Merge commit '683c68232e91f76386db979c461d8fbe2a018782'

15 files changed, 43 insertions, 36 deletions

diff --git a/nixpkgs/pkgs/development/libraries/science/biology/elastix/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/elastix/default.nix
index e5565aae29b1..4d98b12928f5 100644
--- a/nixpkgs/pkgs/development/libraries/science/biology/elastix/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/biology/elastix/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, cmake, itk, python3 }:
+{ stdenv, fetchFromGitHub, fetchpatch, cmake, itk, python3 }:
 
 stdenv.mkDerivation rec {
   pname    = "elastix";
@@ -11,10 +11,24 @@ stdenv.mkDerivation rec {
     sha256 = "1zrl7rz4lwsx88b2shnl985f3a97lmp4ksbd437h9y0hfjq8l0lj";
   };
 
+  patches = [
+    (fetchpatch {
+      name = "itk-5.1-compat.patch";
+      url = "https://github.com/SuperElastix/elastix/commit/402e9a26f22f805b8f2db00c00e59f75fa1783ad.patch";
+      sha256 = "1il6gc1lgy78i0w6gkkppr61nh6g0yjspbfk19hcz20778m5jhz9";
+    })
+    (fetchpatch {
+      name = "fix-osx-build.patch";
+      url = "https://github.com/SuperElastix/elastix/commit/52e1dc3928046f9fbb85d4b2ecd0d5175fa9695d.patch";
+      sha256 = "1hf7kgx1jv497pf0x5wj79sy1wncxcvhrkix9w086lcr8zwxvn9q";
+    })
+  ];
+
+
   nativeBuildInputs = [ cmake python3 ];
   buildInputs = [ itk ];
 
-  doCheck = true;
+  doCheck = !stdenv.isDarwin;  # usual dynamic linker issues
 
   preCheck = "
     export LD_LIBRARY_PATH=$(pwd)/bin
@@ -24,7 +38,7 @@ stdenv.mkDerivation rec {
     homepage = "http://elastix.isi.uu.nl/";
     description = "Image registration toolkit based on ITK";
     maintainers = with maintainers; [ bcdarwin ];
-    platforms = platforms.linux;
+    platforms = platforms.x86_64;  # libitkpng linker issues with ITK 5.1
     license = licenses.asl20;
   };
 }
diff --git a/nixpkgs/pkgs/development/libraries/science/math/arpack/default.nix b/nixpkgs/pkgs/development/libraries/science/math/arpack/default.nix
index a5fbb679df5b..0829557d0f3d 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/arpack/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/arpack/default.nix
@@ -27,7 +27,7 @@ stdenv.mkDerivation {
 
   cmakeFlags = [
     "-DBUILD_SHARED_LIBS=ON"
-    "-DINTERFACE64=${optionalString blas.is64bit "1"}"
+    "-DINTERFACE64=${optionalString blas.isILP64 "1"}"
   ];
 
   preCheck = if stdenv.isDarwin then ''
diff --git a/nixpkgs/pkgs/development/libraries/science/math/ipopt/default.nix b/nixpkgs/pkgs/development/libraries/science/math/ipopt/default.nix
index 647fd82ec0e9..97374fb0d477 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/ipopt/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/ipopt/default.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchurl, unzip, blas, lapack, gfortran }:
 
-assert (!blas.is64bit) && (!lapack.is64bit);
+assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation rec {
   pname = "ipopt";
diff --git a/nixpkgs/pkgs/development/libraries/science/math/magma/default.nix b/nixpkgs/pkgs/development/libraries/science/math/magma/default.nix
index b34139e7f484..dbe162c60b34 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/magma/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/magma/default.nix
@@ -1,8 +1,4 @@
-{ stdenv, fetchurl, cmake, gfortran, cudatoolkit, libpthreadstubs, lapack, blas
-, mklSupport ? false, mkl ? null
-}:
-
-assert !mklSupport || mkl != null;
+{ stdenv, fetchurl, cmake, gfortran, cudatoolkit, libpthreadstubs, lapack, blas }:
 
 with stdenv.lib;
 
@@ -17,13 +13,10 @@ in stdenv.mkDerivation {
     name = "magma-${version}.tar.gz";
   };
 
-  buildInputs = [ gfortran cudatoolkit libpthreadstubs cmake ]
-    ++ (if mklSupport then [ mkl ] else [ lapack blas ]);
+  buildInputs = [ gfortran cudatoolkit libpthreadstubs cmake lapack blas ];
 
   doCheck = false;
 
-  MKLROOT = optionalString mklSupport mkl;
-
   preConfigure = ''
     export CC=${cudatoolkit.cc}/bin/gcc CXX=${cudatoolkit.cc}/bin/g++
   '';
diff --git a/nixpkgs/pkgs/development/libraries/science/math/mkl/default.nix b/nixpkgs/pkgs/development/libraries/science/math/mkl/default.nix
index f9026ec7b997..ee861c14ab44 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/mkl/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/mkl/default.nix
@@ -114,10 +114,10 @@ in stdenvNoCC.mkDerivation {
     '') + ''
 
     # Setup symlinks for blas / lapack
-    ln -s $out/lib/libmkl_rt${stdenvNoCC.hostPlatform.extensions.sharedLibrary} $out/lib/libblas${stdenvNoCC.hostPlatform.extensions.sharedLibrary}
-    ln -s $out/lib/libmkl_rt${stdenvNoCC.hostPlatform.extensions.sharedLibrary} $out/lib/libcblas${stdenvNoCC.hostPlatform.extensions.sharedLibrary}
-    ln -s $out/lib/libmkl_rt${stdenvNoCC.hostPlatform.extensions.sharedLibrary} $out/lib/liblapack${stdenvNoCC.hostPlatform.extensions.sharedLibrary}
-    ln -s $out/lib/libmkl_rt${stdenvNoCC.hostPlatform.extensions.sharedLibrary} $out/lib/liblapacke${stdenvNoCC.hostPlatform.extensions.sharedLibrary}
+    ln -s $out/lib/libmkl_rt${stdenvNoCC.hostPlatform.extensions.sharedLibrary} $out/lib/libblas${stdenvNoCC.hostPlatform.extensions.sharedLibrary}${stdenvNoCC.lib.optionalString stdenvNoCC.hostPlatform.isLinux ".3"}
+    ln -s $out/lib/libmkl_rt${stdenvNoCC.hostPlatform.extensions.sharedLibrary} $out/lib/libcblas${stdenvNoCC.hostPlatform.extensions.sharedLibrary}${stdenvNoCC.lib.optionalString stdenvNoCC.hostPlatform.isLinux ".3"}
+    ln -s $out/lib/libmkl_rt${stdenvNoCC.hostPlatform.extensions.sharedLibrary} $out/lib/liblapack${stdenvNoCC.hostPlatform.extensions.sharedLibrary}${stdenvNoCC.lib.optionalString stdenvNoCC.hostPlatform.isLinux ".3"}
+    ln -s $out/lib/libmkl_rt${stdenvNoCC.hostPlatform.extensions.sharedLibrary} $out/lib/liblapacke${stdenvNoCC.hostPlatform.extensions.sharedLibrary}${stdenvNoCC.lib.optionalString stdenvNoCC.hostPlatform.isLinux ".3"}
   '';
 
   # fixDarwinDylibName fails for libmkl_cdft_core.dylib because the
diff --git a/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix b/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix
index c55a5cb7878f..53c980469932 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix
@@ -96,12 +96,12 @@ let
 in
 stdenv.mkDerivation rec {
   pname = "openblas";
-  version = "0.3.8";
+  version = "0.3.9";
   src = fetchFromGitHub {
     owner = "xianyi";
     repo = "OpenBLAS";
     rev = "v${version}";
-    sha256 = "0s017qqi4n6jzrxl9cyx625wj26smnyn5g8s699s7h8v1srlrw6p";
+    sha256 = "0nq51j45shb32n6086xff3x374kx5qhr2cwjzvppx4s2z0ahflal";
   };
 
   inherit blas64;
@@ -178,10 +178,10 @@ EOF
     done
 
     # Setup symlinks for blas / lapack
-    ln -s $out/lib/libopenblas${stdenv.hostPlatform.extensions.sharedLibrary} $out/lib/libblas${stdenv.hostPlatform.extensions.sharedLibrary}
-    ln -s $out/lib/libopenblas${stdenv.hostPlatform.extensions.sharedLibrary} $out/lib/libcblas${stdenv.hostPlatform.extensions.sharedLibrary}
-    ln -s $out/lib/libopenblas${stdenv.hostPlatform.extensions.sharedLibrary} $out/lib/liblapack${stdenv.hostPlatform.extensions.sharedLibrary}
-    ln -s $out/lib/libopenblas${stdenv.hostPlatform.extensions.sharedLibrary} $out/lib/liblapacke${stdenv.hostPlatform.extensions.sharedLibrary}
+    ln -s $out/lib/libopenblas${stdenv.hostPlatform.extensions.sharedLibrary} $out/lib/libblas${stdenv.hostPlatform.extensions.sharedLibrary}${stdenv.lib.optionalString stdenv.hostPlatform.isLinux ".3"}
+    ln -s $out/lib/libopenblas${stdenv.hostPlatform.extensions.sharedLibrary} $out/lib/libcblas${stdenv.hostPlatform.extensions.sharedLibrary}${stdenv.lib.optionalString stdenv.hostPlatform.isLinux ".3"}
+    ln -s $out/lib/libopenblas${stdenv.hostPlatform.extensions.sharedLibrary} $out/lib/liblapack${stdenv.hostPlatform.extensions.sharedLibrary}${stdenv.lib.optionalString stdenv.hostPlatform.isLinux ".3"}
+    ln -s $out/lib/libopenblas${stdenv.hostPlatform.extensions.sharedLibrary} $out/lib/liblapacke${stdenv.hostPlatform.extensions.sharedLibrary}${stdenv.lib.optionalString stdenv.hostPlatform.isLinux ".3"}
   '';
 
   meta = with stdenv.lib; {
diff --git a/nixpkgs/pkgs/development/libraries/science/math/or-tools/default.nix b/nixpkgs/pkgs/development/libraries/science/math/or-tools/default.nix
index ce6780f0046a..a69ae5af15f3 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/or-tools/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/or-tools/default.nix
@@ -8,13 +8,13 @@ let
 
 in stdenv.mkDerivation rec {
   pname = "or-tools";
-  version = "7.5";
+  version = "7.6";
 
   src = fetchFromGitHub {
     owner = "google";
     repo = "or-tools";
     rev = "v${version}";
-    sha256 = "1p9jwdwzcsaa58ap912hdf2w27vna3xl9g4lh6kjskddwi8l3wac";
+    sha256 = "0605q3y7vh7x7m9azrbkx44blq12zrab6v28b9wmpcn1lmykbw1b";
   };
 
   # The original build system uses cmake which does things like pull
diff --git a/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix b/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix
index 200dd58a4357..6eeeda9e9284 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "petsc";
-  version = "3.13.0";
+  version = "3.13.1";
 
   src = fetchurl {
     url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-${version}.tar.gz";
-    sha256 = "0943bydmsq3sjwj3rxhb8hx58b1fm8vymny731557fs10g5zfbyz";
+    sha256 = "0pr604b9pnryl9q0q5arlhs0xdx7wslca0sbz0pzs9qylmz775qp";
   };
 
   nativeBuildInputs = [ blas gfortran.cc.lib lapack python ];
diff --git a/nixpkgs/pkgs/development/libraries/science/math/scalapack/default.nix b/nixpkgs/pkgs/development/libraries/science/math/scalapack/default.nix
index d20219860296..1cf9c2ed8d53 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/scalapack/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/scalapack/default.nix
@@ -2,7 +2,7 @@
 , gfortran, mpi, blas, lapack
 } :
 
-assert (!blas.is64bit) && (!lapack.is64bit);
+assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation rec {
   pname = "scalapack";
diff --git a/nixpkgs/pkgs/development/libraries/science/math/scs/default.nix b/nixpkgs/pkgs/development/libraries/science/math/scs/default.nix
index 2dcb47f11baa..3820f2b95275 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/scs/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/scs/default.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchFromGitHub, blas, lapack, gfortran, fixDarwinDylibNames }:
 
-assert (!blas.is64bit) && (!lapack.is64bit);
+assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation rec {
   pname = "scs";
diff --git a/nixpkgs/pkgs/development/libraries/science/math/suitesparse-graphblas/default.nix b/nixpkgs/pkgs/development/libraries/science/math/suitesparse-graphblas/default.nix
index 599c1be66461..5a2c28d3c022 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/suitesparse-graphblas/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/suitesparse-graphblas/default.nix
@@ -6,7 +6,7 @@
 
 stdenv.mkDerivation rec {
   pname = "suitesparse-graphblas";
-  version = "3.2.1";
+  version = "3.2.2";
 
   outputs = [ "out" "dev" ];
 
@@ -14,7 +14,7 @@ stdenv.mkDerivation rec {
     owner = "DrTimothyAldenDavis";
     repo = "GraphBLAS";
     rev = "v${version}";
-    sha256 = "AAwwzrpKFHy40Ldm6hTO6L0FWPYwi3kJj3zrshFwYas=";
+    sha256 = "04hprrgj0f44ml2f0w4jfwgrvy8l2s6ya0c9xc8gwlbmkc7a4c62";
   };
 
   nativeBuildInputs = [
diff --git a/nixpkgs/pkgs/development/libraries/science/math/suitesparse/4.2.nix b/nixpkgs/pkgs/development/libraries/science/math/suitesparse/4.2.nix
index 34a1fb7ad9e6..b1c1202c5780 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/suitesparse/4.2.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/suitesparse/4.2.nix
@@ -1,7 +1,7 @@
 { stdenv, fetchurl, gfortran, blas, lapack }:
 
 let
-  int_t = if blas.is64bit then "int64_t" else "int32_t";
+  int_t = if blas.isILP64 then "int64_t" else "int32_t";
 in
 stdenv.mkDerivation rec {
   version = "4.2.1";
diff --git a/nixpkgs/pkgs/development/libraries/science/math/suitesparse/4.4.nix b/nixpkgs/pkgs/development/libraries/science/math/suitesparse/4.4.nix
index b2b7e666b7ef..81a80c920b53 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/suitesparse/4.4.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/suitesparse/4.4.nix
@@ -6,7 +6,7 @@ let
   version = "4.4.4";
   name = "suitesparse-${version}";
 
-  int_t = if blas.is64bit then "int64_t" else "int32_t";
+  int_t = if blas.isILP64 then "int64_t" else "int32_t";
   SHLIB_EXT = stdenv.hostPlatform.extensions.sharedLibrary;
 in
 stdenv.mkDerivation {
diff --git a/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix b/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix
index 48177987a7a2..f0480e1e2381 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix
@@ -44,7 +44,7 @@ stdenv.mkDerivation rec {
     "BLAS=-lblas"
     "LAPACK=-llapack"
     "MY_METIS_LIB=-lmetis"
-  ] ++ stdenv.lib.optionals blas.is64bit [
+  ] ++ stdenv.lib.optionals blas.isILP64 [
     "CFLAGS=-DBLAS64"
   ] ++ stdenv.lib.optionals enableCuda [
     "CUDA_PATH=${cudatoolkit}"
diff --git a/nixpkgs/pkgs/development/libraries/science/math/superlu/default.nix b/nixpkgs/pkgs/development/libraries/science/math/superlu/default.nix
index 05ceb21387d3..ff59297bd839 100644
--- a/nixpkgs/pkgs/development/libraries/science/math/superlu/default.nix
+++ b/nixpkgs/pkgs/development/libraries/science/math/superlu/default.nix
@@ -1,7 +1,7 @@
 { stdenv, fetchurl, cmake,
   gfortran, blas, lapack}:
 
-assert (!blas.is64bit) && (!lapack.is64bit);
+assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation rec {
   version = "5.2.1";