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author | Alyssa Ross <hi@alyssa.is> | 2021-01-26 18:06:19 +0000 |
---|---|---|
committer | Alyssa Ross <hi@alyssa.is> | 2021-01-26 18:21:18 +0000 |
commit | 7ac6743433dd45ceaead2ca96f6356dc0d064ce6 (patch) | |
tree | b68ec89d7d2a8d2b6e6b1ff94ba26d6af4096350 /nixpkgs/pkgs/development/libraries/science | |
parent | c5c7451dbef37b51f52792d6395a670ef5183d27 (diff) | |
parent | 891f607d5301d6730cb1f9dcf3618bcb1ab7f10e (diff) | |
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Merge commit '891f607d5301d6730cb1f9dcf3618bcb1ab7f10e'
Diffstat (limited to 'nixpkgs/pkgs/development/libraries/science')
70 files changed, 263 insertions, 274 deletions
diff --git a/nixpkgs/pkgs/development/libraries/science/benchmark/papi/default.nix b/nixpkgs/pkgs/development/libraries/science/benchmark/papi/default.nix index 00a6e50aa7f7..c265f24c182b 100644 --- a/nixpkgs/pkgs/development/libraries/science/benchmark/papi/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/benchmark/papi/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchurl }: @@ -20,7 +20,7 @@ stdenv.mkDerivation { doCheck = true; checkTarget = "test"; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://icl.utk.edu/papi/"; description = "PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors"; license = licenses.bsdOriginal; diff --git a/nixpkgs/pkgs/development/libraries/science/biology/EBTKS/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/EBTKS/default.nix index c60fe31aaaff..b75ac06627fb 100644 --- a/nixpkgs/pkgs/development/libraries/science/biology/EBTKS/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/biology/EBTKS/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, libminc }: +{ lib, stdenv, fetchFromGitHub, cmake, libminc }: stdenv.mkDerivation rec { pname = "EBTKS"; @@ -16,7 +16,7 @@ stdenv.mkDerivation rec { 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/nixpkgs/pkgs/development/libraries/science/biology/bicgl/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/bicgl/default.nix index 4cc7dcada522..bc2de6e882f9 100644 --- a/nixpkgs/pkgs/development/libraries/science/biology/bicgl/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/biology/bicgl/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, libminc, bicpl, freeglut, mesa_glu }: +{ lib, stdenv, fetchFromGitHub, cmake, libminc, bicpl, freeglut, mesa_glu }: stdenv.mkDerivation rec { pname = "bicgl"; @@ -21,7 +21,7 @@ stdenv.mkDerivation rec { "-DBICPL_DIR=${bicpl}/lib" ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://github.com/${owner}/${pname}"; description = "Brain Imaging Centre graphics library"; maintainers = with maintainers; [ bcdarwin ]; diff --git a/nixpkgs/pkgs/development/libraries/science/biology/bicpl/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/bicpl/default.nix index 96199f0478ea..0bdcbf5a828a 100644 --- a/nixpkgs/pkgs/development/libraries/science/biology/bicpl/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/biology/bicpl/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, libminc, netpbm }: +{ lib, stdenv, fetchFromGitHub, cmake, libminc, netpbm }: stdenv.mkDerivation rec { pname = "bicpl"; @@ -22,7 +22,7 @@ stdenv.mkDerivation rec { doCheck = false; # internal_volume_io.h: No such file or directory - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://github.com/${owner}/${pname}"; description = "Brain Imaging Centre programming library"; maintainers = with maintainers; [ bcdarwin ]; diff --git a/nixpkgs/pkgs/development/libraries/science/biology/bpp-core/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/bpp-core/default.nix index cfbe19d724be..d1eb096e08e6 100644 --- a/nixpkgs/pkgs/development/libraries/science/biology/bpp-core/default.nix +++ b/nixpkgs/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/nixpkgs/pkgs/development/libraries/science/biology/bpp-seq/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/bpp-seq/default.nix index 79fd0fe67716..ef3f3d5756e9 100644 --- a/nixpkgs/pkgs/development/libraries/science/biology/bpp-seq/default.nix +++ b/nixpkgs/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/nixpkgs/pkgs/development/libraries/science/biology/elastix/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/elastix/default.nix index e55a72fb9f84..55ee5ab4fb66 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, fetchpatch, cmake, itk, python3, Cocoa }: +{ lib, stdenv, fetchFromGitHub, fetchpatch, cmake, itk, python3, Cocoa }: stdenv.mkDerivation rec { pname = "elastix"; @@ -20,7 +20,7 @@ stdenv.mkDerivation rec { ]; nativeBuildInputs = [ cmake python3 ]; - buildInputs = [ itk ] ++ stdenv.lib.optionals stdenv.isDarwin [ Cocoa ]; + buildInputs = [ itk ] ++ lib.optionals stdenv.isDarwin [ Cocoa ]; doCheck = !stdenv.isDarwin; # usual dynamic linker issues @@ -28,7 +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/nixpkgs/pkgs/development/libraries/science/biology/gifticlib/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/gifticlib/default.nix index dddf29fb0193..306324129cbd 100644 --- a/nixpkgs/pkgs/development/libraries/science/biology/gifticlib/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/biology/gifticlib/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, expat, nifticlib, zlib }: +{ lib, stdenv, fetchFromGitHub, cmake, expat, nifticlib, zlib }: stdenv.mkDerivation rec { pname = "gifticlib"; @@ -24,7 +24,7 @@ stdenv.mkDerivation rec { runHook postCheck ''; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://www.nitrc.org/projects/gifti"; description = "Medical imaging geometry format C API"; maintainers = with maintainers; [ bcdarwin ]; diff --git a/nixpkgs/pkgs/development/libraries/science/biology/htslib/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/htslib/default.nix index 9da6595e7a43..cb3a543ad2af 100644 --- a/nixpkgs/pkgs/development/libraries/science/biology/htslib/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/biology/htslib/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, zlib, bzip2, lzma, curl, perl }: +{ lib, stdenv, fetchurl, zlib, bzip2, lzma, curl, perl }: stdenv.mkDerivation rec { pname = "htslib"; @@ -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/nixpkgs/pkgs/development/libraries/science/biology/mirtk/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/mirtk/default.nix index 4291e11ed33f..0d23489696f1 100644 --- a/nixpkgs/pkgs/development/libraries/science/biology/mirtk/default.nix +++ b/nixpkgs/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 "$out/share/bash-completion/completions/mirtk" share/completion/bash/mirtk ''; - enableParallelBuilding = true; - nativeBuildInputs = [ cmake gtest ]; buildInputs = [ boost eigen python vtk zlib tbb ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://github.com/BioMedIA/MIRTK"; description = "Medical image registration library and tools"; maintainers = with maintainers; [ bcdarwin ]; diff --git a/nixpkgs/pkgs/development/libraries/science/biology/nifticlib/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/nifticlib/default.nix index 572c31dd1e52..fee2ea8772b4 100644 --- a/nixpkgs/pkgs/development/libraries/science/biology/nifticlib/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/biology/nifticlib/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, zlib }: +{ lib, stdenv, fetchFromGitHub, cmake, zlib }: stdenv.mkDerivation rec { pname = "nifticlib"; @@ -23,7 +23,7 @@ stdenv.mkDerivation rec { ''; doCheck = true; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://nifti-imaging.github.io"; description = "Medical imaging format C API"; maintainers = with maintainers; [ bcdarwin ]; diff --git a/nixpkgs/pkgs/development/libraries/science/biology/oobicpl/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/oobicpl/default.nix index e5ecda0390bd..626e6475ba18 100644 --- a/nixpkgs/pkgs/development/libraries/science/biology/oobicpl/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/biology/oobicpl/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, libminc, bicpl, arguments, pcre-cpp }: +{ lib, stdenv, fetchFromGitHub, cmake, libminc, bicpl, arguments, pcre-cpp }: stdenv.mkDerivation rec { pname = "oobicpl"; @@ -21,7 +21,7 @@ stdenv.mkDerivation rec { "-DARGUMENTS_DIR=${arguments}/lib" "-DOOBICPL_BUILD_SHARED_LIBS=TRUE" ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://github.com/${owner}/${pname}"; description = "Brain Imaging Centre object-oriented programming library (and tools)"; maintainers = with maintainers; [ bcdarwin ]; diff --git a/nixpkgs/pkgs/development/libraries/science/electronics/qcsxcad/default.nix b/nixpkgs/pkgs/development/libraries/science/electronics/qcsxcad/default.nix index 7e73354363ea..a20f6973384a 100644 --- a/nixpkgs/pkgs/development/libraries/science/electronics/qcsxcad/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/electronics/qcsxcad/default.nix @@ -37,8 +37,6 @@ mkDerivation { qtbase ]; - enableParallelBuilding = true; - meta = with lib; { description = "Qt library for CSXCAD"; homepage = "https://github.com/thliebig/QCSXCAD"; diff --git a/nixpkgs/pkgs/development/libraries/science/math/QuadProgpp/default.nix b/nixpkgs/pkgs/development/libraries/science/math/QuadProgpp/default.nix index b5fa5c8825e0..254ce08dc60f 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/QuadProgpp/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/QuadProgpp/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake }: +{ lib, stdenv, fetchFromGitHub, cmake }: stdenv.mkDerivation rec { pname = "QuadProgpp"; @@ -14,7 +14,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake ]; buildInputs = [ ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://github.com/liuq/QuadProgpp"; license = licenses.mit; description = '' diff --git a/nixpkgs/pkgs/development/libraries/science/math/amd-blis/default.nix b/nixpkgs/pkgs/development/libraries/science/math/amd-blis/default.nix index 9bddba0261fe..42c84b3ed610 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/amd-blis/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/amd-blis/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchFromGitHub , perl , python3 @@ -43,7 +43,7 @@ in stdenv.mkDerivation rec { configureFlags = [ "--enable-cblas" "--blas-int-size=${blasIntSize}" - ] ++ stdenv.lib.optionals withOpenMP [ "--enable-threading=openmp" ] + ] ++ lib.optionals withOpenMP [ "--enable-threading=openmp" ] ++ [ withArchitecture ]; postPatch = '' @@ -57,7 +57,7 @@ in stdenv.mkDerivation rec { ln -s $out/lib/libcblas.so.3 $out/lib/libcblas.so ''; - meta = with stdenv.lib; { + meta = with lib; { description = "BLAS-compatible library optimized for AMD CPUs"; homepage = "https://developer.amd.com/amd-aocl/blas-library/"; license = licenses.bsd3; diff --git a/nixpkgs/pkgs/development/libraries/science/math/amd-libflame/default.nix b/nixpkgs/pkgs/development/libraries/science/math/amd-libflame/default.nix index 1e331bca695c..ac35385f9835 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/amd-libflame/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/amd-libflame/default.nix @@ -62,7 +62,7 @@ stdenv.mkDerivation rec { ln -s $out/lib/libflame.so.${version} $out/lib/liblapacke.so.3 ''; - meta = with stdenv.lib; { + meta = with lib; { description = "LAPACK-compatible linear algebra library optimized for AMD CPUs"; homepage = "https://developer.amd.com/amd-aocl/blas-library/"; license = licenses.bsd3; diff --git a/nixpkgs/pkgs/development/libraries/science/math/arpack/default.nix b/nixpkgs/pkgs/development/libraries/science/math/arpack/default.nix index 0b927bb3eac8..382f868a99ac 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/arpack/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/arpack/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake +{ lib, stdenv, fetchFromGitHub, cmake , gfortran, blas, lapack, eigen }: stdenv.mkDerivation rec { @@ -24,7 +24,7 @@ stdenv.mkDerivation rec { cmakeFlags = [ "-DBUILD_SHARED_LIBS=ON" - "-DINTERFACE64=${stdenv.lib.optionalString blas.isILP64 "1"}" + "-DINTERFACE64=${lib.optionalString blas.isILP64 "1"}" ]; preCheck = if stdenv.isDarwin then '' @@ -48,8 +48,8 @@ stdenv.mkDerivation rec { A collection of Fortran77 subroutines to solve large scale eigenvalue problems. ''; - license = stdenv.lib.licenses.bsd3; - maintainers = [ stdenv.lib.maintainers.ttuegel ]; - platforms = stdenv.lib.platforms.unix; + license = lib.licenses.bsd3; + maintainers = [ lib.maintainers.ttuegel ]; + platforms = lib.platforms.unix; }; } diff --git a/nixpkgs/pkgs/development/libraries/science/math/blas/default.nix b/nixpkgs/pkgs/development/libraries/science/math/blas/default.nix index c240a19cca67..332806c495c9 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/blas/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/blas/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, gfortran }: +{ lib, stdenv, fetchurl, gfortran }: stdenv.mkDerivation rec { pname = "blas"; @@ -38,13 +38,13 @@ stdenv.mkDerivation rec { installPhase = # FreeBSD's stdenv doesn't use Coreutils. let dashD = if stdenv.isFreeBSD then "" else "-D"; in - (stdenv.lib.optionalString stdenv.isFreeBSD "mkdir -p $out/lib ;") + (lib.optionalString stdenv.isFreeBSD "mkdir -p $out/lib ;") + '' install ${dashD} -m755 libblas.a "$out/lib/libblas.a" install ${dashD} -m755 libblas.so.${version} "$out/lib/libblas.so.${version}" ln -s libblas.so.${version} "$out/lib/libblas.so.3" ln -s libblas.so.${version} "$out/lib/libblas.so" - # Write pkgconfig alias. + # Write pkg-config alias. # See also openblas/default.nix mkdir $out/lib/pkgconfig cat <<EOF > $out/lib/pkgconfig/blas.pc @@ -55,7 +55,7 @@ Libs: -L$out/lib -lblas EOF ''; - preFixup = stdenv.lib.optionalString stdenv.isDarwin '' + preFixup = lib.optionalString stdenv.isDarwin '' for fn in $(find $out/lib -name "*.so*"); do if [ -L "$fn" ]; then continue; fi install_name_tool -id "$fn" "$fn" @@ -64,8 +64,8 @@ EOF meta = { description = "Basic Linear Algebra Subprograms"; - license = stdenv.lib.licenses.publicDomain; + license = lib.licenses.publicDomain; homepage = "http://www.netlib.org/blas/"; - platforms = stdenv.lib.platforms.unix; + platforms = lib.platforms.unix; }; } diff --git a/nixpkgs/pkgs/development/libraries/science/math/blis/default.nix b/nixpkgs/pkgs/development/libraries/science/math/blis/default.nix index 3943c4dbbcaa..eb91e0a3d222 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/blis/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/blis/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchFromGitHub , perl , python3 @@ -40,7 +40,7 @@ in stdenv.mkDerivation rec { configureFlags = [ "--enable-cblas" "--blas-int-size=${blasIntSize}" - ] ++ stdenv.lib.optionals withOpenMP [ "--enable-threading=openmp" ] + ] ++ lib.optionals withOpenMP [ "--enable-threading=openmp" ] ++ [ withArchitecture ]; postPatch = '' @@ -54,7 +54,7 @@ in stdenv.mkDerivation rec { ln -s $out/lib/libcblas.so.3 $out/lib/libcblas.so ''; - meta = with stdenv.lib; { + meta = with lib; { description = "BLAS-compatible linear algebra library"; homepage = "https://github.com/flame/blis"; license = licenses.bsd3; diff --git a/nixpkgs/pkgs/development/libraries/science/math/brial/default.nix b/nixpkgs/pkgs/development/libraries/science/math/brial/default.nix index 175de67ad7ee..870568c9ac95 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/brial/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/brial/default.nix @@ -1,7 +1,7 @@ -{ stdenv +{ lib, stdenv , fetchFromGitHub , autoreconfHook -, pkgconfig +, pkg-config , boost , m4ri , gd @@ -33,10 +33,10 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ autoreconfHook - pkgconfig + pkg-config ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://github.com/BRiAl/BRiAl"; description = "Legacy version of PolyBoRi maintained by sagemath developers"; license = licenses.gpl2Plus; diff --git a/nixpkgs/pkgs/development/libraries/science/math/caffe2/default.nix b/nixpkgs/pkgs/development/libraries/science/math/caffe2/default.nix index 7755efb30658..fe9a8b671459 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/caffe2/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/caffe2/default.nix @@ -90,26 +90,26 @@ stdenv.mkDerivation rec { ./fix_compilation_on_gcc7.patch ] ++ lib.optional stdenv.cc.isClang [ ./update_clang_cvtsh_bugfix.patch ]; - cmakeFlags = [ ''-DBUILD_TEST=OFF'' - ''-DBUILD_PYTHON=ON'' - ''-DUSE_CUDA=${if useCuda then ''ON''else ''OFF''}'' - ''-DUSE_OPENMP=${if useOpenmp then ''ON''else ''OFF''}'' - ''-DUSE_OPENCV=${if useOpencv3 then ''ON''else ''OFF''}'' - ''-DUSE_MPI=${if useMpi then ''ON''else ''OFF''}'' - ''-DUSE_LEVELDB=${if useLeveldb then ''ON''else ''OFF''}'' - ''-DUSE_LMDB=${if useLmdb then ''ON''else ''OFF''}'' - ''-DUSE_ROCKSDB=${if useRocksdb then ''ON''else ''OFF''}'' - ''-DUSE_ZMQ=${if useZeromq then ''ON''else ''OFF''}'' - ''-DUSE_GLOO=OFF'' - ''-DUSE_NNPACK=OFF'' - ''-DUSE_NCCL=OFF'' - ''-DUSE_REDIS=OFF'' - ''-DUSE_FFMPEG=OFF'' + cmakeFlags = [ "-DBUILD_TEST=OFF" + "-DBUILD_PYTHON=ON" + ''-DUSE_CUDA=${if useCuda then "ON"else "OFF"}'' + ''-DUSE_OPENMP=${if useOpenmp then "ON"else "OFF"}'' + ''-DUSE_OPENCV=${if useOpencv3 then "ON"else "OFF"}'' + ''-DUSE_MPI=${if useMpi then "ON"else "OFF"}'' + ''-DUSE_LEVELDB=${if useLeveldb then "ON"else "OFF"}'' + ''-DUSE_LMDB=${if useLmdb then "ON"else "OFF"}'' + ''-DUSE_ROCKSDB=${if useRocksdb then "ON"else "OFF"}'' + ''-DUSE_ZMQ=${if useZeromq then "ON"else "OFF"}'' + "-DUSE_GLOO=OFF" + "-DUSE_NNPACK=OFF" + "-DUSE_NCCL=OFF" + "-DUSE_REDIS=OFF" + "-DUSE_FFMPEG=OFF" ] ++ lib.optional useCuda [ - ''-DCUDA_TOOLKIT_ROOT_DIR=${cudatoolkit}'' - ''-DCUDA_FAST_MATH=ON'' - ''-DCUDA_HOST_COMPILER=${cudatoolkit.cc}/bin/gcc'' + "-DCUDA_TOOLKIT_ROOT_DIR=${cudatoolkit}" + "-DCUDA_FAST_MATH=ON" + "-DCUDA_HOST_COMPILER=${cudatoolkit.cc}/bin/gcc" ]; preConfigure = '' @@ -126,7 +126,6 @@ stdenv.mkDerivation rec { ''; doCheck = false; - enableParallelBuilding = true; meta = { homepage = "https://caffe2.ai/"; @@ -137,8 +136,8 @@ stdenv.mkDerivation rec { algorithms. You can bring your creations to scale using the power of GPUs in the cloud or to the masses on mobile with Caffe2's cross-platform libraries. ''; - platforms = with stdenv.lib.platforms; linux; - license = stdenv.lib.licenses.asl20; - maintainers = with stdenv.lib.maintainers; [ yuriaisaka ]; + platforms = with lib.platforms; linux; + license = lib.licenses.asl20; + maintainers = with lib.maintainers; [ yuriaisaka ]; }; } diff --git a/nixpkgs/pkgs/development/libraries/science/math/cholmod-extra/default.nix b/nixpkgs/pkgs/development/libraries/science/math/cholmod-extra/default.nix index c381f56277e8..38d1b126ea4e 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/cholmod-extra/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/cholmod-extra/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, gfortran, suitesparse, blas, lapack }: +{ lib, stdenv, fetchFromGitHub, gfortran, suitesparse, blas, lapack }: stdenv.mkDerivation rec { pname = "cholmod-extra"; version = "1.2.0"; @@ -23,7 +23,7 @@ stdenv.mkDerivation rec { doCheck = true; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://github.com/jluttine/cholmod-extra"; description = "A set of additional routines for SuiteSparse CHOLMOD Module"; license = with licenses; [ gpl2Plus ]; diff --git a/nixpkgs/pkgs/development/libraries/science/math/clblas/default.nix b/nixpkgs/pkgs/development/libraries/science/math/clblas/default.nix index 8a474e06e556..aca395001f96 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/clblas/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/clblas/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchFromGitHub , cmake , gfortran @@ -35,27 +35,25 @@ stdenv.mkDerivation rec { "-DBUILD_TEST=OFF" ]; + nativeBuildInputs = [ cmake ]; buildInputs = [ - cmake gfortran blas python boost - ] ++ stdenv.lib.optionals (!stdenv.isDarwin) [ + ] ++ lib.optionals (!stdenv.isDarwin) [ ocl-icd opencl-headers - ] ++ stdenv.lib.optionals stdenv.isDarwin [ + ] ++ lib.optionals stdenv.isDarwin [ Accelerate CoreGraphics CoreVideo ]; - propagatedBuildInputs = stdenv.lib.optionals stdenv.isDarwin [ + propagatedBuildInputs = lib.optionals stdenv.isDarwin [ OpenCL ]; - enableParallelBuilding = true; - - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://github.com/clMathLibraries/clBLAS"; description = "A software library containing BLAS functions written in OpenCL"; longDescription = '' diff --git a/nixpkgs/pkgs/development/libraries/science/math/cliquer/default.nix b/nixpkgs/pkgs/development/libraries/science/math/cliquer/default.nix index 7fe80c323f68..0d8bafffb44f 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/cliquer/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/cliquer/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchFromGitHub , autoreconfHook }: @@ -21,7 +21,7 @@ stdenv.mkDerivation rec { autoreconfHook ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://users.aalto.fi/~pat/cliquer.html"; downloadPage = src.meta.homepage; # autocliquer description = "Routines for clique searching"; diff --git a/nixpkgs/pkgs/development/libraries/science/math/clmagma/default.nix b/nixpkgs/pkgs/development/libraries/science/math/clmagma/default.nix index 2e798a6b83e7..60a3afb50774 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/clmagma/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/clmagma/default.nix @@ -1,6 +1,6 @@ -{ stdenv, fetchurl, gfortran, opencl-headers, clblas, ocl-icd, mkl, intel-ocl }: +{ lib, stdenv, fetchurl, gfortran, opencl-headers, clblas, ocl-icd, mkl, intel-ocl }: -with stdenv.lib; +with lib; let version = "1.3.0"; @@ -65,7 +65,7 @@ in stdenv.mkDerivation { cp ${incfile} make.inc ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Matrix Algebra on GPU and Multicore Architectures, OpenCL port"; license = licenses.bsd3; homepage = "http://icl.cs.utk.edu/magma/index.html"; diff --git a/nixpkgs/pkgs/development/libraries/science/math/cudnn/generic.nix b/nixpkgs/pkgs/development/libraries/science/math/cudnn/generic.nix index e727218c0555..59c0b7f44980 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/cudnn/generic.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/cudnn/generic.nix @@ -57,7 +57,7 @@ stdenv.mkDerivation { majorVersion = lib.versions.major version; }; - meta = with stdenv.lib; { + meta = with lib; { description = "NVIDIA CUDA Deep Neural Network library (cuDNN)"; homepage = "https://developer.nvidia.com/cudnn"; license = licenses.unfree; diff --git a/nixpkgs/pkgs/development/libraries/science/math/ecos/default.nix b/nixpkgs/pkgs/development/libraries/science/math/ecos/default.nix index 2ba69a34a4a7..b60bd1fe76c1 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/ecos/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/ecos/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub }: +{ lib, stdenv, fetchFromGitHub }: stdenv.mkDerivation rec { pname = "ecos"; @@ -27,7 +27,7 @@ stdenv.mkDerivation rec { cp -r include $out/ ''; - meta = with stdenv.lib; { + meta = with lib; { description = "A lightweight conic solver for second-order cone programming"; homepage = "https://www.embotech.com/ECOS"; downloadPage = "https://github.com/embotech/ecos/releases"; diff --git a/nixpkgs/pkgs/development/libraries/science/math/fenics/default.nix b/nixpkgs/pkgs/development/libraries/science/math/fenics/default.nix index 4e89aeebe2b7..e80607ab9556 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/fenics/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/fenics/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchurl , fetchpatch , boost @@ -50,8 +50,8 @@ let meta = { description = "Distributed just-in-time shared library building"; homepage = "https://fenicsproject.org/"; - platforms = stdenv.lib.platforms.all; - license = stdenv.lib.licenses.lgpl3; + platforms = lib.platforms.all; + license = lib.licenses.lgpl3; }; }; @@ -80,8 +80,8 @@ let meta = { description = "Automatic generation of finite element basis functions"; homepage = "https://fenicsproject.org/"; - platforms = stdenv.lib.platforms.all; - license = stdenv.lib.licenses.lgpl3; + platforms = lib.platforms.all; + license = lib.licenses.lgpl3; }; }; @@ -102,8 +102,8 @@ let meta = { description = "A domain-specific language for finite element variational forms"; homepage = "https://fenicsproject.org/"; - platforms = stdenv.lib.platforms.all; - license = stdenv.lib.licenses.lgpl3; + platforms = lib.platforms.all; + license = lib.licenses.lgpl3; }; }; @@ -139,8 +139,8 @@ let meta = { description = "A compiler for finite element variational forms"; homepage = "https://fenicsproject.org/"; - platforms = stdenv.lib.platforms.all; - license = stdenv.lib.licenses.lgpl3; + platforms = lib.platforms.all; + license = lib.licenses.lgpl3; }; }; dolfin = stdenv.mkDerivation { @@ -215,7 +215,7 @@ let meta = { description = "The FEniCS Problem Solving Environment in Python and C++"; homepage = "https://fenicsproject.org/"; - license = stdenv.lib.licenses.lgpl3; + license = lib.licenses.lgpl3; }; }; python-dolfin = pythonPackages.buildPythonPackage rec { @@ -233,8 +233,8 @@ let export CMAKE_PREFIX_PATH=${pybind11}/share/cmake/pybind11:$CMAKE_PREFIX_PATH substituteInPlace setup.py --replace "pybind11==2.2.4" "pybind11" substituteInPlace dolfin/jit/jit.py \ - --replace 'pkgconfig.exists("dolfin")' 'pkgconfig.exists("${dolfin}/lib/pkgconfig/dolfin.pc")' \ - --replace 'pkgconfig.parse("dolfin")' 'pkgconfig.parse("${dolfin}/lib/pkgconfig/dolfin.pc")' + --replace 'pkg-config.exists("dolfin")' 'pkg-config.exists("${dolfin}/lib/pkgconfig/dolfin.pc")' \ + --replace 'pkg-config.parse("dolfin")' 'pkg-config.parse("${dolfin}/lib/pkgconfig/dolfin.pc")' ''; buildInputs = [ dolfin @@ -254,8 +254,8 @@ let meta = { description = "Python bindings for the DOLFIN FEM compiler"; homepage = "https://fenicsproject.org/"; - platforms = stdenv.lib.platforms.all; - license = stdenv.lib.licenses.lgpl3; + platforms = lib.platforms.all; + license = lib.licenses.lgpl3; }; }; in python-dolfin diff --git a/nixpkgs/pkgs/development/libraries/science/math/flintqs/default.nix b/nixpkgs/pkgs/development/libraries/science/math/flintqs/default.nix index 32fb70978cf9..c956eae4f710 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/flintqs/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/flintqs/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchFromGitHub , autoreconfHook , gmp @@ -29,7 +29,7 @@ stdenv.mkDerivation rec { doCheck = true; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://github.com/sagemath/FlintQS"; description = "Highly optimized multi-polynomial quadratic sieve for integer factorization"; license = with licenses; [ gpl2 ]; diff --git a/nixpkgs/pkgs/development/libraries/science/math/ipopt/default.nix b/nixpkgs/pkgs/development/libraries/science/math/ipopt/default.nix index 97374fb0d477..d1d7a9b9f342 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/ipopt/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/ipopt/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, unzip, blas, lapack, gfortran }: +{ lib, stdenv, fetchurl, unzip, blas, lapack, gfortran }: assert (!blas.isILP64) && (!lapack.isILP64); @@ -24,7 +24,7 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; - meta = with stdenv.lib; { + meta = with lib; { description = "A software package for large-scale nonlinear optimization"; homepage = "https://projects.coin-or.org/Ipopt"; license = licenses.epl10; diff --git a/nixpkgs/pkgs/development/libraries/science/math/itpp/default.nix b/nixpkgs/pkgs/development/libraries/science/math/itpp/default.nix index c74a7408e98e..81303a3653ec 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/itpp/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/itpp/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchurl , cmake , gtest @@ -35,8 +35,6 @@ stdenv.mkDerivation rec { "-DGTEST_DIR:PATH=${gtest.src}/googletest" ]; - enableParallelBuilding = true; - doCheck = true; checkPhase = '' @@ -45,7 +43,7 @@ stdenv.mkDerivation rec { ./gtests/itpp_gtests ''; - meta = with stdenv.lib; { + meta = with lib; { description = "IT++ is a C++ library of mathematical, signal processing and communication classes and functions"; homepage = http://itpp.sourceforge.net/; license = licenses.gpl3; diff --git a/nixpkgs/pkgs/development/libraries/science/math/lcalc/default.nix b/nixpkgs/pkgs/development/libraries/science/math/lcalc/default.nix index 6f80e1fd23e0..95034c3637a9 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/lcalc/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/lcalc/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchurl , fetchpatch , pari @@ -68,13 +68,13 @@ stdenv.mkDerivation rec { url = "https://git.archlinux.org/svntogit/community.git/plain/trunk/lcalc-c++11.patch?h=packages/lcalc&id=3607b97df5a8c231191115b0cb5c62426b339e71"; sha256 = "1ccrl61lv2vvx8ggldq54m5d0n1iy6mym7qz0i8nj6yj0dshnpk3"; }) - ] ++ stdenv.lib.optional stdenv.isDarwin + ] ++ lib.optional stdenv.isDarwin (fetchpatch { url = "https://git.sagemath.org/sage.git/plain/build/pkgs/lcalc/patches/clang.patch"; sha256 = "0bb7656z6cp6i4p2qj745cmq0lhh52v2akl9whi760dynfdxbl18"; }); - postPatch = stdenv.lib.optionalString stdenv.isDarwin '' + postPatch = lib.optionalString stdenv.isDarwin '' substituteInPlace src/Makefile --replace g++ c++ ''; @@ -87,7 +87,7 @@ stdenv.mkDerivation rec { "PARI_PREFIX=${pari}" ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "http://oto.math.uwaterloo.ca/~mrubinst/L_function_public/L.html"; description = "A program for calculating with L-functions"; license = with licenses; [ gpl2 ]; diff --git a/nixpkgs/pkgs/development/libraries/science/math/libbraiding/default.nix b/nixpkgs/pkgs/development/libraries/science/math/libbraiding/default.nix index 36d4ad54c3df..cc5d3baf3442 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/libbraiding/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/libbraiding/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchFromGitHub , autoreconfHook }: @@ -21,7 +21,7 @@ stdenv.mkDerivation rec { # no tests included for now (2018-08-05), but can't hurt to activate doCheck = true; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://github.com/miguelmarco/libbraiding/"; description = "C++ library for computations on braid groups"; longDescription = '' diff --git a/nixpkgs/pkgs/development/libraries/science/math/libhomfly/default.nix b/nixpkgs/pkgs/development/libraries/science/math/libhomfly/default.nix index 788f534cc779..b756109aa8fc 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/libhomfly/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/libhomfly/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchFromGitHub , autoreconfHook , boehmgc @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { doCheck = true; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://github.com/miguelmarco/libhomfly/"; description = "Library to compute the homfly polynomial of knots and links"; license = licenses.unlicense; diff --git a/nixpkgs/pkgs/development/libraries/science/math/liblapack/default.nix b/nixpkgs/pkgs/development/libraries/science/math/liblapack/default.nix index 045cccbd2ebf..c742cc60b27f 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/liblapack/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/liblapack/default.nix @@ -1,5 +1,5 @@ { - stdenv, + lib, stdenv, fetchFromGitHub, gfortran, cmake, @@ -7,7 +7,7 @@ shared ? true }: let - inherit (stdenv.lib) optional; + inherit (lib) optional; version = "3.9.0"; in @@ -33,9 +33,7 @@ stdenv.mkDerivation { doCheck = true; - enableParallelBuilding = true; - - meta = with stdenv.lib; { + meta = with lib; { inherit version; description = "Linear Algebra PACKage"; homepage = "http://www.netlib.org/lapack/"; diff --git a/nixpkgs/pkgs/development/libraries/science/math/liblbfgs/default.nix b/nixpkgs/pkgs/development/libraries/science/math/liblbfgs/default.nix index 49108e5e3305..20c5a2070a05 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/liblbfgs/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/liblbfgs/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl }: +{ lib, stdenv, fetchurl }: stdenv.mkDerivation { name = "liblbfgs-1.10"; @@ -11,7 +11,7 @@ stdenv.mkDerivation { meta = { description = "Library of Limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS)"; homepage = "http://www.chokkan.org/software/liblbfgs/"; - license = stdenv.lib.licenses.mit; - platforms = stdenv.lib.platforms.unix; + license = lib.licenses.mit; + platforms = lib.platforms.unix; }; } diff --git a/nixpkgs/pkgs/development/libraries/science/math/libtorch/bin.nix b/nixpkgs/pkgs/development/libraries/science/math/libtorch/bin.nix index fba8bcb9367b..9631f3931cab 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/libtorch/bin.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/libtorch/bin.nix @@ -25,7 +25,7 @@ in stdenv.mkDerivation { nativeBuildInputs = if stdenv.isDarwin then [ fixDarwinDylibNames ] else [ addOpenGLRunpath patchelf ] - ++ stdenv.lib.optionals cudaSupport [ addOpenGLRunpath ]; + ++ lib.optionals cudaSupport [ addOpenGLRunpath ]; buildInputs = [ stdenv.cc.cc @@ -57,9 +57,9 @@ in stdenv.mkDerivation { postFixup = let libPaths = [ stdenv.cc.cc.lib ] - ++ stdenv.lib.optionals cudaSupport [ nvidia_x11 ]; - rpath = stdenv.lib.makeLibraryPath libPaths; - in stdenv.lib.optionalString stdenv.isLinux '' + ++ lib.optionals cudaSupport [ nvidia_x11 ]; + rpath = lib.makeLibraryPath libPaths; + in lib.optionalString stdenv.isLinux '' find $out/lib -type f \( -name '*.so' -or -name '*.so.*' \) | while read lib; do echo "setting rpath for $lib..." patchelf --set-rpath "${rpath}:$out/lib" "$lib" @@ -67,7 +67,7 @@ in stdenv.mkDerivation { addOpenGLRunpath "$lib" ''} done - '' + stdenv.lib.optionalString stdenv.isDarwin '' + '' + lib.optionalString stdenv.isDarwin '' install_name_tool -change @rpath/libshm.dylib $out/lib/libshm.dylib $out/lib/libtorch_python.dylib install_name_tool -change @rpath/libc10.dylib $out/lib/libc10.dylib $out/lib/libtorch_python.dylib install_name_tool -change @rpath/libiomp5.dylib $out/lib/libiomp5.dylib $out/lib/libtorch_python.dylib @@ -110,7 +110,7 @@ in stdenv.mkDerivation { passthru.tests.cmake = callPackage ./test { }; - meta = with stdenv.lib; { + meta = with lib; { description = "C++ API of the PyTorch machine learning framework"; homepage = "https://pytorch.org/"; license = licenses.unfree; # Includes CUDA and Intel MKL. diff --git a/nixpkgs/pkgs/development/libraries/science/math/lrs/default.nix b/nixpkgs/pkgs/development/libraries/science/math/lrs/default.nix index b0cfbca5aa33..f7f981e223b2 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/lrs/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/lrs/default.nix @@ -1,4 +1,4 @@ -{stdenv, fetchurl, gmp}: +{lib, stdenv, fetchurl, gmp}: stdenv.mkDerivation rec { pname = "lrs"; @@ -18,9 +18,9 @@ stdenv.mkDerivation rec { meta = { inherit version; description = "Implementation of the reverse search algorithm for vertex enumeration/convex hull problems"; - license = stdenv.lib.licenses.gpl2 ; - maintainers = [stdenv.lib.maintainers.raskin]; - platforms = stdenv.lib.platforms.linux; + license = lib.licenses.gpl2 ; + maintainers = [lib.maintainers.raskin]; + platforms = lib.platforms.linux; homepage = "http://cgm.cs.mcgill.ca/~avis/C/lrs.html"; }; } diff --git a/nixpkgs/pkgs/development/libraries/science/math/m4ri/default.nix b/nixpkgs/pkgs/development/libraries/science/math/m4ri/default.nix index f50c15abbdf1..26e26e4ffdbc 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/m4ri/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/m4ri/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchFromBitbucket , autoreconfHook }: @@ -20,7 +20,7 @@ stdenv.mkDerivation rec { autoreconfHook ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://malb.bitbucket.io/m4ri/"; description = "Library to do fast arithmetic with dense matrices over F_2"; license = licenses.gpl2Plus; diff --git a/nixpkgs/pkgs/development/libraries/science/math/m4rie/default.nix b/nixpkgs/pkgs/development/libraries/science/math/m4rie/default.nix index 532285991a3c..38a633e58c71 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/m4rie/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/m4rie/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchFromBitbucket , autoreconfHook , m4ri @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { autoreconfHook ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://malb.bitbucket.io/m4rie/"; description = "Library for matrix multiplication, reduction and inversion over GF(2^k) for 2 <= k <= 10"; longDescription = '' diff --git a/nixpkgs/pkgs/development/libraries/science/math/magma/default.nix b/nixpkgs/pkgs/development/libraries/science/math/magma/default.nix index b4ac119ce6cf..b8e3999ffe83 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/magma/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/magma/default.nix @@ -1,6 +1,6 @@ -{ stdenv, fetchurl, cmake, gfortran, ninja, cudatoolkit, libpthreadstubs, lapack, blas }: +{ lib, stdenv, fetchurl, cmake, gfortran, ninja, cudatoolkit, libpthreadstubs, lapack, blas }: -with stdenv.lib; +with lib; let version = "2.5.4"; @@ -43,7 +43,7 @@ in stdenv.mkDerivation { > $out/lib/pkgconfig/magma.pc ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Matrix Algebra on GPU and Multicore Architectures"; license = licenses.bsd3; homepage = "http://icl.cs.utk.edu/magma/index.html"; diff --git a/nixpkgs/pkgs/development/libraries/science/math/metis/default.nix b/nixpkgs/pkgs/development/libraries/science/math/metis/default.nix index 8d6381c8d48d..b06b432372a7 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/metis/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/metis/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, unzip, cmake }: +{ lib, stdenv, fetchurl, unzip, cmake }: stdenv.mkDerivation { name = "metis-5.1.0"; @@ -9,12 +9,12 @@ stdenv.mkDerivation { }; cmakeFlags = [ "-DGKLIB_PATH=../GKlib" ]; - buildInputs = [ unzip cmake ]; + nativeBuildInputs = [ unzip cmake ]; meta = { description = "Serial graph partitioning and fill-reducing matrix ordering"; homepage = "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview"; - license = stdenv.lib.licenses.asl20; - platforms = stdenv.lib.platforms.all; + license = lib.licenses.asl20; + platforms = lib.platforms.all; }; } diff --git a/nixpkgs/pkgs/development/libraries/science/math/mongoose/default.nix b/nixpkgs/pkgs/development/libraries/science/math/mongoose/default.nix index 36c53b2994f5..7dd52f3b663d 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/mongoose/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/mongoose/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchFromGitHub , cmake }: @@ -20,7 +20,7 @@ stdenv.mkDerivation rec { cmake ]; - meta = with stdenv.lib; { + meta = with lib; { description = "Graph Coarsening and Partitioning Library"; homepage = "https://github.com/ScottKolo/Mongoose"; license = licenses.gpl3; diff --git a/nixpkgs/pkgs/development/libraries/science/math/nccl/default.nix b/nixpkgs/pkgs/development/libraries/science/math/nccl/default.nix index eb194c0e9e47..5036ad890799 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/nccl/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/nccl/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, which, cudatoolkit, addOpenGLRunpath }: +{ lib, stdenv, fetchFromGitHub, which, cudatoolkit, addOpenGLRunpath }: stdenv.mkDerivation rec { name = "nccl-${version}-cuda-${cudatoolkit.majorVersion}"; @@ -38,7 +38,7 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; - meta = with stdenv.lib; { + meta = with lib; { description = "Multi-GPU and multi-node collective communication primitives for NVIDIA GPUs"; homepage = "https://developer.nvidia.com/nccl"; license = licenses.bsd3; diff --git a/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix b/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix index 8df04e80ceb3..bd7b739bd77f 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/openblas/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, perl, which +{ lib, stdenv, fetchFromGitHub, perl, which # Most packages depending on openblas expect integer width to match # pointer width, but some expect to use 32-bit integers always # (for compatibility with reference BLAS). @@ -19,7 +19,7 @@ , enableShared ? !stdenv.hostPlatform.isStatic }: -with stdenv.lib; +with lib; let blas64_ = blas64; in @@ -68,7 +68,6 @@ let BINARY = 64; TARGET = setTarget "ATHLON"; DYNAMIC_ARCH = true; - NO_AVX512 = true; USE_OPENMP = !stdenv.hostPlatform.isMusl; }; @@ -106,7 +105,7 @@ let in stdenv.mkDerivation rec { pname = "openblas"; - version = "0.3.12"; + version = "0.3.13"; outputs = [ "out" "dev" ]; @@ -114,7 +113,7 @@ stdenv.mkDerivation rec { owner = "xianyi"; repo = "OpenBLAS"; rev = "v${version}"; - sha256 = "0mk1kjkr96bvvcq2zigzjrs0cnhwsf6gfi0855mp9yifn8lvp20y"; + sha256 = "14jxh0v3jfbw4mfjx4mcz4dd51lyq7pqvh9k8dg94539ypzjr2lj"; }; inherit blas64; @@ -161,7 +160,7 @@ stdenv.mkDerivation rec { NO_BINARY_MODE = if stdenv.isx86_64 then toString (stdenv.hostPlatform != stdenv.buildPlatform) else stdenv.hostPlatform != stdenv.buildPlatform; - } // (stdenv.lib.optionalAttrs singleThreaded { + } // (lib.optionalAttrs singleThreaded { # As described on https://github.com/xianyi/OpenBLAS/wiki/Faq/4bded95e8dc8aadc70ce65267d1093ca7bdefc4c#multi-threaded USE_THREAD = false; USE_LOCKING = true; # available with openblas >= 0.3.7 @@ -189,14 +188,14 @@ EOF ln -s $out/lib/libopenblas${shlibExt} $out/lib/libcblas${shlibExt} ln -s $out/lib/libopenblas${shlibExt} $out/lib/liblapack${shlibExt} ln -s $out/lib/libopenblas${shlibExt} $out/lib/liblapacke${shlibExt} - '' + stdenv.lib.optionalString stdenv.hostPlatform.isLinux '' + '' + lib.optionalString stdenv.hostPlatform.isLinux '' ln -s $out/lib/libopenblas${shlibExt} $out/lib/libblas${shlibExt}.3 ln -s $out/lib/libopenblas${shlibExt} $out/lib/libcblas${shlibExt}.3 ln -s $out/lib/libopenblas${shlibExt} $out/lib/liblapack${shlibExt}.3 ln -s $out/lib/libopenblas${shlibExt} $out/lib/liblapacke${shlibExt}.3 ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Basic Linear Algebra Subprograms"; license = licenses.bsd3; homepage = "https://github.com/xianyi/OpenBLAS"; diff --git a/nixpkgs/pkgs/development/libraries/science/math/openlibm/default.nix b/nixpkgs/pkgs/development/libraries/science/math/openlibm/default.nix index 17197823d6ef..2c4198d9679a 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/openlibm/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/openlibm/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl }: +{ lib, stdenv, fetchurl }: stdenv.mkDerivation rec { pname = "openlibm"; @@ -13,8 +13,8 @@ stdenv.mkDerivation rec { meta = { description = "High quality system independent, portable, open source libm implementation"; homepage = "https://openlibm.org/"; - license = stdenv.lib.licenses.mit; - maintainers = [ stdenv.lib.maintainers.ttuegel ]; - platforms = stdenv.lib.platforms.all; + license = lib.licenses.mit; + maintainers = [ lib.maintainers.ttuegel ]; + platforms = lib.platforms.all; }; } diff --git a/nixpkgs/pkgs/development/libraries/science/math/openspecfun/default.nix b/nixpkgs/pkgs/development/libraries/science/math/openspecfun/default.nix index 3689df607074..a341264d9894 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/openspecfun/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/openspecfun/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, gfortran }: +{ lib, stdenv, fetchurl, gfortran }: stdenv.mkDerivation { name = "openspecfun-0.5.3"; @@ -14,8 +14,8 @@ stdenv.mkDerivation { meta = { description = "A collection of special mathematical functions"; homepage = "https://github.com/JuliaLang/openspecfun"; - license = stdenv.lib.licenses.mit; - maintainers = [ stdenv.lib.maintainers.ttuegel ]; - platforms = stdenv.lib.platforms.all; + license = lib.licenses.mit; + maintainers = [ lib.maintainers.ttuegel ]; + platforms = lib.platforms.all; }; } 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 926f7ba4789c..53c117233d20 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/or-tools/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/or-tools/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, abseil-cpp, gflags, which +{ lib, stdenv, fetchFromGitHub, cmake, abseil-cpp, gflags, which , lsb-release, glog, protobuf, cbc, zlib , ensureNewerSourcesForZipFilesHook, python, swig }: @@ -53,11 +53,9 @@ stdenv.mkDerivation rec { python.pkgs.protobuf python.pkgs.six ]; - enableParallelBuilding = true; - outputs = [ "out" "python" ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://github.com/google/or-tools"; license = licenses.asl20; description = '' diff --git a/nixpkgs/pkgs/development/libraries/science/math/osi/default.nix b/nixpkgs/pkgs/development/libraries/science/math/osi/default.nix index b6f367ff4fe9..b61cd8406064 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/osi/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/osi/default.nix @@ -1,4 +1,4 @@ -{ stdenv, lib, fetchurl, gfortran, pkgconfig +{ stdenv, lib, fetchurl, gfortran, pkg-config , blas, zlib, bzip2 , withGurobi ? false, gurobi , withCplex ? false, cplex }: @@ -16,7 +16,7 @@ stdenv.mkDerivation rec { [ blas zlib bzip2 ] ++ lib.optional withGurobi gurobi ++ lib.optional withCplex cplex; - nativeBuildInputs = [ gfortran pkgconfig ]; + nativeBuildInputs = [ gfortran pkg-config ]; configureFlags = lib.optionals withGurobi [ "--with-gurobi-incdir=${gurobi}/include" "--with-gurobi-lib=-lgurobi${gurobi.libSuffix}" ] ++ lib.optionals withCplex [ "--with-cplex-incdir=${cplex}/cplex/include/ilcplex" "--with-cplex-lib=-lcplex${cplex.libSuffix}" ]; @@ -32,7 +32,7 @@ stdenv.mkDerivation rec { passthru = { inherit withGurobi withCplex; }; - meta = with stdenv.lib; { + meta = with lib; { description = "An abstract base class to a generic linear programming (LP) solver"; homepage = "https://github.com/coin-or/Osi"; license = licenses.epl10; diff --git a/nixpkgs/pkgs/development/libraries/science/math/osqp/default.nix b/nixpkgs/pkgs/development/libraries/science/math/osqp/default.nix index 9cd062d21f2f..00f2726f60fe 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/osqp/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/osqp/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchFromGitHub , cmake }: @@ -17,7 +17,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake ]; - meta = with stdenv.lib; { + meta = with lib; { description = "A quadratic programming solver using operator splitting"; homepage = "https://osqp.org"; license = licenses.asl20; diff --git a/nixpkgs/pkgs/development/libraries/science/math/parmetis/default.nix b/nixpkgs/pkgs/development/libraries/science/math/parmetis/default.nix index 8f24356c7336..db70bf8dd7a4 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/parmetis/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/parmetis/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchurl , cmake , mpi @@ -13,7 +13,8 @@ stdenv.mkDerivation rec { sha256 = "0pvfpvb36djvqlcc3lq7si0c5xpb2cqndjg8wvzg35ygnwqs5ngj"; }; - buildInputs = [ cmake mpi ]; + nativeBuildInputs = [ cmake ]; + buildInputs = [ mpi ]; # metis and GKlib are packaged with distribution # AUR https://aur.archlinux.org/packages/parmetis/ has reported that @@ -23,7 +24,7 @@ stdenv.mkDerivation rec { make config metis_path=$PWD/metis gklib_path=$PWD/metis/GKlib prefix=$out ''; - meta = with stdenv.lib; { + meta = with lib; { description = "An MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices"; homepage = "http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview"; platforms = platforms.all; diff --git a/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix b/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix index a1e9d1e30515..f06a028fe64f 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/petsc/default.nix @@ -1,4 +1,4 @@ -{ stdenv , darwin , fetchurl , blas , gfortran , lapack , python }: +{ lib, stdenv , darwin , fetchurl , blas , gfortran , lapack , python }: stdenv.mkDerivation rec { pname = "petsc"; @@ -20,7 +20,7 @@ stdenv.mkDerivation rec { prePatch = '' substituteInPlace configure \ --replace /bin/sh /usr/bin/python - '' + stdenv.lib.optionalString stdenv.isDarwin '' + '' + lib.optionalString stdenv.isDarwin '' substituteInPlace config/install.py \ --replace /usr/bin/install_name_tool ${darwin.cctools}/bin/install_name_tool ''; @@ -39,7 +39,7 @@ stdenv.mkDerivation rec { ) ''; - meta = with stdenv.lib; { + meta = with lib; { description = '' Library of linear algebra algorithms for solving partial differential equations diff --git a/nixpkgs/pkgs/development/libraries/science/math/planarity/default.nix b/nixpkgs/pkgs/development/libraries/science/math/planarity/default.nix index b1d6a072e130..a257b84ca54b 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/planarity/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/planarity/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchFromGitHub , fetchpatch , autoreconfHook @@ -29,7 +29,7 @@ stdenv.mkDerivation rec { }) ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://github.com/graph-algorithms/edge-addition-planarity-suite"; description = "A library for implementing graph algorithms"; license = licenses.bsd3; diff --git a/nixpkgs/pkgs/development/libraries/science/math/primesieve/default.nix b/nixpkgs/pkgs/development/libraries/science/math/primesieve/default.nix index 46709ff218a0..d99026bc5659 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/primesieve/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/primesieve/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, cmake }: +{ lib, stdenv, fetchurl, cmake }: stdenv.mkDerivation rec { pname = "primesieve"; @@ -11,7 +11,7 @@ stdenv.mkDerivation rec { sha256 = "0g60br3p8di92jx3pr2bb51xh15gg57l7qvwzwn7xf7l585hgi7v"; }; - meta = with stdenv.lib; { + meta = with lib; { description = "Fast C/C++ prime number generator"; homepage = "https://primesieve.org/"; license = licenses.bsd2; diff --git a/nixpkgs/pkgs/development/libraries/science/math/rankwidth/default.nix b/nixpkgs/pkgs/development/libraries/science/math/rankwidth/default.nix index 53f4313a2069..38c9444d0d31 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/rankwidth/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/rankwidth/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchurl }: @@ -18,7 +18,7 @@ stdenv.mkDerivation rec { # check phase is empty for now (as of version 0.7) doCheck = true; - meta = with stdenv.lib; { + meta = with lib; { description = "Calculates rank-width and rank-decompositions"; license = with licenses; [ gpl2Plus ]; maintainers = teams.sage.members; diff --git a/nixpkgs/pkgs/development/libraries/science/math/rubiks/default.nix b/nixpkgs/pkgs/development/libraries/science/math/rubiks/default.nix index 44f8150386e7..b4b670884989 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/rubiks/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/rubiks/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchurl , fetchpatch , coreutils @@ -45,7 +45,7 @@ stdenv.mkDerivation rec { }) ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://wiki.sagemath.org/spkg/rubiks"; description = "Several programs for working with Rubik's cubes"; # The individual websites are no longer available diff --git a/nixpkgs/pkgs/development/libraries/science/math/scalapack/default.nix b/nixpkgs/pkgs/development/libraries/science/math/scalapack/default.nix index 1cf9c2ed8d53..3b84a9d99cbe 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/scalapack/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/scalapack/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, openssh +{ lib, stdenv, fetchFromGitHub, cmake, openssh , gfortran, mpi, blas, lapack } : @@ -18,8 +18,6 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake openssh ]; buildInputs = [ mpi gfortran blas lapack ]; - enableParallelBuilding = true; - doCheck = true; preConfigure = '' @@ -38,13 +36,16 @@ stdenv.mkDerivation rec { # make sure the test starts even if we have less than 4 cores export OMPI_MCA_rmaps_base_oversubscribe=1 + # Fix to make mpich run in a sandbox + export HYDRA_IFACE=lo + # Run single threaded export OMP_NUM_THREADS=1 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH''${LD_LIBRARY_PATH:+:}`pwd`/lib ''; - meta = with stdenv.lib; { + meta = with lib; { homepage = "http://www.netlib.org/scalapack/"; description = "Library of high-performance linear algebra routines for parallel distributed memory machines"; license = licenses.bsd3; diff --git a/nixpkgs/pkgs/development/libraries/science/math/scs/default.nix b/nixpkgs/pkgs/development/libraries/science/math/scs/default.nix index 3820f2b95275..96f543e430f0 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/scs/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/scs/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, blas, lapack, gfortran, fixDarwinDylibNames }: +{ lib, stdenv, fetchFromGitHub, blas, lapack, gfortran, fixDarwinDylibNames }: assert (!blas.isILP64) && (!lapack.isILP64); @@ -20,7 +20,7 @@ stdenv.mkDerivation rec { --replace "gcc" "cc" ''; - nativeBuildInputs = stdenv.lib.optional stdenv.isDarwin fixDarwinDylibNames; + nativeBuildInputs = lib.optional stdenv.isDarwin fixDarwinDylibNames; buildInputs = [ blas lapack gfortran.cc.lib ]; @@ -39,7 +39,7 @@ stdenv.mkDerivation rec { runHook postInstall ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Splitting Conic Solver"; longDescription = '' Numerical optimization package for solving large-scale convex cone problems diff --git a/nixpkgs/pkgs/development/libraries/science/math/spooles/default.nix b/nixpkgs/pkgs/development/libraries/science/math/spooles/default.nix index c55a1b8002e1..6f4ddb3f787e 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/spooles/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/spooles/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, gfortran, perl }: +{ lib, stdenv, fetchurl, gfortran, perl }: stdenv.mkDerivation rec { pname = "spooles"; @@ -15,7 +15,7 @@ stdenv.mkDerivation rec { ./spooles.patch ]; - postPatch = stdenv.lib.optionalString stdenv.hostPlatform.isDarwin '' + postPatch = lib.optionalString stdenv.hostPlatform.isDarwin '' substituteInPlace makefile --replace '-Wl,-soname' '-Wl,-install_name' ''; @@ -42,7 +42,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ perl ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "http://www.netlib.org/linalg/spooles/"; description = "Library for solving sparse real and complex linear systems of equations"; license = licenses.publicDomain; 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 1c910a4f75bb..7696b18e7ca4 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/suitesparse-graphblas/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/suitesparse-graphblas/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchFromGitHub , cmake , gnum4 @@ -22,7 +22,7 @@ stdenv.mkDerivation rec { gnum4 ]; - meta = with stdenv.lib; { + meta = with lib; { description = "Graph algorithms in the language of linear algebra"; homepage = "http://faculty.cse.tamu.edu/davis/GraphBLAS.html"; license = licenses.asl20; 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 b1c1202c5780..b8ce3eca888c 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/suitesparse/4.2.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/suitesparse/4.2.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, gfortran, blas, lapack }: +{ lib, stdenv, fetchurl, gfortran, blas, lapack }: let int_t = if blas.isILP64 then "int64_t" else "int32_t"; @@ -33,7 +33,7 @@ stdenv.mkDerivation rec { "LAPACK=-llapack" ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "http://faculty.cse.tamu.edu/davis/suitesparse.html"; description = "A suite of sparse matrix algorithms"; license = with licenses; [ bsd2 gpl2Plus lgpl21Plus ]; 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 81a80c920b53..1ebac6ac445d 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/suitesparse/4.4.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/suitesparse/4.4.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, gfortran, blas, lapack +{ lib, stdenv, fetchurl, gfortran, blas, lapack , enableCuda ? false, cudatoolkit }: @@ -27,11 +27,11 @@ stdenv.mkDerivation { -e '/CHOLMOD_CONFIG/ s/$/-DNPARTITION -DLONGBLAS=${int_t}/' \ -e '/UMFPACK_CONFIG/ s/$/-DLONGBLAS=${int_t}/' '' - + stdenv.lib.optionalString stdenv.isDarwin '' + + lib.optionalString stdenv.isDarwin '' sed -i "SuiteSparse_config/SuiteSparse_config.mk" \ -e 's/^[[:space:]]*\(LIB = -lm\) -lrt/\1/' '' - + stdenv.lib.optionalString enableCuda '' + + lib.optionalString enableCuda '' sed -i "SuiteSparse_config/SuiteSparse_config.mk" \ -e 's|^[[:space:]]*\(CUDA_ROOT =\)|CUDA_ROOT = ${cudatoolkit}|' \ -e 's|^[[:space:]]*\(GPU_BLAS_PATH =\)|GPU_BLAS_PATH = $(CUDA_ROOT)|' \ @@ -55,7 +55,7 @@ stdenv.mkDerivation { "LAPACK=-llapack" ]; - NIX_CFLAGS_COMPILE = stdenv.lib.optionalString stdenv.isDarwin " -DNTIMER"; + NIX_CFLAGS_COMPILE = lib.optionalString stdenv.isDarwin " -DNTIMER"; postInstall = '' # Build and install shared library @@ -64,7 +64,7 @@ stdenv.mkDerivation { for i in "$out"/lib/lib*.a; do ar -x $i done - ${if enableCuda then cudatoolkit else stdenv.cc.outPath}/bin/${if enableCuda then "nvcc" else "cc"} *.o ${if stdenv.isDarwin then "-dynamiclib" else "--shared"} -o "$out/lib/libsuitesparse${SHLIB_EXT}" -lblas ${stdenv.lib.optionalString enableCuda "-lcublas"} + ${if enableCuda then cudatoolkit else stdenv.cc.outPath}/bin/${if enableCuda then "nvcc" else "cc"} *.o ${if stdenv.isDarwin then "-dynamiclib" else "--shared"} -o "$out/lib/libsuitesparse${SHLIB_EXT}" -lblas ${lib.optionalString enableCuda "-lcublas"} ) for i in umfpack cholmod amd camd colamd spqr; do ln -s libsuitesparse${SHLIB_EXT} "$out"/lib/lib$i${SHLIB_EXT} @@ -90,7 +90,7 @@ stdenv.mkDerivation { nativeBuildInputs = [ gfortran ]; buildInputs = [ blas lapack ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "http://faculty.cse.tamu.edu/davis/suitesparse.html"; description = "A suite of sparse matrix algorithms"; license = with licenses; [ bsd2 gpl2Plus lgpl21Plus ]; diff --git a/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix b/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix index 2e76050aa989..f0c82e7190f9 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/suitesparse/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchFromGitHub , gfortran , blas, lapack @@ -24,7 +24,7 @@ stdenv.mkDerivation rec { }; nativeBuildInputs = [ - ] ++ stdenv.lib.optional stdenv.isDarwin fixDarwinDylibNames; + ] ++ lib.optional stdenv.isDarwin fixDarwinDylibNames; # Use compatible indexing for lapack and blas used buildInputs = assert (blas.isILP64 == lapack.isILP64); [ @@ -33,7 +33,7 @@ stdenv.mkDerivation rec { gfortran.cc.lib gmp mpfr - ] ++ stdenv.lib.optional enableCuda cudatoolkit; + ] ++ lib.optional enableCuda cudatoolkit; preConfigure = '' # Mongoose and GraphBLAS are packaged separately @@ -45,13 +45,13 @@ stdenv.mkDerivation rec { "INSTALL_INCLUDE=${placeholder "dev"}/include" "JOBS=$(NIX_BUILD_CORES)" "MY_METIS_LIB=-lmetis" - ] ++ stdenv.lib.optionals blas.isILP64 [ + ] ++ lib.optionals blas.isILP64 [ "CFLAGS=-DBLAS64" - ] ++ stdenv.lib.optionals enableCuda [ + ] ++ lib.optionals enableCuda [ "CUDA_PATH=${cudatoolkit}" "CUDART_LIB=${cudatoolkit.lib}/lib/libcudart.so" "CUBLAS_LIB=${cudatoolkit}/lib/libcublas.so" - ] ++ stdenv.lib.optionals stdenv.isDarwin [ + ] ++ lib.optionals stdenv.isDarwin [ # Unless these are set, the build will attempt to use `Accelerate` on darwin, see: # https://github.com/DrTimothyAldenDavis/SuiteSparse/blob/v5.8.1/SuiteSparse_config/SuiteSparse_config.mk#L368 "BLAS=-lblas" @@ -64,7 +64,7 @@ stdenv.mkDerivation rec { "library" ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "http://faculty.cse.tamu.edu/davis/suitesparse.html"; description = "A suite of sparse matrix algorithms"; license = with licenses; [ bsd2 gpl2Plus lgpl21Plus ]; diff --git a/nixpkgs/pkgs/development/libraries/science/math/superlu/default.nix b/nixpkgs/pkgs/development/libraries/science/math/superlu/default.nix index ff59297bd839..26dd00d96069 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/superlu/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/superlu/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, cmake, +{ lib, stdenv, fetchurl, cmake, gfortran, blas, lapack}: assert (!blas.isILP64) && (!lapack.isILP64); @@ -12,7 +12,7 @@ stdenv.mkDerivation rec { sha256 = "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"; }; - buildInputs = [ cmake gfortran ]; + nativeBuildInputs = [ cmake gfortran ]; propagatedBuildInputs = [ blas ]; @@ -32,6 +32,6 @@ stdenv.mkDerivation rec { homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"; license = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/License.txt"; description = "A library for the solution of large, sparse, nonsymmetric systems of linear equations"; - platforms = stdenv.lib.platforms.unix; + platforms = lib.platforms.unix; }; } diff --git a/nixpkgs/pkgs/development/libraries/science/math/sympow/default.nix b/nixpkgs/pkgs/development/libraries/science/math/sympow/default.nix index a83e2c835461..3c31ed8a361b 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/sympow/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/sympow/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchFromGitLab , makeWrapper , which @@ -61,7 +61,7 @@ stdenv.mkDerivation rec { "$out/bin/sympow" -sp 2p16 -curve "[1,2,3,4,5]" | grep '8.3705' ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Compute special values of symmetric power elliptic curve L-functions"; license = { shortName = "sympow"; diff --git a/nixpkgs/pkgs/development/libraries/science/math/tensorflow/bin.nix b/nixpkgs/pkgs/development/libraries/science/math/tensorflow/bin.nix index dc0ca5da4cfa..d42026c13cf9 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/tensorflow/bin.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/tensorflow/bin.nix @@ -1,30 +1,25 @@ -{ stdenv +{ lib, stdenv , fetchurl , addOpenGLRunpath , cudaSupport ? false, symlinkJoin, cudatoolkit, cudnn, nvidia_x11 }: -with stdenv.lib; +with lib; let - unavailable = throw "libtensorflow is not available for this platform!"; + broken = !stdenv.isLinux && !stdenv.isDarwin; tfType = if cudaSupport then "gpu" else "cpu"; - system = - if stdenv.isLinux then "linux" - else if stdenv.isDarwin then "darwin" - else unavailable; + system = + if stdenv.isLinux then "linux" + else "darwin"; - platform = - if stdenv.isx86_64 then "x86_64" - else unavailable; + platform = "x86_64"; - rpath = makeLibraryPath ([stdenv.cc.libc stdenv.cc.cc.lib] ++ - optionals cudaSupport [ cudatoolkit.out cudatoolkit.lib cudnn nvidia_x11 ]); + rpath = makeLibraryPath ([stdenv.cc.libc stdenv.cc.cc.lib] + ++ optionals cudaSupport [ cudatoolkit.out cudatoolkit.lib cudnn nvidia_x11 ]); packages = import ./binary-hashes.nix; - packageName = "${tfType}-${system}-${platform}"; - url = packages.${packageName} or unavailable; patchLibs = if stdenv.isDarwin @@ -44,7 +39,7 @@ in stdenv.mkDerivation rec { pname = "libtensorflow"; inherit (packages) version; - src = fetchurl url; + src = fetchurl packages."${tfType}-${system}-${platform}"; nativeBuildInputs = optional cudaSupport addOpenGLRunpath; @@ -55,7 +50,7 @@ in stdenv.mkDerivation rec { chmod -R +w $out ${patchLibs} - # Write pkgconfig file. + # Write pkg-config file. mkdir $out/lib/pkgconfig cat > $out/lib/pkgconfig/tensorflow.pc << EOF Name: TensorFlow @@ -72,6 +67,5 @@ in stdenv.mkDerivation rec { homepage = "https://www.tensorflow.org/install/lang_c"; license = licenses.asl20; platforms = [ "x86_64-linux" "x86_64-darwin" ]; - maintainers = with maintainers; [ basvandijk ]; }; } diff --git a/nixpkgs/pkgs/development/libraries/science/math/tensorflow/binary-hashes.nix b/nixpkgs/pkgs/development/libraries/science/math/tensorflow/binary-hashes.nix index 76f0c5eea7fa..b606e45477a9 100644 --- a/nixpkgs/pkgs/development/libraries/science/math/tensorflow/binary-hashes.nix +++ b/nixpkgs/pkgs/development/libraries/science/math/tensorflow/binary-hashes.nix @@ -1,15 +1,15 @@ { -version = "1.14.0"; -cpu-linux-x86_64 = { - url = "https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-linux-x86_64-1.14.0.tar.gz"; - sha256 = "04bi3ijq4sbb8c5vk964zlv0j9mrjnzzxd9q9knq3h273nc1a36k"; +version = "2.4.0"; +"cpu-linux-x86_64" = { + url = "https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-linux-x86_64-2.4.0.tar.gz"; + sha256 = "022p5jjwmb8rhyyis3cpk2lw45apl2vz49m2rgxmd75h783x1gjk"; }; -gpu-linux-x86_64 = { - url = "https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-linux-x86_64-1.14.0.tar.gz"; - sha256 = "1ffnpyj9jjgwxpjfiyjvq4dm3n6nwiksim5jld9zw7fdswh215x6"; +"gpu-linux-x86_64" = { + url = "https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-linux-x86_64-2.4.0.tar.gz"; + sha256 = "1fclvbrn3fs8qmhmh3lzni7s7wl1w30a071b4gzh9ifnxdhip6lq"; }; -cpu-darwin-x86_64 = { - url = "https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-darwin-x86_64-1.14.0.tar.gz"; - sha256 = "0zsd5ils1a17j6jzh0c7q1z56fw46gkzybbnms7h2rgg8al0rh92"; +"cpu-darwin-x86_64" = { + url = "https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-darwin-x86_64-2.4.0.tar.gz"; + sha256 = "09x096nslg04c8sr7bd5v68a5gfinc0f1h36lbzn8bahs8b1agi3"; }; } diff --git a/nixpkgs/pkgs/development/libraries/science/math/tensorflow/prefetcher.sh b/nixpkgs/pkgs/development/libraries/science/math/tensorflow/prefetcher.sh index 515f25df4c1f..d571d38f7719 100755 --- a/nixpkgs/pkgs/development/libraries/science/math/tensorflow/prefetcher.sh +++ b/nixpkgs/pkgs/development/libraries/science/math/tensorflow/prefetcher.sh @@ -1,7 +1,9 @@ #!/usr/bin/env bash -version=1.14.0 -hashfile=binary-hashes.nix +# ./prefetcher.sh 2.4.0 binary-hashes.nix + +version="$1" +hashfile="$2" rm -f $hashfile echo "{" >> $hashfile echo "version = \"$version\";" >> $hashfile diff --git a/nixpkgs/pkgs/development/libraries/science/networking/ns-3/default.nix b/nixpkgs/pkgs/development/libraries/science/networking/ns-3/default.nix index b611a2baf8e2..4a90f082dc08 100644 --- a/nixpkgs/pkgs/development/libraries/science/networking/ns-3/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/networking/ns-3/default.nix @@ -1,5 +1,6 @@ { stdenv , fetchFromGitLab +, fetchpatch , python , wafHook @@ -32,22 +33,22 @@ let pythonEnv = python.withPackages(ps: - stdenv.lib.optional withManual ps.sphinx - ++ stdenv.lib.optionals pythonSupport (with ps;[ pybindgen pygccxml ]) + lib.optional withManual ps.sphinx + ++ lib.optionals pythonSupport (with ps;[ pybindgen pygccxml ]) ); in stdenv.mkDerivation rec { pname = "ns-3"; - version = "32"; + version = "33"; src = fetchFromGitLab { owner = "nsnam"; repo = "ns-3-dev"; rev = "ns-3.${version}"; - sha256 = "158yjhsrmslj1q4zcq5p16hv9i82qnxx714l7idicncn0wzrfx7k"; + sha256 = "0ds8h0f2qcb0gc2a8bk38cbhdb122i4sbg589bjn59rblzw0hkq4"; }; - nativeBuildInputs = [ wafHook ]; + nativeBuildInputs = [ wafHook python ]; outputs = [ "out" ] ++ lib.optional pythonSupport "py"; @@ -60,11 +61,9 @@ stdenv.mkDerivation rec { postPatch = '' patchShebangs doc/ns3_html_theme/get_version.sh - # FIX/Remove when https://github.com/NixOS/nixpkgs/pull/69310 gets merged - sed -i 's/program.ns3_module_dependencies.copy()/program.ns3_module_dependencies[:]/g' wscript ''; - wafConfigureFlags = with stdenv.lib; [ + wafConfigureFlags = with lib; [ "--enable-modules=${concatStringsSep "," modules}" "--with-python=${pythonEnv.interpreter}" ] @@ -82,7 +81,7 @@ stdenv.mkDerivation rec { # to prevent fatal error: 'backward_warning.h' file not found CXXFLAGS = "-D_GLIBCXX_PERMIT_BACKWARD_HASH"; - postBuild = with stdenv.lib; let flags = concatStringsSep ";" ( + postBuild = with lib; let flags = concatStringsSep ";" ( optional enableDoxygen "./waf doxygen" ++ optional withManual "./waf sphinx" ); @@ -99,14 +98,22 @@ stdenv.mkDerivation rec { ${pythonEnv.interpreter} ./test.py --nowaf ''; + patches = [ + (fetchpatch { + name = "upstream-issue-336.patch"; + url = "https://gitlab.com/nsnam/ns-3-dev/-/commit/673004edae1112e6cb249b698aad856d728530fb.patch"; + sha256 = "0q96ividinbh9xlws014b2ir6gaavygnln5ca9m1db06m4vfwhng"; + }) + ]; + # strictoverflow prevents clang from discovering pyembed when bindings hardeningDisable = [ "fortify" "strictoverflow"]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "http://www.nsnam.org"; license = licenses.gpl3; description = "A discrete time event network simulator"; platforms = with platforms; unix; - maintainers = with maintainers; [ teto ]; + maintainers = with maintainers; [ teto rgrunbla ]; }; } diff --git a/nixpkgs/pkgs/development/libraries/science/robotics/ispike/default.nix b/nixpkgs/pkgs/development/libraries/science/robotics/ispike/default.nix index 39f412e8dd56..b3eed2e326e6 100644 --- a/nixpkgs/pkgs/development/libraries/science/robotics/ispike/default.nix +++ b/nixpkgs/pkgs/development/libraries/science/robotics/ispike/default.nix @@ -1,5 +1,4 @@ -{ stdenv, fetchurl, cmake, boost -}: +{ lib, stdenv, fetchurl, cmake, boost }: stdenv.mkDerivation rec { pname = "ispike"; @@ -10,15 +9,14 @@ stdenv.mkDerivation rec { sha256 = "0khrxp43bi5kisr8j4lp9fl4r5marzf7b4inys62ac108sfb28lp"; }; - buildInputs = [ cmake boost ]; + nativeBuildInputs = [ cmake ]; + buildInputs = [ boost ]; meta = { description = "Spiking neural interface between iCub and a spiking neural simulator"; homepage = "https://sourceforge.net/projects/ispike/"; - license = stdenv.lib.licenses.lgpl3; - platforms = stdenv.lib.platforms.linux; - maintainers = [ stdenv.lib.maintainers.nico202 ]; + license = lib.licenses.lgpl3; + platforms = lib.platforms.linux; + maintainers = [ lib.maintainers.nico202 ]; }; - - } |