{chem}[foss/2024a] pyiron-gpl v0.0.5-20250512, pyiron v0.5.2-20250921, iodata v1.0.0a8 w/ mbocus

easybuild/easyconfigs/g/graphviz-python/graphviz-python-0.21-GCCcore-13.3.0.eb

@@ -0,0 +1,27 @@
+easyblock = 'PythonPackage'
+
+name = 'graphviz-python'
+version = '0.21'
+
+homepage = 'https://pypi.python.org/pypi/graphviz'
+description = """Simple Python interface for Graphviz"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://pypi.python.org/packages/source/g/graphviz']
+sources = ['graphviz-%(version)s.tar.gz']
+checksums = ['20743e7183be82aaaa8ad6c93f8893c923bd6658a04c32ee115edb3c8a835f78']
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('Graphviz', '12.2.0'),
+    ('setuptools', '80.9.0'),
+]
+
+options = {'modulename': 'graphviz'}
+
+moduleclass = 'vis'

easybuild/easyconfigs/i/iodata/iodata-1.0.0a8-foss-2024a.eb

@@ -0,0 +1,28 @@
+easyblock = 'PythonPackage'
+
+name = 'iodata'
+version = '1.0.0a8'
+
+homepage = 'https://github.com/theochem/iodata'
+description = """Python library for reading, writing, and converting computational chemistry file formats and
+generating input files."""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+source_urls = ['https://github.com/theochem/iodata/releases/download/v%(version)s/']
+sources = ['qc_iodata-%(version)s-py3-none-any.whl']
+checksums = ['1365f783448c1ead99a019fabd0bab8f1a82a49e4485eae9c40988aba9e41daa']
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/iodata-convert'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["iodata-convert --help"]
+
+moduleclass = 'chem'

easybuild/easyconfigs/p/pyiron-gpl/pyiron-gpl-0.0.5-20250512-foss-2024a-mbocus.eb

@@ -0,0 +1,48 @@
+easyblock = 'PythonBundle'
+
+name = 'pyiron-gpl'
+version = '0.0.5-20250512'
+local_commit = 'd2d8680'
+versionsuffix = '-mbocus'
+
+homepage = 'https://github.com/mbocus/pyiron_gpl'
+description = """Additional modules for the pyiron IDE licensed under GPLv3.
+Sources are from fork of pyiron-gpl by mbocus.
+"""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+    ('pyiron', '0.5.2-20250921'),
+    ('iodata', '1.0.0a8'),
+]
+
+# fix version and unpin dep versions
+local_preinstallopts = (
+    rf"""sed -i -e "s/\('.*\)==[^']\+',/\1',/g" -e 's/versioneer.get_version(),/"{version}",/' -e "s/==[^']*//" """
+    "setup.py && "
+)
+
+exts_list = [
+    (name, version, {
+        'preinstallopts': local_preinstallopts,
+        'source_urls': ['https://github.com/mbocus/pyiron_gpl/archive/'],
+        'sources':  [{
+            'download_filename': f'{local_commit}.tar.gz',
+            'filename': f'%(name)s-%(version)s-{local_commit}.tar.gz',
+        }],
+        'checksums': ['305ec6688bb7f7c976797aa470e3b6e1009ac46315909b10553e878e912039d6'],
+    }),
+]
+
+# fix __version__
+postinstallcmds = [
+    f"sed -i -e 's/0.1.1/{version}/' -e '/get_versions/d' "
+    "%(installdir)s/lib/python%(pyshortver)s/site-packages/pyiron_gpl/__init__.py"
+]
+
+check_ldshared = True
+
+moduleclass = 'chem'

easybuild/easyconfigs/p/pyiron/pyiron-0.5.2-20250921-foss-2024a.eb

@@ -0,0 +1,163 @@
+easyblock = 'PythonBundle'
+
+name = 'pyiron'
+version = '0.5.2-20250921'
+local_commit = '7ed460'
+
+homepage = 'https://github.com/pyiron/pyiron'
+description = "An integrated development environment (IDE) for computational materials science."
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+builddependencies = [
+    ('poetry', '1.8.3'),
+    ('hatchling', '1.24.2'),
+    ('pybind11', '2.13.6'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+    ('Python-bundle-PyPI', '2024.06'),
+    ('ASE', '3.23.0'),
+    ('phonopy', '2.40.0'),
+    ('scikit-learn', '1.5.2'),
+    ('nglview', '3.1.4'),
+    ('h5py', '3.12.1'),
+    ('SQLAlchemy', '2.0.36'),
+    ('PyYAML', '6.0.2'),
+    ('tqdm', '4.66.5'),
+    ('GitPython', '3.1.43'),
+    ('Pint', '0.24.4'),
+    ('PyTables', '3.10.2'),
+    ('PyZMQ', '26.2.0'),
+    ('ruamel.yaml', '0.18.6'),
+    ('matplotlib', '3.9.2'),
+    ('spglib-python', '2.5.0'),
+    ('graphviz-python', '0.21'),
+    ('flit-core', '3.12.0'),
+    ('pymatgen', '2025.6.14'),
+    ('setuptools', '80.9.0'),
+]
+
+exts_list = [
+    ('packaging', '25.0', {
+        'checksums': ['d443872c98d677bf60f6a1f2f8c1cb748e8fe762d2bf9d3148b5599295b0fc4f'],
+    }),
+    ('typing_extensions', '4.14.0', {
+        'checksums': ['8676b788e32f02ab42d9e7c61324048ae4c6d844a399eebace3d4979d75ceef4'],
+    }),
+    ('isodate', '0.7.2', {
+        'checksums': ['4cd1aa0f43ca76f4a6c6c0292a85f40b35ec2e43e315b59f06e6d32171a953e6'],
+    }),
+    ('rdflib', '7.1.4', {
+        'checksums': ['fed46e24f26a788e2ab8e445f7077f00edcf95abb73bcef4b86cefa8b62dd174'],
+    }),
+    ('prettytable', '3.7.0', {
+        'checksums': ['ef8334ee40b7ec721651fc4d37ecc7bb2ef55fde5098d994438f0dfdaa385c0c'],
+    }),
+    ('typeguard', '4.4.4', {
+        'checksums': ['3a7fd2dffb705d4d0efaed4306a704c89b9dee850b688f060a8b1615a79e5f74'],
+    }),
+    ('owlrl', '7.1.3', {
+        'checksums': ['c9acf66135821ed7a6c4e002387bdb60a5804c86bf0210310df7d5a5da5d2eb1'],
+    }),
+    ('pyshacl', '0.30.1', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['d7e0c21b25e948bb643dbc5db6258da64a90a8ac89055c1fe562b469031072aa'],
+    }),
+    ('deprecated', '1.2.18', {
+        'checksums': ['422b6f6d859da6f2ef57857761bfb392480502a64c3028ca9bbe86085d72115d'],
+    }),
+    ('semantikon', '0.0.20', {
+        'checksums': ['ebd6c2790be5d57955cecb5a670010b1cefb3d32c8f57bb946c8be678b9f5d5d'],
+    }),
+    ('executorlib', '1.7.1', {
+        'checksums': ['fe0e9665aa4179d25acd2be7232bf806bbe19069266c49a795143f224c383fd8'],
+    }),
+    ('sphinx_parser', '0.1.0', {
+        'checksums': ['19a0fb45671fc011e1b0b8f192b6691419a1e3b394bfdac2fb1aaa2a3cf5782f'],
+    }),
+    ('pyscal3', '3.2.7', {
+        'source_urls': ['https://github.com/pyscal/pyscal3/archive'],
+        'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['a5e86e61abe7a0a37aada16ffeb56cbd0d8761c80acb248dd089ca0be2e9cc1f'],
+        # pybind11 is only a build dependency for pyscal3
+        'preinstallopts': """sed -i "s/'pybind11',//g" setup.py && """,
+    }),
+    ('msgpack', '1.1.1', {
+        'checksums': ['77b79ce34a2bdab2594f490c8e80dd62a02d650b91a75159a63ec413b8d104cd'],
+    }),
+    ('h5io', '0.2.4', {
+        'checksums': ['473efdf172f3fc9cddf19131ad281a5ff085c18579b3adce287ba873bbb12603'],
+    }),
+    ('h5io_browser', '0.1.5', {
+        'checksums': ['2ad592da0e9ff65364e4a4554c7ff45b1787b64dc22300364e8ff370ea0bcd5d'],
+    }),
+    ('pysqa', '0.2.3', {
+        'checksums': ['ef7441281ef62fe9418c44a63f9a899a87b276d0183f9389afb3ff8cb9ddbcea'],
+    }),
+    ('pyfileindex', '0.0.32', {
+        'checksums': ['d2ade3c21761fd50395a9cf827618851d6b334cd8cffb19da7434d7c3d8018ac'],
+    }),
+    ('traitlets', '5.14.3', {
+        'checksums': ['9ed0579d3502c94b4b3732ac120375cda96f923114522847de4b3bb98b96b6b7'],
+    }),
+    ('seekpath', '2.1.0', {
+        'checksums': ['31cec579628262e6d4a4c3693fefa70d6ccae1ceeef7c9d10ea3cd48988452c4'],
+    }),
+    ('structuretoolkit', '0.0.34', {
+        'checksums': ['da9fa5f4e07fc9b4798feb622cff778312b9a2cb70ee671665f6a8afb63c66d4'],
+    }),
+    ('defusedxml', '0.7.1', {
+        'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'],
+    }),
+    ('atomistics', '0.2.5', {
+        'checksums': ['9d2e75151a53841e6402373126c59424089008ed4d1cf13bf8e0216bb10fcf53'],
+    }),
+    ('pyfiglet', '0.8.post1', {
+        'checksums': ['c6c2321755d09267b438ec7b936825a4910fec696292139e664ca8670e103639'],
+    }),
+    ('mendeleev', '0.19.0', {
+        'preinstallopts': "sed -i 's/2.9.2/2.9.1/' pyproject.toml && ",
+        'checksums': ['7d513a3be0c2b45369c3c041eb949a76bc92ee42d833b1dee0048a919d3f9a78'],
+    }),
+    ('pylammpsmpi', '0.3.0', {
+        'checksums': ['f2617f38715ac60f8d4fef982acdad41da38d9f2524555beaf0e68eb1dbc11d3'],
+    }),
+    ('pyiron_base', '0.15.1', {
+        'checksums': ['62806100d8a70b82a34b4607dc85815a2c1d2a9e2d2eb34d3607040c0f48c6dc'],
+    }),
+    ('pyiron_dataclasses', '0.0.4', {
+        'checksums': ['4d0889f159dcecdd35353d7ab2fd9eb68c196c73d1bbb6723648a73336a2cd55'],
+    }),
+    ('pyiron_snippets', '0.2.0', {
+        'checksums': ['c46532fe476c79d1182477709b7fa8a66c92e3ae6082c6ccfc0ebef1f69ed046'],
+    }),
+    ('pyiron_atomistics', '0.7.18', {
+        'patches': ['pyiron_atomistics-0.7.18_unpin-dep-versions.patch'],
+        'checksums': [
+            {'pyiron_atomistics-0.7.18.tar.gz': '5d16a3e39abf4bff6be366c8c135a65323bfc648ed9d2cd98a8fe1d497f185fd'},
+            {'pyiron_atomistics-0.7.18_unpin-dep-versions.patch':
+             '6ac9369191dfef4a85b59fc0d3035489d53ad89cc19cb39fa59577843ff9edf6'},
+        ],
+    }),
+    ('pyiron_lammps', '0.4.6', {
+        'checksums': ['ecf36ec09c4c27ab099b234f064712867d14b4ff34760a1c6abd6cece2cfebe6'],
+    }),
+    ('pyiron_vasp', '0.2.12', {
+        'checksums': ['d6c73cd7cc5536a4d40d77bf9823af4fe979ea854f78f2c77a9356084246c495'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/pyiron/pyiron/archive'],
+        'sources': [{
+            'download_filename': f'{local_commit}.tar.gz',
+            'filename': f'%(name)s-%(version)s-{local_commit}.tar.gz'
+        }],
+        'checksums': ['4792bff6c13f7a07a2835bc5b7963400ea6f08392b0ad4ece1e31f6f42e09075'],
+    }),
+]
+
+check_ldshared = True
+
+moduleclass = 'tools'

easybuild/easyconfigs/p/pyiron/pyiron_atomistics-0.7.18_unpin-dep-versions.patch

@@ -0,0 +1,64 @@
+Unpin strict dependencies versions
+Author: Pavel Tomanek
+--- pyproject.toml.orig	2025-09-25 11:08:55.295006783 +0200
++++ pyproject.toml	2025-09-25 11:11:13.137753925 +0200
+@@ -1,5 +1,5 @@
+ [build-system]
+-requires = ["ase", "atomistics", "defusedxml", "h5py", "matplotlib", "mendeleev", "mp-api", "numpy", "pandas", "phonopy", "pint", "pyiron_base", "pylammpsmpi", "scipy", "scikit-learn", "seekpath", "setuptools", "spglib", "structuretoolkit", "hatchling==1.27.0", "hatch-vcs==0.5.0"]
++requires = ["ase", "atomistics", "defusedxml", "h5py", "matplotlib", "mendeleev", "mp-api", "numpy", "pandas", "phonopy", "pint", "pyiron_base", "pylammpsmpi", "scipy", "scikit-learn", "seekpath", "setuptools", "spglib", "structuretoolkit", "hatchling", "hatch-vcs"]
+ build-backend = "hatchling.build"
+
+ [project]
+@@ -24,29 +24,29 @@
+     "Programming Language :: Python :: 3.12",
+ ]
+ dependencies = [
+-    "ase>=3.23.0,<=3.25.0",
+-    "atomistics>=0.1.33,<=0.2.5",
+-    "defusedxml>=0.7.0,<=0.7.1",
+-    "h5py>=3.9.0,<=3.13.0",
+-    "matplotlib>=3.5.3,<=3.10.1",
+-    "mendeleev==0.19.0",
+-    "mp-api>=0.37.0,<=0.45.9",
+-    "numpy==1.26.4",
+-    "pandas>=2.0.3,<=2.3.2",
+-    "phonopy>=2.20.0,<=2.43.2",
+-    "pint>=0.18,<=0.24.4",
+-    "pyiron_base>=0.13.0,<=0.14.3",
+-    "pyiron_lammps>=0.3.2,<=0.4.6",
+-    "pyiron_snippets>=0.1.3,<=0.2.0",
+-    "pyiron_vasp>=0.2.2,<=0.2.12",
+-    "pylammpsmpi>=0.2.18,<=0.3.0",
+-    "pyscal3>=3.2.5,<=3.2.7",
+-    "scipy>=1.15.0,<=1.15.2",
+-    "scikit-learn>=1.2.1,<=1.6.1",
+-    "seekpath>=1.9.5,<=2.1.0",
+-    "spglib>=2.0.2,<=2.6.0",
+-    "structuretoolkit>=0.0.29,<=0.0.34",
+-    "sphinx-parser==0.1.0",
++    "ase",
++    "atomistics",
++    "defusedxml",
++    "h5py",
++    "matplotlib",
++    "mendeleev",
++    "mp-api",
++    "numpy",
++    "pandas",
++    "phonopy",
++    "pint",
++    "pyiron_base",
++    "pyiron_lammps",
++    "pyiron_snippets",
++    "pyiron_vasp",
++    "pylammpsmpi",
++    "pyscal3",
++    "scipy",
++    "scikit-learn",
++    "seekpath",
++    "spglib",
++    "structuretoolkit",
++    "sphinx-parser",
+ ]
+ dynamic = ["version"]
+

test/easyconfigs/easyconfigs.py

@@ -471,6 +471,8 @@ def check_dep_vars(self, gen, dep, dep_vars):
             # filter out one per Python version
             ('Z3', ('-Python-2', True)),
             ('Z3', ('-Python-3', True)),
+            # allow Graphviz coexistence by ignoring the -minimal variant when both exist
+            ('Graphviz', '-minimal'),
         ]
         for dep_name, version_suffix in filter_variants:
             # always retain at least one dep variant