...sts_analysis_interfaces_test__substrate__analyzer.py | 17 -----------------
 4 files changed, 5 insertions(+), 36 deletions(-)

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
@@ -1,7 +1,6 @@
 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}
@@ -15,7 +14,7 @@ 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} \
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,
-     )