{chem}[gompi/2025b] CoordgenLibs v3.0.2, OpenBabel v3.1.1 by Micket · Pull Request #25500 · easybuilders/easybuild-easyconfigs

Micket · 2026-03-04T16:50:24Z

(created using eb --new-pr)

…1-gompi-2025b.eb

github-actions · 2026-03-04T16:51:09Z

Updated software `CoordgenLibs-3.0.2-gompi-2025b.eb`

Diff against CoordgenLibs-3.0.2-gompi-2025a.eb

easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.2-gompi-2025a.eb

diff --git a/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.2-gompi-2025a.eb b/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.2-gompi-2025b.eb
index 34572c0fe1..740f4522f5 100644
--- a/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.2-gompi-2025a.eb
+++ b/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.2-gompi-2025b.eb
@@ -6,26 +6,26 @@ version = '3.0.2'
 homepage = 'https://github.com/schrodinger/coordgenlibs'
 description = "Schrodinger-developed 2D Coordinate Generation"
 
-toolchain = {'name': 'gompi', 'version': '2025a'}
+toolchain = {'name': 'gompi', 'version': '2025b'}
 
 source_urls = ['https://github.com/schrodinger/coordgenlibs/archive/']
 sources = ['v%(version)s.tar.gz']
 checksums = ['f67697434f7fec03bca150a6d84ea0e8409f6ec49d5aab43badc5833098ff4e3']
 
-builddependencies = [('CMake', '3.31.3')]
+builddependencies = [('CMake', '4.0.3')]
 
 dependencies = [
     ('Boost', '1.88.0'),
     ('maeparser', '1.3.3'),
 ]
 
-configopts = "-Dmaeparser_DIR=$EBROOTMAEPARSER/lib/cmake"
+configopts = "-Dmaeparser_DIR=$EBROOTMAEPARSER/lib/cmake -DCMAKE_POLICY_VERSION_MINIMUM=3.5"
 
 # work around compiler warning treated as error by stripping out use of -Werror
 prebuildopts = "sed -i 's/-Werror//g' CMakeFiles/coordgen.dir/flags.make && "
 
 sanity_check_paths = {
-    'files': ['lib/libcoordgen.%s' % SHLIB_EXT],
+    'files': [f'lib/libcoordgen.{SHLIB_EXT}'],
     'dirs': ['include/coordgen', 'lib/cmake'],
 }

Diff against CoordgenLibs-3.0.2-gompi-2024a.eb

easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.2-gompi-2024a.eb

diff --git a/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.2-gompi-2024a.eb b/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.2-gompi-2025b.eb
index d5a216d0ca..740f4522f5 100644
--- a/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.2-gompi-2024a.eb
+++ b/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.2-gompi-2025b.eb
@@ -6,26 +6,26 @@ version = '3.0.2'
 homepage = 'https://github.com/schrodinger/coordgenlibs'
 description = "Schrodinger-developed 2D Coordinate Generation"
 
-toolchain = {'name': 'gompi', 'version': '2024a'}
+toolchain = {'name': 'gompi', 'version': '2025b'}
 
 source_urls = ['https://github.com/schrodinger/coordgenlibs/archive/']
 sources = ['v%(version)s.tar.gz']
 checksums = ['f67697434f7fec03bca150a6d84ea0e8409f6ec49d5aab43badc5833098ff4e3']
 
-builddependencies = [('CMake', '3.29.3')]
+builddependencies = [('CMake', '4.0.3')]
 
 dependencies = [
-    ('Boost', '1.85.0'),
-    ('maeparser', '1.3.1'),
+    ('Boost', '1.88.0'),
+    ('maeparser', '1.3.3'),
 ]
 
-configopts = "-Dmaeparser_DIR=$EBROOTMAEPARSER/lib/cmake"
+configopts = "-Dmaeparser_DIR=$EBROOTMAEPARSER/lib/cmake -DCMAKE_POLICY_VERSION_MINIMUM=3.5"
 
 # work around compiler warning treated as error by stripping out use of -Werror
 prebuildopts = "sed -i 's/-Werror//g' CMakeFiles/coordgen.dir/flags.make && "
 
 sanity_check_paths = {
-    'files': ['lib/libcoordgen.%s' % SHLIB_EXT],
+    'files': [f'lib/libcoordgen.{SHLIB_EXT}'],
     'dirs': ['include/coordgen', 'lib/cmake'],
 }

Diff against CoordgenLibs-3.0.2-gompi-2023b.eb

easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.2-gompi-2023b.eb

diff --git a/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.2-gompi-2023b.eb b/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.2-gompi-2025b.eb
index 10e0d0b2f5..740f4522f5 100644
--- a/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.2-gompi-2023b.eb
+++ b/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.2-gompi-2025b.eb
@@ -6,26 +6,26 @@ version = '3.0.2'
 homepage = 'https://github.com/schrodinger/coordgenlibs'
 description = "Schrodinger-developed 2D Coordinate Generation"
 
-toolchain = {'name': 'gompi', 'version': '2023b'}
+toolchain = {'name': 'gompi', 'version': '2025b'}
 
 source_urls = ['https://github.com/schrodinger/coordgenlibs/archive/']
 sources = ['v%(version)s.tar.gz']
 checksums = ['f67697434f7fec03bca150a6d84ea0e8409f6ec49d5aab43badc5833098ff4e3']
 
-builddependencies = [('CMake', '3.27.6')]
+builddependencies = [('CMake', '4.0.3')]
 
 dependencies = [
-    ('Boost', '1.83.0'),
+    ('Boost', '1.88.0'),
     ('maeparser', '1.3.3'),
 ]
 
-configopts = "-Dmaeparser_DIR=$EBROOTMAEPARSER/lib/cmake"
+configopts = "-Dmaeparser_DIR=$EBROOTMAEPARSER/lib/cmake -DCMAKE_POLICY_VERSION_MINIMUM=3.5"
 
 # work around compiler warning treated as error by stripping out use of -Werror
 prebuildopts = "sed -i 's/-Werror//g' CMakeFiles/coordgen.dir/flags.make && "
 
 sanity_check_paths = {
-    'files': ['lib/libcoordgen.%s' % SHLIB_EXT],
+    'files': [f'lib/libcoordgen.{SHLIB_EXT}'],
     'dirs': ['include/coordgen', 'lib/cmake'],
 }

Updated software `OpenBabel-3.1.1-gompi-2025b.eb`

Diff against OpenBabel-3.1.1-gompi-2025a.eb

easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2025a.eb

diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2025a.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2025b.eb
index 3b5f8c45c0..fdd26e916c 100644
--- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2025a.eb
+++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2025b.eb
@@ -7,7 +7,7 @@ description = """Open Babel is a chemical toolbox designed to speak the many
  to search, convert, analyze, or store data from molecular modeling, chemistry,
  solid-state materials, biochemistry, or related areas."""
 
-toolchain = {'name': 'gompi', 'version': '2025a'}
+toolchain = {'name': 'gompi', 'version': '2025b'}
 toolchainopts = {'pic': True}
 
 source_urls = [GITHUB_LOWER_SOURCE]
@@ -36,13 +36,13 @@ checksums = [
 ]
 
 builddependencies = [
-    ('CMake', '3.31.3'),
+    ('CMake', '3.31.8'),
     ('SWIG', '4.3.1'),
 ]
 dependencies = [
-    ('Python', '3.13.1'),
+    ('Python', '3.13.5'),
     ('zlib', '1.3.1'),
-    ('libxml2', '2.13.4'),
+    ('libxml2', '2.14.3'),
     ('Eigen', '3.4.0'),
     ('RapidJSON', '1.1.0-20250205'),
     ('cairo', '1.18.4'),  # optional: for .png output
@@ -62,7 +62,7 @@ postinstallcmds = [
     'ln -s %(installdir)s/share/openbabel/3.1.0 %(installdir)s/share/openbabel/%(version)s',
 ]
 
-pretestopts = 'cp lib/_openbabel.%s %%(builddir)s/openbabel-*/scripts/python/openbabel/ && ' % SHLIB_EXT
+pretestopts = f'cp lib/_openbabel.{SHLIB_EXT} %(builddir)s/openbabel-*/scripts/python/openbabel/ && '
 runtest = 'test'
 
 moduleclass = 'chem'

Diff against OpenBabel-3.1.1-gompi-2024a.eb

easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2024a.eb

diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2024a.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2025b.eb
index 7d08a69add..fdd26e916c 100644
--- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2024a.eb
+++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2025b.eb
@@ -7,7 +7,7 @@ description = """Open Babel is a chemical toolbox designed to speak the many
  to search, convert, analyze, or store data from molecular modeling, chemistry,
  solid-state materials, biochemistry, or related areas."""
 
-toolchain = {'name': 'gompi', 'version': '2024a'}
+toolchain = {'name': 'gompi', 'version': '2025b'}
 toolchainopts = {'pic': True}
 
 source_urls = [GITHUB_LOWER_SOURCE]
@@ -36,18 +36,18 @@ checksums = [
 ]
 
 builddependencies = [
-    ('CMake', '3.29.3'),
-    ('SWIG', '4.2.1'),
+    ('CMake', '3.31.8'),
+    ('SWIG', '4.3.1'),
 ]
 dependencies = [
-    ('Python', '3.12.3'),
+    ('Python', '3.13.5'),
     ('zlib', '1.3.1'),
-    ('libxml2', '2.12.7'),
+    ('libxml2', '2.14.3'),
     ('Eigen', '3.4.0'),
-    ('RapidJSON', '1.1.0-20240815'),
-    ('cairo', '1.18.0'),  # optional: for .png output
-    ('Boost', '1.85.0'),
-    ('maeparser', '1.3.1'),
+    ('RapidJSON', '1.1.0-20250205'),
+    ('cairo', '1.18.4'),  # optional: for .png output
+    ('Boost', '1.88.0'),
+    ('maeparser', '1.3.3'),
     ('CoordgenLibs', '3.0.2'),
 ]
 
@@ -62,7 +62,7 @@ postinstallcmds = [
     'ln -s %(installdir)s/share/openbabel/3.1.0 %(installdir)s/share/openbabel/%(version)s',
 ]
 
-pretestopts = 'cp lib/_openbabel.%s %%(builddir)s/openbabel-*/scripts/python/openbabel/ && ' % SHLIB_EXT
+pretestopts = f'cp lib/_openbabel.{SHLIB_EXT} %(builddir)s/openbabel-*/scripts/python/openbabel/ && '
 runtest = 'test'
 
 moduleclass = 'chem'

Diff against OpenBabel-3.1.1-gompi-2023b.eb

easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2023b.eb

diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2023b.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2025b.eb
index c9fcaea55e..fdd26e916c 100644
--- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2023b.eb
+++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2025b.eb
@@ -7,7 +7,7 @@ description = """Open Babel is a chemical toolbox designed to speak the many
  to search, convert, analyze, or store data from molecular modeling, chemistry,
  solid-state materials, biochemistry, or related areas."""
 
-toolchain = {'name': 'gompi', 'version': '2023b'}
+toolchain = {'name': 'gompi', 'version': '2025b'}
 toolchainopts = {'pic': True}
 
 source_urls = [GITHUB_LOWER_SOURCE]
@@ -36,17 +36,17 @@ checksums = [
 ]
 
 builddependencies = [
-    ('CMake', '3.27.6'),
-    ('SWIG', '4.1.1'),
+    ('CMake', '3.31.8'),
+    ('SWIG', '4.3.1'),
 ]
 dependencies = [
-    ('Python', '3.11.5'),
-    ('zlib', '1.2.13'),
-    ('libxml2', '2.11.5'),
+    ('Python', '3.13.5'),
+    ('zlib', '1.3.1'),
+    ('libxml2', '2.14.3'),
     ('Eigen', '3.4.0'),
-    ('RapidJSON', '1.1.0-20240409'),
-    ('cairo', '1.18.0'),  # optional: for .png output
-    ('Boost', '1.83.0'),
+    ('RapidJSON', '1.1.0-20250205'),
+    ('cairo', '1.18.4'),  # optional: for .png output
+    ('Boost', '1.88.0'),
     ('maeparser', '1.3.3'),
     ('CoordgenLibs', '3.0.2'),
 ]
@@ -62,7 +62,7 @@ postinstallcmds = [
     'ln -s %(installdir)s/share/openbabel/3.1.0 %(installdir)s/share/openbabel/%(version)s',
 ]
 
-pretestopts = 'cp lib/_openbabel.%s %%(builddir)s/openbabel-*/scripts/python/openbabel/ && ' % SHLIB_EXT
+pretestopts = f'cp lib/_openbabel.{SHLIB_EXT} %(builddir)s/openbabel-*/scripts/python/openbabel/ && '
 runtest = 'test'
 
 moduleclass = 'chem'

Micket · 2026-03-04T16:51:45Z

Test report by @Micket
FAILED
Build succeeded for 0 out of 2 (total: 4 secs) (2 easyconfigs in total)
vera-icelake-build - Linux Rocky Linux 9.6, x86_64, Intel(R) Xeon(R) Silver 4316 CPU @ 2.30GHz, Python 3.9.21
See https://gist.github.com/Micket/8ad4288724deafd9780a9e1a96327e03 for a full test report.

Micket · 2026-03-04T16:55:33Z

Test report by @Micket
FAILED
Build succeeded for 1 out of 2 (total: 57 secs) (2 easyconfigs in total)
vera-icelake-build - Linux Rocky Linux 9.6, x86_64, Intel(R) Xeon(R) Silver 4316 CPU @ 2.30GHz, Python 3.9.21
See https://gist.github.com/Micket/e5682d1a6faf392ce7639ed4c975c0cc for a full test report.

Micket · 2026-03-04T17:01:48Z

Test report by @Micket
FAILED
Build succeeded for 1 out of 2 (total: 1 min 10 secs) (2 easyconfigs in total)
vera-icelake-build - Linux Rocky Linux 9.6, x86_64, Intel(R) Xeon(R) Silver 4316 CPU @ 2.30GHz, Python 3.9.21
See https://gist.github.com/Micket/dc54cc947c681a12653840936454ccd2 for a full test report.

Micket · 2026-03-04T17:29:31Z

Test report by @Micket
SUCCESS
Build succeeded for 2 out of 2 (total: 6 mins 23 secs) (2 easyconfigs in total)
vera-icelake-build - Linux Rocky Linux 9.6, x86_64, Intel(R) Xeon(R) Silver 4316 CPU @ 2.30GHz, Python 3.9.21
See https://gist.github.com/Micket/c9bc9c0ff9b05cd8a0df54c4a8039e44 for a full test report.

adding easyconfigs: CoordgenLibs-3.0.2-gompi-2025b.eb, OpenBabel-3.1.…

ab3ff32

…1-gompi-2025b.eb

Micket added the update label Mar 4, 2026

github-actions bot added the 2025b issues & PRs related to 2025b common toolchains label Mar 4, 2026

Micket added this to the next release (5.2.2?) milestone Mar 4, 2026

CMake bump

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Downgrade CMake

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{chem}[gompi/2025b] CoordgenLibs v3.0.2, OpenBabel v3.1.1#25500

{chem}[gompi/2025b] CoordgenLibs v3.0.2, OpenBabel v3.1.1#25500
Micket wants to merge 4 commits intoeasybuilders:developfrom
Micket:20260304175021_new_pr_CoordgenLibs302

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Updated software CoordgenLibs-3.0.2-gompi-2025b.eb

Updated software OpenBabel-3.1.1-gompi-2025b.eb

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Updated software `CoordgenLibs-3.0.2-gompi-2025b.eb`

Updated software `OpenBabel-3.1.1-gompi-2025b.eb`