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* science/ascent: New port: Visualization and analysis runtime for ↵Yuri Victorovich2021-09-161-0/+1
| | | | multi-physics HPC simulations
* science/helfem: New port: Finite element methods for electronic structure ↵Yuri Victorovich2021-09-111-0/+1
| | | | calculations
* science/py-pyked: New port: Package for manipulating Chemical Kinetics ↵Yuri Victorovich2021-09-111-0/+1
| | | | Experimental Data files
* science/cantera: New port: Chemical kinetics, thermodynamics, and transport ↵Yuri Victorovich2021-09-101-0/+1
| | | | tool suite
* science/openems: New port: Electromagnetic field solver using the EC-FDTD methodYuri Victorovich2021-08-191-0/+1
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* science/openmx: Re-add port: Nanoscale material simulations using density ↵Yuri Victorovich2021-08-151-0/+1
| | | | | | functional theories (DFT) It isn't unfetchable.
* science/dynare: Re-add port: Software platform for handling a wide class of ↵Yuri Victorovich2021-08-141-0/+1
| | | | economic models
* science/siconos: New port: Simulation framework for nonsmooth dynamical systemsYuri Victorovich2021-08-111-0/+1
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* science/orthanc-dicomweb: Revive portFrank Scholl2021-08-091-0/+1
| | | | | | | Plugin to bring support of the DICOMweb standard into Orthanc. PR: 242547 Reviewed by: lwhsu
* science/orthanc-postgresql: Revive portFrank Scholl2021-08-071-0/+1
| | | | | | Orthanc plugin to use PostgreSQL for indexing or storage. PR: 242548
* science/orthanc-mysql: New portFrank Scholl2021-08-071-0/+1
| | | | | | Orthanc plugin to use MySQL/MariaDB for indexing or storage. PR: 242552
* science/orthanc-webviewer: Revive portFrank Scholl2021-08-061-0/+1
| | | | | | Plugin to extend Orthanc with a Web viewer of medical images. PR: 242549
* science/phonopy: New port: Package for phonon calculations at harmonic and ↵Yuri Victorovich2021-08-051-0/+1
| | | | quasi-harmonic levels
* science/py-hiphive: New port: High-order force constants for the massesYuri Victorovich2021-08-051-0/+1
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* science/py-cirq-{aqt,ionq,pasqal}: New ports: Modules for the Cirq quantum ↵Yuri Victorovich2021-07-281-0/+3
| | | | computing framework
* science/py-PubChemPy: New port: Simple Python wrapper around the PubChem PUG ↵Yuri Victorovich2021-07-271-0/+1
| | | | REST API
* science/py-{core,google}: New ports: Writing, manipulating, and optimizing ↵Yuri Victorovich2021-07-261-0/+2
| | | | quantum circuits and running them against quantum computers and simulators
* science/csvtk: Cross-platform and ultrafast toolkit for CSV/TSV processingJason W. Bacon2021-06-181-0/+1
| | | | | | | | | | | | | | 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/orthanc: Hook to the buildGuangyuan Yang2021-06-081-0/+1
| | | | | | PR: 242546 Fixes: d0359493ee0443e596be74b336ea12e6db936a01 Approved by: lwhsu (mentor, implicit), portmgr (fix build)
* science/py-pyscf: New port: Python module for quantum chemistryYuri Victorovich2021-06-051-0/+1
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* science/xcfun: New port: Exchange-correlation functionals with ↵Yuri Victorovich2021-06-051-0/+1
| | | | arbitrary-order derivatives
* science/frontistr adding FrontISTRThierry Thomas2021-04-261-0/+1
| | | | | This is an Open-Source Large-Scale Parallel FEM Program for Nonlinear Structural Analysis.
* science/py-skrebate: Add py-skrebate 0.62Po-Chuan Hsieh2021-04-251-0/+1
| | | | | | | | | | | | This package includes a scikit-learn-compatible Python implementation of ReBATE, a suite of Relief-based feature selection algorithms for Machine Learning. These Relief-Based algorithms (RBAs) are designed for feature weighting/selection as part of a machine learning pipeline (supervised learning). Presently this includes the following core RBAs: ReliefF, SURF, SURF*, MultiSURF*, and MultiSURF. Additionally, an implementation of the iterative TuRF mechanism and VLSRelief is included. WWW: https://github.com/EpistasisLab/scikit-rebate
* One more small cleanup, forgotten yesterday.Mathieu Arnold2021-04-071-1/+0
| | | | Reported by: lwhsu
* Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-061-2/+0
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* New port: science/libecpint: Library for the evaluation of integrals over ↵Yuri Victorovich2021-02-241-0/+1
| | | | | | | effective core potentials Notes: svn path=/head/; revision=566452
* New port: science/dakota: Interface between analysis codes & iterative ↵Yuri Victorovich2021-02-201-0/+1
| | | | | | | systems analysis methods Notes: svn path=/head/; revision=566127
* Sort SUBDIRsSunpoet Po-Chuan Hsieh2021-02-061-1/+1
| | | | Notes: svn path=/head/; revision=564245
* New port: science/thermofun: Code for calculating thermodynamic properties ↵Yuri Victorovich2021-02-021-0/+1
| | | | | | | of materials Notes: svn path=/head/; revision=563780
* Remove expired ports:Rene Ladan2021-02-011-1/+0
| | | | | | | | | | | | | | | | | 2021-01-31 deskutils/orage: Unsupported upstream, cannot work with XFCE 4.16 2021-01-31 sysutils/rubygem-chef-config12 2021-01-31 mail/openwebmail: Does not use modern Perl syntax and no development activity since 2006 2021-01-31 sysutils/rubygem-ohai8 2021-01-31 deskutils/xfce4-volumed: Unsupported upstream, cannot work with XFCE 4.16 2021-01-31 sysutils/rubygem-chef12: Please use sysutils/rubygem-chef instead 2021-01-31 x11/xfce4-embed-plugin: Unsupported upstream, cannot work with XFCE 4.16 2021-01-31 net-p2p/py-transmissionrpc: Unmaintained and dead upstream, use net-p2p/py-transmission-rpc instead 2021-01-31 science/xfce4-equake-plugin: Unsupported upstream, cannot work with XFCE 4.16 2021-01-31 sysutils/xfce4-kbdleds-plugin: Unsupported upstream, cannot work with XFCE 4.16 2021-01-31 textproc/py-gfm: No longer maintained by upstream, please use textproc/py-cmarkgfm instead Notes: svn path=/head/; revision=563574
* New port: science/py-nilearn: Statistical learning for neuroimaging in PythonYuri Victorovich2021-01-211-0/+1
| | | | Notes: svn path=/head/; revision=562173
* New port: science/py-dipy: Python toolbox for analysis of MR diffusion imagingYuri Victorovich2021-01-211-0/+1
| | | | Notes: svn path=/head/; revision=562172
* New port: science/py-nibabel: Read/write some common neuroimaging file formatsYuri Victorovich2021-01-211-0/+1
| | | | Notes: svn path=/head/; revision=562166
* Remove expired ports:Rene Ladan2021-01-171-1/+0
| | | | | | | | | 2021-01-14 net-im/telegram: Upstream unmaintained; please migrate to net-im/telegram-cli 2021-01-14 science/dlpoly-classic: MASTERSITE gone; possibly replaced by https://gitlab.com/DL_POLY_Classic/dl_poly? 2021-01-15 security/py-gtts-token: Obsolete, please use audio/py-gtts instead Notes: svn path=/head/; revision=561814
* New port: science/shelxle: Graphical user interface for small-molecule ↵Yuri Victorovich2021-01-141-0/+1
| | | | | | | structure refinement Notes: svn path=/head/; revision=561586
* Add py-tobler 0.5.4Sunpoet Po-Chuan Hsieh2021-01-031-0/+1
| | | | | | | | | | | tobler is a library for areal interpolation and dasymetric mapping. The name is an homage to the legendary geographer Waldo Tobler. WWW: https://pysal.org/tobler/ WWW: https://github.com/pysal/tobler Notes: svn path=/head/; revision=560056
* Add py-spaghetti 1.4.2Sunpoet Po-Chuan Hsieh2021-01-031-0/+1
| | | | | | | | | | | | | | | | SPAtial GrapHs: nETworks, Topology, & Inference Spaghetti is an open-source Python library for the analysis of network-based spatial data. Originating from the network module in PySAL (Python Spatial Analysis Library), it is under active development for the inclusion of newly proposed methods for building graph-theoretic networks and the analysis of network events. WWW: https://pysal.org/spaghetti/ WWW: https://github.com/pysal/spaghetti Notes: svn path=/head/; revision=560055
* Add py-segregation 1.4.0Sunpoet Po-Chuan Hsieh2021-01-031-0/+1
| | | | | | | | | | | | | | Segregation Analysis, Inference, and Decomposition with PySAL The PySAL segregation package is a tool for analyzing patterns of urban segregation. With only a few lines of code, segregation users can calculate over 40 segregation measures from simple to state-of-the art. WWW: https://pysal.org/segregation/ WWW: https://github.com/pysal/segregation Notes: svn path=/head/; revision=560054
* Add py-libpysal 4.3.0Sunpoet Po-Chuan Hsieh2021-01-031-0/+1
| | | | | | | | | | | | | | | | | Python Spatial Analysis Library Core libpysal offers four modules that form the building blocks in many upstream packages in the PySAL family: - Spatial Weights: libpysal.weights - Input-and output: libpysal.io - Computational geometry: libpysal.cg - Built-in example datasets libpysal.examples WWW: https://pysal.org/libpysal/ WWW: https://github.com/pysal/libpysal Notes: svn path=/head/; revision=560053
* Add py-inequality 1.0.0Sunpoet Po-Chuan Hsieh2021-01-031-0/+1
| | | | | | | | | | | inequality implements measures for the analysis of inequality over space and time and is part of the PySAL family. WWW: https://inequality.readthedocs.io/en/latest/ WWW: https://github.com/pysal/inequality Notes: svn path=/head/; revision=560052
* Add py-esda 2.3.1Sunpoet Po-Chuan Hsieh2021-01-031-0/+1
| | | | | | | | | | | | | | | ESDA: Exploratory Spatial Data Analysis ESDA is an open-source Python library for the exploratory analysis of spatial data. A subpackage of PySAL (Python Spatial Analysis Library), it is under active development and includes methods for global and local spatial autocorrelation analysis. WWW: https://pysal.org/esda/ WWW: https://github.com/pysal/esda Notes: svn path=/head/; revision=560051
* Add py-access 1.1.3Sunpoet Po-Chuan Hsieh2021-01-031-0/+1
| | | | | | | | | | | | | | | Spatial Access for PySAL Whether you work with data in health, retail, employment or other domains, spatial accessibility measures help identify potential spatial mismatches between the supply and demand of services. They indicate how close demand locations are to supply locations. WWW: https://access.readthedocs.io/en/latest/ WWW: https://github.com/pysal/access Notes: svn path=/head/; revision=560050
* Remove expired ports not depending on Python 2.7:Rene Ladan2020-12-311-1/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | 2020-12-31 devel/arm-none-eabi-gdb: This is an old, obsolete version of gdb 2020-12-31 devel/pecl-weakref2: PHP 7.2 extension 2020-12-31 graphics/py-imageio24: Use graphics/py-imageio instead 2020-12-31 mail/bogofilter-tc: TokyoCabinet is being phased out in favor of KyotoCabinet. 2020-12-31 net/pecl-yaz: PHP 7.2 extension 2020-12-31 print/cloudprint: Google Cloud Print is being shut down by Google by end of 2020 2020-12-31 science/py-eccodes-python: Use science/py-eccodes instead 2020-12-31 sysutils/cfengine-masterfiles312: EOL 2020-12-31 sysutils/cfengine-masterfiles313: EOL 2020-12-31 sysutils/cfengine312: EOL 2020-12-31 sysutils/cfengine313: EOL 2020-12-31 sysutils/rubygem-chef-zero5: Please use sysutils/rubygem-chef-zero instead 2020-12-31 sysutils/syslog-ng325: Reduction of syslog-ng ports to one 2020-12-31 sysutils/syslog-ng326: Reduction of syslog-ng ports to one 2020-12-31 sysutils/syslog-ng328: Reduction of syslog-ng ports to one 2020-12-31 sysutils/syslog-ng329: Reduction of syslog-ng ports to one 2020-12-31 www/flashplayer: Depends on a deprecated port 2020-12-31 www/linux-flashplayer: Deprecated by upstream 2020-12-31 www/mediawiki133: Upstream end of life 2020-12-31 www/mediawiki134: Upstream end of life 2020-12-31 www/py-aiohttp2: Use www/py-aiohttp instead sysutils/drm-legacy-kmod is left in for now. Notes: svn path=/head/; revision=559743
* Adding jupyter-jsmol, a JSmol viewer widget for Jupyter Notebooks andThierry Thomas2020-12-221-0/+1
| | | | | | | JupyterLab, to bue used by SageMath 9.3. Notes: svn path=/head/; revision=558904
* Add py-eccodes 1.0.0 (copied from py-eccodes-python)Sunpoet Po-Chuan Hsieh2020-12-191-0/+1
| | | | | | | Changes: https://github.com/ecmwf/eccodes-python/blob/develop/CHANGELOG.rst Notes: svn path=/head/; revision=558476
* Add py-netcdf-flattener 1.2.0Sunpoet Po-Chuan Hsieh2020-12-101-0/+1
| | | | | | | | | | The flattener takes as input and output NetCDF Dataset objects, which the user can create or open from ".nc" files using the netCDF4 API. WWW: https://gitlab.eumetsat.int/open-source/netcdf-flattener Notes: svn path=/head/; revision=557468
* Remove expired ports:Rene Ladan2020-12-011-1/+0
| | | | | | | | | | | | | | | | | | | | | 2020-11-30 databases/datamodeler: depends on expiring java/openjfx8-devel 2020-11-30 devel/gradle4: only needed for expiring biology/igv and java/openjfx8-devel 2020-11-30 devel/py-astroid1: Use devel/py-astroid instead 2020-11-30 devel/pylint1: Use devel/pylint instead 2020-11-30 german/mediathekview: depends on expiring java/openjfx8-devel 2020-11-30 java/openjfx8-devel: No longer maintained upstream 2020-11-30 java/openjfx8-scenebuilder: depends on expiring java/openjfx8-devel 2020-11-30 net-im/py-sleekxmpp: Upstream archived and advices to use net-im/py-slixmpp 2020-12-01 net-mgmt/zabbix44-agent: End of Life 2020-12-01 net-mgmt/zabbix44-frontend: End of Life 2020-12-01 net-mgmt/zabbix44-java: End of Life 2020-12-01 net-mgmt/zabbix44-proxy: End of Life 2020-12-01 net-mgmt/zabbix44-server: End of Life 2020-11-30 print/jabref: depends on expiring java/openjfx8-devel 2020-11-30 science/datawarrior: depends on expiring java/openjfx8-devel Notes: svn path=/head/; revision=556791
* Upgrade Code_Aster to 14.6.0-1.Thierry Thomas2020-11-261-0/+1
| | | | | | | | | | | | | | | | | | | | This implies: - french /aster builds fine with clang, but it seg-faults: switched to Gcc - ASTK is upgraded to 2019.0-1 - math/mumps is upgraded to 5.1.2-aster7 - TFEL/MFront is now required, but when the compilers of tfel and aster are different, it cannot be linked . recopopy science/tfel to science/tfel-edf and depends on science/tfel-edf . science/tfel-edf is built by Gcc, from the sources included in Aster's tarball . register the conflicts Notes: svn path=/head/; revision=556349
* New port: science/py-segyio: Python binding for segyio, the seismic data libraryYuri Victorovich2020-11-081-0/+1
| | | | Notes: svn path=/head/; revision=554431
* New port: science/segyio: Library to interact with SEG-Y & Seismic Unix ↵Yuri Victorovich2020-11-081-0/+1
| | | | | | | formatted seismic data Notes: svn path=/head/; revision=554430
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