Add a recipe for 3dSlicer (https://github.com/Slicer/Slicer)

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
conda-forge · Jan 10, 2025 · 9d50dfa · 9d50dfa
1 parent 0bffd21
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diff --git a/recipes/3dslicer/3dslicer.patch b/recipes/3dslicer/3dslicer.patch
@@ -0,0 +1,26 @@
+diff --git i/SuperBuild/External_CTK.cmake w/SuperBuild/External_CTK.cmake
+index fb41007b04..f2e297de27 100644
+--- i/SuperBuild/External_CTK.cmake
++++ w/SuperBuild/External_CTK.cmake
+@@ -82,6 +82,7 @@ if(NOT DEFINED CTK_DIR AND NOT Slicer_USE_SYSTEM_${proj})
+     ${${proj}_EP_ARGS}
+     GIT_REPOSITORY "${Slicer_${proj}_GIT_REPOSITORY}"
+     GIT_TAG "${Slicer_${proj}_GIT_TAG}"
++    PATCH_COMMAND patch -p1 < $ENV{RECIPE_DIR}/ctk-pythonqt-threads.patch
+     SOURCE_DIR ${EP_SOURCE_DIR}
+     BINARY_DIR ${EP_BINARY_DIR}
+     CMAKE_CACHE_ARGS
+diff --git i/SuperBuild/External_SimpleITK.cmake w/SuperBuild/External_SimpleITK.cmake
+index 694a241408..8fb53b6413 100644
+--- i/SuperBuild/External_SimpleITK.cmake
++++ w/SuperBuild/External_SimpleITK.cmake
+@@ -173,9 +173,6 @@ ExternalProject_Execute(${proj} \"install\" \"${PYTHON_EXECUTABLE}\" \"-m\" \"pi
+       -DCMAKE_CXX_FLAGS:STRING=${ep_common_cxx_flags}
+       -DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER}
+       -DCMAKE_C_FLAGS:STRING=${ep_common_c_flags}
+-      -DCMAKE_CXX_STANDARD:STRING=${CMAKE_CXX_STANDARD}
+-      -DCMAKE_CXX_STANDARD_REQUIRED:BOOL=${CMAKE_CXX_STANDARD_REQUIRED}
+-      -DCMAKE_CXX_EXTENSIONS:BOOL=${CMAKE_CXX_EXTENSIONS}
+       -DCMAKE_CXX_VISIBILITY_PRESET:BOOL=default
+       -DBUILD_SHARED_LIBS:BOOL=${Slicer_USE_SimpleITK_SHARED}
+       -DBUILD_EXAMPLES:BOOL=OFF
diff --git a/recipes/3dslicer/build.sh b/recipes/3dslicer/build.sh
@@ -0,0 +1,48 @@
+#!/usr/bin/env bash
+
+set -xe
+
+mkdir -p build && pushd build
+
+cmake .. -GNinja \
+    -DCMAKE_BUILD_TYPE:STRING=Release \
+    -DCMAKE_INSTALL_PREFIX=${PREFIX} \
+    -DSlicer_RELEASE_TYPE="Stable" \
+    -DQt5_DIR=${PREFIX} \
+    -DSlicer_USE_SYSTEM_python=1 \
+    -DSlicer_USE_SYSTEM_python-numpy=1 \
+    -DSlicer_USE_SYSTEM_python-scipy=1 \
+    -DSlicer_USE_SYSTEM_python-pip=1 \
+    -DSlicer_USE_SYSTEM_python-setuptools=1 \
+    -DSlicer_USE_SYSTEM_python-ensurepip=1 \
+    -DSlicer_USE_SYSTEM_python-wheel=1 \
+    -DSlicer_USE_SYSTEM_LZMA=1 \
+    -DSlicer_USE_SYSTEM_zlib=1 \
+    -DSlicer_USE_SYSTEM_bzip2=1 \
+    -DSlicer_USE_SYSTEM_curl=1 \
+    -DSlicer_USE_SYSTEM_sqlite=1 \
+    -DSlicer_USE_SYSTEM_RapidJSON=1 \
+    -DSlicer_USE_SYSTEM_LibFFI=1 \
+    -DSlicer_USE_SYSTEM_DCMTK=1 \
+    -DSlicer_USE_SYSTEM_OpenSSL=1 \
+    -DSlicer_USE_SYSTEM_LibArchive=1 \
+    -DSlicer_USE_SimpleITK_SHARED="ON" \
+    -DSlicer_VTK_SMP_IMPLEMENTATION_TYPE="TBB" \
+    -DBUILD_TESTING="OFF" \
+    -DCMAKE_MESSAGE_LOG_LEVEL=ERROR
+
+cmake --build . --target Slicer -- -j"${CPU_COUNT}" > build.log
+
+# debug
+ls -la
+
+pushd Slicer-build
+cmake --build . --target install
+
+# debug
+ls -la ${PREFIX}/bin
+
+#    -DSlicer_USE_SYSTEM_ITK=1 \
+#    -DSlicer_USE_SYSTEM_VTK=1 \
+#    -DSlicer_FORCED_WC_LAST_CHANGED_DATE="${last_revision_date}" \
+#    -DSlicer_FORCED_REVISION="${last_revision_hash}"
diff --git a/recipes/3dslicer/ctk-pythonqt-threads.patch b/recipes/3dslicer/ctk-pythonqt-threads.patch
@@ -0,0 +1,10 @@
+--- CTK/CMakeExternals/PythonQt.cmake	2022-07-13 18:42:03.304128760 -0500
++++ CTK/CMakeExternals/PythonQt.cmake.new	2022-07-13 18:41:59.961133207 -0500
+@@ -109,6 +109,7 @@
+     PREFIX ${proj}${ep_suffix}
+     ${location_args}
+     BUILD_COMMAND ""
++    PATCH_COMMAND patch -p1 < $ENV{RECIPE_DIR}/pythonqt-threads.patch
+     CMAKE_CACHE_ARGS
+       ${ep_common_cache_args}
+       -DPythonQt_QT_VERSION:STRING=${CTK_QT_VERSION}
diff --git a/recipes/3dslicer/meta.yaml b/recipes/3dslicer/meta.yaml
@@ -0,0 +1,161 @@
+{% set name = "3dslicer" %}
+{% set version = "5.6.2" %}
+{% set sha256 = "821bd73f0c15b6d599961e5af4a86a32c8468c95927f9eab246ef879f8ff1a20" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/Slicer/Slicer/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+  patches:
+    - 3dslicer.patch
+
+build:
+  number: 0
+  skip: True  # [osx or win]
+  script_env:
+    - QT_QPA_PLATFORM=offscreen
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+    - {{ cdt('mesa-libgl-devel') }}  # [linux]
+    - {{ cdt('mesa-dri-drivers') }}  # [linux]
+    - {{ cdt('libselinux') }}  # [linux]
+    - {{ cdt('libxdamage') }}  # [linux]
+    - {{ cdt('libxxf86vm') }}  # [linux]
+    - {{ cdt('libxext') }}     # [linux]
+    - cmake
+    - ninja
+    - make
+    - git
+    - patch
+  host:
+    - pip
+    - python
+    - xorg-libxfixes  # [linux]
+    - numpy
+    - scipy
+    - setuptools
+    - wheel
+    - packaging
+    - nose
+    - qt
+    - xorg-libxt
+    - xorg-libxext
+    - xorg-libxrender
+    - xorg-libxcomposite
+    - xorg-libxrandr
+    - xorg-libxtst
+    - curl
+    - openssl
+    - xz
+    - zlib
+    - bzip2
+    - curl
+    - sqlite
+    - rapidjson
+    - libffi
+    - dcmtk
+    - libxml2
+    - hdf5
+    - boost
+    - certifi
+    - idna
+    - requests
+    - urllib3
+    - charset-normalizer
+    - chardet
+    - pydicom
+    - six
+    - pillow
+    - dicomweb-client
+    - couchdb-python
+    - gitpython
+    - pyjwt
+    - deprecated
+    - wrapt
+    - cffi
+    - pynacl
+    - pygithub
+    - ffmpeg
+    - libpng
+    - libogg
+    - libtheora
+    - gl2ps
+    # - jpeg
+    - libtiff
+    - eigen
+    - expat
+    - libarchive
+  run:
+    - python
+    - numpy
+    - scipy
+    - wheel
+    - qt
+    - xorg-libxt
+    - xorg-libxext
+    - xorg-libxrender
+    - xorg-libxcomposite
+    - xorg-libxrandr
+    - xorg-libxtst
+    - curl
+    - openssl
+    - xz
+    - zlib
+    - bzip2
+    - curl
+    - sqlite
+    - rapidjson
+    - libffi
+    - dcmtk
+    - libxml2
+    - hdf5
+    - boost
+    - certifi
+    - idna
+    - requests
+    - urllib3
+    - charset-normalizer
+    - chardet
+    - pydicom
+    - six
+    - pillow
+    - dicomweb-client
+    - couchdb-python
+    - gitpython
+    - pyjwt
+    - wrapt
+    - cffi
+    - pynacl
+    - pygithub
+    - ffmpeg
+    - libpng
+    - libogg
+    - libtheora
+    - gl2ps
+    # - jpeg
+    - libtiff
+    - expat
+    - libarchive
+
+test:
+  commands:
+    - Slicer --help
+
+about:
+  home: "https://slicer.org"
+  dev_url: "https://github.com/Slicer/Slicer"
+  doc_url: "https://slicer.readthedocs.io/en/latest/"
+  summary: "Multi-platform, free open source software for visualization and image computing."
+  license: Custom OSS
+  license_family: BSD
+  license_file: License.txt
+
+extra:
+  recipe-maintainers:
+    - martin-g
diff --git a/recipes/3dslicer/pythonqt-threads.patch b/recipes/3dslicer/pythonqt-threads.patch
@@ -0,0 +1,10 @@
+--- PythonQT/src/PythonQtPythonInclude.h	2022-07-13 18:08:39.364858312 -0500
++++ PythonQT/src/PythonQtPythonInclude.h.new	2022-07-13 18:23:21.880628826 -0500
+@@ -35,7 +35,6 @@
+
+ // Undefine macros that Python.h defines to avoid redefinition warning.
+ #undef _POSIX_C_SOURCE
+-#undef _POSIX_THREADS
+ #undef _XOPEN_SOURCE
+
+ // Undefine Qt keywords that conflict with Python headers