diff --git a/science/py-pymatgen/Makefile b/science/py-pymatgen/Makefile index eb813481361f..d2c20a7a5deb 100644 --- a/science/py-pymatgen/Makefile +++ b/science/py-pymatgen/Makefile @@ -1,57 +1,56 @@ PORTNAME= pymatgen DISTVERSIONPREFIX= v -DISTVERSION= 2026.3.23 -PORTREVISION= 1 +DISTVERSION= 2026.5.4 CATEGORIES= science python #MASTER_SITES= PYPI # no tests PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Python Materials Genomics is a robust materials analysis code WWW= https://pymatgen.org/ \ https://github.com/materialsproject/pymatgen LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${PY_SETUPTOOLS} \ - ${PYTHON_PKGNAMEPREFIX}numpy>0:math/py-numpy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}numpy1>0:math/py-numpy1@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pymatgen-core>=2026.3.9:science/py-pymatgen-core@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}certifi>=2024.8.30:security/py-certifi@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}charset-normalizer>=3.4.0:textproc/py-charset-normalizer@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}idna>=3.10:dns/py-idna@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}ruamel.yaml.clib>=0.2.12:devel/py-ruamel.yaml.clib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}ruamel.yaml>=0.18.10:devel/py-ruamel.yaml@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}tenacity>=9.0.0:devel/py-tenacity@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}tzdata>=2024.2:devel/py-tzdata@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}urllib3>=2.6.3:net/py-urllib3@${PY_FLAVOR} RUN_DEPENDS+= ${PYTHON_PKGNAMEPREFIX}ase>=3.23.0:science/py-ase@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}beautifulsoup>0:www/py-beautifulsoup@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}h5py>=3.11.0:science/py-h5py@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}phonopy>=2.33.3:science/py-phonopy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}seekpath>=2.0.1:science/py-seekpath@${PY_FLAVOR} # optional dependencies TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pybtex>0:textproc/py-pybtex@${PY_FLAVOR} USES= compiler:c++11-lang python USE_PYTHON= pep517 cython concurrent autoplist pytest USE_GITHUB= yes GH_ACCOUNT= materialsproject TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} \ PMG_TEST_FILES_DIR=${WRKSRC}/test-files \ MPLBACKEND=Agg TEST_WRKSRC= ${WRKSRC}/tests post-patch: # Remove files owned by py-pymatgen-core (both packages install these from shared namespace) @${RM} ${WRKSRC}/src/pymatgen/analysis/chempot_diagram.py \ ${WRKSRC}/src/pymatgen/analysis/phase_diagram.py \ ${WRKSRC}/src/pymatgen/analysis/reaction_calculator.py # tests as of 2025.2.18: 56 failed, 2912 passed, 149 skipped, 1980 warnings in 11080.55s (3:04:40), see https://github.com/materialsproject/pymatgen/issues/4264 # tests as of 2025.5.28: 56 failed, 3015 passed, 161 skipped, 131 warnings, 7 errors in 5700.13s (1:35:00) # tests as of 2026.3.23: 0 failed (2 spglib-version-sensitive tests patched), 719 passed, 275 skipped, 7 xfailed, 1 xpassed .include diff --git a/science/py-pymatgen/distinfo b/science/py-pymatgen/distinfo index 4f86f328f12c..96e958390982 100644 --- a/science/py-pymatgen/distinfo +++ b/science/py-pymatgen/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1776620172 -SHA256 (materialsproject-pymatgen-v2026.3.23_GH0.tar.gz) = 83c8bc5f92530eeec6c068a56b9530948e9944df5ed54c77625c6ba8142a22d1 -SIZE (materialsproject-pymatgen-v2026.3.23_GH0.tar.gz) = 169183015 +TIMESTAMP = 1778014183 +SHA256 (materialsproject-pymatgen-v2026.5.4_GH0.tar.gz) = 38b88397a9ccd84e40c02e8a5c5109205b93e883bc254950579facd55d50d27c +SIZE (materialsproject-pymatgen-v2026.5.4_GH0.tar.gz) = 165423301 diff --git a/science/py-pymatgen/files/patch-tests_analysis_interfaces_test__coherent__interface.py b/science/py-pymatgen/files/patch-tests_analysis_interfaces_test__coherent__interface.py deleted file mode 100644 index e03965fff1f4..000000000000 --- a/science/py-pymatgen/files/patch-tests_analysis_interfaces_test__coherent__interface.py +++ /dev/null @@ -1,13 +0,0 @@ ---- tests/analysis/interfaces/test_coherent_interface.py.orig 2026-04-20 05:45:36 UTC -+++ tests/analysis/interfaces/test_coherent_interface.py -@@ -46,7 +46,9 @@ class TestInterfaceBuilder(MatSciTest): - assert len(builder.terminations) == 2 - # SP: this test is super fragile and the result fluctuates between 6, 30 and 42 for - # no apparent reason. The author should fix this. -- assert len(list(builder.get_interfaces(termination=("O2_Pmmm_1", "Si_R-3m_1")))) >= 6 -+ # Use the O2 termination dynamically since spglib versions can yield different suffix numbers -+ o2_termination = next(t for t in builder.terminations if t[0].startswith("O2_")) -+ assert len(list(builder.get_interfaces(termination=o2_termination))) >= 6 - - - class TestCoherentInterfaceBuilder: diff --git a/science/py-pymatgen/files/patch-tests_analysis_interfaces_test__substrate__analyzer.py b/science/py-pymatgen/files/patch-tests_analysis_interfaces_test__substrate__analyzer.py deleted file mode 100644 index bb938698160c..000000000000 --- a/science/py-pymatgen/files/patch-tests_analysis_interfaces_test__substrate__analyzer.py +++ /dev/null @@ -1,17 +0,0 @@ ---- tests/analysis/interfaces/test_substrate_analyzer.py.orig 2026-04-20 05:45:36 UTC -+++ tests/analysis/interfaces/test_substrate_analyzer.py -@@ -50,11 +50,11 @@ def test_generate_surface_vectors(): - assert [substrate_millers] == substrate_miller_indices - assert_allclose( - film_vectors, -- [[0, 0, 3.035429], [-2.764654e-16, 4.515023, 2.764654e-16]], -+ [[4.881342e-16, 3.035429e+00, 1.858664e-16], [4.515023e+00, 0.0, 2.764654e-16]], - atol=1e-6, - ) - assert_allclose( - substrate_vectors, -- [[-3.766937, -1.928326, -6.328967], [3.766937, -12.307154, 0.0]], -- atol=1e-6, -+ [[1.928326e+00, 6.328967e+00, -3.766937e+00], [1.2307154e+01, 0.0, 3.766937e+00]], -+ atol=1e-5, - )