{bio,data}[GCCcore/15.2.0] Pint v0.25.3, freesasa v2.2.1, gemmi v0.7.5, PnetCDF v1.14.1 by pavelToman · Pull Request #26378 · easybuilders/easybuild-easyconfigs

pavelToman · 2026-06-26T13:21:46Z

(created using eb --new-pr)
requires:

Biopython from: {bio}[gfbf/2026.1] nglview v4.0.1, MDAnalysis v2.10.0, Seaborn v0.13.2, ASE v3.28.0, Biopython v1.87, Flask v3.1.3, JupyterLab v4.5.8, JupyterNotebook v7.5.7, mrcfile v1.5.4, spglib-python v2.7.0 #26301

…f-2026.1.eb, gemmi-0.7.5-GCCcore-15.2.0.eb, numba-0.65.1-foss-2026.1.eb, LLVM-20.1.8-GCCcore-15.2.0.eb, PnetCDF-1.14.1-gompi-2026.1.eb, netCDF-Fortran-4.6.3-gompi-2026.1.eb

github-actions · 2026-06-26T13:22:37Z

Updated software `gemmi-0.7.5-GCCcore-15.2.0.eb`

Diff against gemmi-0.7.4-GCC-14.2.0.eb

easybuild/easyconfigs/g/gemmi/gemmi-0.7.4-GCC-14.2.0.eb

diff --git a/easybuild/easyconfigs/g/gemmi/gemmi-0.7.4-GCC-14.2.0.eb b/easybuild/easyconfigs/g/gemmi/gemmi-0.7.5-GCCcore-15.2.0.eb
index e88b612553..3161eed108 100644
--- a/easybuild/easyconfigs/g/gemmi/gemmi-0.7.4-GCC-14.2.0.eb
+++ b/easybuild/easyconfigs/g/gemmi/gemmi-0.7.5-GCCcore-15.2.0.eb
@@ -2,7 +2,7 @@
 easyblock = 'CMakePythonPackage'
 
 name = 'gemmi'
-version = '0.7.4'
+version = '0.7.5'
 
 homepage = 'https://gemmi.readthedocs.io/'
 description = """Gemmi is a library, accompanied by a set of programs, developed primarily for
@@ -15,24 +15,23 @@ Parts of this library can be useful in structural bioinformatics (for symmetry-
 aware analysis of protein models), and in other molecular-structure sciences
 that use CIF files (we have the fastest open-source CIF parser)."""
 
-toolchain = {'name': 'GCC', 'version': '14.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '15.2.0'}
 toolchainopts = {'opt': True}
 
 github_account = 'project-gemmi'
 source_urls = [GITHUB_SOURCE]
 sources = ['v%(version)s.tar.gz']
-checksums = ['58ed9023e0f75033ebec1da630461bc6e1af661f29f0c41deed66c20315ebe2a']
+checksums = ['9e2a8a51e62c69bf43f62aadf527ca4312860de8a36c12a8747d3e8ae556f0b3']
 
 builddependencies = [
-    ('pybind11', '2.13.6'),
-    ('pybind11-stubgen', '2.5.5'),
-    ('scikit-build-core', '0.11.1'),
-    ('meson-python', '0.18.0'),
-    ('nanobind', '2.9.2'),
-    ('CMake', '3.31.3'),
+    ('binutils', '2.45'),
+    ('scikit-build-core', '0.12.2'),
+    ('nanobind', '2.13.0'),
+    ('CMake', '4.2.1'),
 ]
 dependencies = [
-    ('Python', '3.13.1'),
+    ('Python', '3.14.2'),
+    ('zlib', '2.3.2'),
 ]
 
 configopts = [
@@ -52,6 +51,11 @@ exts_list = [
     (name, version, {
         'nosource': True,
         'installopts': _pip_opts,
+        'testinstall': True,
+        'runtest': (
+            'LD_LIBRARY_PATH=%(builddir)s/pybuild:$LD_LIBRARY_PATH '
+            'python -s -m unittest discover -v -s %(builddir)s/%(name)s-%(version)s/tests'
+        ),
     }),
 ]

Diff against gemmi-0.7.4-GCC-14.3.0.eb

easybuild/easyconfigs/g/gemmi/gemmi-0.7.4-GCC-14.3.0.eb

diff --git a/easybuild/easyconfigs/g/gemmi/gemmi-0.7.4-GCC-14.3.0.eb b/easybuild/easyconfigs/g/gemmi/gemmi-0.7.5-GCCcore-15.2.0.eb
index 142f4ed90c..3161eed108 100644
--- a/easybuild/easyconfigs/g/gemmi/gemmi-0.7.4-GCC-14.3.0.eb
+++ b/easybuild/easyconfigs/g/gemmi/gemmi-0.7.5-GCCcore-15.2.0.eb
@@ -2,7 +2,7 @@
 easyblock = 'CMakePythonPackage'
 
 name = 'gemmi'
-version = '0.7.4'
+version = '0.7.5'
 
 homepage = 'https://gemmi.readthedocs.io/'
 description = """Gemmi is a library, accompanied by a set of programs, developed primarily for
@@ -15,24 +15,23 @@ Parts of this library can be useful in structural bioinformatics (for symmetry-
 aware analysis of protein models), and in other molecular-structure sciences
 that use CIF files (we have the fastest open-source CIF parser)."""
 
-toolchain = {'name': 'GCC', 'version': '14.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '15.2.0'}
 toolchainopts = {'opt': True}
 
 github_account = 'project-gemmi'
 source_urls = [GITHUB_SOURCE]
 sources = ['v%(version)s.tar.gz']
-checksums = ['58ed9023e0f75033ebec1da630461bc6e1af661f29f0c41deed66c20315ebe2a']
+checksums = ['9e2a8a51e62c69bf43f62aadf527ca4312860de8a36c12a8747d3e8ae556f0b3']
 
 builddependencies = [
-    ('pybind11', '3.0.0'),
-    ('pybind11-stubgen', '2.5.5'),
-    ('scikit-build-core', '0.11.5'),
-    ('meson-python', '0.18.0'),
-    ('nanobind', '2.9.2'),
-    ('CMake', '4.0.3'),
+    ('binutils', '2.45'),
+    ('scikit-build-core', '0.12.2'),
+    ('nanobind', '2.13.0'),
+    ('CMake', '4.2.1'),
 ]
 dependencies = [
-    ('Python', '3.13.5'),
+    ('Python', '3.14.2'),
+    ('zlib', '2.3.2'),
 ]
 
 configopts = [
@@ -52,6 +51,11 @@ exts_list = [
     (name, version, {
         'nosource': True,
         'installopts': _pip_opts,
+        'testinstall': True,
+        'runtest': (
+            'LD_LIBRARY_PATH=%(builddir)s/pybuild:$LD_LIBRARY_PATH '
+            'python -s -m unittest discover -v -s %(builddir)s/%(name)s-%(version)s/tests'
+        ),
     }),
 ]

Diff against gemmi-0.7.1-GCC-13.3.0.eb

easybuild/easyconfigs/g/gemmi/gemmi-0.7.1-GCC-13.3.0.eb

diff --git a/easybuild/easyconfigs/g/gemmi/gemmi-0.7.1-GCC-13.3.0.eb b/easybuild/easyconfigs/g/gemmi/gemmi-0.7.5-GCCcore-15.2.0.eb
index 039e567c7a..3161eed108 100644
--- a/easybuild/easyconfigs/g/gemmi/gemmi-0.7.1-GCC-13.3.0.eb
+++ b/easybuild/easyconfigs/g/gemmi/gemmi-0.7.5-GCCcore-15.2.0.eb
@@ -2,7 +2,7 @@
 easyblock = 'CMakePythonPackage'
 
 name = 'gemmi'
-version = '0.7.1'
+version = '0.7.5'
 
 homepage = 'https://gemmi.readthedocs.io/'
 description = """Gemmi is a library, accompanied by a set of programs, developed primarily for
@@ -15,24 +15,23 @@ Parts of this library can be useful in structural bioinformatics (for symmetry-
 aware analysis of protein models), and in other molecular-structure sciences
 that use CIF files (we have the fastest open-source CIF parser)."""
 
-toolchain = {'name': 'GCC', 'version': '13.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '15.2.0'}
 toolchainopts = {'opt': True}
 
 github_account = 'project-gemmi'
 source_urls = [GITHUB_SOURCE]
 sources = ['v%(version)s.tar.gz']
-checksums = ['5d87c3e82ee159f5642d7c083a74e00ca9cc038ccf9be2522d7ae985f3377393']
+checksums = ['9e2a8a51e62c69bf43f62aadf527ca4312860de8a36c12a8747d3e8ae556f0b3']
 
 builddependencies = [
-    ('pybind11', '2.12.0'),
-    ('pybind11-stubgen', '2.5.4'),
-    ('scikit-build-core', '0.10.6'),
-    ('meson-python', '0.16.0'),
-    ('nanobind', '2.5.0'),
-    ('CMake', '3.29.3'),
+    ('binutils', '2.45'),
+    ('scikit-build-core', '0.12.2'),
+    ('nanobind', '2.13.0'),
+    ('CMake', '4.2.1'),
 ]
 dependencies = [
-    ('Python', '3.12.3'),
+    ('Python', '3.14.2'),
+    ('zlib', '2.3.2'),
 ]
 
 configopts = [
@@ -52,6 +51,11 @@ exts_list = [
     (name, version, {
         'nosource': True,
         'installopts': _pip_opts,
+        'testinstall': True,
+        'runtest': (
+            'LD_LIBRARY_PATH=%(builddir)s/pybuild:$LD_LIBRARY_PATH '
+            'python -s -m unittest discover -v -s %(builddir)s/%(name)s-%(version)s/tests'
+        ),
     }),
 ]

Updated software `Pint-0.25.3-GCCcore-15.2.0.eb`

Diff against Pint-0.25-GCCcore-14.3.0.eb

easybuild/easyconfigs/p/Pint/Pint-0.25-GCCcore-14.3.0.eb

diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.25-GCCcore-14.3.0.eb b/easybuild/easyconfigs/p/Pint/Pint-0.25.3-GCCcore-15.2.0.eb
index 37be0736cd..917f4b5990 100644
--- a/easybuild/easyconfigs/p/Pint/Pint-0.25-GCCcore-14.3.0.eb
+++ b/easybuild/easyconfigs/p/Pint/Pint-0.25.3-GCCcore-15.2.0.eb
@@ -1,7 +1,7 @@
 easyblock = 'PythonBundle'
 
 name = 'Pint'
-version = '0.25'
+version = '0.25.3'
 
 homepage = 'https://github.com/hgrecco/pint'
 description = """Pint is a Python package to define, operate and
@@ -9,16 +9,15 @@ manipulate physical quantities: the product of a numerical value and a
 unit of measurement. It allows arithmetic operations between them and
 conversions from and to different units."""
 
-toolchain = {'name': 'GCCcore', 'version': '14.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '15.2.0'}
 
 builddependencies = [
-    ('binutils', '2.44'),
-    ('hatchling', '1.27.0'),
+    ('binutils', '2.45'),
+    ('hatchling', '1.29.0'),
 ]
-
 dependencies = [
-    ('Python', '3.13.5'),
-    ('Python-bundle-PyPI', '2025.07'),
+    ('Python', '3.14.2'),
+    ('Python-bundle-PyPI', '2026.04'),
 ]
 
 exts_list = [
@@ -29,8 +28,8 @@ exts_list = [
         'checksums': ['266d98905595be2ccc5da964fe0a2c3526fbbffdc45b65b3146d75db992ef6b2'],
     }),
     (name, version, {
-        'sources': ['%(namelower)s-%(version)s.tar.gz'],
-        'checksums': ['22911a30d682ee0540d656571c19a7b1806ce00b2be88a16f67218108b7b8cc2'],
+        'sources': [SOURCELOWER_TAR_GZ],
+        'checksums': ['f8f5df6cf65314d74da1ade1bf96f8e3e4d0c41b51577ac53c49e7d44ca5acee'],
     }),
 ]

Diff against Pint-0.24.4-GCCcore-14.2.0.eb

easybuild/easyconfigs/p/Pint/Pint-0.24.4-GCCcore-14.2.0.eb

diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.24.4-GCCcore-14.2.0.eb b/easybuild/easyconfigs/p/Pint/Pint-0.25.3-GCCcore-15.2.0.eb
index b1a8215a4e..917f4b5990 100644
--- a/easybuild/easyconfigs/p/Pint/Pint-0.24.4-GCCcore-14.2.0.eb
+++ b/easybuild/easyconfigs/p/Pint/Pint-0.25.3-GCCcore-15.2.0.eb
@@ -1,7 +1,7 @@
 easyblock = 'PythonBundle'
 
 name = 'Pint'
-version = '0.24.4'
+version = '0.25.3'
 
 homepage = 'https://github.com/hgrecco/pint'
 description = """Pint is a Python package to define, operate and
@@ -9,16 +9,15 @@ manipulate physical quantities: the product of a numerical value and a
 unit of measurement. It allows arithmetic operations between them and
 conversions from and to different units."""
 
-toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '15.2.0'}
 
 builddependencies = [
-    ('binutils', '2.42'),
-    ('hatchling', '1.27.0'),
+    ('binutils', '2.45'),
+    ('hatchling', '1.29.0'),
 ]
-
 dependencies = [
-    ('Python', '3.13.1'),
-    ('Python-bundle-PyPI', '2025.04'),
+    ('Python', '3.14.2'),
+    ('Python-bundle-PyPI', '2026.04'),
 ]
 
 exts_list = [
@@ -29,8 +28,8 @@ exts_list = [
         'checksums': ['266d98905595be2ccc5da964fe0a2c3526fbbffdc45b65b3146d75db992ef6b2'],
     }),
     (name, version, {
-        'sources': ['%(namelower)s-%(version)s.tar.gz'],
-        'checksums': ['35275439b574837a6cd3020a5a4a73645eb125ce4152a73a2f126bf164b91b80'],
+        'sources': [SOURCELOWER_TAR_GZ],
+        'checksums': ['f8f5df6cf65314d74da1ade1bf96f8e3e4d0c41b51577ac53c49e7d44ca5acee'],
     }),
 ]

Diff against Pint-0.24.4-GCCcore-13.3.0.eb

easybuild/easyconfigs/p/Pint/Pint-0.24.4-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.24.4-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/Pint/Pint-0.25.3-GCCcore-15.2.0.eb
index 83ed499a0c..917f4b5990 100644
--- a/easybuild/easyconfigs/p/Pint/Pint-0.24.4-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/p/Pint/Pint-0.25.3-GCCcore-15.2.0.eb
@@ -1,7 +1,7 @@
 easyblock = 'PythonBundle'
 
 name = 'Pint'
-version = '0.24.4'
+version = '0.25.3'
 
 homepage = 'https://github.com/hgrecco/pint'
 description = """Pint is a Python package to define, operate and
@@ -9,16 +9,15 @@ manipulate physical quantities: the product of a numerical value and a
 unit of measurement. It allows arithmetic operations between them and
 conversions from and to different units."""
 
-toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '15.2.0'}
 
 builddependencies = [
-    ('binutils', '2.42'),
-    ('hatchling', '1.24.2'),
+    ('binutils', '2.45'),
+    ('hatchling', '1.29.0'),
 ]
-
 dependencies = [
-    ('Python', '3.12.3'),
-    ('Python-bundle-PyPI', '2024.06'),
+    ('Python', '3.14.2'),
+    ('Python-bundle-PyPI', '2026.04'),
 ]
 
 exts_list = [
@@ -29,8 +28,8 @@ exts_list = [
         'checksums': ['266d98905595be2ccc5da964fe0a2c3526fbbffdc45b65b3146d75db992ef6b2'],
     }),
     (name, version, {
-        'sources': ['%(namelower)s-%(version)s.tar.gz'],
-        'checksums': ['35275439b574837a6cd3020a5a4a73645eb125ce4152a73a2f126bf164b91b80'],
+        'sources': [SOURCELOWER_TAR_GZ],
+        'checksums': ['f8f5df6cf65314d74da1ade1bf96f8e3e4d0c41b51577ac53c49e7d44ca5acee'],
     }),
 ]

Updated software `PnetCDF-1.14.1-gompi-2026.1.eb`

Diff against PnetCDF-1.14.1-lompi-2025b.eb

easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.14.1-lompi-2025b.eb

diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.14.1-lompi-2025b.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.14.1-gompi-2026.1.eb
index 06586982c4..d0e2a8dad7 100644
--- a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.14.1-lompi-2025b.eb
+++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.14.1-gompi-2026.1.eb
@@ -6,15 +6,15 @@ version = '1.14.1'
 homepage = 'https://parallel-netcdf.github.io/'
 description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access"
 
-toolchain = {'name': 'lompi', 'version': '2025b'}
+toolchain = {'name': 'gompi', 'version': '2026.1'}
 
 source_urls = ['https://parallel-netcdf.github.io/Release']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['6f0f7221006c211fce9ddd2c008796b8c69dd717b2ad1be0b4027fc328fd3220']
 
 builddependencies = [
-    ('Autotools', '20250527'),
-    ('Perl', '5.40.2'),
+    ('Autotools', '20250626'),
+    ('Perl', '5.42.0'),
 ]
 
 preconfigopts = "autoreconf -f -i && "

Diff against PnetCDF-1.13.0-iimpi-2023b.eb

easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.13.0-iimpi-2023b.eb

diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.13.0-iimpi-2023b.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.14.1-gompi-2026.1.eb
index 49bd08fe08..d0e2a8dad7 100644
--- a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.13.0-iimpi-2023b.eb
+++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.14.1-gompi-2026.1.eb
@@ -1,20 +1,20 @@
 easyblock = 'ConfigureMake'
 
 name = 'PnetCDF'
-version = '1.13.0'
+version = '1.14.1'
 
 homepage = 'https://parallel-netcdf.github.io/'
 description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access"
 
-toolchain = {'name': 'iimpi', 'version': '2023b'}
+toolchain = {'name': 'gompi', 'version': '2026.1'}
 
 source_urls = ['https://parallel-netcdf.github.io/Release']
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['aba0f1c77a51990ba359d0f6388569ff77e530ee574e40592a1e206ed9b2c491']
+checksums = ['6f0f7221006c211fce9ddd2c008796b8c69dd717b2ad1be0b4027fc328fd3220']
 
 builddependencies = [
-    ('Autotools', '20220317'),
-    ('Perl', '5.38.0'),
+    ('Autotools', '20250626'),
+    ('Perl', '5.42.0'),
 ]
 
 preconfigopts = "autoreconf -f -i && "

Diff against PnetCDF-1.14.1-iimpi-2025b.eb

easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.14.1-iimpi-2025b.eb

diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.14.1-iimpi-2025b.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.14.1-gompi-2026.1.eb
index 18ae5aaebf..d0e2a8dad7 100644
--- a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.14.1-iimpi-2025b.eb
+++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.14.1-gompi-2026.1.eb
@@ -6,15 +6,15 @@ version = '1.14.1'
 homepage = 'https://parallel-netcdf.github.io/'
 description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access"
 
-toolchain = {'name': 'iimpi', 'version': '2025b'}
+toolchain = {'name': 'gompi', 'version': '2026.1'}
 
 source_urls = ['https://parallel-netcdf.github.io/Release']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['6f0f7221006c211fce9ddd2c008796b8c69dd717b2ad1be0b4027fc328fd3220']
 
 builddependencies = [
-    ('Autotools', '20250527'),
-    ('Perl', '5.40.2'),
+    ('Autotools', '20250626'),
+    ('Perl', '5.42.0'),
 ]
 
 preconfigopts = "autoreconf -f -i && "

pavelToman · 2026-06-26T13:23:04Z

@boegelbot please test @ jsc-zen3

boegelbot · 2026-06-26T13:30:08Z

@pavelToman: 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=26378 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_26378 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 10953

Test results coming soon (I hope)...

Details

- notification for comment with ID 4809975739 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).

boegelbot · 2026-06-26T20:01:29Z

Test report by @boegelbot
SUCCESS
Build succeeded for 7 out of 7 (total: 6 hours 31 mins 4 secs) (7 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.7, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.25
See https://gist.github.com/boegelbot/d6b0eab399d44e90c39ae5b691388e60 for a full test report.

pavelToman · 2026-06-26T20:21:22Z

Test report by @pavelToman
SUCCESS
Build succeeded for 7 out of 7 (total: 6 hours 19 mins 46 secs) (7 easyconfigs in total)
node4246.shinx.os - Linux RHEL 9.6, x86_64, AMD EPYC 9654 96-Core Processor, Python 3.9.21
See https://gist.github.com/pavelToman/8c623d321855592ccc8742cdfec8b468 for a full test report.

Thyre · 2026-06-27T07:30:18Z

Building a second, full LLVM in 2026.1 is a bad idea.
This module clashes with the LLVM toolchain, and since this is built with shared libraries enabled, we risk the chance that some component of an EasyConfig using this as a build dependency will link a shared library of LLVM, causing issues down the line.

There's a good reason why I moved to a static LLVM build for Mesa in #26288.

Older toolchains use a -llvmlite variant, which is basically a minimal LLVM. This is better and should be preferred.
The only downside we'll get is that projects like PyOMP are not supported, as they need OpenMP libraries.

Another option would be to Bundle llvmlite and LLVM in a separate EasyConfig.

In any case, I'd heavily recommend to move this to a separate PR. This needs more discussion.

See also the last meeting notes, where this was discussed as well: https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20260617#qa--other

…mpi-2026.1.eb - merged in PR 26413

…asyconfigs into 20260626152142_new_pr_Pint0253

boegel

lgtm

boegel · 2026-07-09T09:26:34Z

Test report by @boegel
SUCCESS
Build succeeded for 5 out of 5 (total: 28 mins 31 secs) (4 easyconfigs in total)
node4401.skiddo.os - Linux RHEL 9.6, x86_64, AMD EPYC 9755 128-Core Processor (zen5), Python 3.9.21
See https://gist.github.com/boegel/ae2a7d122060507caf53ecac00186483 for a full test report.

boegel · 2026-07-09T09:46:25Z

Going in, thanks @pavelToman!

adding easyconfigs: Pint-0.25.3-GCCcore-15.2.0.eb, freesasa-2.2.1-gfb…

088357f

…f-2026.1.eb, gemmi-0.7.5-GCCcore-15.2.0.eb, numba-0.65.1-foss-2026.1.eb, LLVM-20.1.8-GCCcore-15.2.0.eb, PnetCDF-1.14.1-gompi-2026.1.eb, netCDF-Fortran-4.6.3-gompi-2026.1.eb

pavelToman added new update 2026.1 issues & PRs related to 2026.1 common toolchains labels Jun 26, 2026

pavelToman mentioned this pull request Jun 26, 2026

PhyStack - python bundles with foss/2026.1 vscentrum/vsc-software-stack#650

Open

100 tasks

Update gemmi-0.7.5-GCCcore-15.2.0.eb

48506d0

move numba to separate PR

e73b290

This was referenced Jun 29, 2026

{compiler,lang}[GCCcore/15.2.0,foss/2026.1] numba v0.65.1, LLVM v20.1.8 /w llvmlite #26383

Merged

{data}[gompi/2026.1] netCDF-C++4 v4.3.1, netCDF-Fortran v4.6.3 #26413

Merged

pavelToman and others added 2 commits July 7, 2026 14:07

Delete easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.3-go…

b3b0a77

…mpi-2026.1.eb - merged in PR 26413

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

2995eff

…asyconfigs into 20260626152142_new_pr_Pint0253

boegel changed the title ~~{bio,data}[GCCcore/15.2.0] Pint v0.25.3, freesasa v2.2.1, gemmi v0.7.5, ...~~ {bio,data}[GCCcore/15.2.0] Pint v0.25.3, freesasa v2.2.1, gemmi v0.7.5, PnetCDF v1.14.1 Jul 9, 2026

boegel approved these changes Jul 9, 2026

View reviewed changes

boegel added this to the next release (5.3.2?) milestone Jul 9, 2026

boegel merged commit fdff4c6 into easybuilders:develop Jul 9, 2026
6 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

{bio,data}[GCCcore/15.2.0] Pint v0.25.3, freesasa v2.2.1, gemmi v0.7.5, PnetCDF v1.14.1 - #26378

{bio,data}[GCCcore/15.2.0] Pint v0.25.3, freesasa v2.2.1, gemmi v0.7.5, PnetCDF v1.14.1#26378
boegel merged 5 commits into
easybuilders:developfrom
pavelToman:20260626152142_new_pr_Pint0253

pavelToman commented Jun 26, 2026 •

edited

Loading

Uh oh!

github-actions Bot commented Jun 26, 2026 •

edited

Loading

Uh oh!

pavelToman commented Jun 26, 2026

Uh oh!

boegelbot commented Jun 26, 2026

Uh oh!

boegelbot commented Jun 26, 2026

Uh oh!

pavelToman commented Jun 26, 2026

Uh oh!

Thyre commented Jun 27, 2026 •

edited

Loading

Uh oh!

boegel left a comment

Uh oh!

boegel commented Jul 9, 2026

Uh oh!

boegel commented Jul 9, 2026

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

Uh oh!

Conversation

pavelToman commented Jun 26, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

github-actions Bot commented Jun 26, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Updated software gemmi-0.7.5-GCCcore-15.2.0.eb

Updated software Pint-0.25.3-GCCcore-15.2.0.eb

Updated software PnetCDF-1.14.1-gompi-2026.1.eb

Uh oh!

pavelToman commented Jun 26, 2026

Uh oh!

boegelbot commented Jun 26, 2026

Uh oh!

boegelbot commented Jun 26, 2026

Uh oh!

pavelToman commented Jun 26, 2026

Uh oh!

Thyre commented Jun 27, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

boegel left a comment

Choose a reason for hiding this comment

Uh oh!

boegel commented Jul 9, 2026

Uh oh!

boegel commented Jul 9, 2026

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

pavelToman commented Jun 26, 2026 •

edited

Loading

github-actions Bot commented Jun 26, 2026 •

edited

Loading

Updated software `gemmi-0.7.5-GCCcore-15.2.0.eb`

Updated software `Pint-0.25.3-GCCcore-15.2.0.eb`

Updated software `PnetCDF-1.14.1-gompi-2026.1.eb`

Thyre commented Jun 27, 2026 •

edited

Loading