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-rw-r--r--science/Makefile3
-rw-r--r--science/cdo/Makefile3
-rw-r--r--science/cdo/distinfo6
-rw-r--r--science/csvtk/Makefile2
-rw-r--r--science/molgif/Makefile2
-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
15 files changed, 126 insertions, 7 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/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/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/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.
generated by cgit v1.2.3 (git 2.25.1) at 2025-10-09 05:37:00 +0000