Merge pull request easybuilders#19398 from lcniel/20231211192606_new_…

…pr_pyiron051

{tools}[foss/2023a] pyiron v0.5.1 w/ Python 3.11.3

easybuild/easyconfigs/p/pyiron/pyiron-0.5.1-foss-2023a.eb

@@ -0,0 +1,114 @@
+easyblock = 'PythonBundle'
+
+name = 'pyiron'
+version = '0.5.1'
+
+homepage = 'https://github.com/pyiron/pyiron'
+description = "An integrated development environment (IDE) for computational materials science."
+
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [('poetry', '1.5.1')]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('matplotlib', '3.7.2'),
+    ('h5py', '3.9.0'),
+    ('PyYAML', '6.0'),
+    ('phonopy', '2.20.0'),
+    ('ASE', '3.22.1'),
+    ('PyTables', '3.8.0'),
+    ('nglview', '3.1.2'),
+    ('tqdm', '4.66.1'),
+    ('molmod', '1.4.8'),
+    ('scikit-learn', '1.3.1'),
+    ('yaff', '1.6.0'),
+    ('TAMkin', '1.2.6'),
+    ('QuickFF', '2.2.7'),
+    ('plotly.py', '5.16.0'),
+    ('GitPython', '3.1.40'),
+    ('dill', '0.3.7'),
+    ('sympy', '1.12'),
+    ('pymatgen', '2023.12.18'),
+    ('Pint', '0.23'),
+    ('SQLAlchemy', '2.0.25'),
+]
+
+check_ldshared = True
+use_pip = True
+
+exts_list = [
+    ('h5io', '0.1.2', {
+        'checksums': ['6400543224c489f1cf487be551f892310fa7060fcd4935b84e515efdc1e1fa43'],
+    }),
+    ('defusedxml', '0.6.0', {
+        'checksums': ['f684034d135af4c6cbb949b8a4d2ed61634515257a67299e5f940fbaa34377f5'],
+    }),
+    ('pysqa', '0.1.7', {
+        'checksums': ['fdc37e0178649750e7386b4e9b8287693ee2d47559723c11b9ad42afcfc55900'],
+    }),
+    ('pyfiglet', '0.8.post1', {
+        'checksums': ['c6c2321755d09267b438ec7b936825a4910fec696292139e664ca8670e103639'],
+    }),
+    ('mendeleev', '0.14.0', {
+        'checksums': ['1a89ccf05c708aebe627c5eb19ff5c6379585a2f9e588e1dcf9b03182fe61f3c'],
+    }),
+    ('pyfileindex', '0.0.18', {
+        'checksums': ['6d5acf2500f568667aa5273ae57692c2b62facbcaae7c0bbbf21ba3bdd904961'],
+    }),
+    ('seekpath', '2.1.0', {
+        'checksums': ['31cec579628262e6d4a4c3693fefa70d6ccae1ceeef7c9d10ea3cd48988452c4'],
+    }),
+    (name, version, {
+        'modulename': False,
+        'checksums': ['2e5e3f892b7e49a15443569870aa4ea049951b71fe2ad1ad7f4ac7551d475788'],
+    }),
+    ('pyiron_base', '0.6.12', {
+        'patches': ['pyiron-0.5.1_fix-pyiron-base-version.patch'],
+        'source_urls': ['https://github.com/pyiron/pyiron_base/archive/refs/tags/'],
+        'checksums': [
+            {'pyiron_base-0.6.12.tar.gz': '7ef8fa8b21724776c1ced3ee1efb8484984234150a7f3da296577f90c63751cb'},
+            {'pyiron-0.5.1_fix-pyiron-base-version.patch':
+             'a6390dcd366e17361fb71f26c6d3b75835526bdf773d9ef535c02836fe551b31'},
+        ],
+    }),
+    ('atomistics', '0.1.15', {
+        'patches': ['pyiron-0.5.1_fix-atomistics-requirements.patch'],
+        'source_urls': ['https://github.com/pyiron/atomistics/archive/refs/tags/'],
+        'checksums': [
+            {'atomistics-0.1.15.tar.gz': 'e9c505cace0cbeb9ea5ed33799f332f5cc95230a05ba14b646475cff1bdecaee'},
+            {'pyiron-0.5.1_fix-atomistics-requirements.patch':
+             'deaa57c27be147efc7e4926f6795bfa421280a299fc96de8c0bae342e4770d6c'},
+        ],
+    }),
+    ('pyiron_atomistics', '0.3.11', {
+        'patches': ['pyiron-0.5.1_fix-pyiron-atomistics-version.patch'],
+        'source_urls': ['https://github.com/pyiron/pyiron_atomistics/archive/refs/tags/'],
+        'checksums': [
+            {'pyiron_atomistics-0.3.11.tar.gz': '8c73c452fe60cb808961d22361f9b749488e3d50a8bda7f5c0132aea2f69e00f'},
+            {'pyiron-0.5.1_fix-pyiron-atomistics-version.patch':
+             '5c9b987cb63508f482bff696e252987e10df9b8ee8e860491583c8e547d4568c'},
+        ],
+    }),
+    ('pylammpsmpi', '0.2.10', {
+        'patches': ['pyiron-0.5.1_fix-pylammpsmpi.patch'],
+        'source_urls': ['https://github.com/pyiron/pylammpsmpi/archive/refs/tags/'],
+        'checksums': [
+            {'%(name)s-%(version)s.tar.gz': 'bd5af29a935dacbee743c3cc0bcc799e24e7c2483801f56cb9092a79f016f2ed'},
+            {'pyiron-0.5.1_fix-pylammpsmpi.patch':
+             'd7cacf8eb73cb43e47526bfa3f98157073c01cd88918f191f87d7e75ab4c7c30'},
+        ],
+    }),
+    ('pympipool', '0.7.9', {
+        'checksums': ['5698181bc5dc9a69595fd00ff6a8ba651b77734ccf00df79ae3aea8aaf32790a'],
+    }),
+    ('structuretoolkit', '0.0.15', {
+        'checksums': ['1a258a072055d0c20e9d56156afd4481cfc94c2612c1b908de4b274b423cc6e6'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'

easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-atomistics-requirements.patch

@@ -0,0 +1,17 @@
+Relax requirements of `atomistics`.
+
+--- 0.5.1/foss-2023a/atomistics/atomistics-atomistics-0.1.15/pyproject.toml.orig	2024-01-09 12:42:59.508409527 +0000
++++ 0.5.1/foss-2023a/atomistics/atomistics-atomistics-0.1.15/pyproject.toml 2024-01-09 12:43:44.589293464 +0000
+@@ -26,9 +26,9 @@
+ ]
+ dependencies = [
+     "ase==3.22.1",
+-    "numpy==1.26.2",
+-    "scipy==1.11.4",
+-    "spglib==2.2.0",
++    "numpy>=1.25.1",
++    "scipy>=1.11.1",
++    "spglib>=2.1.0",
+ ]
+ dynamic = ["version"]
+

easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-pyiron-atomistics-version.patch

@@ -0,0 +1,73 @@
+Fixes use of dynamic versioning in pyproject.toml and puts in a specific version instead.
+
+--- 0.5.1/foss-2023a/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml.orig	2024-01-22 10:12:31.768251943 +0000
++++ 0.5.1/foss-2023a/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/pyproject.toml	2024-01-22 10:26:21.997455595 +0000
+@@ -26,24 +26,24 @@
+ dependencies = [
+     "ase==3.22.1",
+-    "atomistics==0.1.12",
+-    "defusedxml==0.7.1",
+-    "h5py==3.10.0",
+-    "matplotlib==3.8.2",
+-    "mendeleev==0.14.0",
+-    "mp-api==0.39.1",
+-    "numpy==1.26.2",
+-    "pandas==2.1.3",
+-    "phonopy==2.21.0",
++    "atomistics>=0.1.12",
++    "defusedxml>=0.6.0",
++    "h5py>=3.9.0",
++    "matplotlib>=3.7.2",
++    "mendeleev>=0.14.0",
++    "mp-api>=0.39.1",
++    "numpy>=1.25.1",
++    "pandas>=2.0.3",
++    "phonopy>=2.20.0",
+-    "pint==0.22",
++    "pint>=0.22",
+     "pyiron_base==0.6.12",
+-    "pylammpsmpi==0.2.9",
++    "pylammpsmpi>=0.2.9",
+-    "scipy==1.11.4",
+-    "scikit-learn==1.3.2",
+-    "seekpath==2.1.0",
+-    "spglib==2.1.0",
++    "scipy>=1.11.1",
++    "scikit-learn>=1.3.1",
++    "seekpath>=2.1.0",
++    "spglib>=2.1.0",
+     "structuretoolkit==0.0.15",
+ ]
+-dynamic = ["version"]
++version = '0.3.11'
+
+ [project.urls]
+ Homepage = "https://pyiron.org"
+@@ -55,13 +55,3 @@
+
+ [tool.setuptools.package-data]
+ "*" = ["data/*.csv"]
+-
+-[tool.setuptools.dynamic]
+-version = {attr = "pyiron_atomistics.__version__"}
+-
+-[tool.versioneer]
+-VCS = "git"
+-style = "pep440-pre"
+-versionfile_source = "pyiron_atomistics/_version.py"
+-parentdir_prefix = "pyiron_atomistics"
+-tag_prefix = "pyiron_atomistics-"
+
+--- 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.11/setup.py.orig	2023-12-13 17:16:26.902513343 +0000
++++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_atomistics/pyiron_atomistics-pyiron_atomistics-0.3.111/setup.py	2023-12-13 17:18:56.504736380 +0000
+@@ -3,6 +3,6 @@
+ import versioneer
+
+ setup(
+-    version=versioneer.get_version(),
+-    cmdclass=versioneer.get_cmdclass(),
+-)
+\ No newline at end
++    version="0.3.11",
++)
++

easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-pyiron-base-version.patch

@@ -0,0 +1,72 @@
+Fixes use of dynamic versioning in pyproject.toml and puts in a specific version instead.
+
+--- 0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml.orig	2023-12-13 15:51:48.895090935 +0000
++++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/pyproject.toml	2023-12-13 15:53:26.626579151 +0000
+@@ -24,23 +24,23 @@
+     "Programming Language :: Python :: 3.11",
+ ]
+ dependencies = [
+-    "dill==0.3.7",
+-    "gitpython==3.1.40",
+-    "h5io==0.1.9",
+-    "h5py==3.10.0",
+-    "jinja2==3.1.2",
+-    "numpy==1.26.2",
+-    "pandas==2.1.3",
+-    "pint==0.22",
+-    "psutil==5.9.5",
+-    "pyfileindex==0.0.18",
+-    "pysqa==0.1.7",
+-    "sqlalchemy==2.0.23",
+-    "tables==3.9.2",
+-    "tqdm==4.66.1",
+-    "traitlets==5.14.0",
++    "dill>=0.3.2",
++    "gitpython>=3.1.8",
++    "h5io>=0.1.2",
++    "h5py>=3.9.0",
++    "jinja2>=3.1.2",
++    "numpy>=1.25.1",
++    "pandas>=2.0.3",
++    "pint>=0.22",
++    "psutil>=5.9.5",
++    "pyfileindex>=0.0.18",
++    "pysqa>=0.1.7",
++    "sqlalchemy>=2.0.23",
++    "tables>=3.8.0",
++    "tqdm>=4.66.1",
++    "traitlets>=5.9.0",
+ ]
+-dynamic = ["version"]
++version = "0.6.12"
+
+ [project.urls]
+ Homepage = "https://github.com/pyiron/pyiron_base"
+@@ -53,12 +53,3 @@
+ [tool.setuptools.packages.find]
+ include = ["pyiron_base*"]
+
+-[tool.setuptools.dynamic]
+-version = {attr = "pyiron_base.__version__"}
+-
+-[tool.versioneer]
+-VCS = "git"
+-style = "pep440-pre"
+-versionfile_source = "pyiron_base/_version.py"
+-parentdir_prefix = "pyiron_base"
+-tag_prefix = "pyiron_base-"
+
+--- 0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/setup.py.orig	2023-12-13 17:16:26.902513343 +0000
++++ 0.5.1/foss-2023a-Python-3.11.3/pyiron_base/pyiron_base-pyiron_base-0.6.12/setup.py	2023-12-13 17:18:56.504736380 +0000
+@@ -3,6 +3,6 @@
+ import versioneer
+
+ setup(
+-    version=versioneer.get_version(),
+-    cmdclass=versioneer.get_cmdclass(),
+-)
+\ No newline at end
++    version="0.6.12",
++)
++
+

easybuild/easyconfigs/p/pyiron/pyiron-0.5.1_fix-pylammpsmpi.patch

@@ -0,0 +1,47 @@
+Fix versioning issue and relax requirements.
+
+--- 0.5.1/foss-2023a/pylammpsmpi/pylammpsmpi-pylammpsmpi-0.2.10/setup.py.orig	2023-12-21 17:27:54.405181324 +0000
++++ 0.5.1/foss-2023a/pylammpsmpi/pylammpsmpi-pylammpsmpi-0.2.10/setup.py	2023-12-21 17:31:38.136048756 +0000
+@@ -1,8 +1,4 @@
+ from setuptools import setup
+
+-import versioneer
++setup(version='0.2.10')
+
+-setup(
+-    version=versioneer.get_version(),
+-    cmdclass=versioneer.get_cmdclass(),
+-)
+\ Ingen nyrad vid filslut
+
+--- 0.5.1/foss-2023a/pylammpsmpi/pylammpsmpi-pylammpsmpi-0.2.10/pyproject.toml.orig	2023-12-21 17:57:36.066162000 +0000
++++ 0.5.1/foss-2023a/pylammpsmpi/pylammpsmpi-pylammpsmpi-0.2.10/pyproject.toml	2023-12-21 17:58:37.373851635 +0000
+@@ -24,11 +24,11 @@
+     "Programming Language :: Python :: 3.11",
+ ]
+ dependencies = [
+-    "mpi4py==3.1.5",
++    "mpi4py>=3.1.4",
+     "pympipool==0.7.9",
+-    "numpy==1.26.2",
++    "numpy>=1.25.1",
+ ]
+-dynamic = ["version"]
++version = '0.2.10'
+
+ [project.urls]
+ Homepage = "https://github.com/pyiron/pylammpsmpi"
+@@ -43,13 +43,3 @@
+
+ [tool.setuptools.packages.find]
+ include = ["pylammpsmpi*"]
+-
+-[tool.setuptools.dynamic]
+-version = {attr = "pylammpsmpi.__version__"}
+-
+-[tool.versioneer]
+-VCS = "git"
+-style = "pep440-pre"
+-versionfile_source = "pylammpsmpi/_version.py"
+-parentdir_prefix = "pylammpsmpi"
+-tag_prefix = "pylammpsmpi-"

easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.7-foss-2023a.eb

@@ -0,0 +1,34 @@
+easyblock = 'PythonPackage'
+
+name = 'QuickFF'
+version = '2.2.7'
+
+homepage = 'https://molmod.github.io/QuickFF/'
+description = """QuickFF is a Python package developed at the Center for
+Molecular Modeling (CMM) to quickly derive accurate force fields from ab initio
+calculations."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/molmod/QuickFF/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['a71922dd39869770b03809355f13bcabdbb8d50429f4d3574cf427ea762f4023']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('matplotlib', '3.7.2'),
+    ('molmod', '1.4.8'),
+    ('yaff', '1.6.0'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'],
+}
+
+sanity_pip_check = True
+
+moduleclass = 'chem'