shogun: refactor build

Main changes are:

- Build with default stdenv instead of forcing GCC 8, by applying upstream
  patches that fix building with newer compilers.

  Together with #134390 and #134393 (and the blas library fixes on #135493
  and #136535), this enables building the derivation on darwin.

- Use multiple outputs.

- Move build-only inputs to nativeBuildInputs.

- Generate the meta examples but do not compile them (they are compiled as
  part of the tests), to not make the build take more time than already is.

  Install the example source files into $doc (but do not install the
  example binaries, only the sources).

- Enable testing by setting the CMake variable CMAKE_SKIP_BUILD_RPATH to
  false (it should not be needed if #108496 is merged). This allows the
  tests to locate the shogun library and run without problems.

  Disable integration and meta tests to speed up the build.

With a few other minor changes:

- Use upstream URL for the json-c patch.

- Be explicit about which optional, commercial dependencies are not used,
  to stop CMake searching for them.

- Do not set NIX_CFLAGS_COMPILE with '-faligned-new' because it causes a
  warning when compiling C files. Set CXXFLAGS instead.

- Remove unnecessary ccache variables from the environment.

- Fix wrong Google Mock download location, which was forcing CMake to need
  network access to download the tarball to the right location (which fails
  within the sandbox).

pkgs/applications/science/machine-learning/shogun/default.nix

@@ -6,6 +6,7 @@
   # build
 , cmake
 , ctags
+, pythonPackages
 , swig
   # math
 , eigen
@@ -30,7 +31,6 @@
 , colpack
   # extra support
 , pythonSupport ? true
-, pythonPackages ? null
 , opencvSupport ? false
 , opencv ? null
 , withSvmLight ? false
@@ -56,7 +56,8 @@ let
       sha256 = "05s9dclmk7x5d7wnnj4qr6r6c827m72a44gizcv09lxr28pr9inz";
       fetchSubmodules = true;
     };
-    # we need the packed archive
+
+    # The CMake external projects expect the packed archives
     rxcpp = fetchurl {
       url = "https://github.com/Reactive-Extensions/RxCpp/archive/v${rxcppVersion}.tar.gz";
       sha256 = "0y2isr8dy2n1yjr9c5570kpc9lvdlch6jv0jvw000amwn5d3krsh";
@@ -71,16 +72,33 @@ in
 stdenv.mkDerivation rec {
   inherit pname version;
 
+  outputs = [ "out" "dev" "doc" ];
+
   src = srcs.toolbox;
 
   patches = [
+    # Fix compile errors with json-c
+    # https://github.com/shogun-toolbox/shogun/pull/4104
     (fetchpatch {
-      url = "https://github.com/awild82/shogun/commit/365ce4c4c700736d2eec8ba6c975327a5ac2cd9b.patch";
+      url = "https://github.com/shogun-toolbox/shogun/commit/365ce4c4c700736d2eec8ba6c975327a5ac2cd9b.patch";
       sha256 = "158hqv4xzw648pmjbwrhxjp7qcppqa7kvriif87gn3zdn711c49s";
     })
+
+    # 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=";
+    })
+
   ] ++ lib.optional (!withSvmLight) ./svmlight-scrubber.patch;
 
-  nativeBuildInputs = [ cmake ];
+  nativeBuildInputs = [ cmake swig ctags ]
+    ++ (with pythonPackages; [ python jinja2 ply ]);
 
   buildInputs = [
     eigen
@@ -100,34 +118,37 @@ stdenv.mkDerivation rec {
     nlopt
     lp_solve
     colpack
-    ctags
-    swig
-  ] ++ lib.optionals pythonSupport (with pythonPackages; [ python ply numpy ])
+  ] ++ lib.optionals pythonSupport (with pythonPackages; [ python numpy ])
     ++ lib.optional opencvSupport opencv;
 
   cmakeFlags = let
     enableIf = cond: if cond then "ON" else "OFF";
   in [
-    "-DBUILD_META_EXAMPLES=${enableIf doCheck}"
-    "-DCMAKE_VERBOSE_MAKEFILE=${enableIf doCheck}"
+    "-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_SKIP_BUILD_RPATH=OFF"
+    "-DCMAKE_CTEST_ARGUMENTS='--exclude-regex;TrainedModelSerialization'"  # Sporadic segfault
     "-DENABLE_TESTING=${enableIf doCheck}"
+    "-DDISABLE_META_INTEGRATION_TESTS=ON"
+    "-DTRAVIS_DISABLE_META_CPP=ON"
     "-DPythonModular=${enableIf pythonSupport}"
     "-DOpenCV=${enableIf opencvSupport}"
     "-DUSE_SVMLIGHT=${enableIf withSvmLight}"
   ];
 
-  CCACHE_DISABLE="1";
-  CCACHE_DIR=".ccache";
+  CXXFLAGS = "-faligned-new";
 
-  NIX_CFLAGS_COMPILE="-faligned-new";
-
-  # broken
-  doCheck = false;
+  doCheck = true;
 
   postUnpack = ''
-    mkdir -p $sourceRoot/third_party/{rxcpp,gtest}
+    mkdir -p $sourceRoot/third_party/{rxcpp,GoogleMock}
     ln -s ${srcs.rxcpp} $sourceRoot/third_party/rxcpp/v${rxcppVersion}.tar.gz
-    ln -s ${srcs.gtest} $sourceRoot/third_party/gtest/release-${gtestVersion}.tar.gz
+    ln -s ${srcs.gtest} $sourceRoot/third_party/GoogleMock/release-${gtestVersion}.tar.gz
   '';
 
   postPatch = ''
@@ -146,6 +167,13 @@ stdenv.mkDerivation rec {
     ./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
+  '';
+
   meta = with lib; {
     description = "A toolbox which offers a wide range of efficient and unified machine learning methods";
     homepage = "http://shogun-toolbox.org/";

pkgs/top-level/all-packages.nix

@@ -26918,16 +26918,7 @@ with pkgs;
   shotcut = libsForQt5.callPackage ../applications/video/shotcut { };
 
   shogun = callPackage ../applications/science/machine-learning/shogun {
-    stdenv = gcc8Stdenv;
-
-    # Workaround for the glibc abi version mismatch.
-    # Please note that opencv builds are by default disabled.
-    opencv = opencv3.override {
-      stdenv = gcc8Stdenv;
-      openexr = openexr.override {
-        stdenv = gcc8Stdenv;
-      };
-    };
+    opencv = opencv3;
   };
 
   smplayer = libsForQt5.callPackage ../applications/video/smplayer { };