#357 imagecodecs pre-PR

357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/LibLZF-2023b.eb

@@ -0,0 +1,31 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+# Update: Thomas Hoffmann (EMBL), Denis Kristak
+easyblock = 'ConfigureMake'
+
+name = 'LibLZF'
+version = '3.6'
+
+homepage = 'http://oldhome.schmorp.de/marc/liblzf.html'
+description = """LibLZF is a very small data compression library. It consists of only two .c and two .h files
+and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still
+written in portable C."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['http://dist.schmorp.de/liblzf/Attic/']
+sources = ['liblzf-%(version)s.tar.gz']
+checksums = ['9c5de01f7b9ccae40c3f619d26a7abec9986c06c36d260c179cedd04b89fb46a']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+sanity_check_commands = ['lzf -h']
+
+sanity_check_paths = {
+    'files': ['bin/lzf', 'lib/liblzf.a'],
+    'dirs': ['bin', 'lib'],
+}
+
+moduleclass = 'lib'

357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/Zopfli-2023.eb

@@ -0,0 +1,37 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Updated: Denis Kristak
+# Updated: Thomas Hoffmann (EMBL), Denis Kristak (Inuits)
+easyblock = 'CMakeMake'
+
+name = 'Zopfli'
+version = '1.0.3'
+
+homepage = 'https://github.com/google/zopfli'
+description = """Zopfli Compression Algorithm is a compression library programmed in C to perform
+very good, but slow, deflate or zlib compression."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/google/zopfli/archive/refs/tags/']
+sources = ['%(namelower)s-%(version)s.tar.gz']
+checksums = ['e955a7739f71af37ef3349c4fa141c648e8775bceb2195be07e86f8e638814bd']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('binutils', '2.40'),
+]
+
+configopts = [
+    '-DBUILD_SHARED_LIBS=ON',
+    '-DBUILD_SHARED_LIBS=OFF',
+]
+
+sanity_check_paths = {
+    'files': ['bin/zopfli', 'include/zopfli.h', 'lib/libzopfli.a', 'lib/libzopfli.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+sanity_check_commands = ["zopfli --help"]
+
+moduleclass = 'tools'

357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/bitshuffle-2023b.eb

@@ -0,0 +1,30 @@
+easyblock = 'PythonPackage'
+
+name = 'bitshuffle'
+version = '0.5.2'
+
+homepage = 'https://github.com/kiyo-masui/bitshuffle'
+description = """
+Filter for improving compression of typed binary data.
+Bitshuffle is an algorithm that rearranges typed, binary data for improving compression, as
+well as a python/C package that implements this algorithm within the Numpy framework.
+The library can be used along side HDF5 to compress and decompress datasets and is integrated
+through the dynamically loaded filters framework. Bitshuffle is HDF5 filter number 32008.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['dc0e3fb7bdbf42be1009cc3028744180600d625a75b31833a24aa32aeaf83d8d']
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('h5py', '3.11.0'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'lib'

357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/imagecodecs-2023b.eb

@@ -28,53 +28,51 @@ dependencies = [
     ('CFITSIO', '4.3.1'),
     ('CharLS', '2.4.2'), # CREATED
     ('giflib', '5.2.1'),
-    # ('jxrlib', '1.1'), # CREATE 1.2
+    ('jxrlib', '1.1'), # CREATED
     ('LittleCMS', '2.15'),
     ('LERC', '4.0.0'),
     ('libaec', '1.0.6'),
-    # ('libavif', '1.0.4'), # CREATE
+    ('libavif', '1.1.1'), # CREATED
     ('libdeflate', '1.19'),
-    # ('libheif', '1.17.6'), # CREATE
+    ('libheif', '1.19.5'), # CREATED
     ('libjpeg-turbo', '3.0.1'),
     ('libjxl', '0.8.2'),
-    # ('LibLZF', '3.6'), # CREATE
+    ('LibLZF', '3.6'), # CREATED
     ('libpng', '1.6.40'),
     ('LibTIFF', '4.6.0'),
     ('libwebp', '1.3.2'),
     ('lz4', '1.9.4'),
     ('OpenJPEG', local_openjpeg_maj_min + '.0'),
     ('snappy', '1.1.10'),
-    # ('zlib-ng', '2.1.6'), # CREATE
-    # ('Zopfli', '1.0.3'), # CREATE
-    # ('zfp', '1.0.1'), # CREATE
+    ('zlib-ng', '2.2.2'), # PR: https://github.com/easybuilders/easybuild-easyconfigs/pull/21861
+    ('Zopfli', '1.0.3'), # CREATED
+    ('zfp', '1.0.1'), # CREATED
     ('zstd', '1.5.5'),
     ('HDF5', '1.14.3'),
     ('h5py', '3.11.0'),
-    # ('bitshuffle', '0.5.1'),  # CREATE # Cannot be as extension because Cython 3.0.8 is too new
+    ('bitshuffle', '0.5.2'),  # CREATED # Cannot be as extension because Cython 3.0.8 is too new
 ]
 
 use_pip = True
 sanity_pip_check = True
 
 exts_list = [
-    ('colorlog', '6.8.2', {
-        'checksums': ['3e3e079a41feb5a1b64f978b5ea4f46040a94f11f0e8bbb8261e3dbbeca64d44'],
+    ('colorlog', '6.9.0', {
+        'checksums': ['bfba54a1b93b94f54e1f4fe48395725a3d92fd2a4af702f6bd70946bdc0c6ac2'],
     }),
     (name, version, {
         'buildopts': '--global-option="build_ext" --global-option="--lite"',
         'extract_cmd': "tar -xvf %s && find . -type f -print0 | xargs -0 dos2unix",
         'patches': ['imagecodecs-2024.1.1_fix-aec-version.patch'],
         'preinstallopts': "export CPATH=$EBROOTOPENJPEG/include/openjpeg-2.5/:$CPATH && ",
-        'source_urls': [
-            'https://github.com/cgohlke/imagecodecs/releases/download/v%(version)s/imagecodecs-2024.1.1.tar.gz'
-        ],
+        'source_urls': ['https://github.com/cgohlke/imagecodecs/releases/download/v%(version)s/'],
         'sources': ['%(name)s-%(version)s.tar.gz'],
         'checksums': [
-            {'imagecodecs-2024.1.1.tar.gz': 'fde46bd698d008255deef5411c59b35c0e875295e835bf6079f7e2ab22f216eb'},
+            {'imagecodecs-2024.6.1.tar.gz': '0f3e94b7f51e2f78287b7ffae82cd850b1007639148894538274fa50bd179886'},
             {'imagecodecs-2024.1.1_fix-aec-version.patch':
              '7feb0a5fe37893d1a186f85c8f6cdb940704605ee2da5ea8e5d555ec5bfa01aa'},
         ],
     }),
 ]
 
-moduleclass = 'lib'
+moduleclass = 'lib'

357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/jxrlib-2023b.eb

@@ -0,0 +1,39 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author::   Denis Kristak (INUITS)
+# Update:    Thomas Hoffmann (EMBL)
+##
+
+easyblock = 'CMakeMake'
+
+name = 'jxrlib'
+version = '1.1'
+
+homepage = 'https://github.com/4creators/jxrlib'
+description = """Open source implementation of jpegxr"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://deb.debian.org/debian/pool/main/j/jxrlib/']
+sources = ['%(name)s_%(version)s.orig.tar.gz']
+patches = [('jxrlib-%(version)s_cmake.patch', 1)]
+checksums = [
+    {'jxrlib_1.1.orig.tar.gz': 'c7287b86780befa0914f2eeb8be2ac83e672ebd4bd16dc5574a36a59d9708303'},
+    {'jxrlib-1.1_cmake.patch': 'e96ea8b418fdab10e9cbc2f4cad95ca1f59a826ce7379c6a3192882050689a74'},
+]
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.27.6'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/JxrDecApp', 'bin/JxrEncApp', "lib/libjpegxr.%s" % SHLIB_EXT],
+    'dirs': [],
+}
+
+sanity_check_commands = ['JxrDecApp', 'JxrEncApp']
+
+modextrapaths = {'CPATH': 'include/jxrlib'}
+
+moduleclass = 'lib'

357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/libavif-2023b.eb

@@ -0,0 +1,36 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak (Inuits)
+# Update: Thomas Hoffmann (EMBL), Denis Kristak (Inuits)
+easyblock = 'CMakeMake'
+
+name = 'libavif'
+version = '1.1.1'
+
+homepage = 'https://github.com/AOMediaCodec/libavif'
+description = """This library aims to be a friendly, portable C implementation of the AV1 Image File Format,
+as described here: https://aomediacodec.github.io/av1-avif/
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/AOMediaCodec/libavif/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['914662e16245e062ed73f90112fbb4548241300843a7772d8d441bb6859de45b']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('binutils', '2.40'),
+    ('NASM', '2.16.01'),
+    ('Meson', '1.2.3'),
+    ('Ninja', '1.11.1'),
+    ('Rust', '1.76.0'),
+    ('pkgconf', '2.0.3'),
+    ('libyuv', '20241125'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libavif.%s' % SHLIB_EXT, 'include/avif/avif.h'],
+    'dirs': [],
+}
+
+moduleclass = 'tools'

357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/libde265-2023b.eb

@@ -0,0 +1,34 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+easyblock = 'CMakeMake'
+
+name = 'libde265'
+version = '1.0.15'
+
+homepage = 'https://github.com/strukturag/libde265'
+description = "libde265 is an open source implementation of the h.265 video codec"
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['00251986c29d34d3af7117ed05874950c875dd9292d016be29d3b3762666511d']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.27.6'),
+]
+
+configopts = "-DENABLE_DECODER=ON -DENABLE_ENCODER=ON"
+
+sanity_check_paths = {
+    'files': ['bin/dec265', 'bin/enc265', 'lib/libde265.%s' % SHLIB_EXT, 'lib/pkgconfig/libde265.pc'],
+    'dirs': ['include/libde265', 'lib/cmake/libde265'],
+}
+
+sanity_check_commands = [
+    "dec265 --help",
+    "enc265 --help",
+]
+
+moduleclass = 'tools'

357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/libheif-2023b.eb

@@ -0,0 +1,43 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+easyblock = 'CMakeMake'
+
+name = 'libheif'
+version = '1.19.5'
+
+homepage = 'https://github.com/strukturag/libheif'
+description = "libheif is an HEIF and AVIF file format decoder and encoder"
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['d3cf0a76076115a070f9bc87cf5259b333a1f05806500045338798486d0afbaf']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.27.6'),
+]
+
+dependencies = [
+    ('libpng', '1.6.40'),
+    ('libjpeg-turbo', '3.0.1'),
+    ('libde265', '1.0.15'),
+    ('x265', '3.5'),
+    ('Gdk-Pixbuf', '2.42.10'),
+]
+
+# build both static and shared libraries
+configopts = [
+    "-DBUILD_SHARED_LIBS=OFF",
+    "-DBUILD_SHARED_LIBS=ON",
+]
+
+sanity_check_paths = {
+    'files': ['bin/heif-info', 'lib/libheif.a', 'lib/libheif.%s' % SHLIB_EXT, 'lib/pkgconfig/libheif.pc'],
+    'dirs': ['include/libheif'],
+}
+
+sanity_check_commands = ["heif-info --help"]
+
+moduleclass = 'tools'

357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/libyuv-2023b.eb

@@ -0,0 +1,29 @@
+easyblock = 'CMakeMake'
+
+name = 'libyuv'
+version = '20241125'
+local_commit = '9a97521'
+
+homepage = 'https://github.com/lemenkov/libyuv'
+description = """libyuv is an open source project that includes YUV scaling and conversion functionality."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/lemenkov/libyuv/archive/']
+sources = [{
+    "download_filename": "%s.tar.gz" % local_commit,
+    "filename": SOURCE_TAR_GZ,
+}]
+checksums = ['25e48eb78c41383e391b68ed017e82e42ded0ae2667fb399f7b2442582ae2af2']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('binutils', '2.40'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/yuvconvert', f'lib/{name}.so', f'lib/{name}.a', f'include/{name}.h'],
+    'dirs': [],
+}
+
+moduleclass = 'tools'

357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/zfp-2023b.eb

@@ -0,0 +1,40 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+# Update: Thomas Hoffmann (EMBL)
+easyblock = 'MakeCp'
+
+name = 'zfp'
+version = '1.0.1'
+
+homepage = 'https://github.com/LLNL/zfp'
+description = """zfp is a compressed format for representing multidimensional floating-point and integer arrays.
+zfp provides compressed-array classes that support high throughput read and write random access to individual array
+elements. zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications
+that read and write large data sets to and from disk."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/LLNL/zfp/archive']
+sources = ['%(version)s.tar.gz']
+checksums = ['4984db6a55bc919831966dd17ba5e47ca7ac58668f4fd278ebd98cd2200da66f']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+prebuildopts = "sed -i 's/FLAGS = -O3/FLAGS = $CFLAGS/g' Makefile && "
+buildopts = 'ZFP_WITH_OPENMP=1'
+
+runtest = 'test'
+
+files_to_copy = ['bin', 'include', 'lib']
+
+sanity_check_paths = {
+    'files': ['bin/zfp', 'bin/testzfp', 'include/zfp.h', 'lib/libzfp.a'],
+    'dirs': ['include/zfp'],
+}
+
+sanity_check_commands = ["zfp --help 2>&1 | grep 'Usage: zfp'"]
+
+moduleclass = 'lib'