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|
{ lib
, stdenv
, fetchFromGitHub
, fetchpatch
, fetchurl
# build
, cmake
, ctags
, python3Packages
, swig
# math
, eigen
, blas
, lapack
, glpk
# data
, protobuf
, json_c
, libxml2
, hdf5
, curl
# compression
, libarchive
, bzip2
, xz
, snappy
, lzo
# more math
, nlopt
, lp_solve
, colpack
# extra support
, pythonSupport ? false
, opencvSupport ? false
, opencv ? null
, withSvmLight ? false
}:
assert pythonSupport -> python3Packages != null;
assert opencvSupport -> opencv != null;
assert (!blas.isILP64) && (!lapack.isILP64);
let
pname = "shogun";
version = "6.1.4";
rxcppVersion = "4.0.0";
gtestVersion = "1.8.0";
srcs = {
toolbox = fetchFromGitHub {
owner = "shogun-toolbox";
repo = "shogun";
rev = "shogun_${version}";
sha256 = "sha256-38aULxK50wQ2+/ERosSpRyBmssmYSGv5aaWfWSlrSRc=";
fetchSubmodules = true;
};
# The CMake external projects expect the packed archives
rxcpp = fetchurl {
url = "https://github.com/Reactive-Extensions/RxCpp/archive/v${rxcppVersion}.tar.gz";
sha256 = "sha256-UOc5WrG8KgAA3xJsaSCjbdPE7gSnFJay9MEK31DWUXg=";
};
gtest = fetchurl {
url = "https://github.com/google/googletest/archive/release-${gtestVersion}.tar.gz";
sha256 = "sha256-WKb0J3yivIVlIis7vVihd2CenEiOinJkk1m6UUUNt9g=";
};
};
in
stdenv.mkDerivation rec {
inherit pname version;
outputs = [ "out" "dev" "doc" ];
src = srcs.toolbox;
patches = [
# Fix compile errors with GCC 9+
# https://github.com/shogun-toolbox/shogun/pull/4811
(fetchpatch {
url = "https://github.com/shogun-toolbox/shogun/commit/c8b670be4790e0f06804b048a6f3d77c17c3ee95.patch";
sha256 = "sha256-MxsR3Y2noFQevfqWK3nmX5iK4OVWeKBl5tfeDNgjcXk=";
})
(fetchpatch {
url = "https://github.com/shogun-toolbox/shogun/commit/5aceefd9fb0e2132c354b9a0c0ceb9160cc9b2f7.patch";
sha256 = "sha256-AgJJKQA8vc5oKaTQDqMdwBR4hT4sn9+uW0jLe7GteJw=";
})
# Fix virtual destruction
(fetchpatch {
url = "https://github.com/shogun-toolbox/shogun/commit/ef0e4dc1cc4a33c9e6b17a108fa38a436de2d7ee.patch";
sha256 = "sha256-a9Rm0ytqkSAgC3dguv8m3SwOSipb+VByBHHdmV0d63w=";
})
./fix-virtual-destruction.patch
# Fix compile errors with json-c
# https://github.com/shogun-toolbox/shogun/pull/4104
(fetchpatch {
url = "https://github.com/shogun-toolbox/shogun/commit/365ce4c4c700736d2eec8ba6c975327a5ac2cd9b.patch";
sha256 = "sha256-OhEWwrHtD/sOcjHmPY/C9zJ8ruww8yXrRcTw38nGEJU=";
})
# Fix compile errors with Eigen 3.4
./eigen-3.4.patch
] ++ lib.optional (!withSvmLight) ./svmlight-scrubber.patch;
nativeBuildInputs = [ cmake swig ctags ]
++ (with python3Packages; [ python jinja2 ply ]);
buildInputs = [
eigen
blas
lapack
glpk
protobuf
json_c
libxml2
hdf5
curl
libarchive
bzip2
xz
snappy
lzo
nlopt
lp_solve
colpack
] ++ lib.optionals pythonSupport (with python3Packages; [ python numpy ])
++ lib.optional opencvSupport opencv;
cmakeFlags = let
enableIf = cond: if cond then "ON" else "OFF";
excludeTestsRegex = lib.concatStringsSep "|" [
# sporadic segfault
"TrainedModelSerialization"
# broken by openblas 0.3.21
"mathematics_lapack"
# these take too long on CI
"evaluation_cross_validation"
"modelselection_combined_kernel"
"modelselection_grid_search"
];
in [
"-DBUILD_META_EXAMPLES=ON"
"-DCMAKE_DISABLE_FIND_PACKAGE_ARPACK=ON"
"-DCMAKE_DISABLE_FIND_PACKAGE_ARPREC=ON"
"-DCMAKE_DISABLE_FIND_PACKAGE_CPLEX=ON"
"-DCMAKE_DISABLE_FIND_PACKAGE_Mosek=ON"
"-DCMAKE_DISABLE_FIND_PACKAGE_TFLogger=ON"
"-DCMAKE_DISABLE_FIND_PACKAGE_ViennaCL=ON"
"-DCMAKE_CTEST_ARGUMENTS=--exclude-regex;'${excludeTestsRegex}'"
"-DENABLE_TESTING=${enableIf doCheck}"
"-DDISABLE_META_INTEGRATION_TESTS=ON"
"-DTRAVIS_DISABLE_META_CPP=ON"
"-DINTERFACE_PYTHON=${enableIf pythonSupport}"
"-DOpenCV=${enableIf opencvSupport}"
"-DUSE_SVMLIGHT=${enableIf withSvmLight}"
];
CXXFLAGS = "-faligned-new";
doCheck = true;
postUnpack = ''
mkdir -p $sourceRoot/third_party/{rxcpp,GoogleMock}
ln -s ${srcs.rxcpp} $sourceRoot/third_party/rxcpp/v${rxcppVersion}.tar.gz
ln -s ${srcs.gtest} $sourceRoot/third_party/GoogleMock/release-${gtestVersion}.tar.gz
'';
postPatch = ''
# Fix preprocessing SVMlight code
sed -i \
-e 's@#ifdef SVMLIGHT@#ifdef USE_SVMLIGHT@' \
-e '/^#ifdef USE_SVMLIGHT/,/^#endif/ s@#endif@#endif //USE_SVMLIGHT@' \
src/shogun/kernel/string/CommUlongStringKernel.cpp
sed -i -e 's/#if USE_SVMLIGHT/#ifdef USE_SVMLIGHT/' src/interfaces/swig/Machine.i
sed -i -e 's@// USE_SVMLIGHT@//USE_SVMLIGHT@' src/interfaces/swig/Transfer.i
sed -i -e 's@/\* USE_SVMLIGHT \*/@//USE_SVMLIGHT@' src/interfaces/swig/Transfer_includes.i
'' + lib.optionalString (!withSvmLight) ''
# Run SVMlight scrubber
patchShebangs scripts/light-scrubber.sh
echo "removing SVMlight code"
./scripts/light-scrubber.sh
'';
postInstall = ''
mkdir -p $doc/share/doc/shogun/examples
mv $out/share/shogun/examples/cpp $doc/share/doc/shogun/examples
cp ../examples/undocumented/libshogun/*.cpp $doc/share/doc/shogun/examples/cpp
rm -r $out/share
'';
postFixup = ''
# CMake incorrectly calculates library path from dev prefix
substituteInPlace $dev/lib/cmake/shogun/ShogunTargets-release.cmake \
--replace "\''${_IMPORT_PREFIX}/lib/" "$out/lib/"
'';
meta = with lib; {
description = "A toolbox which offers a wide range of efficient and unified machine learning methods";
homepage = "http://shogun-toolbox.org/";
license = if withSvmLight then licenses.unfree else licenses.gpl3Plus;
maintainers = with maintainers; [ edwtjo smancill ];
};
}
|
