8688 Commits

Author SHA1 Message Date
Po-Chuan Hsieh
df8e2d1716
science/py-pyteomics: Update to 4.7.5
Changes:	https://github.com/levitsky/pyteomics/releases
		https://pyteomics.readthedocs.io/en/latest/changelog.html
2024-10-25 23:56:47 +08:00
Po-Chuan Hsieh
4d13b25916
textproc/xerces-c3: Update to 3.3.0
- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://issues.apache.org/jira/secure/ReleaseNote.jspa?projectId=10510&version=12355023
2024-10-25 23:56:41 +08:00
Yuri Victorovich
42713e6e9c science/dssp: update 4.4.8 → 4.4.10 2024-10-24 20:27:38 -07:00
Yuri Victorovich
dd5cbb19a7 science/libcifpp: update 7.0.6 → 7.0.7 2024-10-24 20:27:38 -07:00
Max Brazhnikov
678050c8ce science/scidavis: makr broken with PYTHON option
Temporary disable PYTHON option.
2024-10-24 15:26:07 +03:00
Yuri Victorovich
c9e9d2c21f science/py-gsd: update 3.3.2 → 3.4.1
Reported by:	portscout
2024-10-23 02:44:45 -07:00
Max Brazhnikov
39d8976d3b science/scidavis: fix dependence on sip 2024-10-22 11:40:32 +03:00
Robert Clausecker
75ecc581ae science/opensph: port to aarch64
- use sse2neon to build this port on aarch64
 - armv7 might work too, but I can't test it due to dependent ports not
   building right now

Approved by:	yuri (maintainer)
Differential Revision:	https://reviews.freebsd.org/D47140
2024-10-21 11:36:01 +02:00
Po-Chuan Hsieh
b8176fe1eb
science/grib_api: Mark DEPRECATED and set EXPIRATION_DATE to 2024-11-30
PR:		281652
Reported by:	diizzy
Reference:	https://www.ecmwf.int/en/newsletter/152/news/end-road-grib-api
2024-10-21 17:17:41 +08:00
Po-Chuan Hsieh
c418813e03
science/py-eccodes: Update to 2.38.3
Changes:	https://github.com/ecmwf/eccodes-python/releases
		https://github.com/ecmwf/eccodes-python/blob/develop/CHANGELOG.rst
2024-10-21 17:17:29 +08:00
Po-Chuan Hsieh
7ed83197a7
science/eccodes: Update to 2.38.3
Changes:	https://confluence.ecmwf.int/display/ECC/Latest+news
2024-10-21 17:17:29 +08:00
Po-Chuan Hsieh
8873734cb1
science/cgribex: Remove GRIB_API option after grib_api deprecation
- Bump PORTREVISION for dependency change

PR:		281652
2024-10-21 17:17:27 +08:00
Po-Chuan Hsieh
44a45ffd8d
science/cdo: Cosmetic change 2024-10-21 17:17:27 +08:00
Fernando Apesteguía
27df35e109 science/afni: update to 24.3.03 2024-10-19 11:48:36 +02:00
Jason E. Hale
f3eb2459d7 */*: Chase removal of sip from RUN_DEPENDS 2024-10-19 03:33:57 -04:00
Jason E. Hale
0d0b4d9bb9 */*: Remove qtbuilder and sip from RUN_DEPENDS
devel/py-qtbuilder and devel/py-sip should only be used as a
BUILD_DEPENDS. (e.g. USE_PYQT=qtbuilder:build sip:build)
Usually, these are only used to build the PyQt framework, but a few
other ports need them to build. Ports that have them as a BUILD_DEPENDS
unnecessarily haven't been audited yet.

Sip used to be needed for run, but this hasn't been the case for quite
some time. Runtime is provided by the devel/py-qt[56]-sip ports.
(USE_PYQT=pysip). The main PyQt ports provide this automatically, so
it isn't necessary to add it to individual consumers.

While here:
www/onionshare: Remove PyQt stuff completely. It uses PySide.

With hat:	kde@
2024-10-19 03:21:41 -04:00
Po-Chuan Hsieh
ace7fbd08c
science/py-sarpy: Add ALL option 2024-10-18 03:03:16 +08:00
Wen Heping
53a2aaac3e science/py-pydicom: update 3.0.1 2024-10-14 06:32:50 +00:00
Po-Chuan Hsieh
a6fc3871a3
science/py-sarpy: Update to 1.3.59
Changes:	https://github.com/ngageoint/sarpy/blob/master/CHANGELOG.md
2024-10-14 13:25:45 +08:00
Po-Chuan Hsieh
4b4fc73b66
science/py-pyteomics: Update to 4.7.4
Changes:	https://github.com/levitsky/pyteomics/releases
		https://pyteomics.readthedocs.io/en/latest/changelog.html
2024-10-14 13:25:45 +08:00
Po-Chuan Hsieh
64c4b570cf
science/py-h5py: Update to 3.12.1
Changes:	https://github.com/h5py/h5py/releases
		https://github.com/h5py/h5py/tree/master/docs/whatsnew
		https://docs.h5py.org/en/stable/whatsnew/index.html
2024-10-14 13:25:44 +08:00
Po-Chuan Hsieh
494bbdb97e
science/py-eccodes: Update to 2.38.1
Changes:	https://github.com/ecmwf/eccodes-python/releases
		https://github.com/ecmwf/eccodes-python/blob/develop/CHANGELOG.rst
2024-10-14 13:25:44 +08:00
Po-Chuan Hsieh
fb963bddfc
science/py-asdf: Update to 3.5.0
Changes:	https://github.com/asdf-format/asdf/releases
2024-10-14 13:25:44 +08:00
Fernando Apesteguía
0c92380369 science/afni: update to 24.3.02 2024-10-13 13:00:51 +02:00
Yuri Victorovich
f97dbeba67 science/harminv: update 1.3.1 → 1.4.2; add shared libraries
PR:	281283
Approved by:	devel@stasyan.com (maintainer's timeout; 36 days)
2024-10-11 09:45:56 -07:00
Yuri Victorovich
a5bc9af80c science/openmodelica: update 1.23.1 → 1.24.0
Reported by:	portscout
2024-10-10 01:25:20 -07:00
Yuri Victorovich
23feee0e0d science/py-nibabel: update 5.2.1 → 5.3.0
Reported by:	portscout
2024-10-09 18:34:05 -07:00
Daniel Engberg
8db97e44ba science/smoldyn: Fix build with tiff 4.7.0
Use TIFF:tiff to define the library instead of ${TIFF_LIBRARY} and
remove custom logic that tried to replace CMake's own.

PR:		281763
Reviewed by:	yuri
2024-10-09 21:43:26 +02:00
Dimitry Andric
e8b1dca337 science/dlib-cpp: fix build with clang and libc++ 19
As noted in the libc++ 19 release notes [1], std::char_traits<> is now
only provided for char, char8_t, char16_t, char32_t and wchar_t, and any
instantiation for other types will fail.

This causes science/dlib-cpp to fail to compile with clang 19 and
libc++ 19, resulting in errors similar to:

  /usr/include/c++/v1/string:820:42: error: implicit instantiation of undefined template 'std::char_traits<unsigned int>'
    820 |   static_assert(is_same<_CharT, typename traits_type::char_type>::value,
        |                                          ^
  /wrkdirs/usr/ports/science/dlib-cpp/work/dlib-19.24/dlib/bigint/../unicode/unicode.h:496:26: note: in instantiation of template class 'std::basic_string<unsigned int>' requested here
    496 |     inline const ustring convert_utf8_to_utf32 (
        |                          ^
  /usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here
     23 | struct _LIBCPP_TEMPLATE_VIS char_traits;
        |                             ^

These can be fixed by using `char32_t` instead of `uint32_t` for the
`unichar` type.

Also, clang 19 now implements CWG 96 [1], which requires a template
argument list after a 'template' keyword, resulting in errors similar
to:

  /wrkdirs/usr/ports/science/dlib-cpp/work/dlib-19.24/dlib/filtering/../global_optimization/find_max_global.h:61:130: error: a template argument list is expected after a name prefixed by the template keyword [-Wmissing-template-arg-list-after-template-kw]
     61 |             static auto go(T&& f, const matrix<double,0,1>& a) -> decltype(call_function_and_expand_args<max_unpack-1>::template go(std::forward<T>(f),a))
        |                                                                                                                                  ^

This can be fixed by adding `<>` after the `go` identifier.

[1] https://libcxx.llvm.org/ReleaseNotes/19.html#deprecations-and-removals

PR:		281975
Approved by:	arrowd (maintainer)
MFH:		2024Q3
2024-10-09 21:10:15 +02:00
Yuri Victorovich
60f7fa5281 science/libcifpp: update 7.0.5 → 7.0.6
Reported by:	portscout
2024-10-09 02:42:00 -07:00
Yuri Victorovich
6f37bc3867 science/hypre: update 2.31.0 → 2.32.0
Reported by:	portscout
2024-10-09 02:41:59 -07:00
Yuri Victorovich
a71fb1c3c7 science/dssp: update 4.4.7 → 4.4.8
Reported by:	portscout
2024-10-08 01:48:12 -07:00
Po-Chuan Hsieh
c69810d6f5
science/py-h5py: Update to 3.12.0
Changes:	https://github.com/h5py/h5py/releases
		https://github.com/h5py/h5py/tree/master/docs/whatsnew
		https://docs.h5py.org/en/stable/whatsnew/index.html
2024-10-07 22:16:48 +08:00
Po-Chuan Hsieh
c26cf9c596
science/libaec: Remove CMAKE_TESTING_ON
CMAKE_TESTING_ON defaults to BUILD_TESTING.
2024-10-07 22:16:42 +08:00
Po-Chuan Hsieh
232b56f7db
devel/protobuf: Update to 28.2
- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://github.com/protocolbuffers/protobuf/releases
2024-10-07 22:16:41 +08:00
Yuri Victorovich
969c67a78e science/elk: update 10.0.15 → 10.1.12
Reported by:	portscout
2024-10-07 02:42:12 -07:00
Yuri Victorovich
8005b5ffec science/bout++-merging-filaments: Broken
Reported by:	fallout
2024-10-06 11:31:38 -07:00
TAKATSU Tomonari
7a3dd95cac science/R-cran-Epi: Update to 2.56
Reported by:	portscout
2024-10-06 07:36:27 +00:00
Fernando Apesteguía
572c4f97e3 science/afni: update to 24.3.00 2024-10-03 18:16:23 +02:00
Dima Panov
55cfbcf56c
*/*: bump consumers after devel/boost* update
With hat:	office
Sponsored by:	Future Crew, LLC
2024-10-03 13:25:14 +03:00
Dima Panov
debf8b0ac5
science/dakota: mark as BROKEN, fails to build with boost-1.85+
With hat:	office
Sponsored by:	Future Crew, LLC
2024-10-03 13:25:02 +03:00
Dima Panov
edfa7f02f9
science/orthanc-webviewer: unbreak build with boost-1.85
With hat:	office
Sponsored by:	Future Crew, LLC
2024-10-03 13:24:59 +03:00
Dima Panov
a0dd41749a
science/orthanc-postgresql: unbreak build with boost-1.85
With hat:	office
Sponsored by:	Future Crew, LLC
2024-10-03 13:24:58 +03:00
Dima Panov
7e9cadbb16
science/orthanc-mysql: unbreak build with boost-1.85
With hat:	office
Sponsored by:	Future Crew, LLC
2024-10-03 13:24:58 +03:00
Dima Panov
e40868a34d
science/orthanc-dicomweb: unbreak build with boost-1.85
With hat:	office
Sponsored by:	Future Crew, LLC
2024-10-03 13:24:57 +03:00
Dima Panov
26f80525e4
science/orthanc: unbreak build with boost-1.85
With hat:	office
Sponsored by:	Future Crew, LLC
2024-10-03 13:24:56 +03:00
Yuri Victorovich
91889f3275 science/PETSc: update 3.21.6 → 3.22.0 2024-10-03 02:17:10 -07:00
Rene Ladan
4485bd8221 all: drop support for expired FreeBSD 14.0
Simplify expressions for FreeBSD 13.X

Reviewed by:	many

Differential Revision:	https://reviews.freebsd.org/D46601
2024-10-01 20:56:20 +02:00
Rene Ladan
f49cd2fa7a science/py-nilearn: expire on 2024-12-31 for devel/py-codecov 2024-09-30 21:37:15 +02:00
Po-Chuan Hsieh
286ab7a3e8
science/py-scikit-optimize: Update to 0.10.2
Changes:	https://github.com/holgern/scikit-optimize/releases
		https://scikit-optimize.readthedocs.io/en/latest/whats_new.html
2024-09-30 21:36:36 +08:00