{vis}[GCCcore/12.2.0] MONAI v1.3.0, einops v0.7.0, ITK v5.3.0, ... w/ largefiles

easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.2.0.eb

@@ -0,0 +1,29 @@
+easyblock = 'PythonPackage'
+
+name = 'einops'
+version = '0.7.0'
+
+homepage = 'https://einops.rocks/'
+description = """
+Flexible and powerful tensor operations for readable and reliable code.
+Supports numpy, pytorch, tensorflow, jax, and others."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['b2b04ad6081a3b227080c9bf5e3ace7160357ff03043cd66cc5b2319eb7031d1']
+
+builddependencies = [
+    ('binutils', '2.39'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+sanity_pip_check = True
+
+moduleclass = 'math'

easybuild/easyconfigs/g/grpcio/grpcio-1.57.0-GCCcore-12.2.0.eb

@@ -0,0 +1,54 @@
+easyblock = 'PythonBundle'
+
+name = 'grpcio'
+version = '1.57.0'
+
+homepage = 'https://grpc.io/'
+description = """gRPC is a modern, open source, high-performance remote procedure call (RPC)
+framework that can run anywhere. gRPC enables client and server applications to
+communicate transparently, and simplifies the building of connected systems."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchainopts = {'pic': True}
+
+use_pip = True
+sanity_pip_check = True
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('OpenSSL', '1.1', '', SYSTEM),
+    ('RE2', '2023-03-01'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('protobuf-python', '4.23.0'),
+    ('Abseil', '20230125.2'),
+]
+
+exts_list = [
+    (name, version, {
+        'modulename': 'grpc',
+        'preinstallopts': (
+            # patch hardcoded /usr paths to prefix them with alternate sysroot path (if defined)
+            "sed -i 's@/usr@%(sysroot)s/usr@g' setup.py && "
+            "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && "
+            # Required to avoid building with non-default C++ standard but keep other flags,
+            # see https://github.com/grpc/grpc/issues/34256
+            'export GRPC_PYTHON_CFLAGS="-fvisibility=hidden -fno-wrapv -fno-exceptions" &&'
+            "GRPC_PYTHON_BUILD_SYSTEM_OPENSSL=True "
+            "GRPC_PYTHON_BUILD_SYSTEM_ZLIB=True "
+            "GRPC_PYTHON_BUILD_SYSTEM_RE2=True "
+            "GRPC_PYTHON_BUILD_SYSTEM_ABSL=True "
+        ),
+        'patches': ['grpcio-1.57.0_use-ebroot.patch'],
+        'checksums': [
+            {'grpcio-1.57.0.tar.gz':
+             '4b089f7ad1eb00a104078bab8015b0ed0ebcb3b589e527ab009c53893fd4e613'},
+            {'grpcio-1.57.0_use-ebroot.patch':
+             '5faf822cd817b723ae9361e43656d0ecc7b3333a166bbab2df80b43ae588e510'},
+        ],
+    }),
+]
+
+moduleclass = 'lib'

easybuild/easyconfigs/i/ITK/ITK-5.3.0-foss-2022b.eb

@@ -0,0 +1,78 @@
+# Contributors:
+# Fenglai Liu ([email protected]) - Vanderbilt University
+# Alex Domingo ([email protected]) - Vrije Universiteit Brussel (VUB)
+# Denis Kristak, Pavel Tománek (INUITS)
+#
+easyblock = 'CMakeMake'
+
+name = 'ITK'
+version = '5.3.0'
+
+homepage = 'https://itk.org'
+description = """Insight Segmentation and Registration Toolkit (ITK) provides
+ an extensive suite of software tools for registering and segmenting
+ multidimensional imaging data."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+toolchainopts = {'pic': True, 'cstd': 'c++11'}
+
+github_account = 'InsightSoftwareConsortium'
+source_urls = [GITHUB_SOURCE]
+sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+patches = [
+    'ITK-5.3.0_vtk-include.patch',
+    'ITK-5.3.0_fix-compatibility-swig-4-1.patch',
+]
+checksums = [
+    {'ITK-5.3.0.tar.gz': '64e7e8094a5023c8f68ee042459d6319581fadb35e2fe90a4ae230ce36369db1'},
+    {'ITK-5.3.0_vtk-include.patch': '138ebd2e0e7f9001aba5f4a7e8145ffcf0093913d50f109ecff447773fd52a48'},
+    {'ITK-5.3.0_fix-compatibility-swig-4-1.patch': '0138878d96e90d6bfdc81fd4f2b5ec413d61c1de666a16842b417c2686ebf506'},
+]
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('Bison', '3.8.2'),
+    ('Eigen', '3.4.0'),
+    ('SWIG', '4.1.1'),
+    ('Perl', '5.36.0'),
+]
+dependencies = [
+    ('Python', '3.10.8'),
+    ('double-conversion', '3.2.1'),
+    ('expat', '2.4.9'),
+    ('HDF5', '1.14.0'),
+    ('libjpeg-turbo', '2.1.4'),
+    ('libpng', '1.6.38'),
+    ('LibTIFF', '4.4.0'),
+    ('VTK', '9.2.6'),
+    ('zlib', '1.2.12'),
+]
+
+# Features
+configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF '
+configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON '
+# Enable Python bindings
+configopts += '-DITK_WRAP_PYTHON:BOOL=ON -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python '
+configopts += '-DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig -DSWIG_DIR=$EBROOTSWIG '
+configopts += '-DPY_SITE_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages '
+# Dependencies from EB
+local_sys_deps = ['DOUBLECONVERSION', 'EIGEN', 'EXPAT', 'FFTW', 'HDF5', 'JPEG', 'PNG', 'SWIG', 'TIFF', 'ZLIB']
+local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps]
+configopts += ' '.join(local_sys_cmake)
+
+prebuildopts = "LC_ALL=C "
+
+local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF',
+                   'ITKReview', 'ITKVTK', 'ITKVtkGlue', 'itkSimpleITKFilters']
+
+sanity_check_paths = {
+    'files': ['bin/itkTestDriver'] +
+             ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (l, SHLIB_EXT) for l in local_lib_names],
+    'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'lib/python%(pyshortver)s/site-packages', 'share'],
+}
+
+sanity_check_commands = ["python -c 'import itk'"]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'data'

easybuild/easyconfigs/i/ITK/ITK-5.3.0_vtk-include.patch

@@ -0,0 +1,13 @@
+Manually add the include directory of VTK
+dirty fix for issue https://github.com/InsightSoftwareConsortium/ITK/issues/4375
+author: Alex Domingo (Vrije Universiteit Brussel)
+--- Wrapping/CMakeLists.txt.orig	2023-12-21 13:41:44.845008000 +0100
++++ Wrapping/CMakeLists.txt	2023-12-21 13:42:14.794328946 +0100
+@@ -112,6 +112,7 @@
+ ###############################################################################
+ # Configure specific wrapper modules
+ ###############################################################################
++include_directories("$ENV{EBROOTVTK}/include/vtk-9.2/")
+
+ unset(WRAP_ITK_MODULES CACHE)
+

easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2022b.eb

@@ -0,0 +1,96 @@
+easyblock = 'PythonBundle'
+
+name = 'MONAI'
+version = '1.3.0'
+
+homepage = 'https://monai.io/'
+description = """
+MONAI is a PyTorch-based, open-source framework for deep learning in healthcare
+imaging, part of PyTorch Ecosystem.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+github_account = 'Project-MONAI'
+
+builddependencies = [
+    ('Ninja', '1.11.1'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('PyTorch', '1.13.1'),
+    ('einops', '0.7.0'),
+    ('ITK', '5.3.0'),
+    ('NiBabel', '5.2.0'),
+    ('scikit-image', '0.21.0'),
+    ('tensorboard', '2.15.1'),
+    ('torchvision', '0.14.1'),
+    ('tqdm', '4.64.1'),
+    ('Pillow', '9.4.0'),
+    ('openslide-python', '1.3.1'),
+    ('BeautifulSoup', '4.11.1'),
+]
+
+use_pip = True
+
+# install MONAI with list of 'extras', which require additional dependencies
+local_pip_extras = "einops,fire,gdown,ignite,itk,jsonschema,lmdb,nibabel,"
+local_pip_extras += "openslide,pandas,pillow,psutil,pydicom,pyyaml,scipy,"
+local_pip_extras += "skimage,tensorboard,torchvision,tqdm"
+
+# PyTorch-Ignite v0.4.11 bundled as an extension because MONAI v1.3.0 has a strict requirement on it
+exts_list = [
+    ('gdown', '4.7.1', {
+        'checksums': ['347f23769679aaf7efa73e5655270fcda8ca56be65eb84a4a21d143989541045'],
+    }),
+    ('lmdb', '1.4.1', {
+        'checksums': ['1f4c76af24e907593487c904ef5eba1993beb38ed385af82adb25a858f2d658d'],
+    }),
+    ('termcolor', '2.3.0', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['3afb05607b89aed0ffe25202399ee0867ad4d3cb4180d98aaf8eefa6a5f7d475'],
+    }),
+    ('fire', '0.5.0', {
+        'checksums': ['a6b0d49e98c8963910021f92bba66f65ab440da2982b78eb1bbf95a0a34aacc6'],
+    }),
+    ('pytorch-ignite', '0.4.11', {
+        'modulename': 'ignite',
+        'patches': ['PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch'],
+        'checksums': [
+            {'pytorch-ignite-0.4.11.tar.gz': 'ee31096a58679417097ef7f3f27d88bec40b789ac5e13cd9ed08bc89ca8ce2e2'},
+            {'PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch':
+             'd45c0da30c01f7ce47b7be49a6d5d6eb9529c94a0b9de89260d4b07d9d2359e0'},
+        ],
+    }),
+    (name, version, {
+        'preinstallopts': 'BUILD_MONAI=1',
+        'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
+        'use_pip_extras': local_pip_extras,
+        # 2 valid checksums, as source tarball provided by GitHub for MONAI 1.3.0 slightly changed at some point
+        # see also https://github.com/easybuilders/easybuild-easyconfigs/issues/20617
+        'checksums': [('67e0f55678faad4bd38b1ea69d5de94586b20b551b8ad745415623a8b6c1c5e2',
+                       '076d75458d490b4f2dafbf5974fcc8e07a86c03f39f5ef48c6689ab6e4347da9')],
+    }),
+]
+
+sanity_pip_check = True
+
+# 'pip check' does not verify whether all optional dependencies required to support 'extras'
+# are actually available, so we do it here via an import check;
+local_extra_mod_check = {x: x for x in local_pip_extras.split(",")}
+# Some special cases with different module name than extra name
+local_extra_mod_check['pillow'] = 'PIL'
+local_extra_mod_check['pyyaml'] = 'yaml'
+
+sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"]
+sanity_check_commands += ["python -c 'import %s'" % local_extra_mod_check[x] for x in local_extra_mod_check]
+
+sanity_check_paths = {
+    'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/ignite'],
+}
+
+moduleclass = 'vis'

easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-gfbf-2022b.eb

@@ -0,0 +1,46 @@
+easyblock = 'PythonBundle'
+
+name = 'NiBabel'
+version = '5.2.0'
+
+homepage = 'https://nipy.github.io/nibabel'
+description = """NiBabel provides read/write access to some common medical and neuroimaging file formats,
+ including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT
+ as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and
+ annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI."""
+
+toolchain = {'name': 'gfbf', 'version': '2022b'}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('Pillow', '9.4.0'),
+    ('pydicom', '2.4.4'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('bz2file', '0.98', {
+        'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'],
+    }),
+    ('nibabel', version, {
+        'checksums': ['3df8f1ab981d1bd92f4331d565528d126ab9717fdbd4cfe68f43fcd1c2bf3f52'],
+    }),
+]
+
+fix_python_shebang_for = ['bin/*']
+
+sanity_check_paths = {
+    'files': ['bin/nib-dicomfs', 'bin/nib-diff', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "nib-diff --help",
+    "parrec2nii --help",
+]
+
+sanity_pip_check = True
+
+moduleclass = 'vis'

easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-12.2.0-largefiles.eb

@@ -0,0 +1,56 @@
+easyblock = 'ConfigureMake'
+
+name = 'OpenSlide'
+version = '3.4.1'
+versionsuffix = '-largefiles'
+
+homepage = 'https://openslide.org/'
+description = """OpenSlide is a C library that provides a simple interface to
+read whole-slide images (also known as virtual slides)."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = [GITHUB_SOURCE]
+sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+patches = ['%(name)s-%(version)s_large_file_support.patch']
+checksums = [
+    # v3.4.1.tar.gz
+    'a5d869916e370125421535dcce778b2ba625dc50d920aa4ca93bbaaa6a7b470c',
+    # %(name)s-%(version_major_minor)s.1_large_file_support.patch
+    'cb618053f4ae6c3ce37d1b8b0e4ef7c55fd17378776d13be4aa4efab91706b8c',
+]
+
+builddependencies = [
+    ('Autotools', '20220317'),
+    ('M4', '1.4.19'),
+    ('pkgconf', '1.9.3'),
+    ('binutils', '2.39'),
+]
+
+dependencies = [
+    ('zlib', '1.2.12'),
+    ('libpng', '1.6.38'),
+    ('libjpeg-turbo', '2.1.4'),
+    ('LibTIFF', '4.4.0'),
+    ('OpenJPEG', '2.5.0'),
+    ('libxml2', '2.10.3'),
+    ('SQLite', '3.39.4'),
+    ('cairo', '1.17.4'),
+    ('Gdk-Pixbuf', '2.42.10'),
+]
+
+preconfigopts = "autoreconf -f -i && "
+
+sanity_check_paths = {
+    'files': [
+        'bin/openslide-quickhash1sum',
+        'bin/openslide-show-properties',
+        'bin/openslide-write-png',
+        'lib/libopenslide.la',
+        'lib/libopenslide.%s' % SHLIB_EXT
+    ],
+    'dirs': ['include/openslide']
+}
+
+
+moduleclass = 'vis'