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-rw-r--r--science/R-cran-Epi/Makefile2
-rw-r--r--science/R-cran-Epi/distinfo6
-rw-r--r--science/abinit/Makefile3
-rw-r--r--science/abinit/distinfo6
-rw-r--r--science/packmol/Makefile2
-rw-r--r--science/packmol/distinfo6
-rw-r--r--science/phonopy/Makefile2
-rw-r--r--science/phonopy/distinfo6
-rw-r--r--science/py-OpenMC/Makefile4
-rw-r--r--science/py-obspy/Makefile3
-rw-r--r--science/py-phonopy/Makefile4
-rw-r--r--science/py-phonopy/distinfo6
-rw-r--r--science/py-pycsw/Makefile3
-rw-r--r--science/py-pygeometa/Makefile4
-rw-r--r--science/py-pyteomics/Makefile5
-rw-r--r--science/py-rmf/Makefile2
-rw-r--r--science/rmf/Makefile2
-rw-r--r--science/votca/Makefile4
18 files changed, 36 insertions, 34 deletions
diff --git a/science/R-cran-Epi/Makefile b/science/R-cran-Epi/Makefile
index 6bdc6a33695d..371fe4129bcb 100644
--- a/science/R-cran-Epi/Makefile
+++ b/science/R-cran-Epi/Makefile
@@ -1,5 +1,5 @@
PORTNAME= Epi
-PORTVERSION= 2.59
+PORTVERSION= 2.60
CATEGORIES= science
DISTNAME= ${PORTNAME}_${PORTVERSION}
diff --git a/science/R-cran-Epi/distinfo b/science/R-cran-Epi/distinfo
index f8021114727e..ec0e369f065d 100644
--- a/science/R-cran-Epi/distinfo
+++ b/science/R-cran-Epi/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1736910907
-SHA256 (Epi_2.59.tar.gz) = 00d630908d1cd06a13d0df12d32e56840992021b6d3769e2b2b5d68078967637
-SIZE (Epi_2.59.tar.gz) = 3198148
+TIMESTAMP = 1752227410
+SHA256 (Epi_2.60.tar.gz) = 29d6d91a7a0f04369852738fce009b3aefa59c65380174b6eec24ba7046aec57
+SIZE (Epi_2.60.tar.gz) = 3976720
diff --git a/science/abinit/Makefile b/science/abinit/Makefile
index a310bee72cd0..2347581589fd 100644
--- a/science/abinit/Makefile
+++ b/science/abinit/Makefile
@@ -1,6 +1,5 @@
PORTNAME= abinit
-DISTVERSION= 10.2.7
-PORTREVISION= 1
+DISTVERSION= 10.4.5
CATEGORIES= science
MAINTAINER= yuri@FreeBSD.org
diff --git a/science/abinit/distinfo b/science/abinit/distinfo
index fa923cfa81d0..3cc29d915b5d 100644
--- a/science/abinit/distinfo
+++ b/science/abinit/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1739946724
-SHA256 (abinit-abinit-10.2.7_GH0.tar.gz) = 0cd5c5755d151ef6a95b107cdcf0ec496818e34356ae8d26b2b4842bf641aec4
-SIZE (abinit-abinit-10.2.7_GH0.tar.gz) = 141254516
+TIMESTAMP = 1753132807
+SHA256 (abinit-abinit-10.4.5_GH0.tar.gz) = ccb3af00603f574208b6d5bea6f857d7040be5748e7a93a689ffad84eb6a65ce
+SIZE (abinit-abinit-10.4.5_GH0.tar.gz) = 153582604
diff --git a/science/packmol/Makefile b/science/packmol/Makefile
index 51c3da1f9c11..627188fa12eb 100644
--- a/science/packmol/Makefile
+++ b/science/packmol/Makefile
@@ -1,6 +1,6 @@
PORTNAME= packmol
DISTVERSIONPREFIX= v
-DISTVERSION= 21.0.3
+DISTVERSION= 21.0.4
CATEGORIES= science
MAINTAINER= eduardo@FreeBSD.org
diff --git a/science/packmol/distinfo b/science/packmol/distinfo
index 275ea14103c6..1e7f2f2c9e84 100644
--- a/science/packmol/distinfo
+++ b/science/packmol/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1752270287
-SHA256 (m3g-packmol-v21.0.3_GH0.tar.gz) = 902e885e4b08ca728333b7cb56c9d8e46c4581f9f8d503ac42d13e24e00dc185
-SIZE (m3g-packmol-v21.0.3_GH0.tar.gz) = 630746
+TIMESTAMP = 1752317019
+SHA256 (m3g-packmol-v21.0.4_GH0.tar.gz) = ca2398a6f8f2a326f52cda8e45a8818ea430a1b195fd3801d017e1a18f38fde8
+SIZE (m3g-packmol-v21.0.4_GH0.tar.gz) = 630743
diff --git a/science/phonopy/Makefile b/science/phonopy/Makefile
index 79dae27c15f8..87062e5bc90e 100644
--- a/science/phonopy/Makefile
+++ b/science/phonopy/Makefile
@@ -1,6 +1,6 @@
PORTNAME= phonopy
DISTVERSIONPREFIX= v
-DISTVERSION= 2.38.0
+DISTVERSION= 2.42.0
CATEGORIES= science python
MAINTAINER= yuri@FreeBSD.org
diff --git a/science/phonopy/distinfo b/science/phonopy/distinfo
index fd9b3ed7de36..7a515ee74037 100644
--- a/science/phonopy/distinfo
+++ b/science/phonopy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1741068945
-SHA256 (phonopy-phonopy-v2.38.0_GH0.tar.gz) = e98c2b63f5cd847aa2efe6aa714ed1e656a3a2dba6f167830fc3149ee6bef4f1
-SIZE (phonopy-phonopy-v2.38.0_GH0.tar.gz) = 7712107
+TIMESTAMP = 1753085727
+SHA256 (phonopy-phonopy-v2.42.0_GH0.tar.gz) = db7efd4acb881114a9679a8f6730f127c196090d82077009746325ad2bc53041
+SIZE (phonopy-phonopy-v2.42.0_GH0.tar.gz) = 7718436
diff --git a/science/py-OpenMC/Makefile b/science/py-OpenMC/Makefile
index 6a295606f93b..77f10b2454d9 100644
--- a/science/py-OpenMC/Makefile
+++ b/science/py-OpenMC/Makefile
@@ -1,7 +1,7 @@
PORTNAME= OpenMC
DISTVERSIONPREFIX= v
DISTVERSION= 0.15.0
-PORTREVISION= 1
+PORTREVISION= 2
CATEGORIES= science
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
@@ -15,7 +15,7 @@ LICENSE_FILE= ${WRKSRC}/LICENSE
PY_DEPENDS= ${PYNUMPY} \
${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}ipython>0:devel/ipython@${PY_FLAVOR} \
- ${PYTHON_PKGNAMEPREFIX}lxml>0:devel/py-lxml@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}lxml5>0:devel/py-lxml5@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \
diff --git a/science/py-obspy/Makefile b/science/py-obspy/Makefile
index 682927b7f136..b0a3b8b4c973 100644
--- a/science/py-obspy/Makefile
+++ b/science/py-obspy/Makefile
@@ -1,5 +1,6 @@
PORTNAME= obspy
PORTVERSION= 1.4.2
+PORTREVISION= 1
CATEGORIES= science python
MASTER_SITES= PYPI
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
@@ -14,7 +15,7 @@ BUILD_DEPENDS= ${PYNUMPY} \
${PYTHON_PKGNAMEPREFIX}scipy>=1.7.0:science/py-scipy@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}future>=0.12.4:devel/py-future@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}matplotlib>=3.3.0:math/py-matplotlib@${PY_FLAVOR} \
- ${PYTHON_PKGNAMEPREFIX}lxml>=2.2:devel/py-lxml@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}lxml5>=2.2:devel/py-lxml5@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}requests>=0:www/py-requests@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}decorator>=0:devel/py-decorator@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}sqlalchemy10>=0:databases/py-sqlalchemy10@${PY_FLAVOR}
diff --git a/science/py-phonopy/Makefile b/science/py-phonopy/Makefile
index bb9438585200..b298e416ecf5 100644
--- a/science/py-phonopy/Makefile
+++ b/science/py-phonopy/Makefile
@@ -1,5 +1,5 @@
PORTNAME= phonopy
-DISTVERSION= 2.38.0
+DISTVERSION= 2.42.0
CATEGORIES= science python
MASTER_SITES= PYPI
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
@@ -36,6 +36,6 @@ TEST_WRKSRC= ${WRKSRC}/test
post-install:
@${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/phonopy/_phonopy${PYTHON_TAG}.so
-# tests as of 2.37.0: 3 failed, 270 passed, 4 skipped, 4 warnings, 5 errors in 1448.81s (0:24:08) (failures are likely in science/py-symfc with -9999 error)
+# tests as of 2.41.2: 6 failed, 159 passed, 5 skipped, 21 warnings, 130 errors in 502.46s (0:08:22) (failures are likely in science/py-symfc with -9999 error)
.include <bsd.port.mk>
diff --git a/science/py-phonopy/distinfo b/science/py-phonopy/distinfo
index 73eee825c0b9..fa7a9f63de51 100644
--- a/science/py-phonopy/distinfo
+++ b/science/py-phonopy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1741068971
-SHA256 (phonopy-2.38.0.tar.gz) = f2c285affe76b45fcef59d6323c7da727bbcfcdf25e0684cbdae46fccdcf40cf
-SIZE (phonopy-2.38.0.tar.gz) = 4712135
+TIMESTAMP = 1753085744
+SHA256 (phonopy-2.42.0.tar.gz) = f157afabc461d6b86c3ff09b139534890ca365ac4fd468cad1a0d0e9233776ce
+SIZE (phonopy-2.42.0.tar.gz) = 4715307
diff --git a/science/py-pycsw/Makefile b/science/py-pycsw/Makefile
index be76bccd65c7..0e08e20fb106 100644
--- a/science/py-pycsw/Makefile
+++ b/science/py-pycsw/Makefile
@@ -1,5 +1,6 @@
PORTNAME= pycsw
PORTVERSION= 2.6.2
+PORTREVISION= 1
CATEGORIES= science python
MASTER_SITES= PYPI
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
@@ -15,7 +16,7 @@ LICENSE_FILE= ${WRKSRC}/LICENSE.txt
BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR}
RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}geolinks>=0:science/py-geolinks@${PY_FLAVOR} \
- ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}lxml5>=0:devel/py-lxml5@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}OWSLib>=0:graphics/py-OWSLib@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}pyproj>=0:graphics/py-pyproj@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}shapely>=0:devel/py-shapely@${PY_FLAVOR} \
diff --git a/science/py-pygeometa/Makefile b/science/py-pygeometa/Makefile
index dd1b60da1fc8..df12a82e2163 100644
--- a/science/py-pygeometa/Makefile
+++ b/science/py-pygeometa/Makefile
@@ -1,6 +1,6 @@
PORTNAME= pygeometa
PORTVERSION= 0.15.3
-PORTREVISION= 3
+PORTREVISION= 4
CATEGORIES= science python
MASTER_SITES= PYPI
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
@@ -18,7 +18,7 @@ BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>=0:devel/py-setuptools@${PY_FLA
RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}click>=0:devel/py-click@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}Jinja2>=0:devel/py-Jinja2@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}jsonschema>=0:devel/py-jsonschema@${PY_FLAVOR} \
- ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}lxml5>=0:devel/py-lxml5@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}OWSLib>=0:graphics/py-OWSLib@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}pyyaml>=0:devel/py-pyyaml@${PY_FLAVOR}
diff --git a/science/py-pyteomics/Makefile b/science/py-pyteomics/Makefile
index cbcc08f885f8..6ef21f18727d 100644
--- a/science/py-pyteomics/Makefile
+++ b/science/py-pyteomics/Makefile
@@ -1,5 +1,6 @@
PORTNAME= pyteomics
PORTVERSION= 4.7.5
+PORTREVISION= 1
CATEGORIES= science python
MASTER_SITES= PYPI
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
@@ -30,9 +31,9 @@ XML_DESC= XML support
DF_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pandas>=0.17,1:math/py-pandas@${PY_FLAVOR}
GRAPHICS_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}matplotlib>=0:math/py-matplotlib@${PY_FLAVOR}
TDA_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR}
-UNIMOD_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \
+UNIMOD_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml5>=0:devel/py-lxml5@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}sqlalchemy14>=0:databases/py-sqlalchemy14@${PY_FLAVOR}
-XML_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml>=0:devel/py-lxml@${PY_FLAVOR} \
+XML_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}lxml5>=0:devel/py-lxml5@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR}
.include <bsd.port.mk>
diff --git a/science/py-rmf/Makefile b/science/py-rmf/Makefile
index 1d13d19df62c..dbe6e2950396 100644
--- a/science/py-rmf/Makefile
+++ b/science/py-rmf/Makefile
@@ -6,7 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
MAINTAINER= yuri@FreeBSD.org
COMMENT= Library to support reading and writing of Rich Molecular Format files
WWW= https://integrativemodeling.org/rmf/ \
- https://github.com/open-rmf/rmf
+ https://github.com/salilab/rmf
LICENSE= APACHE20
LICENSE_FILE= ${WRKSRC}/COPYING
diff --git a/science/rmf/Makefile b/science/rmf/Makefile
index 5d09f287b9f7..9a1b1c673a5d 100644
--- a/science/rmf/Makefile
+++ b/science/rmf/Makefile
@@ -6,7 +6,7 @@ CATEGORIES= science graphics
MAINTAINER= yuri@FreeBSD.org
COMMENT= Library to support reading and writing of Rich Molecular Format files
WWW= https://integrativemodeling.org/rmf/ \
- https://github.com/open-rmf/rmf
+ https://github.com/salilab/rmf
LICENSE= APACHE20
LICENSE_FILE= ${WRKSRC}/COPYING
diff --git a/science/votca/Makefile b/science/votca/Makefile
index 24ce596890b3..4e9868987d20 100644
--- a/science/votca/Makefile
+++ b/science/votca/Makefile
@@ -1,7 +1,7 @@
PORTNAME= votca
DISTVERSIONPREFIX= v
DISTVERSION= 2025
-PORTREVISION= 1
+PORTREVISION= 2
CATEGORIES= science
MAINTAINER= yuri@FreeBSD.org
@@ -15,7 +15,7 @@ BROKEN_i386= undefined reference to `__atomic_load'
PY_DEPENDS= \
${PYTHON_PKGNAMEPREFIX}ase>0:science/py-ase@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \
- ${PYTHON_PKGNAMEPREFIX}lxml>0:devel/py-lxml@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}lxml5>0:devel/py-lxml5@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}xmltodict>0:devel/py-xmltodict@${PY_FLAVOR} \
rdkit>0:science/rdkit
BUILD_DEPENDS= bash:shells/bash \
generated by cgit v1.2.3 (git 2.25.1) at 2025-07-22 04:20:37 +0000