Merge branch 'nixpkgs-update' into master

11 files changed, 111 insertions, 68 deletions

diff --git a/pkgs/development/libraries/science/biology/EBTKS/default.nix b/pkgs/development/libraries/science/biology/EBTKS/default.nix
index f4353f51d66..2a832fc7c37 100644
--- a/pkgs/development/libraries/science/biology/EBTKS/default.nix
+++ b/pkgs/development/libraries/science/biology/EBTKS/default.nix
@@ -1,8 +1,8 @@
-{ stdenv, fetchFromGitHub, cmake, libminc }:
+{ lib, stdenv, fetchFromGitHub, cmake, libminc }:
 
 stdenv.mkDerivation rec {
   pname = "EBTKS";
-  name  = "${pname}-2017-09-23";
+  version  = "unstable-2017-09-23";
 
   src = fetchFromGitHub {
     owner  = "BIC-MNI";
@@ -14,9 +14,9 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ cmake ];
   buildInputs = [ libminc ];
 
-  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" ];
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "https://github.com/BIC-MNI/${pname}";
     description = "Library for working with MINC files";
     maintainers = with maintainers; [ bcdarwin ];
diff --git a/pkgs/development/libraries/science/biology/bicgl/default.nix b/pkgs/development/libraries/science/biology/bicgl/default.nix
index 3c9b8f8257c..bc2de6e882f 100644
--- a/pkgs/development/libraries/science/biology/bicgl/default.nix
+++ b/pkgs/development/libraries/science/biology/bicgl/default.nix
@@ -1,24 +1,27 @@
-{ stdenv, fetchFromGitHub, cmake, libminc, bicpl, freeglut, mesa_glu }:
+{ lib, stdenv, fetchFromGitHub, cmake, libminc, bicpl, freeglut, mesa_glu }:
 
 stdenv.mkDerivation rec {
   pname = "bicgl";
-  name  = "${pname}-2017-09-10";
+  version = "unstable-2018-04-06";
 
   owner = "BIC-MNI";
 
   src = fetchFromGitHub {
     inherit owner;
     repo   = pname;
-    rev    = "b7f7e52d1039d6202a93d9055f516186033656cc";
+    rev    = "61a035751c9244fcca1edf94d6566fa2a709ce90";
     sha256 = "0lzirdi1mf4yl8srq7vjn746sbydz7h0wjh7wy8gycy6hq04qrg4";
   };
 
   nativeBuildInputs = [ cmake ];
   buildInputs = [ libminc bicpl freeglut mesa_glu ];
 
-  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib" "-DBICPL_DIR=${bicpl}/lib" ];
+  cmakeFlags = [
+    "-DLIBMINC_DIR=${libminc}/lib/cmake"
+    "-DBICPL_DIR=${bicpl}/lib"
+  ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "https://github.com/${owner}/${pname}";
     description = "Brain Imaging Centre graphics library";
     maintainers = with maintainers; [ bcdarwin ];
diff --git a/pkgs/development/libraries/science/biology/bicpl/default.nix b/pkgs/development/libraries/science/biology/bicpl/default.nix
index 0c634c0f265..5cf63e34224 100644
--- a/pkgs/development/libraries/science/biology/bicpl/default.nix
+++ b/pkgs/development/libraries/science/biology/bicpl/default.nix
@@ -1,29 +1,27 @@
-{ stdenv, fetchFromGitHub, cmake, libminc, netpbm }:
+{ lib, stdenv, fetchFromGitHub, cmake, libminc, netpbm }:
 
 stdenv.mkDerivation rec {
   pname = "bicpl";
-  name  = "${pname}-2017-09-10";
-
-  owner = "BIC-MNI";
+  version = "unstable-2020-10-15";
 
   # current master is significantly ahead of most recent release, so use Git version:
   src = fetchFromGitHub {
-    inherit owner;
+    owner  = "BIC-MNI";
     repo   = pname;
-    rev    = "612a63e740fadb162fcf27ee00da6a18dec4d5a9";
-    sha256 = "1vv9gi184bkvp3f99v9xmmw1ly63ip5b09y7zdjn39g7kmwzrga7";
+    rev    = "a58af912a71a4c62014975b89ef37a8e72de3c9d";
+    sha256 = "0iw0pmr8xrifbx5l8a0xidfqbm1v8hwzqrw0lcmimxlzdihyri0g";
   };
 
   nativeBuildInputs = [ cmake ];
   buildInputs = [ libminc netpbm ];
 
-  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib" ];
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" ];
 
   doCheck = false;
   # internal_volume_io.h: No such file or directory
 
-  meta = with stdenv.lib; {
-    homepage = "https://github.com/${owner}/${pname}";
+  meta = with lib; {
+    homepage = "https://github.com/BIC-MNI/bicpl";
     description = "Brain Imaging Centre programming library";
     maintainers = with maintainers; [ bcdarwin ];
     platforms = platforms.unix;
diff --git a/pkgs/development/libraries/science/biology/bpp-core/default.nix b/pkgs/development/libraries/science/biology/bpp-core/default.nix
index cfbe19d724b..d1eb096e08e 100644
--- a/pkgs/development/libraries/science/biology/bpp-core/default.nix
+++ b/pkgs/development/libraries/science/biology/bpp-core/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, cmake }:
+{ lib, stdenv, fetchFromGitHub, cmake }:
 
 stdenv.mkDerivation rec {
   pname = "bpp-core";
@@ -26,7 +26,7 @@ stdenv.mkDerivation rec {
 
   doCheck = !stdenv.isDarwin;
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Main_Page";
     changelog = "https://github.com/BioPP/bpp-core/blob/master/ChangeLog";
     description = "C++ bioinformatics libraries and tools";
diff --git a/pkgs/development/libraries/science/biology/bpp-seq/default.nix b/pkgs/development/libraries/science/biology/bpp-seq/default.nix
index 79fd0fe6771..ef3f3d5756e 100644
--- a/pkgs/development/libraries/science/biology/bpp-seq/default.nix
+++ b/pkgs/development/libraries/science/biology/bpp-seq/default.nix
@@ -29,7 +29,7 @@ stdenv.mkDerivation rec {
 
   doCheck = !stdenv.isDarwin;
 
-  meta = bpp-core.meta // { 
+  meta = bpp-core.meta // {
     changelog = "https://github.com/BioPP/bpp-seq/blob/master/ChangeLog";
   };
 }
diff --git a/pkgs/development/libraries/science/biology/elastix/default.nix b/pkgs/development/libraries/science/biology/elastix/default.nix
index 4d98b12928f..55ee5ab4fb6 100644
--- a/pkgs/development/libraries/science/biology/elastix/default.nix
+++ b/pkgs/development/libraries/science/biology/elastix/default.nix
@@ -1,32 +1,26 @@
-{ stdenv, fetchFromGitHub, fetchpatch, cmake, itk, python3 }:
+{ lib, stdenv, fetchFromGitHub, fetchpatch, cmake, itk, python3, Cocoa }:
 
 stdenv.mkDerivation rec {
   pname    = "elastix";
-  version = "5.0.0";
+  version = "5.0.1";
 
   src = fetchFromGitHub {
     owner  = "SuperElastix";
     repo   = pname;
     rev    = version;
-    sha256 = "1zrl7rz4lwsx88b2shnl985f3a97lmp4ksbd437h9y0hfjq8l0lj";
+    sha256 = "1mx8kkak2d3ibfrxrh8jkmh2zkdlgl9h578wiw3617zcwaa97bxw";
   };
 
   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";
+      name = "install-executables.patch";  # https://github.com/SuperElastix/elastix/issues/305
+      url = "https://github.com/SuperElastix/elastix/commit/8e26cdc0d66f6030c7be085fdc424d84d4fc7546.patch";
+      sha256 = "12y9wbpi9jlarnw6fk4iby97jxvx5g4daq9zqblbcmn51r134bj5";
     })
   ];
 
-
   nativeBuildInputs = [ cmake python3 ];
-  buildInputs = [ itk ];
+  buildInputs = [ itk ] ++ lib.optionals stdenv.isDarwin [ Cocoa ];
 
   doCheck = !stdenv.isDarwin;  # usual dynamic linker issues
 
@@ -34,7 +28,7 @@ stdenv.mkDerivation rec {
     export LD_LIBRARY_PATH=$(pwd)/bin
   ";
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "http://elastix.isi.uu.nl/";
     description = "Image registration toolkit based on ITK";
     maintainers = with maintainers; [ bcdarwin ];
diff --git a/pkgs/development/libraries/science/biology/gifticlib/default.nix b/pkgs/development/libraries/science/biology/gifticlib/default.nix
new file mode 100644
index 00000000000..306324129cb
--- /dev/null
+++ b/pkgs/development/libraries/science/biology/gifticlib/default.nix
@@ -0,0 +1,34 @@
+{ lib, stdenv, fetchFromGitHub, cmake, expat, nifticlib, zlib }:
+
+stdenv.mkDerivation rec {
+  pname = "gifticlib";
+  version = "unstable-2020-07-07";
+
+  src = fetchFromGitHub {
+    owner = "NIFTI-Imaging";
+    repo = "gifti_clib";
+    rev = "5eae81ba1e87ef3553df3b6ba585f12dc81a0030";
+    sha256 = "0gcab06gm0irjnlrkpszzd4wr8z0fi7gx8f7966gywdp2jlxzw19";
+  };
+
+  cmakeFlags = [ "-DUSE_SYSTEM_NIFTI=ON" "-DDOWNLOAD_TEST_DATA=OFF" ];
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ expat nifticlib zlib ];
+
+  # without the test data, this is only a few basic tests
+  doCheck = !stdenv.isDarwin;
+  checkPhase = ''
+    runHook preCheck
+    ctest -LE 'NEEDS_DATA'
+    runHook postCheck
+  '';
+
+  meta = with lib; {
+    homepage = "https://www.nitrc.org/projects/gifti";
+    description = "Medical imaging geometry format C API";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.unix;
+    license = licenses.publicDomain;
+  };
+}
diff --git a/pkgs/development/libraries/science/biology/htslib/default.nix b/pkgs/development/libraries/science/biology/htslib/default.nix
index 7ee63e9bb41..3233a29449a 100644
--- a/pkgs/development/libraries/science/biology/htslib/default.nix
+++ b/pkgs/development/libraries/science/biology/htslib/default.nix
@@ -1,18 +1,18 @@
-{ stdenv, fetchurl, zlib, bzip2, lzma, curl, perl }:
+{ lib, stdenv, fetchurl, zlib, bzip2, xz, curl, perl }:
 
 stdenv.mkDerivation rec {
   pname = "htslib";
-  version = "1.10.2";
+  version = "1.11";
 
   src = fetchurl {
     url = "https://github.com/samtools/htslib/releases/download/${version}/${pname}-${version}.tar.bz2";
-    sha256 = "0f8rglbvf4aaw41i2sxlpq7pvhly93sjqiz0l4q3hwki5zg47dg3";
+    sha256 = "1mrq4mihzx37yqhj3sfz6da6mw49niia808bzsw2gkkgmadxvyng";
   };
 
   # perl is only used during the check phase.
   nativeBuildInputs = [ perl ];
 
-  buildInputs = [ zlib bzip2 lzma curl ];
+  buildInputs = [ zlib bzip2 xz curl ];
 
   configureFlags = [ "--enable-libcurl" ]; # optional but strongly recommended
 
@@ -26,7 +26,7 @@ stdenv.mkDerivation rec {
 
   doCheck = true;
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     description = "A C library for reading/writing high-throughput sequencing data";
     license = licenses.mit;
     homepage = "http://www.htslib.org/";
diff --git a/pkgs/development/libraries/science/biology/mirtk/default.nix b/pkgs/development/libraries/science/biology/mirtk/default.nix
index 4291e11ed33..0d23489696f 100644
--- a/pkgs/development/libraries/science/biology/mirtk/default.nix
+++ b/pkgs/development/libraries/science/biology/mirtk/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, gtest, fetchFromGitHub, cmake, boost, eigen, python, vtk, zlib, tbb }:
+{ lib, stdenv, gtest, fetchFromGitHub, cmake, boost, eigen, python, vtk, zlib, tbb }:
 
 stdenv.mkDerivation rec {
   version = "2.0.0";
@@ -31,12 +31,10 @@ stdenv.mkDerivation rec {
     install -Dm644 -t "$out/share/bash-completion/completions/mirtk" share/completion/bash/mirtk
   '';
 
-  enableParallelBuilding = true;
-
   nativeBuildInputs = [ cmake gtest ];
   buildInputs = [ boost eigen python vtk zlib tbb ];
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "https://github.com/BioMedIA/MIRTK";
     description = "Medical image registration library and tools";
     maintainers = with maintainers; [ bcdarwin ];
diff --git a/pkgs/development/libraries/science/biology/nifticlib/default.nix b/pkgs/development/libraries/science/biology/nifticlib/default.nix
index 37055259e7c..fee2ea8772b 100644
--- a/pkgs/development/libraries/science/biology/nifticlib/default.nix
+++ b/pkgs/development/libraries/science/biology/nifticlib/default.nix
@@ -1,22 +1,30 @@
-{ stdenv, fetchurl, cmake, zlib }:
+{ lib, stdenv, fetchFromGitHub, cmake, zlib }:
 
 stdenv.mkDerivation rec {
-  pname    = "nifticlib";
-  pversion = "2.0.0";
-  name  = "${pname}-${pversion}";
+  pname = "nifticlib";
+  version = "3.0.1";
 
-  src = fetchurl {
-    url    = "mirror://sourceforge/project/niftilib/${pname}/${pname}_2_0_0/${name}.tar.gz";
-    sha256 = "123z9bwzgin5y8gi5ni8j217k7n683whjsvg0lrpii9flgk8isd3";
+  src = fetchFromGitHub {
+    owner = "NIFTI-Imaging";
+    repo = "nifti_clib";
+    rev = "v${version}";
+    sha256 = "0hamm6nvbjdjjd5md4jahzvn5559frigxaiybnjkh59ckxwb1hy4";
   };
 
+  cmakeFlags = [ "-DDOWNLOAD_TEST_DATA=OFF" ];
+
   nativeBuildInputs = [ cmake ];
   buildInputs = [ zlib ];
 
-  doCheck = false; # fails 7 out of 293 tests
+  checkPhase = ''
+    runHook preCheck
+    ctest -LE 'NEEDS_DATA'
+    runHook postCheck
+  '';
+  doCheck = true;
 
-  meta = with stdenv.lib; {
-    homepage = "https://sourceforge.net/projects/niftilib";
+  meta = with lib; {
+    homepage = "https://nifti-imaging.github.io";
     description = "Medical imaging format C API";
     maintainers = with maintainers; [ bcdarwin ];
     platforms = platforms.unix;
diff --git a/pkgs/development/libraries/science/biology/oobicpl/default.nix b/pkgs/development/libraries/science/biology/oobicpl/default.nix
index 8755b7fd2eb..7f1112311d6 100644
--- a/pkgs/development/libraries/science/biology/oobicpl/default.nix
+++ b/pkgs/development/libraries/science/biology/oobicpl/default.nix
@@ -1,28 +1,36 @@
-{ stdenv, fetchFromGitHub, cmake, libminc, bicpl, arguments, pcre-cpp }:
+{ lib
+, stdenv
+, fetchFromGitHub
+, cmake
+, libminc
+, bicpl
+, arguments
+, pcre-cpp }:
 
 stdenv.mkDerivation rec {
   pname = "oobicpl";
-  name  = "${pname}-2016-03-02";
-
-  owner = "BIC-MNI";
+  version = "unstable-2020-08-12";
 
   src = fetchFromGitHub {
-    inherit owner;
+    owner  = "BIC-MNI";
     repo   = pname;
-    rev    = "bc062a65dead2e58461f5afb37abedfa6173f10c";
-    sha256 = "05l4ml9djw17bgdnrldhcxydrzkr2f2scqlyak52ph5azj5n4zsx";
+    rev    = "a9409da8a5bb4925438f32aff577b6333faec28b";
+    sha256 = "0b4chjhr32wbb1sash8cq1jfnr7rzdq84hif8anlrjqd3l0gw357";
   };
 
   nativeBuildInputs = [ cmake ];
+
   buildInputs = [ libminc bicpl arguments pcre-cpp ];
 
-  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib"
-                 "-DBICPL_DIR=${bicpl}/lib"
-                 "-DARGUMENTS_DIR=${arguments}/lib"
-                 "-DOOBICPL_BUILD_SHARED_LIBS=TRUE" ];
+  cmakeFlags = [
+    "-DLIBMINC_DIR=${libminc}/lib/cmake"
+    "-DBICPL_DIR=${bicpl}/lib"
+    "-DARGUMENTS_DIR=${arguments}/lib"
+    "-DOOBICPL_BUILD_SHARED_LIBS=TRUE"
+  ];
 
-  meta = with stdenv.lib; {
-    homepage = "https://github.com/${owner}/${pname}";
+  meta = with lib; {
+    homepage = "https://github.com/BIC-MNI/oobicpl";
     description = "Brain Imaging Centre object-oriented programming library (and tools)";
     maintainers = with maintainers; [ bcdarwin ];
     platforms = platforms.unix;