science/py-pymatgen-core: New port: Python Materials Genomics core data structures and algorithms

6 files changed, 120 insertions, 0 deletions

diff --git a/science/Makefile b/science/Makefile
index 9f9003d9c5a9..98911db6b1b1 100644
--- a/science/Makefile
+++ b/science/Makefile
@@ -409,6 +409,7 @@
     SUBDIR += py-pygmo2
     SUBDIR += py-pyked
     SUBDIR += py-pymatgen
+    SUBDIR += py-pymatgen-core
     SUBDIR += py-pymatgen-analysis-alloys
     SUBDIR += py-pymbd
     SUBDIR += py-pymol
diff --git a/science/py-pymatgen-core/Makefile b/science/py-pymatgen-core/Makefile
new file mode 100644
index 000000000000..f8c6cc4d6a55
--- /dev/null
+++ b/science/py-pymatgen-core/Makefile
@@ -0,0 +1,61 @@
+PORTNAME=	pymatgen-core
+DISTVERSIONPREFIX=	v
+DISTVERSION=	2026.4.16
+CATEGORIES=	science python
+PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	Python Materials Genomics core data structures and algorithms
+WWW=		https://pymatgen.org/ \
+		https://github.com/materialsproject/pymatgen-core
+
+LICENSE=	MIT
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+BUILD_DEPENDS=	${PY_SETUPTOOLS} \
+		${PYTHON_PKGNAMEPREFIX}numpy1>0:math/py-numpy1@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR}
+RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}bibtexparser>=1.4.3:textproc/py-bibtexparser@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}contourpy>=1.3.1:math/py-contourpy@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}cycler>=0.12.1:devel/py-cycler@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}fonttools>=4.61.0:print/py-fonttools@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}joblib>=1.3.2:devel/py-joblib@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}kiwisolver>=1.4.7:math/py-kiwisolver@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}lxml>=4.9:devel/py-lxml@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}matplotlib>=3.8:math/py-matplotlib@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}monty>=2026.2.18:devel/py-monty@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}mpmath>=1.3.0:math/py-mpmath@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}networkx>=2.7:math/py-networkx@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}numpy1>0:math/py-numpy1@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}orjson>=3.10.18:devel/py-orjson@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}packaging>=24.2:devel/py-packaging@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}palettable>=3.3.3:misc/py-palettable@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}pandas>=2.2.3:math/py-pandas@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}pillow>=9.0.0:graphics/py-pillow@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}plotly>=5:graphics/py-plotly@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}pyparsing>=3.2.0:devel/py-pyparsing@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}python-dateutil>=2.9.0:devel/py-python-dateutil@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}pytz>=2024.2:devel/py-pytz@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}requests>=2.32.5:www/py-requests@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}scipy>=1.14.1:science/py-scipy@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}six>=1.16.0:devel/py-six@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}spglib>=2.5.0:science/py-spglib@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}sympy>=1.3:math/py-sympy@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}tabulate>=0.9.0:devel/py-tabulate@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}tqdm>=4.67.1:misc/py-tqdm@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}uncertainties>=3.1:math/py-uncertainties@${PY_FLAVOR}
+
+USES=		compiler:c++11-lang python
+USE_PYTHON=	pep517 cython concurrent autoplist pytest
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	materialsproject
+GH_PROJECT=	pymatgen-core
+
+TEST_ENV=	${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} \
+		PMG_TEST_FILES_DIR=${WRKSRC}/test-files \
+		MPLBACKEND=Agg
+
+# tests as of 2026.4.16: 2557 passed, 116 skipped, 5 xfailed, 1 xpassed, 53 warnings in 330.65s (0:05:30)
+
+.include <bsd.port.mk>
diff --git a/science/py-pymatgen-core/distinfo b/science/py-pymatgen-core/distinfo
new file mode 100644
index 000000000000..d60548e4cdf2
--- /dev/null
+++ b/science/py-pymatgen-core/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1776629591
+SHA256 (materialsproject-pymatgen-core-v2026.4.16_GH0.tar.gz) = 25cf7dc091c68207c052365bd4218da6bd77ffb6b9b2c5e2539ceceb2b68fb21
+SIZE (materialsproject-pymatgen-core-v2026.4.16_GH0.tar.gz) = 232470453
diff --git a/science/py-pymatgen-core/files/patch-pyproject.toml b/science/py-pymatgen-core/files/patch-pyproject.toml
new file mode 100644
index 000000000000..a9b320cf89f1
--- /dev/null
+++ b/science/py-pymatgen-core/files/patch-pyproject.toml
@@ -0,0 +1,32 @@
+--- pyproject.toml.orig	2026-04-16 01:03:44 UTC
++++ pyproject.toml
+@@ -3,8 +3,8 @@ requires = [
+     "Cython>=0.29.23",
+     # Building against NPY2 will support both NPY1 and NPY2
+     # https://numpy.org/devdocs/dev/depending_on_numpy.html#build-time-dependency
+-    "numpy>=2.1.0",
+-    "setuptools>=65.0.0",
++    "numpy",
++    "setuptools",
+ ]
+ build-backend = "setuptools.build_meta"
+ 
+@@ -72,7 +72,7 @@ dependencies = [
+     "spglib>=2.5",
+     "sympy>=1.3", # PR #4116
+     "uncertainties>=3.1",
+-    "plotly>=6.0",
++    "plotly",
+     "joblib>=1.3.2",
+     "lxml>=4.9",
+     "bibtexparser",
+@@ -118,9 +118,6 @@ zeopp = ["pyzeo; platform_system != 'Windows'"]  # Not
+ # https://github.com/tblite/tblite/issues/175
+ tblite = ["tblite[ase]>=0.3.0; platform_system=='Linux' and python_version<'3.12'"]
+ zeopp = ["pyzeo; platform_system != 'Windows'"]  # Note: requires Voro++ and Zeo++ to be installed
+-
+-[project.scripts]
+-pmg = "pymatgen.cli.pmg:main"
+ 
+ [tool.setuptools]
+ include-package-data = false
diff --git a/science/py-pymatgen-core/files/patch-src_pymatgen_core_structure.py b/science/py-pymatgen-core/files/patch-src_pymatgen_core_structure.py
new file mode 100644
index 000000000000..949ef97a271e
--- /dev/null
+++ b/science/py-pymatgen-core/files/patch-src_pymatgen_core_structure.py
@@ -0,0 +1,11 @@
+--- src/pymatgen/core/structure.py.orig	2026-04-20 04:32:30 UTC
++++ src/pymatgen/core/structure.py
+@@ -1172,7 +1172,7 @@ class IStructure(SiteCollection, MSONable):
+                 )
+                 new_sites.append(periodic_site)
+ 
+-        new_charge = self._charge * np.linalg.det(scale_matrix) if self._charge else None
++        new_charge = self._charge * round(float(np.linalg.det(scale_matrix))) if self._charge else None
+         return Structure.from_sites(new_sites, charge=new_charge, to_unit_cell=True).relabel_sites(ignore_uniq=True)
+ 
+     def __rmul__(self, scaling_matrix):
diff --git a/science/py-pymatgen-core/pkg-descr b/science/py-pymatgen-core/pkg-descr
new file mode 100644
index 000000000000..7f814a666199
--- /dev/null
+++ b/science/py-pymatgen-core/pkg-descr
@@ -0,0 +1,12 @@
+Python Materials Genomics is a robust materials analysis code that defines
+core object representations for structures and molecules with support for
+many electronic structure codes.
+
+This is the pymatgen-core package, which implements the core data structures
+and algorithms of pymatgen, including:
+- Core data structures (Structure, Molecule, Element, etc.)
+- Electronic structure modules
+- IO modules for VASP, FEFF, CP2K, LAMMPS and more
+- Symmetry analysis
+- Transformation modules
+- Optimization utilities