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

easybuild/easyconfigs/f/freesasa/freesasa-2.2.1-gfbf-2026.1.eb

@@ -0,0 +1,24 @@
+easyblock = 'PythonBundle'
+
+name = 'freesasa'
+version = '2.2.1'
+
+homepage = 'https://github.com/freesasa/freesasa-python'
+description = "The module provides Python bindings for the FreeSASA C Library."
+
+toolchain = {'name': 'gfbf', 'version': '2026.1'}
+
+builddependencies = [('Cython', '3.2.4')]
+dependencies = [
+    ('Python', '3.14.2'),
+    ('Biopython', '1.87'),
+]
+
+exts_list = [
+    (name, version, {
+        'preinstallopts': 'USE_CYTHON=1 ',
+        'checksums': ['5630e65d619cf6a062028d7c6297afe8c5b18c677c75f1c32a0938399f4f6850'],
+    }),
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/g/gemmi/gemmi-0.7.5-GCCcore-15.2.0.eb

@@ -0,0 +1,69 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/05
+easyblock = 'CMakePythonPackage'
+
+name = 'gemmi'
+version = '0.7.5'
+
+homepage = 'https://gemmi.readthedocs.io/'
+description = """Gemmi is a library, accompanied by a set of programs, developed primarily for
+use in macromolecular crystallography (MX). For working with:
+
+macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files), refinement
+restraints (CIF files), reflection data (MTZ and mmCIF formats), data on a 3D
+grid (electron density maps, masks, MRC/CCP4 format) crystallographic symmetry.
+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': 'GCCcore', 'version': '15.2.0'}
+toolchainopts = {'opt': True}
+
+github_account = 'project-gemmi'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['9e2a8a51e62c69bf43f62aadf527ca4312860de8a36c12a8747d3e8ae556f0b3']
+
+builddependencies = [
+    ('binutils', '2.45'),
+    ('scikit-build-core', '0.12.2'),
+    ('nanobind', '2.13.0'),
+    ('CMake', '4.2.1'),
+]
+dependencies = [
+    ('Python', '3.14.2'),
+    ('zlib', '2.3.2'),
+]
+
+configopts = [
+    f'-DSTRIP_BINARY=ON -DUSE_FORTRAN=1 -DBUILD_SHARED_LIBS={x} -DPYTHON_INSTALL_DIR=%(installdir)s'
+    for x in ['OFF', 'ON']
+]
+
+_pip_opts = ' '.join([
+    '--config-settings="cmake.args=-DSTANDALONE_PYTHON_MODULE=OFF"',  # use lib/libgemmi_cpp.so
+    '--config-settings="cmake.args=-DBUILD_GEMMI_PROGRAM=OFF"',
+    '--config-settings="cmake.args=-DINSTALL_DEV_FILES=OFF"',
+    '-Cbuild-dir=%(builddir)s/pybuild'
+])
+
+exts_defaultclass = 'PythonPackage'
+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'
+        ),
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/gemmi', f'lib/libgemmi_cpp.{SHLIB_EXT}', 'lib/libgemmi_cpp.a'],
+    'dirs': ['bin', 'lib', 'include/gemmi', 'lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s.dist-info']
+}
+
+sanity_check_commands = ['gemmi -h']
+
+moduleclass = 'bio'

easybuild/easyconfigs/p/Pint/Pint-0.25.3-GCCcore-15.2.0.eb

@@ -0,0 +1,36 @@
+easyblock = 'PythonBundle'
+
+name = 'Pint'
+version = '0.25.3'
+
+homepage = 'https://github.com/hgrecco/pint'
+description = """Pint is a Python package to define, operate and
+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': '15.2.0'}
+
+builddependencies = [
+    ('binutils', '2.45'),
+    ('hatchling', '1.29.0'),
+]
+dependencies = [
+    ('Python', '3.14.2'),
+    ('Python-bundle-PyPI', '2026.04'),
+]
+
+exts_list = [
+    ('flexcache', '0.3', {
+        'checksums': ['18743bd5a0621bfe2cf8d519e4c3bfdf57a269c15d1ced3fb4b64e0ff4600656'],
+    }),
+    ('flexparser', '0.4', {
+        'checksums': ['266d98905595be2ccc5da964fe0a2c3526fbbffdc45b65b3146d75db992ef6b2'],
+    }),
+    (name, version, {
+        'sources': [SOURCELOWER_TAR_GZ],
+        'checksums': ['f8f5df6cf65314d74da1ade1bf96f8e3e4d0c41b51577ac53c49e7d44ca5acee'],
+    }),
+]
+
+moduleclass = 'numlib'

easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.14.1-gompi-2026.1.eb

@@ -0,0 +1,35 @@
+easyblock = 'ConfigureMake'
+
+name = 'PnetCDF'
+version = '1.14.1'
+
+homepage = 'https://parallel-netcdf.github.io/'
+description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access"
+
+toolchain = {'name': 'gompi', 'version': '2026.1'}
+
+source_urls = ['https://parallel-netcdf.github.io/Release']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['6f0f7221006c211fce9ddd2c008796b8c69dd717b2ad1be0b4027fc328fd3220']
+
+builddependencies = [
+    ('Autotools', '20250626'),
+    ('Perl', '5.42.0'),
+]
+
+preconfigopts = "autoreconf -f -i && "
+configopts = [
+    '',
+    '--enable-shared',
+]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['ncmpidiff', 'ncmpidump', 'ncmpigen', 'ncoffsets',
+                                     'ncvalidator', 'pnetcdf-config', 'pnetcdf_version']] +
+             ['lib/lib%(namelower)s.a', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT],
+    'dirs': ['include'],
+}
+
+modextrapaths = {'PNETCDF': ''}
+
+moduleclass = 'data'