{astro}[foss/2023b] LoSoTo v2.5.0, LSMTool v1.7.0, LINC v5.0, dysco v1.3, LofarStMan v1.0, PyVO v1.7. RMextract v0.5.1, SAGECal v0.8.4, toil-cwl v8.2.0 by casparvl · Pull Request #23155 · easybuilders/easybuild-easyconfigs

casparvl · 2025-06-19T14:27:59Z

(created using eb --new-pr)

Edit: just to be clear why this is still in draft: I aim to implement a test step, but it requires editing several config files (with sed or equivalent) so that I can run a test LINC pipeline.

Depends on add patch to Python easyconfigs to fix ctypes when $LD_LIBRARY_PATH is not being set #23499 and add support to Python easyblock for conditionally applying extra patch to fix ctypes when EasyBuild is configured to filter $LD_LIBRARY_PATH easybuild-easyblocks#3860 for PyTables to build correctly IF you filter LD_LIBRARY_PATH in your EasyBuild config (e.g. in EESSI when building with EESSI-extend).

….5.0-foss-2023b.eb, LSMTool-1.7.0-foss-2023b.eb, SAGECal-0.8.4-foss-2023b.eb, RMextract-0.5.1-foss-2023b.eb, LofarStMan-1.0-foss-2023b.eb, dysco-1.3-foss-2023b.eb, cwltool-3.1.20250110105449-foss-2023b.eb, toil-cwl-8.2.0-foss-2023b.eb, PyVO-1.7-foss-2023b.eb

github-actions · 2025-06-19T14:28:23Z

Updated software `cwltool-3.1.20250110105449-foss-2023b.eb`

Diff against cwltool-3.1.20221008225030-foss-2021a.eb

easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221008225030-foss-2021a.eb

diff --git a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221008225030-foss-2021a.eb b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20250110105449-foss-2023b.eb
index 8edf05ee21..6cc69f7f4b 100644
--- a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221008225030-foss-2021a.eb
+++ b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20250110105449-foss-2023b.eb
@@ -1,47 +1,54 @@
-##
-# This is a contribution from SIB Swiss Institute of Bioinformatics
-# Homepage:     https://www.sib.swiss/research-infrastructure/competence-centers/vital-it
-#
-# Authors::     Sebastien Moretti <sebastien.moretti@sib.swiss>
-#
-##
-
 easyblock = 'PythonBundle'
 
 name = 'cwltool'
-version = '3.1.20221008225030'
+version = '3.1.20250110105449'
+
+homepage = "https://cwltool.readthedocs.io/"
 
-homepage = 'https://github.com/common-workflow-language/cwltool'
-description = """Common workflow language (CWL) reference implementation."""
+description = """
+This is the reference implementation of the Common Workflow Language open
+standards. It is intended to be feature complete and provide comprehensive
+validation of CWL files as well as provide other tools related to working with
+CWL.
+"""
 
-toolchain = {'name': 'foss', 'version': '2021a'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 
 builddependencies = [
-    ('binutils', '2.36.1'),
-    ('CMake',    '3.20.1'),
-    ('make',     '4.3'),
-    ('Check',    '0.15.2'),
-    ('SWIG',     '4.0.2'),
-    ('expat',    '2.2.9'),
-    ('bzip2',    '1.0.8'),
-    ('zlib',     '1.2.11'),
+    ('hatchling', '1.18.0')
 ]
 
-# The Qt5 dependency of Graphviz (required by pydot) may be long to build and
-# requires a lot of disk space and memory!
+# Based on https://github.com/common-workflow-language/cwltool/blob/3.1.20250110105449/pyproject.toml
 dependencies = [
-    ('Python',            '3.9.5'),
-    ('typing-extensions', '3.10.0.0'),
-    ('pydot',             '1.4.2'),
-    ('lxml',              '4.6.3'),
-    ('ruamel.yaml',       '0.17.21'),
-    ('networkx',          '2.5.1'),
+    ('nodejs', '20.9.0'),
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('ruamel.yaml', '0.18.6'),
+    ('RDFlib', '7.1.4'),
+    ('lxml', '4.9.3'),
+    ('networkx', '3.2.1'),
+    ('pydot', '2.0.0'),
 ]
 
-# Fetch the tar.gz, not the whl files!
 exts_list = [
-    ('argcomplete', '2.0.0', {
-        'checksums': ['6372ad78c89d662035101418ae253668445b391755cfe94ea52f1b9d22425b20'],
+    ('mistune', '3.0.2', {
+        'checksums': ['fc7f93ded930c92394ef2cb6f04a8aabab4117a91449e72dcc8dfa646a508be8'],
+    }),
+    ('mypy-extensions', '1.1.0', {
+        'patches': ['mypy-extensions-1.1.0_license.patch'],
+        'source_tmpl': 'mypy_extensions-%(version)s.tar.gz',
+        'checksums': [
+            {'mypy_extensions-1.1.0.tar.gz': '52e68efc3284861e772bbcd66823fde5ae21fd2fdb51c62a211403730b916558'},
+            {'mypy-extensions-1.1.0_license.patch': 'ad6f0666755104f94fc33f5da56dbf218517312d2be5bdc2877e3bfd879d20af'},
+        ],
+    }),
+    ('schema-salad', '8.9.20250408123006', {
+        'modulename': 'schema_salad',
+        'source_tmpl': 'schema_salad-%(version)s.tar.gz',
+        'checksums': ['7b95bf6ab6960b4b60605e4a908cd56f1a30ec7c16901af6e46a98e152b9f069'],
+    }),
+    ('prov', '1.5.1', {
+        'checksums': ['7a2d72b0df43cd9c6e374d815c8ce3cd5ca371d54f98f837853ac9fcc98aee4c'],
     }),
     ('humanfriendly', '10.0', {
         'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'],
@@ -49,56 +56,33 @@ exts_list = [
     ('coloredlogs', '15.0.1', {
         'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'],
     }),
-    ('isodate', '0.6.1', {
-        'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'],
-    }),
-    ('rdflib', '6.2.0', {
-        'checksums': ['62dc3c86d1712db0f55785baf8047f63731fa59b2682be03219cb89262065942'],
-    }),
-    ('mistune', '2.0.4', {
-        'checksums': ['9ee0a66053e2267aba772c71e06891fa8f1af6d4b01d5e84e267b4570d4d9808'],
+    ('argcomplete', '3.6.2', {
+        'checksums': ['d0519b1bc867f5f4f4713c41ad0aba73a4a5f007449716b16f385f2166dc6adf'],
     }),
-    ('schema-salad', '8.3.20230109181936', {
-        'modulename': 'schema_salad',
-        'checksums': ['e0fb8fbe793dda42133f374642be9f1af1651bbfb3ca37e341d8866d695de45a'],
-    }),
-    ('shellescape', '3.8.1', {
-        'checksums': ['40b310b30479be771bf3ab28bd8d40753778488bd46ea0969ba0b35038c3ec26'],
-    }),
-    ('cwlformat', '2022.2.18', {
-        'modulename': 'cwlformat',
-        'source_tmpl': 'cwlformat-%(version)s-py3-none-any.whl',
-        'checksums': ['d3e2dca192ce10e703ed4eb0bae26539db08d8ddd7c6a6fe9d1406c3f1b53cda'],
-    }),
-    ('cwl-upgrader', '1.2.4', {
+    ('cwl-upgrader', '1.2.12', {
+        'source_tmpl': 'cwl_upgrader-%(version)s.tar.gz',
         'modulename': 'cwlupgrader',
-        'checksums': ['b25fc236407343d44cc830ac3f63eed395b8d872fc7e17db92cde583d4a3b2ec'],
-    }),
-    ('cwl-utils', '0.21', {
-        'modulename': 'cwl_utils',
-        'checksums': ['583f05010f7572f3a69310325472ccb6efc2db7f43dc6428d03552e0ffcbaaf9'],
+        'checksums': ['0d4e514d32d96b60c5300de9baa30a583b09066c9aa78dd6aa7744164d72dc5c'],
     }),
-    ('mypy-extensions', '0.4.3', {
-        'modulename': 'mypy_extensions',
-        'source_tmpl': 'mypy_extensions-%(version)s.tar.gz',
-        'checksums': ['2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8'],
+    ('spython', '0.3.14', {
+        'checksums': ['8ad53ef034395cfa2d8a710cc1c3638e4475e5bbc6a2842d317db8013c2e4188'],
     }),
-    ('prov', '1.5.1', {
-        'checksums': ['7a2d72b0df43cd9c6e374d815c8ce3cd5ca371d54f98f837853ac9fcc98aee4c'],
+    ('rich-argparse', '1.7.1', {
+        'patches': ['rich-argparse-1.7.1_unkown_classifier.patch'],
+        'source_tmpl': 'rich_argparse-%(version)s.tar.gz',
+        'checksums': [
+            {'rich_argparse-1.7.1.tar.gz': 'd7a493cde94043e41ea68fb43a74405fa178de981bf7b800f7a3bd02ac5c27be'},
+            {'rich-argparse-1.7.1_unkown_classifier.patch':
+             '63e62dba328b2b857425798986af180b1baf228be5f8fd63e5b3cc43e546f972'},
+        ],
     }),
-    ('bagit', '1.8.1', {
-        'checksums': ['37df1330d2e8640c8dee8ab6d0073ac701f0614d25f5252f9e05263409cee60c'],
+    ('cwl-utils', '0.38', {
+        'source_tmpl': 'cwl_utils-%(version)s.tar.gz',
+        'checksums': ['1122e1f4cc8f48f9f51ddcb8114fa9e3862d717fd4aacb00f4428008f19e9fec'],
     }),
     (name, version, {
-        'checksums': ['9fbf2996ba673d83eaf28c745560f68992c08ab668eab2447957dbaaee8881b0'],
+        'checksums': ['91d3a5946a2afd3e8c4d7e38a53690ad06e3dd88c1d1e1afa368caa41ec3038f'],
     }),
 ]
 
-sanity_check_paths = {
-    'files': ['bin/cwltool'],
-    'dirs': ['lib/python%(pyshortver)s/site-packages'],
-}
-
-sanity_check_commands = ["cwltool --version"]
-
 moduleclass = 'tools'

Diff against cwltool-3.1.20221018083734-foss-2021a.eb

easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb

diff --git a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20250110105449-foss-2023b.eb
index d3fb741e01..6cc69f7f4b 100644
--- a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb
+++ b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20250110105449-foss-2023b.eb
@@ -1,47 +1,54 @@
-##
-# This is a contribution from SIB Swiss Institute of Bioinformatics
-# Homepage:     https://www.sib.swiss/research-infrastructure/competence-centers/vital-it
-#
-# Authors::     Sebastien Moretti <sebastien.moretti@sib.swiss>
-#
-##
-
 easyblock = 'PythonBundle'
 
 name = 'cwltool'
-version = '3.1.20221018083734'
+version = '3.1.20250110105449'
+
+homepage = "https://cwltool.readthedocs.io/"
 
-homepage = 'https://github.com/common-workflow-language/cwltool'
-description = """Common workflow language (CWL) reference implementation."""
+description = """
+This is the reference implementation of the Common Workflow Language open
+standards. It is intended to be feature complete and provide comprehensive
+validation of CWL files as well as provide other tools related to working with
+CWL.
+"""
 
-toolchain = {'name': 'foss', 'version': '2021a'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 
 builddependencies = [
-    ('binutils', '2.36.1'),
-    ('CMake',    '3.20.1'),
-    ('make',     '4.3'),
-    ('Check',    '0.15.2'),
-    ('SWIG',     '4.0.2'),
-    ('expat',    '2.2.9'),
-    ('bzip2',    '1.0.8'),
-    ('zlib',     '1.2.11'),
+    ('hatchling', '1.18.0')
 ]
 
-# The Qt5 dependency of Graphviz (required by pydot) may be long to build and
-# requires a lot of disk space and memory!
+# Based on https://github.com/common-workflow-language/cwltool/blob/3.1.20250110105449/pyproject.toml
 dependencies = [
-    ('Python',            '3.9.5'),
-    ('typing-extensions', '3.10.0.0'),
-    ('pydot',             '1.4.2'),
-    ('lxml',              '4.6.3'),
-    ('ruamel.yaml',       '0.17.21'),
-    ('networkx',          '2.5.1'),
+    ('nodejs', '20.9.0'),
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('ruamel.yaml', '0.18.6'),
+    ('RDFlib', '7.1.4'),
+    ('lxml', '4.9.3'),
+    ('networkx', '3.2.1'),
+    ('pydot', '2.0.0'),
 ]
 
-# Fetch the tar.gz, not the whl files!
 exts_list = [
-    ('argcomplete', '2.0.0', {
-        'checksums': ['6372ad78c89d662035101418ae253668445b391755cfe94ea52f1b9d22425b20'],
+    ('mistune', '3.0.2', {
+        'checksums': ['fc7f93ded930c92394ef2cb6f04a8aabab4117a91449e72dcc8dfa646a508be8'],
+    }),
+    ('mypy-extensions', '1.1.0', {
+        'patches': ['mypy-extensions-1.1.0_license.patch'],
+        'source_tmpl': 'mypy_extensions-%(version)s.tar.gz',
+        'checksums': [
+            {'mypy_extensions-1.1.0.tar.gz': '52e68efc3284861e772bbcd66823fde5ae21fd2fdb51c62a211403730b916558'},
+            {'mypy-extensions-1.1.0_license.patch': 'ad6f0666755104f94fc33f5da56dbf218517312d2be5bdc2877e3bfd879d20af'},
+        ],
+    }),
+    ('schema-salad', '8.9.20250408123006', {
+        'modulename': 'schema_salad',
+        'source_tmpl': 'schema_salad-%(version)s.tar.gz',
+        'checksums': ['7b95bf6ab6960b4b60605e4a908cd56f1a30ec7c16901af6e46a98e152b9f069'],
+    }),
+    ('prov', '1.5.1', {
+        'checksums': ['7a2d72b0df43cd9c6e374d815c8ce3cd5ca371d54f98f837853ac9fcc98aee4c'],
     }),
     ('humanfriendly', '10.0', {
         'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'],
@@ -49,56 +56,33 @@ exts_list = [
     ('coloredlogs', '15.0.1', {
         'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'],
     }),
-    ('isodate', '0.6.1', {
-        'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'],
-    }),
-    ('rdflib', '6.2.0', {
-        'checksums': ['62dc3c86d1712db0f55785baf8047f63731fa59b2682be03219cb89262065942'],
-    }),
-    ('mistune', '0.8.4', {
-        'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'],
+    ('argcomplete', '3.6.2', {
+        'checksums': ['d0519b1bc867f5f4f4713c41ad0aba73a4a5f007449716b16f385f2166dc6adf'],
     }),
-    ('schema-salad', '8.3.20221016151607', {
-        'modulename': 'schema_salad',
-        'checksums': ['c61a517c945cd383445ebecbc085b00766913a3fdd7df9699a0fa4c41728ca1f'],
-    }),
-    ('shellescape', '3.8.1', {
-        'checksums': ['40b310b30479be771bf3ab28bd8d40753778488bd46ea0969ba0b35038c3ec26'],
-    }),
-    ('cwlformat', '2022.2.18', {
-        'modulename': 'cwlformat',
-        'source_tmpl': 'cwlformat-%(version)s-py3-none-any.whl',
-        'checksums': ['d3e2dca192ce10e703ed4eb0bae26539db08d8ddd7c6a6fe9d1406c3f1b53cda'],
-    }),
-    ('cwl-upgrader', '1.2.4', {
+    ('cwl-upgrader', '1.2.12', {
+        'source_tmpl': 'cwl_upgrader-%(version)s.tar.gz',
         'modulename': 'cwlupgrader',
-        'checksums': ['b25fc236407343d44cc830ac3f63eed395b8d872fc7e17db92cde583d4a3b2ec'],
-    }),
-    ('cwl-utils', '0.20', {
-        'modulename': 'cwl_utils',
-        'checksums': ['28472aaba50ab4e8380c29f31c27beb63f60a1af1690369ab7bb7e31e71e66d9'],
+        'checksums': ['0d4e514d32d96b60c5300de9baa30a583b09066c9aa78dd6aa7744164d72dc5c'],
     }),
-    ('mypy-extensions', '0.4.3', {
-        'modulename': 'mypy_extensions',
-        'source_tmpl': 'mypy_extensions-%(version)s.tar.gz',
-        'checksums': ['2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8'],
+    ('spython', '0.3.14', {
+        'checksums': ['8ad53ef034395cfa2d8a710cc1c3638e4475e5bbc6a2842d317db8013c2e4188'],
     }),
-    ('prov', '1.5.1', {
-        'checksums': ['7a2d72b0df43cd9c6e374d815c8ce3cd5ca371d54f98f837853ac9fcc98aee4c'],
+    ('rich-argparse', '1.7.1', {
+        'patches': ['rich-argparse-1.7.1_unkown_classifier.patch'],
+        'source_tmpl': 'rich_argparse-%(version)s.tar.gz',
+        'checksums': [
+            {'rich_argparse-1.7.1.tar.gz': 'd7a493cde94043e41ea68fb43a74405fa178de981bf7b800f7a3bd02ac5c27be'},
+            {'rich-argparse-1.7.1_unkown_classifier.patch':
+             '63e62dba328b2b857425798986af180b1baf228be5f8fd63e5b3cc43e546f972'},
+        ],
     }),
-    ('bagit', '1.8.1', {
-        'checksums': ['37df1330d2e8640c8dee8ab6d0073ac701f0614d25f5252f9e05263409cee60c'],
+    ('cwl-utils', '0.38', {
+        'source_tmpl': 'cwl_utils-%(version)s.tar.gz',
+        'checksums': ['1122e1f4cc8f48f9f51ddcb8114fa9e3862d717fd4aacb00f4428008f19e9fec'],
     }),
-    ('cwltool', '3.1.20221018083734', {
-        'checksums': ['06d08f390ed7577ac66c6eef0c98f915363b5e36c04daa1353e3f2d0c5e19f17'],
+    (name, version, {
+        'checksums': ['91d3a5946a2afd3e8c4d7e38a53690ad06e3dd88c1d1e1afa368caa41ec3038f'],
     }),
 ]
 
-sanity_check_paths = {
-    'files': ['bin/cwltool'],
-    'dirs': ['lib/python%(pyshortver)s/site-packages'],
-}
-
-sanity_check_commands = ["cwltool --version"]
-
 moduleclass = 'tools'

Updated software `pydot-2.0.0-GCCcore-13.2.0.eb`

Diff against pydot-3.0.4-GCCcore-13.2.0.eb

easybuild/easyconfigs/p/pydot/pydot-3.0.4-GCCcore-13.2.0.eb

diff --git a/easybuild/easyconfigs/p/pydot/pydot-3.0.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-13.2.0.eb
index eb9f7fd64b..95fd542804 100644
--- a/easybuild/easyconfigs/p/pydot/pydot-3.0.4-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-13.2.0.eb
@@ -2,14 +2,16 @@
 easyblock = 'PythonBundle'
 
 name = 'pydot'
-version = '3.0.4'
+version = '2.0.0'
 
 homepage = 'https://github.com/pydot/pydot'
 description = "Python interface to Graphviz's Dot language."
 
 toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
-builddependencies = [('binutils', '2.40')]
+builddependencies = [
+    ('binutils', '2.40'),
+]
 
 dependencies = [
     ('Python', '3.11.5'),
@@ -17,9 +19,7 @@ dependencies = [
 ]
 
 exts_list = [
-    (name, version, {
-        'checksums': ['3ce88b2558f3808b0376f22bfa6c263909e1c3981e2a7b629b65b451eee4a25d'],
-    }),
+    ('pydot', '2.0.0', {'checksums': ['60246af215123fa062f21cd791be67dda23a6f280df09f68919e637a1e4f3235']}),
 ]
 
 moduleclass = 'vis'

Diff against pydot-3.0.3-GCCcore-13.3.0.eb

easybuild/easyconfigs/p/pydot/pydot-3.0.3-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/p/pydot/pydot-3.0.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-13.2.0.eb
index 326a57df47..95fd542804 100644
--- a/easybuild/easyconfigs/p/pydot/pydot-3.0.3-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-13.2.0.eb
@@ -2,24 +2,24 @@
 easyblock = 'PythonBundle'
 
 name = 'pydot'
-version = '3.0.3'
+version = '2.0.0'
 
 homepage = 'https://github.com/pydot/pydot'
 description = "Python interface to Graphviz's Dot language."
 
-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'),
-    ('Python-bundle-PyPI', '2024.06'),
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
 ]
 
 exts_list = [
-    (name, version, {
-        'checksums': ['5e009d97b2fff92b7a88f09ec1fd5b163f07f3b10469c927d362471d6faa0d50'],
-    }),
+    ('pydot', '2.0.0', {'checksums': ['60246af215123fa062f21cd791be67dda23a6f280df09f68919e637a1e4f3235']}),
 ]
 
 moduleclass = 'vis'

Diff against pydot-2.0.0-GCCcore-12.2.0.eb

easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-13.2.0.eb
index 668b1a0caf..95fd542804 100644
--- a/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-13.2.0.eb
@@ -7,16 +7,19 @@ version = '2.0.0'
 homepage = 'https://github.com/pydot/pydot'
 description = "Python interface to Graphviz's Dot language."
 
-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'),
+    ('Python-bundle-PyPI', '2023.10'),
+]
 
 exts_list = [
-    (name, version, {
-        'checksums': ['60246af215123fa062f21cd791be67dda23a6f280df09f68919e637a1e4f3235'],
-    }),
+    ('pydot', '2.0.0', {'checksums': ['60246af215123fa062f21cd791be67dda23a6f280df09f68919e637a1e4f3235']}),
 ]
 
 moduleclass = 'vis'

Updated software `RDFlib-7.1.4-GCCcore-13.2.0.eb`

Diff against RDFlib-7.1.4-GCCcore-14.2.0.eb

easybuild/easyconfigs/r/RDFlib/RDFlib-7.1.4-GCCcore-14.2.0.eb

diff --git a/easybuild/easyconfigs/r/RDFlib/RDFlib-7.1.4-GCCcore-14.2.0.eb b/easybuild/easyconfigs/r/RDFlib/RDFlib-7.1.4-GCCcore-13.2.0.eb
index 5231560c2f..7ad7db1fcb 100644
--- a/easybuild/easyconfigs/r/RDFlib/RDFlib-7.1.4-GCCcore-14.2.0.eb
+++ b/easybuild/easyconfigs/r/RDFlib/RDFlib-7.1.4-GCCcore-13.2.0.eb
@@ -7,22 +7,19 @@ homepage = 'https://github.com/RDFLib/rdflib'
 description = """RDFLib is a Python library for working with RDF, a simple yet powerful language
  for representing information."""
 
-toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 builddependencies = [
-    ('binutils', '2.42'),
-    ('poetry', '2.1.2'),
+    ('binutils', '2.40'),
+    ('poetry', '1.6.1'),
 ]
 
 dependencies = [
-    ('Python', '3.13.1'),
-    ('Python-bundle-PyPI', '2025.04'),
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
 ]
 
 exts_list = [
-    ('isodate', '0.7.2', {
-        'checksums': ['4cd1aa0f43ca76f4a6c6c0292a85f40b35ec2e43e315b59f06e6d32171a953e6'],
-    }),
     ('rdflib', version, {
         'checksums': ['fed46e24f26a788e2ab8e445f7077f00edcf95abb73bcef4b86cefa8b62dd174'],
     }),

Diff against RDFlib-7.1.4-GCCcore-14.3.0.eb

easybuild/easyconfigs/r/RDFlib/RDFlib-7.1.4-GCCcore-14.3.0.eb

diff --git a/easybuild/easyconfigs/r/RDFlib/RDFlib-7.1.4-GCCcore-14.3.0.eb b/easybuild/easyconfigs/r/RDFlib/RDFlib-7.1.4-GCCcore-13.2.0.eb
index d7a85f286b..7ad7db1fcb 100644
--- a/easybuild/easyconfigs/r/RDFlib/RDFlib-7.1.4-GCCcore-14.3.0.eb
+++ b/easybuild/easyconfigs/r/RDFlib/RDFlib-7.1.4-GCCcore-13.2.0.eb
@@ -7,22 +7,19 @@ homepage = 'https://github.com/RDFLib/rdflib'
 description = """RDFLib is a Python library for working with RDF, a simple yet powerful language
  for representing information."""
 
-toolchain = {'name': 'GCCcore', 'version': '14.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 builddependencies = [
-    ('binutils', '2.44'),
-    ('poetry', '2.1.3'),
+    ('binutils', '2.40'),
+    ('poetry', '1.6.1'),
 ]
 
 dependencies = [
-    ('Python', '3.13.5'),
-    ('Python-bundle-PyPI', '2025.07'),
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
 ]
 
 exts_list = [
-    ('isodate', '0.7.2', {
-        'checksums': ['4cd1aa0f43ca76f4a6c6c0292a85f40b35ec2e43e315b59f06e6d32171a953e6'],
-    }),
     ('rdflib', version, {
         'checksums': ['fed46e24f26a788e2ab8e445f7077f00edcf95abb73bcef4b86cefa8b62dd174'],
     }),

Diff against RDFlib-7.0.0-GCCcore-13.3.0.eb

easybuild/easyconfigs/r/RDFlib/RDFlib-7.0.0-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/r/RDFlib/RDFlib-7.0.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/RDFlib/RDFlib-7.1.4-GCCcore-13.2.0.eb
index 92447d79e7..7ad7db1fcb 100644
--- a/easybuild/easyconfigs/r/RDFlib/RDFlib-7.0.0-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/r/RDFlib/RDFlib-7.1.4-GCCcore-13.2.0.eb
@@ -1,30 +1,27 @@
 easyblock = 'PythonBundle'
 
 name = 'RDFlib'
-version = '7.0.0'
+version = '7.1.4'
 
 homepage = 'https://github.com/RDFLib/rdflib'
 description = """RDFLib is a Python library for working with RDF, a simple yet powerful language
  for representing information."""
 
-toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 builddependencies = [
-    ('binutils', '2.42'),
-    ('poetry', '1.8.3'),
+    ('binutils', '2.40'),
+    ('poetry', '1.6.1'),
 ]
 
 dependencies = [
-    ('Python', '3.12.3'),
-    ('Python-bundle-PyPI', '2024.06'),
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
 ]
 
 exts_list = [
-    ('isodate', '0.6.1', {
-        'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'],
-    }),
     ('rdflib', version, {
-        'checksums': ['9995eb8569428059b8c1affd26b25eac510d64f5043d9ce8c84e0d0036e995ae'],
+        'checksums': ['fed46e24f26a788e2ab8e445f7077f00edcf95abb73bcef4b86cefa8b62dd174'],
     }),
 ]

…ttps://git.astron.nl/RD/LINC/-/blob/b4356321a88504de89c13bb459dbbc625958626f/.gitlab-ci.yml

casparvl · 2025-10-15T19:47:45Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-10-15T19:50:10Z

@casparvl: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=23155 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23155 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 8414

Test results coming soon (I hope)...

Details

- notification for comment with ID 3408011434 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

casparvl · 2025-10-15T19:56:49Z

Test report by @casparvl
FAILED
Build succeeded for 16 out of 20 (13 easyconfigs in total)
tcn1190.local.snellius.surf.nl - Linux RHEL 9.4 (Plow), x86_64, AMD EPYC 9654 96-Core Processor (zen4), Python 3.11.4
See https://gist.github.com/casparvl/33235b8c5701f4ce05d54f2261d3f99c for a full test report.

boegelbot · 2025-10-15T19:59:13Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 13 (12 easyconfigs in total)
jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/059538cca2bd3732406e048ef1a243f1 for a full test report.

casparvl · 2025-10-15T21:58:29Z

Python was being rebuild in #23499 at the same time, causing all the failures on jsczen3.

For the failure on tcn1190, this was due to not having the changes from #23499 and easybuilders/easybuild-easyblocks#3860 yet, which are required for PyTables.

casparvl · 2025-10-15T22:03:53Z

Will need to make some exceptions for the easyconfig unit tests to pass. E.g. PyDot needs to be < v3 according to https://github.com/common-workflow-language/cwltool/blob/a67c898958f6affc8cb9de05fe87c9228a4fc63e/requirements.txt#L10

….com:sara-nl/easybuild-easyconfigs into 20250619162753_new_pr_Boost.Python-NumPy1830

casparvl · 2025-10-16T10:05:30Z

@boegelbot please test @ jsc-zen3

easybuild/easyconfigs/l/LINC/LINC-5.0-foss-2023b.eb

bedroge · 2025-10-17T09:09:33Z

Test report by @bedroge
SUCCESS
Build succeeded for 12 out of 12 (12 easyconfigs in total)
bob-Latitude-5300 - Linux Ubuntu 25.04 (Plucky Puffin), x86_64, Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz, Python 3.13.3
See https://gist.github.com/bedroge/6beb792b3d5d0e39c10a156584f2f2f5 for a full test report.

…not yet in 2.5.0

….com:sara-nl/easybuild-easyconfigs into 20250619162753_new_pr_Boost.Python-NumPy1830

bedroge · 2025-10-20T17:52:53Z

Test report by @bedroge
SUCCESS
Build succeeded for 12 out of 12 (12 easyconfigs in total)
interactive1 - Linux Rocky Linux 8.10, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.6.8
See https://gist.github.com/bedroge/d99c41cff1efe638b69606da6596010e for a full test report.

bedroge · 2025-10-20T17:59:51Z

Test report by @bedroge
SUCCESS
Build succeeded for 12 out of 12 (12 easyconfigs in total)
bob-Latitude-5300 - Linux Ubuntu 25.04 (Plucky Puffin), x86_64, Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz, Python 3.13.3
See https://gist.github.com/bedroge/f072724bd37bb44590bae846e36c21e5 for a full test report.

easybuild/easyconfigs/l/LINC/LINC-5.0-foss-2023b.eb

easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-13.2.0.eb

easybuild/easyconfigs/s/SAGECal/SAGECal-0.8.4-foss-2023b.eb

easybuild/easyconfigs/t/toil-cwl/toil-cwl-8.2.0-foss-2023b.eb

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>

…S_NUM_THREADS, and optionally unsetting all SLURM env. We don't want the module to do this for us, as setting OMP_NUM_THREADS=1 and OPENBLAS_NUM_THREADS=1 might cripple other codes without the user noticing, hence the user should set them manually so they are aware

bedroge · 2025-10-21T10:13:39Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-10-21T10:20:12Z

@bedroge: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=23155 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23155 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 8501

Test results coming soon (I hope)...

Details

- notification for comment with ID 3425791326 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

bedroge · 2025-10-21T10:30:05Z

Test report by @bedroge
SUCCESS
Build succeeded for 12 out of 12 (12 easyconfigs in total)
bob-Latitude-5300 - Linux Ubuntu 25.04 (Plucky Puffin), x86_64, Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz, Python 3.13.3
See https://gist.github.com/bedroge/b39e4b18129e0be555c6799f39d485fc for a full test report.

boegelbot · 2025-10-21T11:01:19Z

Test report by @boegelbot
SUCCESS
Build succeeded for 12 out of 12 (12 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/6e1d594385122002a071ed05fc018fbb for a full test report.

bedroge · 2025-10-21T12:12:18Z

Going in, thanks @casparvl!

casparvl added new update labels Jun 19, 2025

casparvl marked this pull request as draft June 19, 2025 14:28

casparl and others added 7 commits June 23, 2025 18:02

Added LINC, which was the whole point of this PR

d401df5

Added missing patches

a915a3d

Added missing RDFlib

887a05b

Added missing pydot

5708a17

Disable failing script from sanity check for now

9da45b8

Fix checksum

770465d

Remove checksum for linc, since it is not reproducible

49b8436

Thyre added the 2023b label Aug 18, 2025

Caspar van Leeuwen and others added 3 commits October 15, 2025 17:46

Added a test step that runs the run_hba_target test from LINCs own CI h…

0ac0d51

…ttps://git.astron.nl/RD/LINC/-/blob/b4356321a88504de89c13bb459dbbc625958626f/.gitlab-ci.yml

Fix typo

b20555c

Merge branch 'develop' into 20250619162753_new_pr_Boost.Python-NumPy1830

53b1c49

casparvl changed the title ~~{astro}[foss/2023b] Boost.Python-NumPy v1.83.0, LoSoTo v2.5.0, LSMTool v1.7.0, ...~~ {astro}[foss/2023b] LoSoTo v2.5.0, LSMTool v1.7.0, ... Oct 15, 2025

casparvl changed the title ~~{astro}[foss/2023b] LoSoTo v2.5.0, LSMTool v1.7.0, ...~~ {astro}[foss/2023b] LoSoTo v2.5.0, LSMTool v1.7.0, LINC v5.0 ... Oct 15, 2025

casparvl changed the title ~~{astro}[foss/2023b] LoSoTo v2.5.0, LSMTool v1.7.0, LINC v5.0 ...~~ {astro}[foss/2023b] LoSoTo v2.5.0, LSMTool v1.7.0, LINC v5.0, ... Oct 15, 2025

Caspar van Leeuwen added 4 commits October 16, 2025 00:07

Fix LINC code style errors

42779b8

Fix too long line in PyVO

7cdda1d

Add missing checksums for dysco, LofarStMan and SAGECal

c4a64d0

Merge branch '20250619162753_new_pr_Boost.Python-NumPy1830' of github…

dd661fa

….com:sara-nl/easybuild-easyconfigs into 20250619162753_new_pr_Boost.Python-NumPy1830

bedroge reviewed Oct 17, 2025

View reviewed changes

easybuild/easyconfigs/l/LINC/LINC-5.0-foss-2023b.eb Show resolved Hide resolved

Update easybuild/easyconfigs/l/LINC/LINC-5.0-foss-2023b.eb

5f39cf7

Caspar van Leeuwen added 2 commits October 20, 2025 17:14

Use tagged tarball, as setuptools_scm was only introduced in master, …

40f7b77

…not yet in 2.5.0

Merge branch '20250619162753_new_pr_Boost.Python-NumPy1830' of github…

de09744

….com:sara-nl/easybuild-easyconfigs into 20250619162753_new_pr_Boost.Python-NumPy1830

casparvl marked this pull request as ready for review October 20, 2025 19:21

bedroge reviewed Oct 21, 2025

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easybuild/easyconfigs/l/LINC/LINC-5.0-foss-2023b.eb Outdated Show resolved Hide resolved

fix small typo

cee8866

bedroge reviewed Oct 21, 2025

View reviewed changes

easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-13.2.0.eb Show resolved Hide resolved

add and remove blank line

7d7afcf

bedroge reviewed Oct 21, 2025

View reviewed changes

easybuild/easyconfigs/s/SAGECal/SAGECal-0.8.4-foss-2023b.eb Outdated Show resolved Hide resolved

bedroge reviewed Oct 21, 2025

View reviewed changes

easybuild/easyconfigs/t/toil-cwl/toil-cwl-8.2.0-foss-2023b.eb Outdated Show resolved Hide resolved

bedroge and others added 3 commits October 21, 2025 09:37

fix typo

7cb198e

Update easybuild/easyconfigs/s/SAGECal/SAGECal-0.8.4-foss-2023b.eb

0c9f4a5

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>

bedroge approved these changes Oct 21, 2025

View reviewed changes

bedroge added this to the next release (5.2.0?) milestone Oct 21, 2025

bedroge merged commit b35081d into easybuilders:develop Oct 21, 2025
8 checks passed

boegel changed the title ~~{astro}[foss/2023b] LoSoTo v2.5.0, LSMTool v1.7.0, LINC v5.0, ...~~ {astro}[foss/2023b] LoSoTo v2.5.0, LSMTool v1.7.0, LINC v5.0, dysco v1.3 Dec 23, 2025

boegel changed the title ~~{astro}[foss/2023b] LoSoTo v2.5.0, LSMTool v1.7.0, LINC v5.0, dysco v1.3~~ {astro}[foss/2023b] LoSoTo v2.5.0, LSMTool v1.7.0, LINC v5.0, dysco v1.3, LofarStMan v1.0 Dec 23, 2025

boegel changed the title ~~{astro}[foss/2023b] LoSoTo v2.5.0, LSMTool v1.7.0, LINC v5.0, dysco v1.3, LofarStMan v1.0~~ {astro}[foss/2023b] LoSoTo v2.5.0, LSMTool v1.7.0, LINC v5.0, dysco v1.3, LofarStMan v1.0, PyVO v1.7 Dec 23, 2025

boegel changed the title ~~{astro}[foss/2023b] LoSoTo v2.5.0, LSMTool v1.7.0, LINC v5.0, dysco v1.3, LofarStMan v1.0, PyVO v1.7~~ {astro}[foss/2023b] LoSoTo v2.5.0, LSMTool v1.7.0, LINC v5.0, dysco v1.3, LofarStMan v1.0, PyVO v1.7. RMextract v0.5.1 Dec 23, 2025

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Updated software cwltool-3.1.20250110105449-foss-2023b.eb

Updated software pydot-2.0.0-GCCcore-13.2.0.eb

Updated software RDFlib-7.1.4-GCCcore-13.2.0.eb

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casparvl commented Jun 19, 2025 •

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Updated software `cwltool-3.1.20250110105449-foss-2023b.eb`

Updated software `pydot-2.0.0-GCCcore-13.2.0.eb`

Updated software `RDFlib-7.1.4-GCCcore-13.2.0.eb`