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{tools}[GCCcore/13.2.0] bakta v1.10.0, PyHMMER v0.10.15, psutil v6.1.0, ... #21861

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{tools}[GCCcore/13.2.0] bakta v1.10.0, PyHMMER v0.10.15, psutil v6.1.0, ... #21861

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@PetrKralCZ PetrKralCZ commented Nov 15, 2024 •
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(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#174

@PetrKralCZ
adding easyconfigs: bakta-1.10.0-foss-2023b.eb, PyHMMER-0.10.15-gompi…
1fbe073 
…-2023b.eb, psutil-6.1.0-GCCcore-13.2.0.eb, zlib-ng-2.2.2-GCCcore-13.2.0.eb, versioningit-3.1.2-GCCcore-13.2.0.eb
@PetrKralCZ PetrKralCZ mentioned this pull request Nov 15, 2024
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Updated software PyHMMER-0.10.15-gompi-2023b.eb

Diff against PyHMMER-0.10.6-gompi-2023a.eb

easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.6-gompi-2023a.eb

diff --git a/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.6-gompi-2023a.eb b/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.15-gompi-2023b.eb
index a9a329832b..2d6165976d 100644
--- a/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.6-gompi-2023a.eb
+++ b/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.15-gompi-2023b.eb
@@ -1,8 +1,10 @@
 # Thomas Hoffmann, EMBL Heidelberg, [email protected], 2024/02
+# Update: Petr Král (INUITS)
+
 easyblock = 'PythonBundle'
 
 name = 'PyHMMER'
-version = '0.10.6'
+version = '0.10.15'
 
 homepage = 'https://github.com/althonos/pyhmmer'
 description = """
@@ -14,22 +16,26 @@ pyhmmer is a Python package, implemented using the Cython language, that
 provides bindings to HMMER3. It directly interacts with the HMMER internals,    
 which has the following advantages over CLI wrappers (like hmmer-py)"""
 
-toolchain = {'name': 'gompi', 'version': '2023a'}
+toolchain = {'name': 'gompi', 'version': '2023b'}
 
 builddependencies = [
-    ('Cython', '3.0.7'),
+    ('Cython', '3.0.10'),
 ]
+
 dependencies = [
-    ('Python', '3.11.3'),
+    ('Python', '3.11.5'),
     ('HMMER', '3.4'),
-    ('psutil', '5.9.8')
+    ('psutil', '6.1.0')
 ]
 
 use_pip = True
+sanity_pip_check = True
 
 exts_list = [
-    ('pyhmmer', version, {
-        'checksums': ['47e017ccc523046400312afc937d4d68306f6ca0ed82e313deb3697d4fd8ccff'],
+    ('%(namelower)s', version, {
+        # Requirement for `psutil` is too strict.
+        'preinstallopts': "sed -i 's/psutil ~=5.8/psutil >=5.8/g' setup.cfg && ",
+        'checksums': ['bf8e97ce8da6fb5850298f3074640f3e998d5a655877f865c1592eb057dc7921'],
     }),
 ]
 
@@ -38,6 +44,4 @@ sanity_check_paths = {
     'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'],
 }
 
-sanity_pip_check = True
-
 moduleclass = 'bio'

Updated software psutil-6.1.0-GCCcore-13.2.0.eb

Diff against psutil-6.0.0-GCCcore-13.3.0.eb

easybuild/easyconfigs/p/psutil/psutil-6.0.0-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/p/psutil/psutil-6.0.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/psutil/psutil-6.1.0-GCCcore-13.2.0.eb
index d6b6501e7d..5ba7c5d938 100644
--- a/easybuild/easyconfigs/p/psutil/psutil-6.0.0-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/p/psutil/psutil-6.1.0-GCCcore-13.2.0.eb
@@ -1,16 +1,16 @@
 easyblock = 'PythonBundle'
 
 name = 'psutil'
-version = '6.0.0'
+version = '6.1.0'
 
 homepage = 'https://github.com/giampaolo/psutil'
 description = """A cross-platform process and system utilities module for Python"""
 
-toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
-builddependencies = [('binutils', '2.42')]
+builddependencies = [('binutils', '2.40')]
 
-dependencies = [('Python', '3.12.3')]
+dependencies = [('Python', '3.11.5')]
 
 use_pip = True
 sanity_pip_check = True
@@ -18,8 +18,8 @@ sanity_pip_check = True
 exts_list = [
     (name, version, {
         'source_urls': ['https://github.com/giampaolo/psutil/archive'],
-        'sources': ['%(name)s-%(version)s.tar.gz'],
-        'checksums': ['8faae4f310b6d969fa26ca0545338b21f73c6b15db7c4a8d934a5482faa818f2'],
+        'sources': ['release-%(version)s.tar.gz'],
+        'checksums': ['0ffb8a92fac0e89c10b0beb152acae27975fd488d0b9938e441106f319e7599c'],
     }),
 ]
Diff against psutil-5.9.8-GCCcore-12.3.0.eb

easybuild/easyconfigs/p/psutil/psutil-5.9.8-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.9.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/psutil/psutil-6.1.0-GCCcore-13.2.0.eb
index 554ec684e8..5ba7c5d938 100644
--- a/easybuild/easyconfigs/p/psutil/psutil-5.9.8-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/p/psutil/psutil-6.1.0-GCCcore-13.2.0.eb
@@ -1,16 +1,16 @@
 easyblock = 'PythonBundle'
 
 name = 'psutil'
-version = '5.9.8'
+version = '6.1.0'
 
 homepage = 'https://github.com/giampaolo/psutil'
 description = """A cross-platform process and system utilities module for Python"""
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 builddependencies = [('binutils', '2.40')]
 
-dependencies = [('Python', '3.11.3')]
+dependencies = [('Python', '3.11.5')]
 
 use_pip = True
 sanity_pip_check = True
@@ -18,8 +18,8 @@ sanity_pip_check = True
 exts_list = [
     (name, version, {
         'source_urls': ['https://github.com/giampaolo/psutil/archive'],
-        'sources': ['%(name)s-%(version)s.tar.gz'],
-        'checksums': ['6be126e3225486dff286a8fb9a06246a5253f4c7c53b475ea5f5ac934e64194c'],
+        'sources': ['release-%(version)s.tar.gz'],
+        'checksums': ['0ffb8a92fac0e89c10b0beb152acae27975fd488d0b9938e441106f319e7599c'],
     }),
 ]
Diff against psutil-5.9.5-GCCcore-12.2.0.eb

easybuild/easyconfigs/p/psutil/psutil-5.9.5-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.9.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/psutil/psutil-6.1.0-GCCcore-13.2.0.eb
index f51a55120b..5ba7c5d938 100644
--- a/easybuild/easyconfigs/p/psutil/psutil-5.9.5-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/p/psutil/psutil-6.1.0-GCCcore-13.2.0.eb
@@ -1,16 +1,16 @@
 easyblock = 'PythonBundle'
 
 name = 'psutil'
-version = '5.9.5'
+version = '6.1.0'
 
 homepage = 'https://github.com/giampaolo/psutil'
 description = """A cross-platform process and system utilities module for Python"""
 
-toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
-builddependencies = [('binutils', '2.39')]
+builddependencies = [('binutils', '2.40')]
 
-dependencies = [('Python', '3.10.8')]
+dependencies = [('Python', '3.11.5')]
 
 use_pip = True
 sanity_pip_check = True
@@ -18,8 +18,8 @@ sanity_pip_check = True
 exts_list = [
     (name, version, {
         'source_urls': ['https://github.com/giampaolo/psutil/archive'],
-        'sources': [SOURCE_TAR_GZ],
-        'checksums': ['5410638e4df39c54d957fc51ce03048acd8e6d60abc0f5107af51e5fb566eb3c'],
+        'sources': ['release-%(version)s.tar.gz'],
+        'checksums': ['0ffb8a92fac0e89c10b0beb152acae27975fd488d0b9938e441106f319e7599c'],
     }),
 ]

Updated software versioningit-3.1.2-GCCcore-13.2.0.eb

Diff against versioningit-3.1.2-GCCcore-13.3.0.eb

easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.3.0.eb b/easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.2.0.eb
index ab4e77dea4..3ea3731df7 100644
--- a/easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/v/versioningit/versioningit-3.1.2-GCCcore-13.2.0.eb
@@ -9,13 +9,13 @@ package’s version based on your version control repository’s tags.
 Unlike others, it allows easy customization of the version format and even lets you easily override
 the separate functions used for version extraction & calculation."""
 
-toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 builddependencies = [
-    ('binutils', '2.42'),
-    ('hatchling', '1.24.2'),
+    ('binutils', '2.40'),
+    ('hatchling', '1.18.0'),
 ]
-dependencies = [('Python', '3.12.3')]
+dependencies = [('Python', '3.11.5')]
 
 sources = [SOURCE_TAR_GZ]
 checksums = ['4db83ed99f56b07d83940bee3445ca46ca120d13b6b304cdb5fb44e5aa4edec0']

Updated software zlib-ng-2.2.2-GCCcore-13.2.0.eb

Diff against zlib-ng-2.2.1-GCCcore-13.3.0.eb

easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.1-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.2-GCCcore-13.2.0.eb
index 266b927072..8e1cf20a94 100644
--- a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.1-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.2-GCCcore-13.2.0.eb
@@ -1,21 +1,21 @@
 easyblock = 'PythonBundle'
 
 name = 'zlib-ng'
-version = '2.2.1'
+version = '2.2.2'
 
 homepage = 'https://github.com/zlib-ng/zlib-ng'
 description = """zlib data compression library for the next generation systems"""
 
-toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 builddependencies = [
-    ('CMake', '3.29.3'),
-    ('binutils', '2.42'),
+    ('CMake', '3.27.6'),
+    ('binutils', '2.40'),
     ('versioningit', '3.1.2'),
 ]
 
 dependencies = [
-    ('Python', '3.12.3'),
+    ('Python', '3.11.5'),
 ]
 
 components = [
@@ -23,7 +23,7 @@ components = [
         'easyblock': 'CMakeMake',
         'source_urls': ['https://github.com/zlib-ng/zlib-ng/archive/'],
         'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
-        'checksums': ['ec6a76169d4214e2e8b737e0850ba4acb806c69eeace6240ed4481b9f5c57cdf'],
+        'checksums': ['fcb41dd59a3f17002aeb1bb21f04696c9b721404890bb945c5ab39d2cb69654c'],
         'start_dir': '%(name)s-%(version)s',
         'configopts': '-DZLIB_ENABLE_TESTS=ON',
     }),
@@ -34,9 +34,9 @@ use_pip = True
 sanity_pip_check = True
 
 exts_list = [
-    (name, '0.5.0', {
+    (name, '0.5.1', {
         'source_tmpl': 'zlib_ng-%(version)s.tar.gz',
-        'checksums': ['3322c4300253a054af3d3aafa2f3858dceee3a577810122ba55eff756bf35ef2'],
+        'checksums': ['32a46649e8efc21ddd74776a55366a8d8be4e3a95b93dc1f0ffe3880718990d9'],
         'preinstallopts': 'PYTHON_ZLIB_NG_LINK_DYNAMIC=true',
         'modulename': 'zlib_ng',
     }),
Diff against zlib-ng-2.1.6-GCCcore-12.3.0.eb

easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.1.6-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.1.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.2-GCCcore-13.2.0.eb
index c29b31ffb3..8e1cf20a94 100644
--- a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.1.6-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.2-GCCcore-13.2.0.eb
@@ -1,26 +1,46 @@
-# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
-# Updated: Denis Kristak (Inuits)
-# Updated: Thomas Hoffmann (EMBL), Denis Kristak (Inuits)
-easyblock = 'CMakeMake'
+easyblock = 'PythonBundle'
 
 name = 'zlib-ng'
-version = '2.1.6'
+version = '2.2.2'
 
 homepage = 'https://github.com/zlib-ng/zlib-ng'
 description = """zlib data compression library for the next generation systems"""
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
-
-source_urls = ['https://github.com/zlib-ng/zlib-ng/archive/']
-sources = ['%(version)s.tar.gz']
-checksums = ['a5d504c0d52e2e2721e7e7d86988dec2e290d723ced2307145dedd06aeb6fef2']
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 builddependencies = [
-    ('CMake', '3.26.3'),
+    ('CMake', '3.27.6'),
     ('binutils', '2.40'),
+    ('versioningit', '3.1.2'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+]
+
+components = [
+    (name, version, {
+        'easyblock': 'CMakeMake',
+        'source_urls': ['https://github.com/zlib-ng/zlib-ng/archive/'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
+        'checksums': ['fcb41dd59a3f17002aeb1bb21f04696c9b721404890bb945c5ab39d2cb69654c'],
+        'start_dir': '%(name)s-%(version)s',
+        'configopts': '-DZLIB_ENABLE_TESTS=ON',
+    }),
+
 ]
 
-configopts = ' -DZLIB_ENABLE_TESTS=True '
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    (name, '0.5.1', {
+        'source_tmpl': 'zlib_ng-%(version)s.tar.gz',
+        'checksums': ['32a46649e8efc21ddd74776a55366a8d8be4e3a95b93dc1f0ffe3880718990d9'],
+        'preinstallopts': 'PYTHON_ZLIB_NG_LINK_DYNAMIC=true',
+        'modulename': 'zlib_ng',
+    }),
+]
 
 sanity_check_paths = {
     'files': ['include/zconf-ng.h', 'include/zlib-ng.h', 'lib/libz-ng.a', 'lib/libz-ng.%s' % SHLIB_EXT],
Diff against zlib-ng-2.0.7-GCCcore-11.3.0.eb

easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.7-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.2-GCCcore-13.2.0.eb
index 2f4e46a256..8e1cf20a94 100644
--- a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.7-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.2.2-GCCcore-13.2.0.eb
@@ -1,26 +1,46 @@
-# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
-# Updated: Denis Kristak (Inuits)
-# Updated: Thomas Hoffmann (EMBL), Denis Kristak (Inuits)
-easyblock = 'CMakeMake'
+easyblock = 'PythonBundle'
 
 name = 'zlib-ng'
-version = '2.0.7'
+version = '2.2.2'
 
 homepage = 'https://github.com/zlib-ng/zlib-ng'
 description = """zlib data compression library for the next generation systems"""
 
-toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
-
-source_urls = ['https://github.com/zlib-ng/zlib-ng/archive/']
-sources = ['%(version)s.tar.gz']
-checksums = ['6c0853bb27738b811f2b4d4af095323c3d5ce36ceed6b50e5f773204fb8f7200']
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 builddependencies = [
-    ('CMake', '3.23.1'),
-    ('binutils', '2.38'),
+    ('CMake', '3.27.6'),
+    ('binutils', '2.40'),
+    ('versioningit', '3.1.2'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+]
+
+components = [
+    (name, version, {
+        'easyblock': 'CMakeMake',
+        'source_urls': ['https://github.com/zlib-ng/zlib-ng/archive/'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
+        'checksums': ['fcb41dd59a3f17002aeb1bb21f04696c9b721404890bb945c5ab39d2cb69654c'],
+        'start_dir': '%(name)s-%(version)s',
+        'configopts': '-DZLIB_ENABLE_TESTS=ON',
+    }),
+
 ]
 
-configopts = ' -DZLIB_ENABLE_TESTS=True '
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    (name, '0.5.1', {
+        'source_tmpl': 'zlib_ng-%(version)s.tar.gz',
+        'checksums': ['32a46649e8efc21ddd74776a55366a8d8be4e3a95b93dc1f0ffe3880718990d9'],
+        'preinstallopts': 'PYTHON_ZLIB_NG_LINK_DYNAMIC=true',
+        'modulename': 'zlib_ng',
+    }),
+]
 
 sanity_check_paths = {
     'files': ['include/zconf-ng.h', 'include/zlib-ng.h', 'lib/libz-ng.a', 'lib/libz-ng.%s' % SHLIB_EXT],

@PetrKralCZ PetrKralCZ marked this pull request as draft November 16, 2024 07:18
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bakta
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@PetrKralCZ