[ENH][packages/slicer] Introduce external packages

guix-systole/packages/openigtlink.scm

@@ -0,0 +1,138 @@
+(define-module (guix-systole packages openigtlink)
+  #:use-module ((guix licenses)
+                #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix build-system cmake)
+  #:use-module (guix build-system copy)
+  #:use-module (gnu packages algebra)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages fontutils)
+  #:use-module (gnu packages geo)
+  #:use-module (gnu packages gl)
+  #:use-module (gnu packages image)
+  #:use-module (gnu packages xml)
+  #:use-module (gnu packages gnome)
+  #:use-module (gnu packages maths)
+  #:use-module (gnu packages mpi)
+  #:use-module (gnu packages pdf)
+  #:use-module (gnu packages qt)
+  #:use-module (gnu packages serialization)
+  #:use-module (gnu packages tbb)
+  #:use-module (gnu packages xiph)
+  #:use-module (guix-systole packages)
+  #:use-module (guix-systole packages vtk)
+  #:use-module (guix-systole packages ctk))
+
+(define-public openigtlink
+  (package
+    (name "openigtlink")
+    (version "c512727") ;version used by PlusBuild (Plus 2.8)
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        "https://github.com/openigtlink/OpenIGTLink/archive/c512727425c2b7a594fabb9cd1fbfac512bf376e.tar.gz")
+       (sha256
+        (base32 "0s2rxa4igs2d354205vnp57bf81yj5fpqh91hy5v3zz34gri46j5"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:configure-flags (list "-DBUILD_EXAMPLES:BOOL=OFF"
+                          "-DBUILD_TESTING:BOOL=OFF"
+                          "-DOpenIGTLink_SUPERBUILD:BOOL=OFF"
+                          "-DOpenIGTLink_PROTOCOL_VERSION_2:BOOL=OFF"
+                          "-DOpenIGTLink_PROTOCOL_VERSION_3:BOOL=ON"
+                          "-DOpenIGTLink_ENABLE_VIDEOSTREAMING:BOOL=ON"
+                          "-DOpenIGTLink_USE_VP9:BOOL=OFF"
+
+                          "-DOpenIGTLink_INSTALL_PACKAGE_DIR:PATH=lib/cmake/OpenIGTLink"
+
+                          "-DBUILD_SHARED_LIBS:BOOL=ON")
+       #:tests? #f))
+    (inputs (list glew))
+    (home-page "openigtlink.org")
+    (synopsis
+     "Free, open-source network communication library for image-guided therapy")
+    (description
+     "The OpenIGTLink Library is a C/C++ implementation of The OpenIGTLink 
+Protocol. OpenIGTLink is an open-source network communication interface 
+specifically designed for image-guided interventions. It aims to provide a 
+plug-and-play unified real-time communications (URTC) in operating rooms (ORs) 
+for image-guided interventions, where imagers, sensors, surgical robots,and 
+computers from different vendors work cooperatively. This URTC will ensure the 
+seamless data flow among those components and enable a closed-loop process of 
+planning, control, delivery, and feedback. The specification of OpenIGTLink is 
+open, and can be used without any license fee; hence OpenIGTLink is suitable for 
+both industrial and academic developers.")
+    (license license:bsd-3)))
+
+(define-public openigtlinkio
+  (package
+    (name "openigtlinkio")
+    (version "a262c1f")
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        "https://github.com/IGSIO/OpenIGTLinkIO/archive/a262c1f5e63c00831cbf67d5284f4734f8a7b143.tar.gz")
+       (sha256
+        (base32 "01y6nhv7c5m57clpql8vg1g43k4k37mvb0bvasl28r90mqm4dvsm"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:configure-flags (list "-DBUILD_TESTING:BOOL=OFF"
+                               "-DIGTLIO_USE_EXAMPLES:BOOL=OFF"
+                               "-DBUILD_SHARED_LIBS:BOOL=ON")
+       #:tests? #f))
+    (inputs (list double-conversion
+                  eigen
+                  expat
+                  ctk
+                  freetype
+                  glew
+                  gl2ps
+                  glew
+                  hdf5
+                  jsoncpp
+                  libharu
+                  libjpeg-turbo
+                  libtheora
+                  libxml++
+                  lz4
+                  mpich
+                  netcdf
+                  openigtlink
+                  proj
+                  qtbase-5
+                  qtx11extras
+                  tbb
+                  vtk-slicer))
+    (home-page "openigtlink.org")
+    (synopsis
+     "Library for interfacing to openigtlink/OpenIGTLink, dependent on VTK and Qt. Based on openigtlink/OpenIGTLinkIF ")
+    (description
+     "Library for interfacing to openigtlink/OpenIGTLink, dependent on VTK and Qt. Based on openigtlink/OpenIGTLinkIF.")
+    (license license:asl2.0)))
+
+(define-public sliceropenigtlinkif-src
+  (package
+    (name "openigtlinkif-src")
+    (version "6fbdadf")
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        "https://github.com/openigtlink/SlicerOpenIGTLink/archive/73df3c26e169f539123de54096c2eff8de0871c9.tar.gz")
+       (sha256
+        (base32 "053vczsadhxm2c9nqg1bmjx7lbzkzpsjqx9jj2jyqypcc9ry31mx"))
+       (patches (search-patches
+                 "0019-COMP-packages-slicer-Port-OpenIGTLinkIF-to-slicer.patch"))))
+    (build-system copy-build-system)
+    (arguments
+     `(#:install-plan '(("." "/"))
+       #:phases (modify-phases %standard-phases
+                  (delete 'build))))
+    (home-page
+     "https://slicer.readthedocs.io/en/latest/user_guide/modules/plots.html")
+    (synopsis "OpenIGTLink interface module for 3D Slicer 4.x ")
+    (description "OpenIGTLink interface module for 3D Slicer 4.x ")
+    (license license:bsd-2)))

guix-systole/packages/patches/0016-ENH-packages-slicer-Add-External-Modules-directory.patch

@@ -0,0 +1,28 @@
+diff --git a/Modules/CMakeLists.txt b/Modules/CMakeLists.txt
+index 3f6fa9eab4..a29305d328 100644
+--- a/Modules/CMakeLists.txt
++++ b/Modules/CMakeLists.txt
+@@ -12,3 +12,6 @@ endif()
+ if(Slicer_BUILD_CLI_SUPPORT AND Slicer_BUILD_CLI)
+   add_subdirectory(CLI)
+ endif()
++
++# Build external modules
++add_subdirectory(External)
+diff --git a/Modules/External/CMakeLists.txt b/Modules/External/CMakeLists.txt
+new file mode 100644
+index 0000000000..fde9267043
+--- /dev/null
++++ b/Modules/External/CMakeLists.txt
+@@ -0,0 +1,11 @@
++## External dependencies can be added to this directory. Slicer will
++## automatically build them.
++
++file(GLOB children RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} */)
++
++foreach(child ${children})
++    if(IS_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/${child}" AND EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/${child}/CMakeLists.txt")
++      add_subdirectory(${child})
++    endif()
++endforeach()
++

guix-systole/packages/patches/0017-ENH-packages-slicer-Include-macros-to-Plots-module.patch

@@ -0,0 +1,25 @@
+diff --git a/Modules/Loadable/CMakeLists.txt b/Modules/Loadable/CMakeLists.txt
+index 606011bac6..745232e19b 100644
+--- a/Modules/Loadable/CMakeLists.txt
++++ b/Modules/Loadable/CMakeLists.txt
+@@ -18,7 +18,7 @@ set(qtmodules
+   Transforms
+   Data
+   Models
+-  Plots
++  #Plots
+   Segmentations
+   Sequences
+   SlicerWelcome
+diff --git a/Modules/Loadable/Plots/CMakeLists.txt b/Modules/Loadable/Plots/CMakeLists.txt
+index 4685399f1f..4a8c56dee6 100644
+--- a/Modules/Loadable/Plots/CMakeLists.txt
++++ b/Modules/Loadable/Plots/CMakeLists.txt
+@@ -2,6 +2,7 @@
+ #-----------------------------------------------------------------------------
+ set(MODULE_NAME Plots)
+
++include(${Slicer_CMAKE_DIR}/SlicerMacroBuildLoadableModule.cmake)
+ string(TOUPPER ${MODULE_NAME} MODULE_NAME_UPPER)
+
+ #-----------------------------------------------------------------------------

guix-systole/packages/patches/0018-COMP-packages-openigtlink-Include-Slicer-macros-in-OpenIGTLinkIF.patch

@@ -0,0 +1,50 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 6f43133..4f0b8b8 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -17,8 +17,8 @@ set(SUPERBUILD_TOPLEVEL_PROJECT inner)
+
+ #-----------------------------------------------------------------------------
+ # Extension dependencies
+-find_package(Slicer REQUIRED)
+-include(${Slicer_USE_FILE})
++#find_package(Slicer REQUIRED)
++#include(${Slicer_USE_FILE})
+ mark_as_superbuild(Slicer_DIR)
+
+ #-----------------------------------------------------------------------------
+@@ -30,10 +30,10 @@ mark_as_superbuild(SlicerOpenIGTLink_USE_VP9)
+ # SuperBuild setup
+ option(${EXTENSION_NAME}_SUPERBUILD "Build ${EXTENSION_NAME} and the projects it depends on." ON)
+ mark_as_advanced(${EXTENSION_NAME}_SUPERBUILD)
+-if(${EXTENSION_NAME}_SUPERBUILD)
+-  include("${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild.cmake")
+-  return()
+-endif()
++#if(${EXTENSION_NAME}_SUPERBUILD)
++#  include("${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild.cmake")
++#  return()
++#endif()
+
+ #-----------------------------------------------------------------------------
+ # Extension modules
+@@ -55,11 +55,11 @@ include(${Slicer_EXTENSION_GENERATE_CONFIG})
+
+ #-----------------------------------------------------------------------------
+ # Packaging
+-set(EXTENSION_CPACK_INSTALL_CMAKE_PROJECTS)
+-list(APPEND EXTENSION_CPACK_INSTALL_CMAKE_PROJECTS "${OpenIGTLink_DIR};OpenIGTLink;RuntimeLibraries;/")
+-list(APPEND EXTENSION_CPACK_INSTALL_CMAKE_PROJECTS "${OpenIGTLinkIO_DIR};OpenIGTLinkIO;RuntimeLibraries;/")
+-set(${EXTENSION_NAME}_CPACK_INSTALL_CMAKE_PROJECTS "${EXTENSION_CPACK_INSTALL_CMAKE_PROJECTS}" CACHE STRING "List of external projects to install" FORCE)
+-list(APPEND CPACK_INSTALL_CMAKE_PROJECTS "${CMAKE_BINARY_DIR};${EXTENSION_NAME};ALL;/")
+-list(APPEND CPACK_INSTALL_CMAKE_PROJECTS "${${EXTENSION_NAME}_CPACK_INSTALL_CMAKE_PROJECTS}")
+-include(${CMAKE_CURRENT_SOURCE_DIR}/CMake/SlicerBlockInstallVP9.cmake)
+-include(${Slicer_EXTENSION_CPACK})
++#set(EXTENSION_CPACK_INSTALL_CMAKE_PROJECTS)
++#list(APPEND EXTENSION_CPACK_INSTALL_CMAKE_PROJECTS "${OpenIGTLink_DIR};OpenIGTLink;RuntimeLibraries;/")
++#list(APPEND EXTENSION_CPACK_INSTALL_CMAKE_PROJECTS "${OpenIGTLinkIO_DIR};OpenIGTLinkIO;RuntimeLibraries;/")
++#set(${EXTENSION_NAME}_CPACK_INSTALL_CMAKE_PROJECTS "${EXTENSION_CPACK_INSTALL_CMAKE_PROJECTS}" CACHE STRING "List of external projects to install" FORCE)
++#list(APPEND CPACK_INSTALL_CMAKE_PROJECTS "${CMAKE_BINARY_DIR};${EXTENSION_NAME};ALL;/")
++#list(APPEND CPACK_INSTALL_CMAKE_PROJECTS "${${EXTENSION_NAME}_CPACK_INSTALL_CMAKE_PROJECTS}")
++#include(${CMAKE_CURRENT_SOURCE_DIR}/CMake/SlicerBlockInstallVP9.cmake)
++#include(${Slicer_EXTENSION_CPACK})