febio: 3.6 -> 4.7

pkgs/by-name/fe/febio/fix-cmake.patch

@@ -1,6 +1,16 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index c1bc953edf..f6aaf92fb5 100644
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -47,7 +47,7 @@ function(findLib libName libDir libOut)
+@@ -2,6 +2,7 @@
+ set(CMAKE_CXX_STANDARD 14)
+ set(CMAKE_CXX_STANDARD_REQUIRED ON)
+ mark_as_advanced(FORCE CMAKE_INSTALL_PREFIX)
++include(GNUInstallDirs)
+ 
+ project(FEBio)
+ set(FEBIO_LIBS FEBioFluid FEBioLib FEBioMech FEBioMix FEBioOpt FECore NumCore FEAMR FEBioRVE FEImgLib)
+@@ -51,7 +52,7 @@
          find_library(TEMP NAMES ${libName}.lib ${ARGV3}.lib ${ARGV4}.lib ${ARGV5}.lib ${ARGV6}.lib
              PATHS ${${libDir}} NO_DEFAULT_PATH)
      else()
@@ -9,18 +19,53 @@
              PATHS ${${libDir}} NO_DEFAULT_PATH)
      endif()
      
-diff --git a/FindDependencies.cmake b/FindDependencies.cmake
-index 2d644005f..7261ba923 100644
---- a/FindDependencies.cmake
-+++ b/FindDependencies.cmake
-@@ -46,8 +46,8 @@ if(MKLROOT)
-             NO_DEFAULT_PATH)
-             
-         find_library(MKL_OMP_LIB 
--            NAMES iomp5 iomp5md libiomp5md.lib
--            PATHS ${MKLROOT}/../lib ${MKLROOT}/../compiler/lib
-+            NAMES libiomp5@so@ libiomp5 iomp5 iomp5md libiomp5md.lib
-+            PATHS ${MKLROOT}/lib ${MKLROOT}/../lib ${MKLROOT}/../compiler/lib
-             PATH_SUFFIXES "intel64" "intel32"
-             NO_DEFAULT_PATH
-             DOC "MKL OMP Library")
+@@ -154,7 +155,7 @@
+ ##### Find Source Files #####
+ 
+ macro(findHdrSrc name)
+-	file(GLOB HDR_${name} "${name}/*.h")
++	file(GLOB HDR_${name} "${name}/*.h" "${name}/*.hpp")
+ 	file(GLOB SRC_${name} "${name}/*.cpp")
+ endmacro()
+ 
+@@ -171,8 +172,9 @@
+ 
+ macro(addLib name TYPE)
+     string(TOLOWER ${name} lname)
+-	add_library(${lname} ${TYPE} ${HDR_${name}} ${SRC_${name}})
++	add_library(${lname} ${TYPE} ${SRC_${name}})
+ 	set_property(TARGET ${lname} PROPERTY AUTOGEN_BUILD_DIR ${CMAKE_BINARY_DIR}/CMakeFiles/AutoGen/${name}_autogen)
++    target_sources(${lname} PUBLIC FILE_SET HEADERS TYPE HEADERS FILES ${HDR_${name}})
+     
+     if(NOT WIN32)
+         set_property(TARGET ${lname} PROPERTY POSITION_INDEPENDENT_CODE ON)
+@@ -181,6 +183,8 @@
+     if(APPLE)
+         target_link_libraries(${lname} PRIVATE "-undefined dynamic_lookup")
+     endif()
++
++    install(TARGETS ${lname} FILE_SET HEADERS)
+ endmacro()
+ 
+ foreach(name IN LISTS FEBIO_LIBS)
+@@ -194,6 +198,7 @@
+ ##### Set up executable compilation #####
+ file(GLOB SOURCES "FEBio/*.cpp")
+ add_executable (febio4 ${SOURCES})
++install(TARGETS febio4)
+ 
+ if(WIN32)
+     target_compile_options(febio4 PRIVATE /openmp)
+@@ -269,7 +274,6 @@
+ mark_as_advanced(EXTRA_INC)
+ 
+ ##### Setup includes, defnitions, and linking options #####
+-include_directories(${PROJECT_SOURCE_DIR})
+ 
+ # Link LEVMAR
+ if(USE_LEVMAR)
+@@ -438,3 +442,4 @@
+     file(WRITE ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/febio.xml "${filedata}")
+ endif()
+ 
++install(FILES ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/febio.xml TYPE BIN)

pkgs/by-name/fe/febio/package.nix

@@ -1,68 +1,66 @@
 {
   lib,
   stdenv,
+  overrideSDK,
   fetchFromGitHub,
+  fetchpatch2,
+  substituteAll,
   cmake,
-  boost,
-  eigen,
-  libxml2,
-  mpi,
-  python3,
+  ninja,
+  zlib,
+  darwin,
   mklSupport ? true,
   mkl,
-  substituteAll,
 }:
 
-stdenv.mkDerivation rec {
+let
+  stdenv' = if stdenv.isDarwin then overrideSDK stdenv "11.0" else stdenv;
+in
+
+stdenv'.mkDerivation (finalAttrs: {
   pname = "FEBio";
-  version = "3.6";
+  version = "4.7";
 
   src = fetchFromGitHub {
     owner = "febiosoftware";
-    repo = pname;
-    rev = "v${version}";
-    sha256 = "187s4lyzr806xla3smq3lsvj3f6wxlhfkban89w0fnyfmfb8w9am";
+    repo = "FEBio";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-RRdIOyXg4jYW76ABfJdMfVtCYMLYFdvyOI98nHXCof8=";
   };
 
   patches = [
+    # Fix library searching and installation
     (substituteAll {
-      src = ./fix-cmake.patch; # cannot find mkl libraries without this
+      src = ./fix-cmake.patch;
       so = stdenv.hostPlatform.extensions.sharedLibrary;
     })
+
+    # Fixed missing header include for strcpy
+    # https://github.com/febiosoftware/FEBio/pull/92
+    (fetchpatch2 {
+      url = "https://github.com/febiosoftware/FEBio/commit/ad9e80e2aa8737828855458a703822f578db2fd3.patch?full_index=1";
+      hash = "sha256-/uLnJB/oAwLQnsZtJnUlaAEpyZVLG6o2riRwwMCH8rI=";
+    })
   ];
 
-  cmakeFlags = lib.optional mklSupport "-DUSE_MKL=On" ++ lib.optional mklSupport "-DMKLROOT=${mkl}";
+  cmakeFlags = lib.optionals mklSupport [
+    (lib.cmakeBool "USE_MKL" true)
+    (lib.cmakeFeature "MKLROOT" "${mkl}")
+  ];
 
-  env.CXXFLAGS = lib.optionalString stdenv.isLinux "-include cstring";
+  nativeBuildInputs = [
+    cmake
+    ninja
+  ];
 
-  installPhase = ''
-    runHook preInstall
-
-    mkdir -p $out/include
-    cp -R lib bin $out/
-    cp -R ../FECore \
-      ../FEBioFluid \
-      ../FEBioLib \
-      ../FEBioMech \
-      ../FEBioMix \
-      ../FEBioOpt \
-      ../FEBioPlot \
-      ../FEBioXML \
-      ../NumCore \
-      $out/include
-
-    runHook postInstall
-  '';
-
-  nativeBuildInputs = [ cmake ];
-  buildInputs = [
-    boost
-    eigen
-    libxml2
-    mpi
-    python3
-    python3.pkgs.numpy
-  ] ++ lib.optional mklSupport mkl;
+  buildInputs =
+    [ zlib ]
+    ++ lib.optionals mklSupport [ mkl ]
+    ++ lib.optionals stdenv.isDarwin [
+      darwin.apple_sdk.frameworks.CoreGraphics
+      darwin.apple_sdk.frameworks.CoreVideo
+      darwin.apple_sdk.frameworks.Accelerate
+    ];
 
   meta = {
     description = "FEBio Suite Solver";
@@ -71,4 +69,4 @@ stdenv.mkDerivation rec {
     platforms = lib.platforms.unix;
     maintainers = with lib.maintainers; [ Scriptkiddi ];
   };
-}
+})