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-rw-r--r--science/Makefile3
-rw-r--r--science/afni/Makefile2
-rw-r--r--science/afni/distinfo6
-rw-r--r--science/cdo/Makefile3
-rw-r--r--science/cdo/distinfo6
-rw-r--r--science/csvtk/Makefile2
-rw-r--r--science/isaac-cfd/Makefile9
-rw-r--r--science/molgif/Makefile2
-rw-r--r--science/packmol/Makefile2
-rw-r--r--science/packmol/distinfo6
-rw-r--r--science/py-asdf/Makefile1
-rw-r--r--science/py-mne/Makefile34
-rw-r--r--science/py-mne/distinfo3
-rw-r--r--science/py-mne/pkg-descr4
-rw-r--r--science/py-neo/Makefile26
-rw-r--r--science/py-neo/distinfo3
-rw-r--r--science/py-neo/pkg-descr8
-rw-r--r--science/py-pynrrd/Makefile31
-rw-r--r--science/py-pynrrd/distinfo3
-rw-r--r--science/py-pynrrd/pkg-descr4
-rw-r--r--science/py-qiskit/Makefile1
-rw-r--r--science/qt6-quick3dphysics/distinfo6
-rw-r--r--science/tinker/Makefile1
-rw-r--r--science/tinker/distinfo6
-rw-r--r--science/tinker/files/patch-cmake_CMakeLists.txt15
-rw-r--r--science/tinker/files/patch-make_Makefile13
26 files changed, 166 insertions, 34 deletions
diff --git a/science/Makefile b/science/Makefile
index 7a7615c8776f..9713030b534d 100644
--- a/science/Makefile
+++ b/science/Makefile
@@ -370,6 +370,7 @@
SUBDIR += py-meshio
SUBDIR += py-mmcif
SUBDIR += py-mmtf-python
+ SUBDIR += py-mne
SUBDIR += py-molmod
SUBDIR += py-mp-api
SUBDIR += py-mpcontribs-client
@@ -377,6 +378,7 @@
SUBDIR += py-mplhep-data
SUBDIR += py-mrchem
SUBDIR += py-ncrystal
+ SUBDIR += py-neo
SUBDIR += py-netCDF4
SUBDIR += py-netcdf-flattener
SUBDIR += py-nglview
@@ -408,6 +410,7 @@
SUBDIR += py-pymatgen-analysis-alloys
SUBDIR += py-pymbd
SUBDIR += py-pymol
+ SUBDIR += py-pynrrd
SUBDIR += py-pyosf
SUBDIR += py-pyphot
SUBDIR += py-pyprecice
diff --git a/science/afni/Makefile b/science/afni/Makefile
index 74ad2cbe7f50..60a9c6179d87 100644
--- a/science/afni/Makefile
+++ b/science/afni/Makefile
@@ -1,6 +1,6 @@
PORTNAME= afni
DISTVERSIONPREFIX= AFNI_
-DISTVERSION= 25.2.17
+DISTVERSION= 25.2.18
CATEGORIES= science biology graphics perl5 python
MAINTAINER= fernape@FreeBSD.org
diff --git a/science/afni/distinfo b/science/afni/distinfo
index a69fa3d8ee34..86a0070395b4 100644
--- a/science/afni/distinfo
+++ b/science/afni/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1758872368
-SHA256 (afni-afni-AFNI_25.2.17_GH0.tar.gz) = e97fba22be67fd931b753047e536f5cb919a507a2e2769f258a82ad0f0dec959
-SIZE (afni-afni-AFNI_25.2.17_GH0.tar.gz) = 53342709
+TIMESTAMP = 1759213947
+SHA256 (afni-afni-AFNI_25.2.18_GH0.tar.gz) = 9f21faf0f8ed66eba8a2c1473a4c5c0421909e0f386fc699ed599bebced96003
+SIZE (afni-afni-AFNI_25.2.18_GH0.tar.gz) = 53390003
diff --git a/science/cdo/Makefile b/science/cdo/Makefile
index 43c111203c7c..3189b691bce4 100644
--- a/science/cdo/Makefile
+++ b/science/cdo/Makefile
@@ -1,7 +1,8 @@
PORTNAME= cdo
PORTVERSION= 2.5.3
+PORTREVISION= 1
CATEGORIES= science
-MASTER_SITES= https://code.mpimet.mpg.de/attachments/download/30034/ \
+MASTER_SITES= https://code.mpimet.mpg.de/attachments/download/30045/ \
LOCAL/sunpoet
MAINTAINER= sunpoet@FreeBSD.org
diff --git a/science/cdo/distinfo b/science/cdo/distinfo
index 99abd7f5e917..1924307377b3 100644
--- a/science/cdo/distinfo
+++ b/science/cdo/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1755062464
-SHA256 (cdo-2.5.3.tar.gz) = 0145cdba866a02b3e9b269e2ff7728ce61e21761332888041f05dc033676fa08
-SIZE (cdo-2.5.3.tar.gz) = 14007141
+TIMESTAMP = 1757515934
+SHA256 (cdo-2.5.3.tar.gz) = 470fee8f4d2b4eddf9ec82d0adccf1f6b4821ddf34b33bfe6b7069b6b6457b40
+SIZE (cdo-2.5.3.tar.gz) = 13973520
diff --git a/science/csvtk/Makefile b/science/csvtk/Makefile
index acaa471d2f00..3d2c9d80ac57 100644
--- a/science/csvtk/Makefile
+++ b/science/csvtk/Makefile
@@ -1,7 +1,7 @@
PORTNAME= csvtk
DISTVERSIONPREFIX= v
DISTVERSION= 0.34.0
-PORTREVISION= 2
+PORTREVISION= 3
CATEGORIES= science
MAINTAINER= jwb@FreeBSD.org
diff --git a/science/isaac-cfd/Makefile b/science/isaac-cfd/Makefile
index dfe1e852aff2..7ebbbae934ac 100644
--- a/science/isaac-cfd/Makefile
+++ b/science/isaac-cfd/Makefile
@@ -20,7 +20,6 @@ NO_WRKSUBDIR= yes
MAKEFILE= makefile
MAKE_ARGS= CPPFLAGS=-I.
USES= fortran gmake
-FFLAGS+= -std=legacy
PLIST_FILES= bin/isaac
PORTDOCS= man.4_2.ps.gz
@@ -34,6 +33,12 @@ EXAMPLES_DISTFILES= example_cases${EXTRACT_SUFX}
OPTIMIZED_FFLAGS_DESC= Use extra compiler (fortran) optimizations
OPTIMIZED_FFLAGS_VARS= FFLAGS+="-O2 -ffast-math"
+.include <bsd.port.pre.mk>
+
+.if ${FORTRAN_DEFAULT} != flang
+FFLAGS= -std=legacy
+.endif
+
pre-configure:
@${REINPLACE_CMD} -e 's+%%FC%%+${FC}+g ; s+%%FFLAGS%%+${FFLAGS}+;' \
${WRKSRC}/makefile
@@ -53,4 +58,4 @@ do-install-EXAMPLES-on:
${TAR} -xzf ${DISTDIR}/${DIST_SUBDIR}/example_cases${EXTRACT_SUFX} \
-C ${STAGEDIR}${EXAMPLESDIR}
-.include <bsd.port.mk>
+.include <bsd.port.post.mk>
diff --git a/science/molgif/Makefile b/science/molgif/Makefile
index 9998275f996b..af14421a80b8 100644
--- a/science/molgif/Makefile
+++ b/science/molgif/Makefile
@@ -1,6 +1,6 @@
PORTNAME= molgif
DISTVERSION= g20180108
-PORTREVISION= 30
+PORTREVISION= 31
CATEGORIES= science
MAINTAINER= yuri@FreeBSD.org
diff --git a/science/packmol/Makefile b/science/packmol/Makefile
index 8f1bef5e46ce..5f2d5ae0c487 100644
--- a/science/packmol/Makefile
+++ b/science/packmol/Makefile
@@ -1,6 +1,6 @@
PORTNAME= packmol
DISTVERSIONPREFIX= v
-DISTVERSION= 21.1.0
+DISTVERSION= 21.1.1
CATEGORIES= science
MAINTAINER= eduardo@FreeBSD.org
diff --git a/science/packmol/distinfo b/science/packmol/distinfo
index a62a7e08f6a6..a48cfe0d0a3d 100644
--- a/science/packmol/distinfo
+++ b/science/packmol/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1755694551
-SHA256 (m3g-packmol-v21.1.0_GH0.tar.gz) = bcb64849bd490c329018210cf91375871108004ac8bf3e8cf9463e42e551fe46
-SIZE (m3g-packmol-v21.1.0_GH0.tar.gz) = 634772
+TIMESTAMP = 1759409929
+SHA256 (m3g-packmol-v21.1.1_GH0.tar.gz) = 4bad785e6e1b91d8b80934eeebf91013e940c577693bbecd7ec56eb563f5d97f
+SIZE (m3g-packmol-v21.1.1_GH0.tar.gz) = 634943
diff --git a/science/py-asdf/Makefile b/science/py-asdf/Makefile
index 150580aa2496..5a7e1522c875 100644
--- a/science/py-asdf/Makefile
+++ b/science/py-asdf/Makefile
@@ -43,7 +43,6 @@ OPTIONS_DEFAULT=ALL HTTP LZ4
ALL_IMPLIES= HTTP LZ4
ALL_DESC= All optional dependencies
HTTP_DESC= HTTP support via fsspec
-LZ4_DESC= Lz4 compression algorithm support
HTTP_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}aiohttp>=0:www/py-aiohttp@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}fsspec>=2022.8.2:filesystems/py-fsspec@${PY_FLAVOR}
diff --git a/science/py-mne/Makefile b/science/py-mne/Makefile
new file mode 100644
index 000000000000..3f15411d9c98
--- /dev/null
+++ b/science/py-mne/Makefile
@@ -0,0 +1,34 @@
+PORTNAME= mne
+PORTVERSION= 1.10.1
+CATEGORIES= science python
+MASTER_SITES= PYPI
+PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
+
+MAINTAINER= yuri@FreeBSD.org
+COMMENT= Python project for MEG and EEG data analysis
+WWW= https://mne.tools/stable/ \
+ https://github.com/mne-tools/mne-python
+
+LICENSE= BSD3CLAUSE
+LICENSE_FILE= ${WRKSRC}/LICENSE.txt
+
+BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}hatchling>0:devel/py-hatchling@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}hatch-vcs>0:devel/py-hatch-vcs@${PY_FLAVOR}
+RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}decorator>0:devel/py-decorator@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}Jinja2>0:devel/py-Jinja2@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}lazy_loader>=0.3:devel/py-lazy_loader@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.7:math/py-matplotlib@${PY_FLAVOR} \
+ ${PYNUMPY} \
+ ${PYTHON_PKGNAMEPREFIX}packaging>0:devel/py-packaging@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}pooch>=1.5:devel/py-pooch@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}scipy>=1.11:science/py-scipy@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}tqdm>0:misc/py-tqdm@${PY_FLAVOR}
+
+USES= python
+USE_PYTHON= pep517 concurrent autoplist
+
+NO_ARCH= yes
+
+# tests as of 1.10.1: pytest tests available but require extra dependencies, skipped for packaging
+
+.include <bsd.port.mk>
diff --git a/science/py-mne/distinfo b/science/py-mne/distinfo
new file mode 100644
index 000000000000..f63a12725683
--- /dev/null
+++ b/science/py-mne/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1759525649
+SHA256 (mne-1.10.1.tar.gz) = a93e3d772d551e43ec5ddcd3495fffe0f98e3e384045bcd96497636e86a32a0b
+SIZE (mne-1.10.1.tar.gz) = 7123187
diff --git a/science/py-mne/pkg-descr b/science/py-mne/pkg-descr
new file mode 100644
index 000000000000..06c74b93513a
--- /dev/null
+++ b/science/py-mne/pkg-descr
@@ -0,0 +1,4 @@
+MNE-Python is an open-source Python package for exploring, visualizing,
+and analyzing human neurophysiological data: MEG, EEG, sEEG, ECoG, and more.
+It includes algorithms for preprocessing, source estimation, time-frequency
+analysis, statistics, and machine learning.
diff --git a/science/py-neo/Makefile b/science/py-neo/Makefile
new file mode 100644
index 000000000000..af57025f1e56
--- /dev/null
+++ b/science/py-neo/Makefile
@@ -0,0 +1,26 @@
+PORTNAME= neo
+PORTVERSION= 0.14.2
+CATEGORIES= science python
+MASTER_SITES= PYPI
+PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
+
+MAINTAINER= yuri@FreeBSD.org
+COMMENT= Package for representing electrophysiology data in Python
+WWW= https://neo.readthedocs.io/en/latest/ \
+ https://github.com/NeuralEnsemble/python-neo
+
+LICENSE= BSD3CLAUSE
+LICENSE_FILE= ${WRKSRC}/LICENSE.txt
+
+RUN_DEPENDS= ${PYNUMPY} \
+ ${PYTHON_PKGNAMEPREFIX}packaging>0:devel/py-packaging@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}quantities>=0.16.1:science/py-quantities@${PY_FLAVOR}
+
+USES= python
+USE_PYTHON= distutils autoplist concurrent pytest
+
+NO_ARCH= yes
+
+# tests as of 0.14.2: 669 passed, 731 skipped in 80.29s
+
+.include <bsd.port.mk>
diff --git a/science/py-neo/distinfo b/science/py-neo/distinfo
new file mode 100644
index 000000000000..11e758623a41
--- /dev/null
+++ b/science/py-neo/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1759525621
+SHA256 (neo-0.14.2.tar.gz) = 76517503e114fffcc38aa3600c04dd8be48b1ee5e2c8162bc0db8fb92476811f
+SIZE (neo-0.14.2.tar.gz) = 5067423
diff --git a/science/py-neo/pkg-descr b/science/py-neo/pkg-descr
new file mode 100644
index 000000000000..3104e132bd32
--- /dev/null
+++ b/science/py-neo/pkg-descr
@@ -0,0 +1,8 @@
+Neo is a package for representing electrophysiology data in Python, together
+with support for reading a wide range of neurophysiology file formats.
+
+The goal of Neo is to improve interoperability between Python tools for
+analyzing, visualizing and generating electrophysiology data, by providing
+a common, shared object model. In order to be as lightweight a dependency
+as possible, Neo is deliberately limited to representation of data, with
+no functions for data analysis or visualization.
diff --git a/science/py-pynrrd/Makefile b/science/py-pynrrd/Makefile
new file mode 100644
index 000000000000..11058c29480c
--- /dev/null
+++ b/science/py-pynrrd/Makefile
@@ -0,0 +1,31 @@
+PORTNAME= pynrrd
+DISTVERSIONPREFIX= v
+DISTVERSION= 1.1.3
+CATEGORIES= science python
+#MASTER_SITES= PYPI # no tests
+PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
+
+MAINTAINER= yuri@FreeBSD.org
+COMMENT= Pure Python module for reading and writing NRRD files
+WWW= https://pynrrd.readthedocs.io/en/stable/ \
+ https://github.com/mhe/pynrrd
+
+LICENSE= MIT
+LICENSE_FILE= ${WRKSRC}/LICENSE
+
+BUILD_DEPENDS= ${PY_SETUPTOOLS} \
+ ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR}
+RUN_DEPENDS= ${PYNUMPY} \
+ ${PYTHON_PKGNAMEPREFIX}typing-extensions>=0:devel/py-typing-extensions@${PY_FLAVOR}
+
+USES= python
+USE_PYTHON= pep517 autoplist pytest
+
+USE_GITHUB= yes
+GH_ACCOUNT= mhe
+
+NO_ARCH= yes
+
+# tests as of 1.1.3: 159 passed in 3.03s
+
+.include <bsd.port.mk>
diff --git a/science/py-pynrrd/distinfo b/science/py-pynrrd/distinfo
new file mode 100644
index 000000000000..fc154510a78b
--- /dev/null
+++ b/science/py-pynrrd/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1759736084
+SHA256 (mhe-pynrrd-v1.1.3_GH0.tar.gz) = 10ce743d69ecf54b41ecab56b74dc8a5f806d299c45fcc1ef07d7d8aef5949ea
+SIZE (mhe-pynrrd-v1.1.3_GH0.tar.gz) = 47813
diff --git a/science/py-pynrrd/pkg-descr b/science/py-pynrrd/pkg-descr
new file mode 100644
index 000000000000..2f8cf8ad7e91
--- /dev/null
+++ b/science/py-pynrrd/pkg-descr
@@ -0,0 +1,4 @@
+NRRD (Nearly Raw Raster Data) is a library and file format designed to
+support scientific visualization and image processing involving N-dimensional
+raster data. This library provides the ability to read and write NRRD files
+using pure Python.
diff --git a/science/py-qiskit/Makefile b/science/py-qiskit/Makefile
index 25eb454a3612..9e1c3667b27d 100644
--- a/science/py-qiskit/Makefile
+++ b/science/py-qiskit/Makefile
@@ -1,5 +1,6 @@
PORTNAME= qiskit
DISTVERSION= 2.1.2
+PORTREVISION= 1
CATEGORIES= science python
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
diff --git a/science/qt6-quick3dphysics/distinfo b/science/qt6-quick3dphysics/distinfo
index 8e99d6679edf..a1a299cb31b7 100644
--- a/science/qt6-quick3dphysics/distinfo
+++ b/science/qt6-quick3dphysics/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1756197855
-SHA256 (KDE/Qt/6.9.2/qtquick3dphysics-everywhere-src-6.9.2.tar.xz) = 87fc6485638f52cd33dc1a755a11c78fd992e438fe77ef53e0ca57c63505cc8b
-SIZE (KDE/Qt/6.9.2/qtquick3dphysics-everywhere-src-6.9.2.tar.xz) = 4668516
+TIMESTAMP = 1759303916
+SHA256 (KDE/Qt/6.9.3/qtquick3dphysics-everywhere-src-6.9.3.tar.xz) = dcd7b22d745d249eb602c5d4d8af8a8e9d11217ccb42b3dd611bb047153b5a6e
+SIZE (KDE/Qt/6.9.3/qtquick3dphysics-everywhere-src-6.9.3.tar.xz) = 4668392
diff --git a/science/tinker/Makefile b/science/tinker/Makefile
index 9249e98239ef..5723eb9b39db 100644
--- a/science/tinker/Makefile
+++ b/science/tinker/Makefile
@@ -1,5 +1,6 @@
PORTNAME= tinker
DISTVERSION= 25.5
+PORTREVISION= 1
CATEGORIES= science
MASTER_SITES= https://dasher.wustl.edu/tinker/downloads/
diff --git a/science/tinker/distinfo b/science/tinker/distinfo
index 327e627a7d9e..b452890259c0 100644
--- a/science/tinker/distinfo
+++ b/science/tinker/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1758258766
-SHA256 (tinker-25.5.tar.gz) = 01b50ad3680c0bfb77c77e4f9c653c47a39da1510286cb8a5dbc14f8f7b86d18
-SIZE (tinker-25.5.tar.gz) = 81152948
+TIMESTAMP = 1759481421
+SHA256 (tinker-25.5.tar.gz) = 10e24742d262a09a4b191eb73ef994cc8987e1e5e18ac7759420b36f07a02036
+SIZE (tinker-25.5.tar.gz) = 81137927
diff --git a/science/tinker/files/patch-cmake_CMakeLists.txt b/science/tinker/files/patch-cmake_CMakeLists.txt
new file mode 100644
index 000000000000..e4d2d621ed7f
--- /dev/null
+++ b/science/tinker/files/patch-cmake_CMakeLists.txt
@@ -0,0 +1,15 @@
+--- cmake/CMakeLists.txt.orig 2025-10-03 08:52:37 UTC
++++ cmake/CMakeLists.txt
+@@ -68,12 +68,6 @@ set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+
+ # Set compiler flags
+
+-if(APPLE)
+- set(ARCH_FLAGS "-mtune=native")
+-else()
+- set(ARCH_FLAGS "-march=native")
+-endif()
+-
+ if(WIN32)
+ if(CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
+ set(CMAKE_Fortran_FLAGS_RELEASE "/O3 /QxHost /Qip- /Qprec-div- /w")
diff --git a/science/tinker/files/patch-make_Makefile b/science/tinker/files/patch-make_Makefile
index 4b7b308532ab..7e1f679a86a0 100644
--- a/science/tinker/files/patch-make_Makefile
+++ b/science/tinker/files/patch-make_Makefile
@@ -1,15 +1,6 @@
---- make/Makefile.orig 2024-05-04 16:08:28 UTC
+--- make/Makefile.orig 2025-09-30 16:25:57 UTC
+++ make/Makefile
-@@ -68,7 +68,7 @@ F77FLAGS = -c
-
- F77 = gfortran
- F77FLAGS = -c
--OPTFLAGS = -Ofast -march=native -fopenmp
-+OPTFLAGS = -Ofast $(PORT_SIMD_FLAGS) -fopenmp
- OPTFLAGS = -Ofast -fopenmp
- OPTFLAGS = -Og -g -fbacktrace -fcheck=bounds -Wunused -Wmaybe-uninitialized
- LIBDIR = -L. -L$(TINKER_LIBDIR)/linux -Wl,--no-as-needed -ldl
-@@ -829,138 +829,138 @@ rename_bin:
+@@ -813,138 +813,138 @@ rename_bin:
cat *.f *.c > tinker.txt
rename_bin:
generated by cgit v1.2.3 (git 2.25.1) at 2025-10-09 01:39:32 +0000