Merge pull request #331864 from emilazy/push-posunwslrptx

febio: 3.6 -> 4.7; febio-studio: 1.6.1 -> 2.7

pkgs/applications/science/biology/febio-studio/default.nix

@@ -1,62 +0,0 @@
-{ lib, stdenv, fetchFromGitHub, cmake, zlib, libglvnd, libGLU, wrapQtAppsHook
-, sshSupport ? true, openssl, libssh
-, tetgenSupport ? true, tetgen
-, ffmpegSupport ? true, ffmpeg_4
-, dicomSupport  ? false, dcmtk
-, withModelRepo ? true
-, withCadFeatures ? false
-}:
-
-stdenv.mkDerivation rec {
-  pname = "febio-studio";
-  version = "1.6.1";
-
-  src = fetchFromGitHub {
-    owner = "febiosoftware";
-    repo = "FEBioStudio";
-    rev = "v${version}";
-    sha256 = "0r6pg49i0q9idp7pjymj7mlxd63qjvmfvg0l7fmx87y1yd2hfw4h";
-  };
-
-  patches = [
-    ./febio-studio-cmake.patch # Fix Errors that appear with certain Cmake flags
-  ];
-
-  cmakeFlags = [
-    "-DQt_Ver=5"
-    "-DNOT_FIRST=On"
-    "-DOpenGL_GL_PREFERENCE=GLVND"
-  ]
-    ++ lib.optional sshSupport "-DUSE_SSH=On"
-    ++ lib.optional tetgenSupport "-DUSE_TETGEN=On"
-    ++ lib.optional ffmpegSupport "-DUSE_FFMPEG=On"
-    ++ lib.optional dicomSupport "-DUSE_DICOM=On"
-    ++ lib.optional withModelRepo "-DMODEL_REPO=On"
-    ++ lib.optional withCadFeatures "-DCAD_FEATURES=On"
-  ;
-
-
-  installPhase = ''
-    runHook preInstall
-    mkdir -p $out/
-    cp -R bin $out/
-    runHook postInstall
-  '';
-
-  nativeBuildInputs = [ cmake wrapQtAppsHook ];
-  buildInputs = [ zlib libglvnd libGLU openssl libssh ]
-    ++ lib.optional sshSupport openssl
-    ++ lib.optional tetgenSupport tetgen
-    ++ lib.optional ffmpegSupport ffmpeg_4
-    ++ lib.optional dicomSupport dcmtk
-  ;
-
-  meta = with lib; {
-    description = "FEBio Suite Solver";
-    mainProgram = "FEBioStudio";
-    license = with licenses; [ mit ];
-    homepage = "https://febio.org/";
-    platforms = platforms.unix;
-    maintainers = with maintainers; [ Scriptkiddi ];
-  };
-}

pkgs/applications/science/biology/febio-studio/febio-studio-cmake.patch

@@ -1,38 +0,0 @@
-diff --git a/FEBioStudio/RepositoryPanel.cpp b/FEBioStudio/RepositoryPanel.cpp
-index 382db303..314cdc68 100644
---- a/FEBioStudio/RepositoryPanel.cpp
-+++ b/FEBioStudio/RepositoryPanel.cpp
-@@ -1364,10 +1364,10 @@ void CRepositoryPanel::loadingPageProgress(qint64 bytesSent, qint64 bytesTotal)
- 
- #else
- 
--CRepositoryPanel::CRepositoryPanel(CMainWindow* pwnd, QWidget* parent){}
-+CRepositoryPanel::CRepositoryPanel(CMainWindow* pwnd, QDockWidget* parent){}
- CRepositoryPanel::~CRepositoryPanel(){}
- void CRepositoryPanel::OpenLink(const QString& link) {}
--// void CRepositoryPanel::Raise() {}
-+void CRepositoryPanel::Raise() {}
- void CRepositoryPanel::SetModelList(){}
- void CRepositoryPanel::ShowMessage(QString message) {}
- void CRepositoryPanel::ShowWelcomeMessage(QByteArray messages) {}
-@@ -1396,6 +1396,7 @@ void CRepositoryPanel::on_actionSearch_triggered() {}
- void CRepositoryPanel::on_actionClearSearch_triggered() {}
- void CRepositoryPanel::on_actionDeleteRemote_triggered() {}
- void CRepositoryPanel::on_actionModify_triggered() {}
-+void CRepositoryPanel::on_actionCopyPermalink_triggered() {}
- void CRepositoryPanel::on_treeWidget_itemSelectionChanged() {}
- void CRepositoryPanel::on_treeWidget_customContextMenuRequested(const QPoint &pos) {}
- void CRepositoryPanel::DownloadItem(CustomTreeWidgetItem *item) {}
-diff --git a/FEBioStudio/WzdUpload.cpp b/FEBioStudio/WzdUpload.cpp
-index 5ce74346..20062e06 100644
---- a/FEBioStudio/WzdUpload.cpp
-+++ b/FEBioStudio/WzdUpload.cpp
-@@ -1183,7 +1183,7 @@ void CWzdUpload::on_saveJson_triggered()
- 		getProjectJson(&projectInfo);
- 
- 		QFile file(filedlg.selectedFiles()[0]);
--		file.open(QIODeviceBase::WriteOnly);
-+		file.open(QIODevice::WriteOnly);
- 		file.write(projectInfo);
- 		file.close();
- 	}

pkgs/applications/science/geometry/tetgen/default.nix

@@ -27,6 +27,6 @@ stdenv.mkDerivation rec {
     mainProgram = "tetgen";
     homepage = "http://tetgen.org/";
     license = lib.licenses.agpl3Plus;
-    platforms = lib.platforms.linux;
+    platforms = lib.platforms.unix;
   };
 }

pkgs/by-name/fe/febio-studio/cmake-install.patch

@@ -0,0 +1,14 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 7ad2c68eb2..0e3e978bd9 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -449,6 +449,9 @@
+ 	set_property(TARGET ${FBS_BIN_NAME} PROPERTY AUTOGEN_BUILD_DIR ${CMAKE_BINARY_DIR}/CMakeFiles/AutoGen/FEBioStudio_autogen)
+ endif()
+ 
++include(GNUInstallDirs)
++install(TARGETS ${FBS_BIN_NAME} BUNDLE DESTINATION Applications)
++
+ macro(addLib name)
+ 	add_library(${name} ${HDR_${name}} ${SRC_${name}})
+ 	set_property(TARGET ${name} PROPERTY AUTOGEN_BUILD_DIR ${CMAKE_BINARY_DIR}/CMakeFiles/AutoGen/${name}_autogen)

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

@@ -0,0 +1,89 @@
+{
+  lib,
+  stdenv,
+  overrideSDK,
+  fetchFromGitHub,
+  cmake,
+  ninja,
+  zlib,
+  libGLU,
+  qt6Packages,
+  febio,
+  glew,
+  sshSupport ? true,
+  openssl,
+  libssh,
+  tetgenSupport ? true,
+  tetgen,
+  ffmpegSupport ? true,
+  ffmpeg_7,
+  dicomSupport ? false,
+  dcmtk,
+  withModelRepo ? true,
+  withCadFeatures ? false,
+}:
+
+let
+  stdenv' =
+    if stdenv.isDarwin then
+      overrideSDK stdenv {
+        darwinSdkVersion = "11.0";
+        darwinMinVersion = "10.15";
+      }
+    else
+      stdenv;
+in
+
+stdenv'.mkDerivation (finalAttrs: {
+  pname = "febio-studio";
+  version = "2.7";
+
+  src = fetchFromGitHub {
+    owner = "febiosoftware";
+    repo = "FEBioStudio";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-ggIzz6bvNjqlI8s31EVnbM0TOspBSc9/myKpWukS3MU=";
+  };
+
+  patches = [ ./cmake-install.patch ];
+
+  cmakeFlags =
+    [ (lib.cmakeFeature "Qt_Root" "${qt6Packages.qtbase}") ]
+    ++ lib.optional sshSupport "-DUSE_SSH=On"
+    ++ lib.optional tetgenSupport "-DUSE_TETGEN=On"
+    ++ lib.optional ffmpegSupport "-DUSE_FFMPEG=On"
+    ++ lib.optional dicomSupport "-DUSE_DICOM=On"
+    ++ lib.optional withModelRepo "-DMODEL_REPO=On"
+    ++ lib.optional withCadFeatures "-DCAD_FEATURES=On";
+
+  nativeBuildInputs = [
+    cmake
+    ninja
+    qt6Packages.wrapQtAppsHook
+  ];
+
+  buildInputs =
+    [
+      zlib
+      libGLU
+      glew
+      qt6Packages.qtbase
+      febio
+    ]
+    ++ lib.optionals sshSupport [
+      openssl
+      libssh
+    ]
+    ++ lib.optional tetgenSupport tetgen
+    ++ lib.optional ffmpegSupport ffmpeg_7
+    ++ lib.optional dicomSupport dcmtk;
+
+  meta = {
+    description = "FEBio Suite Solver";
+    mainProgram = "FEBioStudio";
+    license = with lib.licenses; [ mit ];
+    homepage = "https://febio.org/";
+    platforms = lib.platforms.unix;
+    maintainers = with lib.maintainers; [ Scriptkiddi ];
+  };
+})

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

@@ -0,0 +1,71 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index c1bc953edf..f6aaf92fb5 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -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()
+-        find_library(TEMP NAMES lib${libName}.a lib${ARGV3}.a lib${ARGV4}.a lib${ARGV5}.a lib${ARGV6}.a
++        find_library(TEMP NAMES lib${libName}.a lib${ARGV3}.a lib${ARGV4}.a lib${ARGV5}.a lib${ARGV6}.a lib${libName}@so@ lib${ARGV3}@so@ lib${ARGV4}@so@ lib${ARGV5}@so@ lib${ARGV6}@so@
+             PATHS ${${libDir}} NO_DEFAULT_PATH)
+     endif()
+     
+@@ -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

@@ -0,0 +1,72 @@
+{
+  lib,
+  stdenv,
+  overrideSDK,
+  fetchFromGitHub,
+  fetchpatch2,
+  substituteAll,
+  cmake,
+  ninja,
+  zlib,
+  darwin,
+  mklSupport ? true,
+  mkl,
+}:
+
+let
+  stdenv' = if stdenv.isDarwin then overrideSDK stdenv "11.0" else stdenv;
+in
+
+stdenv'.mkDerivation (finalAttrs: {
+  pname = "FEBio";
+  version = "4.7";
+
+  src = fetchFromGitHub {
+    owner = "febiosoftware";
+    repo = "FEBio";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-RRdIOyXg4jYW76ABfJdMfVtCYMLYFdvyOI98nHXCof8=";
+  };
+
+  patches = [
+    # Fix library searching and installation
+    (substituteAll {
+      src = ./fix-cmake.patch;
+      so = stdenv.hostPlatform.extensions.sharedLibrary;
+    })
+
+    # Fixed missing header include for strcpy
+    # https://github.com/febiosoftware/FEBio/pull/92
+    (fetchpatch2 {
+      url = "https://github.com/febiosoftware/FEBio/commit/ad9e80e2aa8737828855458a703822f578db2fd3.patch?full_index=1";
+      hash = "sha256-/uLnJB/oAwLQnsZtJnUlaAEpyZVLG6o2riRwwMCH8rI=";
+    })
+  ];
+
+  cmakeFlags = lib.optionals mklSupport [
+    (lib.cmakeBool "USE_MKL" true)
+    (lib.cmakeFeature "MKLROOT" "${mkl}")
+  ];
+
+  nativeBuildInputs = [
+    cmake
+    ninja
+  ];
+
+  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";
+    license = with lib.licenses; [ mit ];
+    homepage = "https://febio.org/";
+    platforms = lib.platforms.unix;
+    maintainers = with lib.maintainers; [ Scriptkiddi ];
+  };
+})

pkgs/development/libraries/febio/default.nix

@@ -1,61 +0,0 @@
-{ lib, stdenv, fetchFromGitHub, cmake, boost, eigen, libxml2, mpi, python3
-, mklSupport ? true, mkl
-, substituteAll
-}:
-
-stdenv.mkDerivation rec {
-  pname = "FEBio";
-  version = "3.6";
-
-  src = fetchFromGitHub {
-    owner = "febiosoftware";
-    repo = pname;
-    rev = "v${version}";
-    sha256 = "187s4lyzr806xla3smq3lsvj3f6wxlhfkban89w0fnyfmfb8w9am";
-  };
-
-  patches = [
-    (substituteAll {
-      src = ./fix-cmake.patch;  # cannot find mkl libraries without this
-      so = stdenv.hostPlatform.extensions.sharedLibrary;
-    })
-  ];
-
-  cmakeFlags = lib.optional mklSupport "-DUSE_MKL=On"
-    ++ lib.optional mklSupport "-DMKLROOT=${mkl}"
-  ;
-
-  env.CXXFLAGS = lib.optionalString stdenv.isLinux "-include cstring";
-
-  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
-  ;
-
-  meta = {
-    description = "FEBio Suite Solver";
-    license = with lib.licenses; [ mit ];
-    homepage = "https://febio.org/";
-    platforms = lib.platforms.unix;
-    maintainers = with lib.maintainers; [ Scriptkiddi ];
-  };
-}

pkgs/development/libraries/febio/fix-cmake.patch

@@ -1,26 +0,0 @@
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -47,7 +47,7 @@ function(findLib libName libDir libOut)
-         find_library(TEMP NAMES ${libName}.lib ${ARGV3}.lib ${ARGV4}.lib ${ARGV5}.lib ${ARGV6}.lib
-             PATHS ${${libDir}} NO_DEFAULT_PATH)
-     else()
--        find_library(TEMP NAMES lib${libName}.a lib${ARGV3}.a lib${ARGV4}.a lib${ARGV5}.a lib${ARGV6}.a
-+        find_library(TEMP NAMES lib${libName}.a lib${ARGV3}.a lib${ARGV4}.a lib${ARGV5}.a lib${ARGV6}.a lib${libName}@so@ lib${ARGV3}@so@ lib${ARGV4}@so@ lib${ARGV5}@so@ lib${ARGV6}@so@
-             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")

pkgs/top-level/all-packages.nix

@@ -20113,8 +20113,6 @@ with pkgs;
 
   fcl = callPackage ../development/libraries/fcl { };
 
-  febio = callPackage ../development/libraries/febio { };
-
   ffcast = callPackage ../tools/X11/ffcast { };
 
   fflas-ffpack = callPackage ../development/libraries/fflas-ffpack { };
@@ -37016,8 +37014,6 @@ with pkgs;
 
   fastp = callPackage ../applications/science/biology/fastp { };
 
-  febio-studio = libsForQt5.callPackage ../applications/science/biology/febio-studio { };
-
   flywheel-cli = callPackage ../applications/science/biology/flywheel-cli { };
 
   hh-suite = callPackage ../applications/science/biology/hh-suite {