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* graphics/mesa-libs: Bump reverse deps for libglvndKevin Bowling2021-06-2227-19/+27
| | | | | | | | | | Per discussion with bapt on helping pkg handle the changing of these deps and avoiding impossible upgrade senarios. PR: 246767 Reviewed by: manu, bapt Approved by: x11 Differential Revision: https://reviews.freebsd.org/D30824
* science/py-pygeodesy: Update to 21.6.16Po-Chuan Hsieh2021-06-202-4/+4
| | | | Changes: https://github.com/mrJean1/PyGeodesy/commits/master
* science/libaec: Update to 1.0.5Po-Chuan Hsieh2021-06-203-7/+7
| | | | | | - Update LICENSE_FILE Changes: https://gitlab.dkrz.de/k202009/libaec/-/blob/master/CHANGELOG.md
* science/smoldyn: Update 2.65 -> 2.66Yuri Victorovich2021-06-202-5/+4
| | | | Reported by: portscout
* science/py-chainer: Update 7.7.0 -> 7.8.0Yuri Victorovich2021-06-202-5/+4
| | | | Reported by: portscout
* science/py-jupyter_jsmol: Remove PY_PYGMENTSPo-Chuan Hsieh2021-06-201-1/+1
| | | | With hat: python
* science/abinit: Remove PY_PYGMENTSPo-Chuan Hsieh2021-06-201-1/+1
| | | | With hat: python
* science/py-segregation: Update to 2.0.0Po-Chuan Hsieh2021-06-202-5/+7
| | | | Changes: https://github.com/pysal/segregation/releases
* science/py-eccodes: Update to 1.3.3Po-Chuan Hsieh2021-06-202-4/+4
| | | | Changes: https://github.com/ecmwf/eccodes-python/blob/develop/CHANGELOG.rst
* science/csvtk: Cross-platform and ultrafast toolkit for CSV/TSV processingJason W. Bacon2021-06-184-0/+38
| | | | | | | | | | | | | | CSV/TSV formats are basic and ubiquitous file formats in both Bioinformatics and data science. People usually use spreadsheet software like MS Excel to process table data. However this is all by clicking and typing, which is not automated and is time-consuming to repeat, especially when you want to apply similar operations with different datasets or purposes. csvtk is convenient for rapid data investigation and also easy to integrate into analysis pipelines. It could save you lots of time in (not) writing Python/R scripts.
* science/py-nilearn: Update 0.7.1 -> 0.8.0Yuri Victorovich2021-06-182-4/+4
| | | | Reported by: portscout
* science/code_saturne: upgrade to 7.0Thierry Thomas2021-06-183-233/+327
| | | | Changelog at <https://github.com/code-saturne/code_saturne/blob/v7.0/NEWS.md>.
* science/hdf: add back the previously removed powerpc workaroundPiotr Kubaj2021-06-161-0/+3
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* math/gsl: update to 2.7Tobias C. Berner2021-06-1613-5/+13
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | From [1] * What is new in gsl-2.7: * fixed doc bug for gsl_histogram_min_bin (lhcsky at 163.com) * fixed bug #60335 (spmatrix test failure, J. Lamb) * fixed bug #36577 * clarified documentation on interpolation accelerators (V. Krishnan) * fixed bug #45521 (erroneous GSL_ERROR_NULL in ode-initval2, thanks to M. Sitte) * fixed doc bug #59758 * fixed bug #58202 (rstat median for n=5) * added support for native C complex number types in gsl_complex when using a C11 compiler * upgraded to autoconf 2.71, automake 1.16.3, libtool 2.4.6 * updated exponential fitting example for nonlinear least squares * added banded LU decomposition and solver (gsl_linalg_LU_band) * New functions added to the library: - gsl_matrix_norm1 - gsl_spmatrix_norm1 - gsl_matrix_complex_conjtrans_memcpy - gsl_linalg_QL: decomp, unpack - gsl_linalg_complex_QR_* (thanks to Christian Krueger) - gsl_vector_sum - gsl_matrix_scale_rows - gsl_matrix_scale_columns - gsl_multilarge_linear_matrix_ptr - gsl_multilarge_linear_rhs_ptr - gsl_spmatrix_dense_add (renamed from gsl_spmatrix_add_to_dense) - gsl_spmatrix_dense_sub - gsl_linalg_cholesky_band: solvem, svxm, scale, scale_apply - gsl_linalg_QR_UD: decomp, lssolve - gsl_linalg_QR_UU: decomp, lssolve, QTvec - gsl_linalg_QR_UZ: decomp - gsl_multifit_linear_lcurvature - gsl_spline2d_eval_extrap * bug fix in checking vector lengths in gsl_vector_memcpy (dieggsy@pm.me) * made gsl_sf_legendre_array_index() inline and documented - gsl_sf_legendre_nlm() [1] http://git.savannah.gnu.org/cgit/gsl.git/tree/NEWS PR: 256423 Exp-run by: antoine
* science/afni: update to 21.1.12Fernando Apesteguía2021-06-164-13/+19
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* science/shelxle: Update 1.0.1267 -> 1.0.1273Yuri Victorovich2021-06-152-4/+4
| | | | Reported by: portscout
* science/gabedit: fix build on powerpcPiotr Kubaj2021-06-151-0/+1
| | | | LLVM on powerpc doesn't have libomp.
* science/elk: Update 7.1.14 -> 7.2.42Yuri Victorovich2021-06-142-4/+4
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* science/py-spaghetti: Update to 1.6.0Po-Chuan Hsieh2021-06-142-4/+4
| | | | Changes: https://github.com/pysal/spaghetti/releases
* science/py-asdf: Update to 2.8.1Po-Chuan Hsieh2021-06-142-4/+4
| | | | Changes: https://github.com/asdf-format/asdf/releases
* */*: Zpdate KDE Gear to 21.04.2Tobias C. Berner2021-06-134-6/+18
| | | | | | | | | | Thursday, 10 June 2021 Over 120 individual programs plus dozens of programmer libraries and feature plugins are released simultaneously as part of KDE Gear. The full changelog can be found here: https://kde.org/announcements/changelogs/gear/21.04.2/
* misc/openvdb: Update 8.0.1 -> 8.1.0Yuri Victorovich2021-06-131-1/+1
| | | | Reported by: portscout
* devel/googletest: update to 1.11.0Jan Beich2021-06-121-1/+1
| | | | | | Changes: https://github.com/google/googletest/compare/53495a2a...release-1.11.0 Changes: https://github.com/google/googletest/releases/tag/release-1.11.0 Reported by: GitHub (watch releases)
* science/agrum: Update 0.20.2 -> 0.20.3Yuri Victorovich2021-06-123-5/+6
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* science/rdkit: Update 2020.09.5 -> 2021.03.3Yuri Victorovich2021-06-114-20/+72
| | | | Reported by: portscout
* science/coordgenlibs: Update 1.4.2 -> 2.0.3Yuri Victorovich2021-06-115-10/+26
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* science/py-phonopy: Update 2.9.3 -> 2.10.0Yuri Victorovich2021-06-112-4/+4
| | | | Reported by: portscout
* science/py-eccodes: Remove PYNUMPYPo-Chuan Hsieh2021-06-101-1/+1
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* science/eccodes: Update to 2.22.0Po-Chuan Hsieh2021-06-103-4/+132
| | | | Changes: https://confluence.ecmwf.int/display/ECC/Latest+news
* science/smoldyn: Fix build - release was rerolledYuri Victorovich2021-06-102-3/+4
| | | | | | The upstream has confirmed that they rerolled it. Reported by: fallout
* science/py-phono3py: Remove unnecessary build dependency on math/lapackeYuri Victorovich2021-06-091-2/+1
| | | | | PR: 256493 Reported by: John Hein <jcfyecrayz@liamekaens.com>
* science/orthanc: Hook to the buildGuangyuan Yang2021-06-081-0/+1
| | | | | | PR: 242546 Fixes: d0359493ee0443e596be74b336ea12e6db936a01 Approved by: lwhsu (mentor, implicit), portmgr (fix build)
* science/orthanc: Revive portFrank Scholl2021-06-087-0/+230
| | | | | | | | Orthanc is a Lightweight DICOM server for healthcare and medical research. PR: 242546 Approved by: lwhsu (mentor)
* science/xcfun: fix build on GCC-based systemsMark Linimon2021-06-071-1/+1
| | | | | | | | by adding compiler:c++11-lang to USES: CMake Error in /wrkdirs/usr/ports/science/xcfun/work/.build/CMakeFiles/CMakeTmp/CMakeLists.txt: Target "cmTC_6be99" requires the language dialect "CXX11" , but CMake does not know the compile flags to use to enable it.
* science/xcfun: Remove redundant 'v' from DISTVERSIONYuri Victorovich2021-06-062-4/+4
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* science/libcint: Fix tests by adding the science/py-pyscf dependencyYuri Victorovich2021-06-051-1/+2
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* science/py-pyscf: New port: Python module for quantum chemistryYuri Victorovich2021-06-056-0/+76
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* science/xcfun: New port: Exchange-correlation functionals with ↵Yuri Victorovich2021-06-055-0/+63
| | | | arbitrary-order derivatives
* science/libcint: Update 4.4.0 -> 4.4.1Yuri Victorovich2021-06-052-4/+4
| | | | Reported by: portscout
* science/py-PyFR: Update 1.12.0 -> 1.12.1Yuri Victorovich2021-06-052-5/+5
| | | | Reported by: portscout
* science/avogadro2: Update 1.93.0 -> 1.94.0Yuri Victorovich2021-06-042-4/+4
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* science/avogadrolibs: Remove redundant lineYuri Victorovich2021-06-041-2/+0
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* science/py-avogadrolibs: Update 1.93.0 -> 1.94.0Yuri Victorovich2021-06-043-11/+11
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* science/avogadrolibs: Update 1.93.1 -> 1.94.0Yuri Victorovich2021-06-045-49/+989
| | | | Reported by: portscout
* devel/googletest: update to 1.10.0.667Jan Beich2021-06-031-1/+1
| | | | | | | | Upstream no longer makes releases, see https://github.com/google/googletest/commit/861d535e2595 Changes: https://github.com/google/googletest/compare/release-1.10.0...53495a2a Reported by: ngie (1 year ago)
* science/jmol: Update 14.31.40 -> 14.31.41Yuri Victorovich2021-06-022-4/+4
| | | | Reported by: portscout
* science/shelxle: Update 1.0.1264 -> 1.0.1267Yuri Victorovich2021-06-022-4/+4
| | | | Reported by: portscout
* science/py-scipy: Fix required python versionJohn W. O'Brien2021-06-011-1/+1
| | | | | | | | | scipy dropped support for 3.6 as of 1.6.0: https://github.com/scipy/scipy/commit/0a4f408d9bd560f9a379d2e33b136b93f3583042 PR: 256083 MFH: 2021Q2
* science/afni: update to 21.1.09Fernando Apesteguía2021-05-312-4/+4
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* science/shelxle: Update 1.0.1260 -> 1.0.1264Yuri Victorovich2021-05-312-4/+4
| | | | Reported by: portscout
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