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-rw-r--r--science/atompaw/Makefile3
-rw-r--r--science/atompaw/files/patch-src_input__dataset__mod.F9011
-rw-r--r--science/berkeleygw/Makefile2
-rw-r--r--science/csvtk/Makefile2
-rw-r--r--science/kim-api/Makefile6
-rw-r--r--science/kim-api/distinfo6
-rw-r--r--science/kim-api/pkg-plist3
-rw-r--r--science/molgif/Makefile2
-rw-r--r--science/py-ase/Makefile12
-rw-r--r--science/py-ase/distinfo6
-rw-r--r--science/py-ase/files/patch-pyproject.toml11
-rw-r--r--science/py-kimpy/Makefile7
-rw-r--r--science/py-kimpy/distinfo6
13 files changed, 53 insertions, 24 deletions
diff --git a/science/atompaw/Makefile b/science/atompaw/Makefile
index 61ccc526fadb..5e23ebdb9006 100644
--- a/science/atompaw/Makefile
+++ b/science/atompaw/Makefile
@@ -1,6 +1,6 @@
PORTNAME= atompaw
DISTVERSION= 4.2.0.3
-PORTREVISION= 2
+PORTREVISION= 3
CATEGORIES= science
MASTER_SITES= http://users.wfu.edu/natalie/papers/pwpaw/
@@ -16,6 +16,7 @@ LIB_DEPENDS= liblapack.so:math/lapack \
USES= fortran gmake libtool
GNU_CONFIGURE= yes
+CONFIGURE_ARGS= --with-linalg-prefix=${LOCALBASE}
OPTIONS_DEFINE= DOCS LIBXC
OPTIONS_DEFAULT= LIBXC
diff --git a/science/atompaw/files/patch-src_input__dataset__mod.F90 b/science/atompaw/files/patch-src_input__dataset__mod.F90
new file mode 100644
index 000000000000..cca7d9e3d6ae
--- /dev/null
+++ b/science/atompaw/files/patch-src_input__dataset__mod.F90
@@ -0,0 +1,11 @@
+--- src/input_dataset_mod.F90.orig 2023-06-02 20:37:00 UTC
++++ src/input_dataset_mod.F90
+@@ -2097,7 +2097,7 @@ END IF
+ INTEGER :: input_unit,echo_unit
+ INTEGER :: i_all,i_dx,i_xmin,i_zmesh,i_range
+ LOGICAL :: has_to_echo
+- CHARACTER(200) :: inputline
++ CHARACTER(256) :: inputline
+ TYPE(input_dataset_t),POINTER :: dataset
+
+ !------------------------------------------------------------------
diff --git a/science/berkeleygw/Makefile b/science/berkeleygw/Makefile
index 36f76867eaaa..bc988171c441 100644
--- a/science/berkeleygw/Makefile
+++ b/science/berkeleygw/Makefile
@@ -18,7 +18,7 @@ BUILD_DEPENDS= bash:shells/bash
LIB_DEPENDS= libfftw3.so:math/fftw3
RUN_DEPENDS= bash:shells/bash
-USES= blaslapack:openblas gmake fortran python shebangfix
+USES= blaslapack:openblas gmake fortran:gfortran python shebangfix
SHEBANG_GLOB= *.sh *.py *awk
diff --git a/science/csvtk/Makefile b/science/csvtk/Makefile
index e4b2b99739a4..acaa471d2f00 100644
--- a/science/csvtk/Makefile
+++ b/science/csvtk/Makefile
@@ -1,7 +1,7 @@
PORTNAME= csvtk
DISTVERSIONPREFIX= v
DISTVERSION= 0.34.0
-PORTREVISION= 1
+PORTREVISION= 2
CATEGORIES= science
MAINTAINER= jwb@FreeBSD.org
diff --git a/science/kim-api/Makefile b/science/kim-api/Makefile
index bcfc3fe9f454..154452adc611 100644
--- a/science/kim-api/Makefile
+++ b/science/kim-api/Makefile
@@ -1,12 +1,12 @@
PORTNAME= kim-api
-DISTVERSION= 2.3.0
-PORTREVISION= 1
+DISTVERSION= 2.4.1
CATEGORIES= science
MASTER_SITES= https://s3.openkim.org/kim-api/
MAINTAINER= yuri@FreeBSD.org
COMMENT= Framework for reliable, reproducible, portable molecular simulations
-WWW= https://openkim.org/
+WWW= https://openkim.org/ \
+ https://github.com/openkim/kim-api
LICENSE= LGPL3
LICENSE_FILE= ${WRKSRC}/LICENSE.LGPL
diff --git a/science/kim-api/distinfo b/science/kim-api/distinfo
index 34ec678ecd72..aa9436bebfa7 100644
--- a/science/kim-api/distinfo
+++ b/science/kim-api/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1647738438
-SHA256 (kim-api-2.3.0.txz) = 93673bb8fbc0625791f2ee67915d1672793366d10cabc63e373196862c14f991
-SIZE (kim-api-2.3.0.txz) = 357580
+TIMESTAMP = 1757122898
+SHA256 (kim-api-2.4.1.txz) = 225e3136d43e416a4424551e9e5f6d92cc6ecfe11389a1b6e97d6dcdfed83d44
+SIZE (kim-api-2.4.1.txz) = 364020
diff --git a/science/kim-api/pkg-plist b/science/kim-api/pkg-plist
index 544dee8e567d..8ad13559dacb 100644
--- a/science/kim-api/pkg-plist
+++ b/science/kim-api/pkg-plist
@@ -134,8 +134,9 @@ lib/kim-api/portable-models/ex_model_Ar_SLJ_MultiCutoff/libkim-api-portable-mode
lib/kim-api/simulator-models/Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu/libkim-api-simulator-model.so
lib/libkim-api.so
lib/libkim-api.so.2
-lib/libkim-api.so.2.3.0
+lib/libkim-api.so.2.4.1
libdata/pkgconfig/libkim-api.pc
+libexec/kim-api/kim-api-base64-encode
libexec/kim-api/kim-api-collections-info
libexec/kim-api/kim-api-portable-model-info
libexec/kim-api/kim-api-shared-library-test
diff --git a/science/molgif/Makefile b/science/molgif/Makefile
index 280dc2503615..9998275f996b 100644
--- a/science/molgif/Makefile
+++ b/science/molgif/Makefile
@@ -1,6 +1,6 @@
PORTNAME= molgif
DISTVERSION= g20180108
-PORTREVISION= 29
+PORTREVISION= 30
CATEGORIES= science
MAINTAINER= yuri@FreeBSD.org
diff --git a/science/py-ase/Makefile b/science/py-ase/Makefile
index 27c665165e36..f3e0a8056fdc 100644
--- a/science/py-ase/Makefile
+++ b/science/py-ase/Makefile
@@ -1,21 +1,21 @@
PORTNAME= ase
-DISTVERSION= 3.23.0
-PORTREVISION= 2
+DISTVERSION= 3.26.0
CATEGORIES= science python # chemistry
MASTER_SITES= PYPI
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
MAINTAINER= yuri@FreeBSD.org
COMMENT= Atomic simulation environment
-WWW= https://wiki.fysik.dtu.dk/ase/
+WWW= https://ase-lib.org/ \
+ https://gitlab.com/ase/ase
LICENSE= LGPL21
LICENSE_FILE= ${WRKSRC}/COPYING.LESSER
RUN_DEPENDS= ${PYNUMPY} \
${PYTHON_PKGNAMEPREFIX}matplotlib>=3.1.0:math/py-matplotlib@${PY_FLAVOR} \
- ${PYTHON_PKGNAMEPREFIX}scipy>=1.1.0:science/py-scipy@${PY_FLAVOR} \
- nwchem:science/nwchem
+ ${PYTHON_PKGNAMEPREFIX}scipy>=1.1.0:science/py-scipy@${PY_FLAVOR}
+# nwchem:science/nwchem
TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest-mock>0:devel/py-pytest-mock@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}pytest-xdist>=1.30.0:devel/py-pytest-xdist@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}asap3>0:science/py-asap3@${PY_FLAVOR} \
@@ -29,4 +29,6 @@ USE_PYTHON= distutils concurrent autoplist pytest
NO_ARCH= yes
+# tests as of 3.26.0: 25 failed, 3036 passed, 538 skipped, 5 xfailed, 49 warnings, 10 errors in 2377.98s (0:39:37), see https://gitlab.com/ase/ase/-/issues/1746, https://gitlab.com/ase/ase/-/issues/1747
+
.include <bsd.port.mk>
diff --git a/science/py-ase/distinfo b/science/py-ase/distinfo
index 856920eb9664..eb2ad2c0fbb6 100644
--- a/science/py-ase/distinfo
+++ b/science/py-ase/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1720836089
-SHA256 (ase-3.23.0.tar.gz) = 91a2aa31d89bd90b0efdfe4a7e84264f32828b2abfc9f38e65e041ad76fec8ae
-SIZE (ase-3.23.0.tar.gz) = 2336462
+TIMESTAMP = 1757118068
+SHA256 (ase-3.26.0.tar.gz) = a071a355775b0a8062d23e9266e9d811b19d9f6d9ec5215e8032f7d93dc65075
+SIZE (ase-3.26.0.tar.gz) = 2405567
diff --git a/science/py-ase/files/patch-pyproject.toml b/science/py-ase/files/patch-pyproject.toml
new file mode 100644
index 000000000000..f1ffc89d09c4
--- /dev/null
+++ b/science/py-ase/files/patch-pyproject.toml
@@ -0,0 +1,11 @@
+--- pyproject.toml.orig 2025-09-06 00:22:04 UTC
++++ pyproject.toml
+@@ -7,8 +7,6 @@ readme = 'README.rst'
+ description='Atomic Simulation Environment'
+ dynamic = ['version']
+ readme = 'README.rst'
+-license = 'LGPL-2.1-or-later'
+-license-files = ['LICENSE']
+ maintainers = [{ name = 'ASE Community', email = 'ase-users@listserv.fysik.dtu.dk' }]
+ classifiers = [
+ 'Development Status :: 6 - Mature',
diff --git a/science/py-kimpy/Makefile b/science/py-kimpy/Makefile
index 442b5c9a82d3..0c537ae18c1e 100644
--- a/science/py-kimpy/Makefile
+++ b/science/py-kimpy/Makefile
@@ -1,6 +1,5 @@
PORTNAME= kimpy
-DISTVERSION= 2.1.1
-PORTREVISION= 1
+DISTVERSION= 2.1.3
CATEGORIES= science python
MASTER_SITES= PYPI
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
@@ -19,7 +18,11 @@ RUN_DEPENDS= ${PYNUMPY}
USES= compiler:c++20-lang pkgconfig python
USE_PYTHON= distutils autoplist pytest # tests fail to run, see https://github.com/openkim/kimpy/issues/16
+TEST_WRKSRC= ${WRKSRC}/tests
+
post-install:
@${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/kimpy/*${PYTHON_TAG}.so
+# tests as of 2.1.3: 21 passed in 2.91s
+
.include <bsd.port.mk>
diff --git a/science/py-kimpy/distinfo b/science/py-kimpy/distinfo
index e7d3c6deaef7..6d692faf3795 100644
--- a/science/py-kimpy/distinfo
+++ b/science/py-kimpy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1726458544
-SHA256 (kimpy-2.1.1.tar.gz) = 3ab9ab64179cdf8b7d41704330d12bbb78461792664354e9e9144098709bc636
-SIZE (kimpy-2.1.1.tar.gz) = 50141
+TIMESTAMP = 1757123909
+SHA256 (kimpy-2.1.3.tar.gz) = 2a4a4455dfc5aeb5b8379a96b7c1e7a3f34bfe6bd3c077e23a3e27b8829c2aed
+SIZE (kimpy-2.1.3.tar.gz) = 49856
generated by cgit v1.2.3 (git 2.25.1) at 2025-09-06 07:34:03 +0000