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* science/openems: Update 0.0.35-71 -> 0.0.35-76Yuri Victorovich2022-06-262-9/+7
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* science/shelxle: Update 1.0.1395 -> 1.0.1396Yuri Victorovich2022-06-262-4/+4
| | | | Reported by: portscout
* science/libint2: Update 2.7.1 -> 2.7.2Yuri Victorovich2022-06-262-5/+4
| | | | Reported by: portscout
* science/jmol: Update 14.32.59 -> 14.32.61Yuri Victorovich2022-06-262-4/+4
| | | | Reported by: portscout
* devel/googletest: update to 1.12.0Jan Beich2022-06-252-1/+2
| | | | | Changes: https://github.com/google/googletest/releases/tag/release-1.12.0 Reported by: GitHub (watch releases)
* science/helfem: Fix build with clang-14Yuri Victorovich2022-06-242-1/+6
| | | | | | | Due to a regression in clang-14 and the improper C++ include line caused build failure. Reference: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=264877
* science/gramps: Optional dependency on py-bsddb3Benjamin Takacs2022-06-232-8/+26
| | | | | | | | | | | | | databases/py-bsddb3 is deprecated. Make science/gramps use py-bsddb3 as an option to facilitate the migration and remove the DEPRECATE note since it does not apply anymore. Add UPDATING note with instructions for the migration. While here pet linters. PR: 264529 Reported by: nimaje+fbz@bureaucracy.de
* science/bagel: Update 1.2.2 -> 1.2.2-132Yuri Victorovich2022-06-232-13/+19
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* science/lammps: patch_2Jun2022 -> stable_23Jun2022Yuri Victorovich2022-06-232-4/+4
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* science/precice: Add options; Backport patch provided by upstreamYuri Victorovich2022-06-212-6/+24
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* science/netcdf: Update to 4.9.0Po-Chuan Hsieh2022-06-213-23/+38
| | | | Changes: https://github.com/Unidata/netcdf-c/releases
* science/py-MDAnalysis*: upgrade to 2.2.0Thierry Thomas2022-06-218-24/+129
| | | | | | | | | | | | | Version 0.19.2 is too old and does not support Python-3.9. Remark: threadpoolctl is disabled in this port. See <https://github.com/MDAnalysis/mdanalysis/pull/2950> for the impacts on performance. Releases notes at <https://github.com/MDAnalysis/mdanalysis/releases>. PR: 264716 Approved by: yuri (maintainer)
* science/py-pygeometa: Update to 0.11.1Po-Chuan Hsieh2022-06-212-4/+4
| | | | | Changes: https://github.com/geopython/pygeometa/releases https://github.com/geopython/pygeometa/blob/master/debian/changelog
* lang/fpc: Fix build issues building some fpc based appsJose Alonso Cardenas Marquez2022-06-212-2/+2
| | | | | | | - Add missing parameter to getdirentries syscall function - Re-build i386 and amd64 bootstrap - Revert fpc-i386 (FPC_USE_LIBC) build to syscall build - Bump PORTREVISION in all ports dependant of freepascal compiler
* science/py-pyprecice: New port: Coupling library for partitioned ↵Yuri Victorovich2022-06-204-0/+42
| | | | multi-physics simulations
* science/precice: New port: Coupling library for partitioned multi-physics ↵Yuri Victorovich2022-06-206-0/+69
| | | | simulations
* science/ghemical: Fix path to mopac portYuri Victorovich2022-06-191-1/+1
| | | | | ... after it was recently moved. Reported by: cperciva@
* science/py-ase: Add test targetYuri Victorovich2022-06-191-1/+7
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* science/py-asap3: New port: Classical potentials for MD with ASEYuri Victorovich2022-06-194-0/+32
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* biology/mopac: Move to science/mopac; Add TIMESTAMP to distinfo; Take ↵Yuri Victorovich2022-06-195-0/+60
| | | | maintainership
* science/siesta: Add commentYuri Victorovich2022-06-191-1/+1
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* science/py-ase: Add commentYuri Victorovich2022-06-191-1/+1
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* science/shelxle: Update 1.0.1393 -> 1.0.1395Yuri Victorovich2022-06-192-4/+4
| | | | Reported by: portscout
* */*: Bump PORTREVISIONJose Alonso Cardenas Marquez2022-06-182-2/+2
| | | | - lang/fpc was update to new bootstrap
* science/gromacs: Update 2022.1 -> 2022.2Yuri Victorovich2022-06-173-7/+11
| | | | Reported by: portscout
* science/hypre: Update 2.24.0 -> 2.25.0Yuri Victorovich2022-06-177-189/+4
| | | | Reported by: portscout
* science/dakota: Fix LIB_DEPENDS after science/szip removalPo-Chuan Hsieh2022-06-161-1/+1
| | | | | science/szip has been replaced by science/libaec in 328ae4074233a5b85e0e38efece1af5dcc218160. And it has been removed in 3110404349b2df7a416cef5e76af82f9e888c0db.
* science/dakota: Update 6.15.0 -> 6.16.0Yuri Victorovich2022-06-165-32/+60
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* science/libcint: Update 5.1.2 -> 5.1.3Yuri Victorovich2022-06-162-4/+4
| | | | Reported by: portscout
* science/hdf5: Sort PLISTPo-Chuan Hsieh2022-06-161-1/+1
| | | | - Fix PLIST change in f791baebff9d739e1b9c7d1ab963ecf7406a705d
* science/silo: Fix build with HDF5 1.10.8+Po-Chuan Hsieh2022-06-161-0/+42
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* science/hdf5: Update to 1.10.9Po-Chuan Hsieh2022-06-163-25/+132
| | | | | | Changes: https://portal.hdfgroup.org/display/support/HDF5+1.10.7 https://portal.hdfgroup.org/display/support/HDF5+1.10.8 https://portal.hdfgroup.org/display/support/HDF5+1.10.9
* science/szip: Remove obsoleted portPo-Chuan Hsieh2022-06-165-43/+0
| | | | Use science/libaec instead.
* */*: Replace science/szip with science/libaecPo-Chuan Hsieh2022-06-1629-43/+59
| | | | | | | | | | | - Bump PORTREVISION of dependent ports for dependency change szip does not allow redistribution in binary form without proper commercial license. Its LICENSE_PERMS should be set to no-auto-accept which blocks building this port, therefore building dependent ports are also blocked. Switch all dependent ports to science/libaec to avoid conflicts and license issue. PR: 228743, 246097, 250165
* science/py-qcelemental: Update 0.24.0 -> 0.25.0Yuri Victorovich2022-06-152-7/+10
| | | | Reported by: portscout
* science/py-py3Dmol: New port: IPython interface for embedding 3Dmol.js viewsYuri Victorovich2022-06-154-0/+25
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* science/atompaw: Update 4.2.0.0 -> 4.2.0.1Yuri Victorovich2022-06-142-4/+4
| | | | Reported by: portscout
* cience/py-scikit-learn: Update to 1.1.1Wen Heping2022-06-132-4/+4
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* science/libtensorflow1: disallow newer BazelChris Rees2022-06-121-1/+1
| | | | | | | | | | | Does not build with newer Bazel: Repository rule git_repository defined at: /usr/ports/science/libtensorflow1/work-default/bazel_out/98e92f9393bc83ca8c28c921fe93f245/external/bazel_tools/tools/build_defs/repo/git.bzl:199:33: in <toplevel> ERROR: /usr/ports/science/libtensorflow1/work-default/bazel_out/98e92f9393bc83ca8c28c921fe93f245/external/io_bazel_rules_docker/container/image.bzl:550:31: invalid escape sequence: \s. Use '\\' to insert '\'. PR: ports/260694 Discovered by: Dario <darioml@gmail.com>
* science/libtensorflow1: add flavour without AVXPaul Armstrong2022-06-121-3/+14
| | | | | | | | | | | | Not all processors bought these days support AVX, for example Pentium Gold. People would most likely wish to have a working package in this case. While here, remove march=native. PR: ports/260694 Discussed with: diizzy Discussed with: William Miur <wamuir@gmail.com>
* misc/openvdb: Update 9.0.0 -> 9.1.0Yuri Victorovich2022-06-111-1/+1
| | | | Reported by: portscout
* science/agrum: Update 1.1.0 -> 1.1.1Yuri Victorovich2022-06-113-6/+6
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* science/shelxle: Update 1.0.1391 -> 1.0.1393Yuri Victorovich2022-06-112-4/+4
| | | | Reported by: portscout
* KDE: Update KDE Gear to 22.04.2 (June bugfix release)Tobias C. Berner2022-06-102-6/+6
| | | | | | | | | | | | | | | | Over 120 individual programs plus dozens of programmer libraries and feature plugins are released simultaneously as part of KDE Gear. Today they all get new bugfix source releases with updated translations, including: * ark: Support ‘7zip’ as well as ‘p7zip’. * konsole: Fix scroll position jumps regression. * okular: Fix crash while undoing with the menu on an empty annotation. Distro and app store packagers should update their application packages. Full Changelog: https://kde.org/announcements/changelogs/gear/22.04.2/
* science/libtensorflow1: Add new portPaul Armstrong2022-06-108-0/+397
| | | | | | | | | | | | | | | | C API for TensorFlow, an open source platform for machine learning TensorFlow is an end-to-end open source platform for machine learning. It has a comprehensive, flexible ecosystem of tools, libraries, and community resources that lets researchers push the state-of-the-art in ML and developers easily build and deploy ML-powered applications. The TensorFlow C API is typically a requirement of TensorFlow APIs in other languages such as Go and Rust. This is version 1 of the API, which is deprecated but still widely used. PR: ports/260694 Improved by: delphij
* science/R-cran-kernlab: Update to 0.9-31TAKATSU Tomonari2022-06-102-4/+4
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* science/R-cran-e1071: Update to 1.7-11TAKATSU Tomonari2022-06-092-4/+4
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* science/afni: update to 22.1.13Fernando Apesteguía2022-06-093-4/+5
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* science/R-cran-DCluster: Update to 0.2-8TAKATSU Tomonari2022-06-092-6/+5
| | | | - Fix LICENSE section
* science/py-pygeometa: Update to 0.11.0Po-Chuan Hsieh2022-06-092-4/+4
| | | | Changes: https://github.com/geopython/pygeometa/releases
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