Merge commit 'b09661d41fb93562fd53f31574dbf781b130ac44'

9 files changed, 73 insertions, 46 deletions

diff --git a/nixpkgs/pkgs/development/libraries/science/astronomy/wcslib/default.nix b/nixpkgs/pkgs/development/libraries/science/astronomy/wcslib/default.nix
index 58c2744605a2..6adf52514710 100644
--- a/nixpkgs/pkgs/development/libraries/science/astronomy/wcslib/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/astronomy/wcslib/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "wcslib";
-  version = "7.6";
+  version = "7.7";
 
   src = fetchurl {
     url = "ftp://ftp.atnf.csiro.au/pub/software/wcslib/${pname}-${version}.tar.bz2";
-    sha256 = "sha256-VLuMkhZ6fxP4qnP8S4oJeFJW0smCE0Z968eigqQxMYs=";
+    sha256 = "sha256-pwjmtOkOLNZCdDRxW1kbucPUAFyZcl7ElLjgvtLeU1U=";
   };
 
   nativeBuildInputs = [ flex ];
diff --git a/nixpkgs/pkgs/development/libraries/science/biology/EBTKS/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/EBTKS/default.nix
index b75ac06627fb..2a832fc7c37a 100644
--- a/nixpkgs/pkgs/development/libraries/science/biology/EBTKS/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/biology/EBTKS/default.nix
@@ -2,7 +2,7 @@
 
 stdenv.mkDerivation rec {
   pname = "EBTKS";
-  name  = "${pname}-2017-09-23";
+  version  = "unstable-2017-09-23";
 
   src = fetchFromGitHub {
     owner  = "BIC-MNI";
diff --git a/nixpkgs/pkgs/development/libraries/science/math/lcalc/default.nix b/nixpkgs/pkgs/development/libraries/science/math/lcalc/default.nix
index 95034c3637a9..3f0cf45062f1 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/lcalc/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/lcalc/default.nix
@@ -65,7 +65,7 @@ stdenv.mkDerivation rec {
 
     (fetchpatch {
       name = "c++11.patch";
-      url = "https://git.archlinux.org/svntogit/community.git/plain/trunk/lcalc-c++11.patch?h=packages/lcalc&id=3607b97df5a8c231191115b0cb5c62426b339e71";
+      url = "https://raw.githubusercontent.com/archlinux/svntogit-community/3607b97df5a8c231191115b0cb5c62426b339e71/trunk/lcalc-c++11.patch";
       sha256 = "1ccrl61lv2vvx8ggldq54m5d0n1iy6mym7qz0i8nj6yj0dshnpk3";
     })
   ] ++ lib.optional stdenv.isDarwin
diff --git a/nixpkgs/pkgs/development/libraries/science/math/liblapack/default.nix b/nixpkgs/pkgs/development/libraries/science/math/liblapack/default.nix
index 66f343d4912d..79e494a053b8 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/liblapack/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/liblapack/default.nix
@@ -7,12 +7,11 @@
 }:
 let
   inherit (lib) optional;
-  version = "3.9.1";
 in
 
 stdenv.mkDerivation rec {
   pname = "liblapack";
-  inherit version;
+  version = "3.9.1";
 
   src = fetchFromGitHub {
     owner = "Reference-LAPACK";
@@ -57,7 +56,6 @@ stdenv.mkDerivation rec {
   '';
 
   meta = with lib; {
-    inherit version;
     description = "Linear Algebra PACKage";
     homepage = "http://www.netlib.org/lapack/";
     license = licenses.bsd3;
diff --git a/nixpkgs/pkgs/development/libraries/science/math/liblbfgs/default.nix b/nixpkgs/pkgs/development/libraries/science/math/liblbfgs/default.nix
index 20c5a2070a05..3c194648c2a3 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/liblbfgs/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/liblbfgs/default.nix
@@ -1,10 +1,11 @@
 { lib, stdenv, fetchurl }:
-stdenv.mkDerivation {
-  name = "liblbfgs-1.10";
+stdenv.mkDerivation rec {
+  pname = "liblbfgs";
+  version = "1.10";
 
   configureFlags = [ "--enable-sse2" ];
   src = fetchurl {
-    url = "https://github.com/downloads/chokkan/liblbfgs/liblbfgs-1.10.tar.gz";
+    url = "https://github.com/downloads/chokkan/liblbfgs/liblbfgs-${version}.tar.gz";
     sha256 = "1kv8d289rbz38wrpswx5dkhr2yh4fg4h6sszkp3fawxm09sann21";
   };
 
diff --git a/nixpkgs/pkgs/development/libraries/science/math/lrs/default.nix b/nixpkgs/pkgs/development/libraries/science/math/lrs/default.nix
index f7f981e223b2..063fead11650 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/lrs/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/lrs/default.nix
@@ -16,7 +16,6 @@ stdenv.mkDerivation rec {
   '';
 
   meta = {
-    inherit version;
     description = "Implementation of the reverse search algorithm for vertex enumeration/convex hull problems";
     license = lib.licenses.gpl2 ;
     maintainers = [lib.maintainers.raskin];
diff --git a/nixpkgs/pkgs/development/libraries/science/math/metis/default.nix b/nixpkgs/pkgs/development/libraries/science/math/metis/default.nix
index b06b432372a7..da79f6d62499 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/metis/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/metis/default.nix
@@ -1,10 +1,11 @@
 { lib, stdenv, fetchurl, unzip, cmake }:
 
-stdenv.mkDerivation {
-  name = "metis-5.1.0";
+stdenv.mkDerivation rec {
+  name = "metis";
+  version = "5.1.0";
 
   src = fetchurl {
-    url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz";
+    url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-${version}.tar.gz";
     sha256 = "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn";
   };
 
diff --git a/nixpkgs/pkgs/development/libraries/science/math/openspecfun/default.nix b/nixpkgs/pkgs/development/libraries/science/math/openspecfun/default.nix
index a341264d9894..cb72fbd2ca48 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/openspecfun/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/openspecfun/default.nix
@@ -1,10 +1,13 @@
-{ lib, stdenv, fetchurl, gfortran }:
+{ lib, stdenv, fetchFromGitHub, gfortran }:
 
-stdenv.mkDerivation {
-  name = "openspecfun-0.5.3";
-  src = fetchurl {
-    url = "https://github.com/JuliaLang/openspecfun/archive/v0.5.3.tar.gz";
-    sha256 = "1rs1bv8jq751fv9vq79890wqf9xlbjc7lvz3ighzyfczbyjcf18m";
+stdenv.mkDerivation rec {
+  pname = "openspecfun";
+  version = "0.5.3";
+  src = fetchFromGitHub {
+    owner = "JuliaLang";
+    repo = "openspecfun";
+    rev = "v${version}";
+    sha256 = "0pfw6l3ch7isz403llx7inxlvavqh01jh1hb9dpidi86sjjx9kfh";
   };
 
   makeFlags = [ "prefix=$(out)" ];
diff --git a/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix b/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix
index f06a028fe64f..ee495deedc1e 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix
@@ -1,4 +1,20 @@
-{ lib, stdenv , darwin , fetchurl , blas , gfortran , lapack , python }:
+{ lib
+, stdenv
+, fetchurl
+, darwin
+, gfortran
+, python3
+, blas
+, lapack
+, mpi                   # generic mpi dependency
+, openssh               # required for openmpi tests
+, petsc-withp4est ? true
+, p4est
+, zlib                  # propagated by p4est but required by petsc
+}:
+
+# This version of PETSc does not support a non-MPI p4est build
+assert petsc-withp4est -> p4est.mpiSupport;
 
 stdenv.mkDerivation rec {
   pname = "petsc";
@@ -9,44 +25,53 @@ stdenv.mkDerivation rec {
     sha256 = "04vy3qyakikslc58qyv8c9qrwlivix3w6znc993i37cvfg99dch9";
   };
 
-  nativeBuildInputs = [ blas gfortran gfortran.cc.lib lapack python ];
-
-  # Upstream does some hot she-py-bang stuff, this change streamlines that
-  # process. The original script in upstream is both a shell script and a
-  # python script, where the shellscript just finds a suitable python
-  # interpreter to execute the python script. See
-  # https://github.com/NixOS/nixpkgs/pull/89299#discussion_r450203444
-  # for more details.
-  prePatch = ''
-    substituteInPlace configure \
-      --replace /bin/sh /usr/bin/python
-  '' + lib.optionalString stdenv.isDarwin ''
+  mpiSupport = !withp4est || p4est.mpiSupport;
+  withp4est = petsc-withp4est;
+
+  nativeBuildInputs = [ python3 gfortran ];
+  buildInputs = [ blas lapack ]
+    ++ lib.optional mpiSupport mpi
+    ++ lib.optional (mpiSupport && mpi.pname == "openmpi") openssh
+    ++ lib.optional withp4est p4est
+  ;
+
+  prePatch = lib.optionalString stdenv.isDarwin ''
     substituteInPlace config/install.py \
       --replace /usr/bin/install_name_tool ${darwin.cctools}/bin/install_name_tool
   '';
 
   preConfigure = ''
     export FC="${gfortran}/bin/gfortran" F77="${gfortran}/bin/gfortran"
-    patchShebangs .
+    patchShebangs ./lib/petsc/bin
     configureFlagsArray=(
       $configureFlagsArray
-      "--CC=$CC"
-      "--with-cxx=$CXX"
-      "--with-fc=$FC"
-      "--with-mpi=0"
-      "--with-blas-lib=[${blas}/lib/libblas.so,${gfortran.cc.lib}/lib/libgfortran.a]"
-      "--with-lapack-lib=[${lapack}/lib/liblapack.so,${gfortran.cc.lib}/lib/libgfortran.a]"
+      ${if !mpiSupport then ''
+        "--with-mpi=0"
+      '' else ''
+        "--CC=mpicc"
+        "--with-cxx=mpicxx"
+        "--with-fc=mpif90"
+        "--with-mpi=1"
+      ''}
+      ${if withp4est then ''
+        "--with-p4est=1"
+        "--with-zlib-include=${zlib.dev}/include"
+        "--with-zlib-lib=-L${zlib}/lib -lz"
+      '' else ""}
+      "--with-blas=1"
+      "--with-lapack=1"
     )
   '';
 
+  configureScript = "python ./configure";
+
+  enableParallelBuilding = true;
+  doCheck = stdenv.hostPlatform == stdenv.buildPlatform;
+
   meta = with lib; {
-    description = ''
-      Library of linear algebra algorithms for solving partial differential
-      equations
-    '';
+    description = "Portable Extensible Toolkit for Scientific computation";
     homepage = "https://www.mcs.anl.gov/petsc/index.html";
     license = licenses.bsd2;
-    maintainers = with maintainers; [ wucke13 ];
-    platforms = platforms.all;
+    maintainers = with maintainers; [ wucke13 cburstedde ];
   };
 }