Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

…asyconfigs into 20240628004822_new_pr_imkl-FFTW202420

easybuild/easyconfigs/b/biom-format/biom-format-2.1.16-foss-2023b.eb

@@ -0,0 +1,49 @@
+##
+# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia
+# Homepage:     https://staff.flinders.edu.au/research/deep-thought
+#
+# Authors::     Robert Qiao <[email protected]>
+# License::     Revised BSD
+#
+# Notes:: updated by Kenneth Hoste (HPC-UGent) for foss/2021b
+##
+# Updated: Petr Král (INUITS)
+# Updated: Lara Peeters (Ghent University)
+
+easyblock = 'PythonPackage'
+
+name = 'biom-format'
+version = '2.1.16'
+
+homepage = 'https://biom-format.org'
+description = """
+The BIOM file format (canonically pronounced biome) is designed to be
+ a general-use format for representing biological sample by observation
+ contingency tables. BIOM is a recognized standard for the Earth Microbiome
+ Project and is a Genomics Standards Consortium supported project.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'usempi': True}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['47f88d57a94ecaa4d06f3578ca394e78db6d12e46ab0886634743181e67dcfc9']
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('h5py', '3.11.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+download_dep_fail = True
+
+sanity_check_paths = {
+    'files': ['bin/biom'],
+    'dirs': ['lib'],
+}
+
+options = {'modulename': 'biom'}
+
+moduleclass = 'bio'

easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2023a.eb

@@ -0,0 +1,37 @@
+# This easyconfig was created by the BEAR Software team at the University of Birmingham.
+# Update: Petr Král (INUITS)
+easyblock = 'PythonBundle'
+
+name = 'CSBDeep'
+version = '0.7.4'
+
+homepage = "https://csbdeep.bioimagecomputing.com/"
+description = """CSBDeep is a toolbox for Content-aware Image Restoration (CARE)."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('TensorFlow', '2.13.0'),
+    ('matplotlib', '3.7.2'),
+    ('tqdm', '4.66.1'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('tifffile', '2024.6.18', {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['67299c0445fc47463bbc71f3cb4676da2ab0242b0c6c6542a0680801b4b97d8a'],
+    }),
+    ('%(namelower)s', version, {
+        'source_tmpl': SOURCE_WHL,
+        'checksums': ['155d61827439373dc9c2a730a1ef621f7e373fea16599d583e0a70f1e48bd6db'],
+    }),
+]
+
+sanity_check_commands = ['care_predict']
+
+moduleclass = 'bio'

easybuild/easyconfigs/i/iimpi/iimpi-2024.06.eb

@@ -0,0 +1,18 @@
+# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild
+easyblock = 'Toolchain'
+
+name = 'iimpi'
+version = '2024.06'
+
+homepage = 'https://software.intel.com/parallel-studio-xe'
+description = """Intel C/C++ and Fortran compilers, alongside Intel MPI."""
+
+toolchain = SYSTEM
+
+local_comp_ver = '2024.2.0'
+dependencies = [
+    ('intel-compilers', local_comp_ver),
+    ('impi', '2021.13.0', '', ('intel-compilers', local_comp_ver)),
+]
+
+moduleclass = 'toolchain'

easybuild/easyconfigs/i/impi/impi-2021.13.0-intel-compilers-2024.2.0.eb

@@ -0,0 +1,16 @@
+name = 'impi'
+version = '2021.13.0'
+
+homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html'
+description = "Intel MPI Library, compatible with MPICH ABI"
+
+toolchain = {'name': 'intel-compilers', 'version': '2024.2.0'}
+
+# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/9f84e1e8-11b2-4bd1-8512-3e3343585956']
+sources = ['l_mpi_oneapi_p_%(version)s.719_offline.sh']
+checksums = ['5e23cf495c919e17032577e3059438f632297ee63f2cdb906a2547298823cc64']
+
+dependencies = [('UCX', '1.16.0')]
+
+moduleclass = 'mpi'

easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb

@@ -11,21 +11,20 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['a7298207f72f2b27b2ab1ce392a6ea37afbd1fbee0f1f8d190b054dcaba878fe']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.10.0-linux-x86_64.tar.gz': 'a7298207f72f2b27b2ab1ce392a6ea37afbd1fbee0f1f8d190b054dcaba878fe'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
+]
+
+# install wrapper with linking safeguards for Julia libraries
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
 
 sanity_check_commands = ['julia --help']
 
-modextrapaths_append = {
-    # Use default DEPOT_PATH where first entry is user's depot.
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths.
-    # Appending ':' to make sure we don't override the user's custom JULIA_DEPOT_PATH if set.
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'

easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb

@@ -15,20 +15,20 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/aarch64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['0f496972d26cea88151204d03e6bd87702aa1ff983de3b1e4f320c48ef67325f']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.6.0-linux-aarch64.tar.gz': '0f496972d26cea88151204d03e6bd87702aa1ff983de3b1e4f320c48ef67325f'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
+]
+
+# install wrapper with linking safeguards for Julia libraries
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
 
 sanity_check_commands = ['julia --help']
 
-modextravars = {
-    # Use default DEPOT_PATH where first entry is user's depot
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'

easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb

@@ -19,20 +19,20 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['b8fe23ee547254a2fe14be587284ed77c78c06c2d8e9aad5febce0d21cab8e2c']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.6.5-linux-x86_64.tar.gz': 'b8fe23ee547254a2fe14be587284ed77c78c06c2d8e9aad5febce0d21cab8e2c'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
+]
+
+# install wrapper with linking safeguards for Julia libraries
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
 
 sanity_check_commands = ['julia --help']
 
-modextravars = {
-    # Use default DEPOT_PATH where first entry is user's depot
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'

easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb

@@ -19,20 +19,19 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['c25ff71a4242207ab2681a0fcc5df50014e9d99f814e77cacbc5027e20514945']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.6.6-linux-x86_64.tar.gz': 'c25ff71a4242207ab2681a0fcc5df50014e9d99f814e77cacbc5027e20514945'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
+]
+
+# install wrapper with linking safeguards for Julia libraries
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
-
 sanity_check_commands = ['julia --help']
 
-modextravars = {
-    # Use default DEPOT_PATH where first entry is user's depot
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'

easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb

@@ -19,20 +19,19 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['6c4522d595e4cbcd00157ac458a72f8aec01757053d2073f99daa39e442b2a36']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.6.7-linux-x86_64.tar.gz': '6c4522d595e4cbcd00157ac458a72f8aec01757053d2073f99daa39e442b2a36'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
+]
+
+# install wrapper with linking safeguards for Julia libraries
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
-
 sanity_check_commands = ['julia --help']
 
-modextravars = {
-    # Use default DEPOT_PATH where first entry is user's depot
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'

easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb

@@ -19,20 +19,19 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['7299f3a638aec5e0b9e14eaf0e6221c4fe27189aa0b38ac5a36f03f0dc4c0d40']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.7.0-linux-x86_64.tar.gz': '7299f3a638aec5e0b9e14eaf0e6221c4fe27189aa0b38ac5a36f03f0dc4c0d40'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
+]
+
+# install wrapper with linking safeguards for Julia libraries
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
-
 sanity_check_commands = ['julia --help']
 
-modextravars = {
-    # Use default DEPOT_PATH where first entry is user's depot
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'

easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb

@@ -19,20 +19,19 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['44658e9c7b45e2b9b5b59239d190cca42de05c175ea86bc346c294a8fe8d9f11']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.7.1-linux-x86_64.tar.gz': '44658e9c7b45e2b9b5b59239d190cca42de05c175ea86bc346c294a8fe8d9f11'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
+]
+
+# install wrapper with linking safeguards for Julia libraries
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
-
 sanity_check_commands = ['julia --help']
 
-modextravars = {
-    # Use default DEPOT_PATH where first entry is user's depot
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'

easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb

@@ -19,20 +19,19 @@ toolchain = SYSTEM
 
 source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/']
 sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz']
-checksums = ['a75244724f3b2de0e7249c861fbf64078257c16fb4203be78f1cf4dd5973ba95']
+patches = [('julia.wrapper', 'bin/')]
+checksums = [
+    {'julia-1.7.2-linux-x86_64.tar.gz': 'a75244724f3b2de0e7249c861fbf64078257c16fb4203be78f1cf4dd5973ba95'},
+    {'julia.wrapper': 'd10aeaff53cca9875f7b0ce9218eae3bd21870b654e26c4c52aa8bfcc9da702d'},
+]
+
+# install wrapper with linking safeguards for Julia libraries
+postinstallcmds = ["cd %(installdir)s/bin && mv julia julia.bin && mv julia.wrapper julia"]
 
 sanity_check_paths = {
-    'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
-    'dirs': ['bin', 'etc', 'include', 'lib', 'share']
+    'files': ['bin/julia', 'bin/julia.bin', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'etc', 'include', 'lib', 'lib/julia', 'share']
 }
-
 sanity_check_commands = ['julia --help']
 
-modextravars = {
-    # Use default DEPOT_PATH where first entry is user's depot
-    # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have
-    # those installations appended to DEPOT_PATH without disabling any of the default paths
-    'JULIA_DEPOT_PATH': ':',
-}
-
 moduleclass = 'lang'