn68l82ky3q";
+    sha256 = "0bvgmkgz37n2bi9niskpl05hf7rsj1lj972fbrgnlz25s4ywxrwy";
   };
 
   nativeBuildInputs = [ cmake pkgconfig ];
diff --git a/nixpkgs/pkgs/applications/science/logic/z3/0001-fix-2131.patch b/nixpkgs/pkgs/applications/science/logic/z3/0001-fix-2131.patch
deleted file mode 100644
index 0b21b8fffd40..000000000000
--- a/nixpkgs/pkgs/applications/science/logic/z3/0001-fix-2131.patch
+++ /dev/null
@@ -1,66 +0,0 @@
-From c5df6ce96e068eceb77019e48634721c6a5bb607 Mon Sep 17 00:00:00 2001
-From: Nikolaj Bjorner <nbjorner@microsoft.com>
-Date: Sun, 10 Feb 2019 10:07:24 -0800
-Subject: [PATCH 1/1] fix #2131
-
-Signed-off-by: Nikolaj Bjorner <nbjorner@microsoft.com>
----
- src/api/python/README.txt    | 10 +++-------
- src/api/python/setup.py      |  2 +-
- src/ast/recfun_decl_plugin.h |  2 +-
- 3 files changed, 5 insertions(+), 9 deletions(-)
-
-diff --git a/src/api/python/README.txt b/src/api/python/README.txt
-index 9312b1119..561b8dedc 100644
---- a/src/api/python/README.txt
-+++ b/src/api/python/README.txt
-@@ -1,8 +1,4 @@
--You can learn more about Z3Py at:
--http://rise4fun.com/Z3Py/tutorial/guide
--
--On Windows, you must build Z3 before using Z3Py.
--To build Z3, you should executed the following command
-+On Windows, to build Z3, you should executed the following command
- in the Z3 root directory at the Visual Studio Command Prompt
- 
-        msbuild /p:configuration=external
-@@ -12,8 +8,8 @@ If you are using a 64-bit Python interpreter, you should use
-        msbuild /p:configuration=external /p:platform=x64
- 
- 
--On Linux and macOS, you must install Z3Py, before trying example.py.
--To install Z3Py on Linux and macOS, you should execute the following
-+On Linux and macOS, you must install python bindings, before trying example.py.
-+To install python on Linux and macOS, you should execute the following
- command in the Z3 root directory
- 
-         sudo make install-z3py
-diff --git a/src/api/python/setup.py b/src/api/python/setup.py
-index 2a750fee6..063680e2b 100644
---- a/src/api/python/setup.py
-+++ b/src/api/python/setup.py
-@@ -178,7 +178,7 @@ setup(
-     name='z3-solver',
-     version=_z3_version(),
-     description='an efficient SMT solver library',
--    long_description='Z3 is a theorem prover from Microsoft Research with support for bitvectors, booleans, arrays, floating point numbers, strings, and other data types.\n\nFor documentation, please read http://z3prover.github.io/api/html/z3.html\n\nIn the event of technical difficulties related to configuration, compiliation, or installation, please submit issues to https://github.com/angr/angr-z3',
-+    long_description='Z3 is a theorem prover from Microsoft Research with support for bitvectors, booleans, arrays, floating point numbers, strings, and other data types.\n\nFor documentation, please read http://z3prover.github.io/api/html/z3.html\n\nIn the event of technical difficulties related to configuration, compilation, or installation, please submit issues to https://github.com/angr/angr-z3',
-     author="The Z3 Theorem Prover Project",
-     maintainer="Audrey Dutcher",
-     maintainer_email="audrey@rhelmot.io",
-diff --git a/src/ast/recfun_decl_plugin.h b/src/ast/recfun_decl_plugin.h
-index 0247335e8..b294cdfce 100644
---- a/src/ast/recfun_decl_plugin.h
-+++ b/src/ast/recfun_decl_plugin.h
-@@ -56,7 +56,7 @@ namespace recfun {
-         friend class def;
-         func_decl_ref       m_pred; //<! predicate used for this case
-         expr_ref_vector     m_guards; //<! conjunction that is equivalent to this case
--        expr_ref            m_rhs; //<! if guard is true, `f(t1…tn) = rhs` holds
-+        expr_ref            m_rhs; //<! if guard is true, `f(t1...tn) = rhs` holds
-         def *               m_def; //<! definition this is a part of
-         bool                m_immediate; //<! does `rhs` contain no defined_fun/case_pred?
- 
--- 
-2.19.2
-
diff --git a/nixpkgs/pkgs/applications/science/logic/z3/default.nix b/nixpkgs/pkgs/applications/science/logic/z3/default.nix
index 8c1c0ca23024..14f75fb68b5e 100644
--- a/nixpkgs/pkgs/applications/science/logic/z3/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/z3/default.nix
@@ -1,20 +1,16 @@
 { stdenv, fetchFromGitHub, python, fixDarwinDylibNames }:
 
 stdenv.mkDerivation rec {
-  name = "z3-${version}";
-  version = "4.8.4";
+  pname = "z3";
+  version = "4.8.5";
 
   src = fetchFromGitHub {
     owner  = "Z3Prover";
-    repo   = "z3";
-    rev    = name;
-    sha256 = "014igqm5vwswz0yhz0cdxsj3a6dh7i79hvhgc3jmmmz3z0xm1gyn";
+    repo   = pname;
+    rev    = "Z3-${version}";
+    sha256 = "11sy98clv7ln0a5vqxzvh6wwqbswsjbik2084hav5kfws4xvklfa";
   };
 
-  patches = [
-    ./0001-fix-2131.patch
-  ];
-
   buildInputs = [ python fixDarwinDylibNames ];
   propagatedBuildInputs = [ python.pkgs.setuptools ];
   enableParallelBuilding = true;