Number of commits found XX: 518 (showing only 100 on this page)

1 | 2 | 3 | 4 | 5 | 6  »  

New port: science/py-pygmo2: Python platform to perform parallel computations of
optimisation tasks

Clean up some things

Reported by:	portscan

new port: science/xtb

xtb is a semiempirical extended tight-binding program package with
application in computational chemistry and matrials science.

Port is configured to use OpenBLAS to facilitate performance.

WWW: https://github.com/grimme-lab/xtb

New port: science/fastjet: Package for jet finding in pp and e+e- collisions

New port: science/hepmc3: Event record for High Energy Physics Monte Carlo
generators/simulation

Re-add port: science/cp2k: Quantum chemistry and solid state physics software
package; Update 6.1.0 -> 7.1.0-20200518

Re-add port: science/abinit: Full-featured atomic-scale first-principles
simulation software

The taball for the 8.10.3 version was replaced on the upstream website with
significant updates in it.
The new tarball doesn't compile.
I preserved the previous 8.10.3 version tarball so that the package can build.
The new, 9.x version is upcoming.

Add py-liac-arff 2.4.0

The liac-arff module implements functions to read and write ARFF files in
Python. It was created in the Connectionist Artificial Intelligence Laboratory
(LIAC), which takes place at the Federal University of Rio Grande do Sul
(UFRGS), in Brazil.

ARFF (Attribute-Relation File Format) is an file format specially created for
describe datasets which are used commonly for machine learning experiments and
softwares. This file format was created to be used in Weka, the best
representative software for machine learning automated experiments.

WWW: https://github.com/renatopp/liac-arff

New port: science/py-moltemplate: Tool to prepare simulations of molecules,
complex molecular assemblies

New port: science/ergo: Quantum chemistry program for large-scale atomic
calculations

Remove expired ports:

Adjusted for ports rescued since r534032

2020-05-05 audio/festvox-czech: Broken for more than 6 months
2020-05-05 audio/gkrellmvolume2: Broken for more than 6 months
2020-05-05 audio/mixmos: Broken for more than 6 months
2020-05-05 audio/mma: Broken for more than 6 months
2020-05-05 audio/pd-cyclone: Broken for more than 6 months
2020-05-05 audio/shorten: Broken for more than 6 months
2020-05-05 audio/taglib-sharp: Broken for more than 6 months
2020-05-05 audio/xhippo: Broken for more than 6 months
2020-05-05 biology/consed: Broken for more than 6 months
2020-05-05 biology/plinkseq: Broken for more than 6 months
2020-05-05 biology/seqtools: Broken for more than 6 months

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Sort

New port: science/votca: CSG and XTP: libraries for atomistic simulations

New port: science/plumed: PLUgin for MolEcular Dynamics

New port: science/py-kliff: KIM-based Learning-Integrated Fitting Framework

New port: science/py-kim-query: Helper routines for querying the OpenKIM
repository

Add py-scikit-optimize 0.7.4

Scikit-Optimize, or skopt, is a simple and efficient library to minimize (very)
expensive and noisy black-box functions. It implements several methods for
sequential model-based optimization. skopt aims to be accessible and easy to use
in many contexts.

WWW: https://github.com/scikit-optimize/scikit-optimize

science/ncnn: Move to misc/ncnn; Update 20200226 -> 20200413

Reported by:	portscout (update)

New port: science/qiskit-aer: Simulator for quantum circuits, including noise
models

Remove expired ports, all Python-2.7-only:

2020-02-17 audio/decibel-audio-player: Old, uses EOLed python27
2020-02-17 audio/soundconverter: Old, uses EOLed python27
2020-02-19 cad/linuxcnc-devel: Broken, uses EOLed python27
2020-02-19 databases/monetdb: Broken, uses EOLed python27
2020-02-19 databases/py-cql: Broken, uses EOLed python27
2020-02-18 databases/zodb3: Old, uses EOLed python27
2020-02-17 deskutils/gourmet: Old, uses EOLed python27
2020-02-18 devel/py-Products.PlacelessTranslationService: Old, uses EOLed
python27
2020-02-18 devel/py-Products.ZopeVersionControl: Old, uses EOLed python27
2020-02-18 devel/py-Products.statusmessages: Old, uses EOLed python27
2020-02-18 devel/py-collective.z3cform.datetimewidget: Old, uses EOLed python27
2020-02-20 devel/py-five.formlib: Old, uses EOLed python27
2020-02-18 devel/py-five.localsitemanager: Old, uses EOLed python27

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Adding R-cran-FAdist, a R package with a collection of probability distributions
that are sometimes used in hydrology, used by math/rkward-kde for its non-
regression tests.

Remove expired ports:

2020-01-27 accessibility/py-papi: Unmaintained, uses EOLed python27
2020-01-27 archivers/py-czipfile: Unmaintained, uses EOLed python27
2020-01-27 audio/boodler: Unmaintained, uses EOLed python27
2020-01-27 audio/dir2ogg: Unmaintained, uses EOLed python27
2020-01-27 audio/jokosher: Unmaintained, uses EOLed python27
2020-01-27 audio/mpdbrowser: Unmaintained, uses EOLed python27
2020-01-27 audio/nekobee: Unmaintained, uses EOLed python27
2020-01-27 audio/patchage: Unmaintained, uses EOLed python27
2020-01-27 audio/py-ao: Unmaintained, uses EOLed python27
2020-01-27 audio/py-id3: Unmaintained, uses EOLed python27
2020-01-27 audio/py-shout: Unmaintained, uses EOLed python27
2020-01-27 audio/py-speex: Unmaintained, uses EOLed python27
2020-01-27 audio/pytone: Unmaintained, uses EOLed python27

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New port: science/py-h5json: Tools and library for representing HDF5 in JSON

Add py-pygeometa 0.5.0

pygeometa is a Python package to generate metadata for geospatial datasets.

WWW: https://github.com/geopython/pygeometa

Add py-pycsw 2.4.2

pycsw is an OGC CSW server implementation written in Python. Started in 2010
(more formally announced in 2011), pycsw allows for the publishing and discovery
of geospatial metadata via numerous APIs (CSW 2/CSW 3, OpenSearch, OAI-PMH,
SRU), providing a standards-based metadata and catalogue component of spatial
data infrastructures. pycsw is Open Source, released under an MIT license, and
runs on all major platforms (Windows, Linux, Mac OS X).

WWW: https://pycsw.org/
WWW: https://github.com/geopython/pycsw

Add py-geolinks 0.2.0

geolinks provides utilities to deal with geospatial links.

WWW: https://github.com/geopython/geolinks

Move cad/elmerfem -> science/elmerfem

Also:
* Update COMMENT to reflect how their website decribes it
* Update WWW
* Group USExx lines

Remove expired ports:

2020-01-10 astro/viking: Depends on broken and expiring graphics/mapnik
2020-01-10 audio/slv2: Broken for more than 5 months
2020-01-10 audio/triceratops-lv2: Broken for more than 5 months
2020-01-10 cad/brickutils: Broken for more than 3 months, unmaintained
2020-01-10 deskutils/zanshin: Broken for more than 5 months
2020-01-10 devel/elixir-gen_state_machine: Broken for more than 6 months
2020-01-10 devel/elixir-swarm: Depends on broken and expiring
devel/elixir-gen_state_machine
2020-01-10 devel/erlang-clique: Depends on broken and expiring
devel/erlang-cuttlefish
2020-01-10 devel/erlang-gen_rpc: Broken for more than 6 months
2020-01-10 devel/erlang-msgpack: Broken for more than 6 months
2020-01-10 devel/ocaml-deriving-ocsigen: Broken for more than 6 months
2020-01-10 devel/p5-rpm-build-perl: Broken for more than 7 months
2020-01-10 devel/shedskin: Broken for more than 3 months, unmaintained

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New port: science/cdk: Chemistry Development Kit

Resurrect ports depending on devel/openmp.

These ports will transition transparantly to openmp from base once
FreeBSD 12.0 reaches end-of-life.

Reported by:	jbeich [1] [2]

[1] https://lists.freebsd.org/pipermail/svn-ports-head/2019-May/210482.html
[2] https://lists.freebsd.org/pipermail/svn-ports-head/2019-December/229648.html

Remove expired ports:

2019-12-31 accessibility/linux-c6-atk: Superseded by CentOS 7
2019-12-31 audio/exaile-devel: this port is older than audio/exaile
2019-12-31 audio/linux-c6-alsa-lib: Superseded by CentOS 7
2019-12-31 audio/linux-c6-alsa-plugins-oss: Superseded by CentOS 7
2019-12-31 audio/linux-c6-alsa-plugins-pulseaudio: Superseded by CentOS 7
2019-12-31 audio/linux-c6-alsa-utils: Superseded by CentOS 7
2019-12-31 audio/linux-c6-flac: Superseded by CentOS 7
2019-12-31 audio/linux-c6-libaudiofile: Superseded by CentOS 7
2019-12-31 audio/linux-c6-libogg: Superseded by CentOS 7
2019-12-31 audio/linux-c6-libsndfile: Superseded by CentOS 7
2019-12-31 audio/linux-c6-libvorbis: Superseded by CentOS 7
2019-12-31 audio/linux-c6-mikmod: Superseded by CentOS 7
2019-12-31 audio/linux-c6-nas-libs: Superseded by CentOS 7

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Add py-geomet 0.2.1

GeoMet converts GeoJSON to WKT/WKB (Well-Known Text/Binary), and vice versa.
Extended WKB/WKT are also supported. Conversion functions are exposed through
idiomatic load/loads/dump/dumps interfaces.

GeoMet is intended to cover all common use cases for dealing with 2D, 3D, and 4D
geometries (including 'Z', 'M', and 'ZM').

WWW: https://github.com/geomet/geomet

New port: science/highfive: Header-only C++ HDF5 interface

Remove deprecated ports

Remove deprecated ports depending on the soon to be removed
x11/libXxf86misc and graphics/libGLw

2019-11-01 games/xpilot-ng-client: Depends on deprecated x11/libXxf86misc
2019-11-01 science/xmakemol: Depends on expiring graphics/libGLw

Remove expired ports:

2019-10-16 archivers/freetar: Unfetchable, unmaintained
2019-10-16 archivers/hffzip: Unfetchable, unmaintained
2019-10-16 archivers/hpack.non-usa.only: Unfetchable, unmaintained
2019-10-16 archivers/untar: Unfetchable, unmaintained
2019-10-16 astro/gpsdrive: Unfetchable, unmaintained
2019-10-16 astro/planets: Unfetchable, unmaintained
2019-10-16 audio/ascd: Unfetchable, unmaintained
2019-10-16 audio/audiotag: Unfetchable, unmaintained
2019-10-16 audio/gmidimonitor: Unfetchable, unmaintained
2019-10-16 audio/gmpc-lyricwiki: Unfetchable, unmaintained
2019-10-16 audio/jack_mixer: Unfetchable, unmaintained
2019-10-16 audio/jmusic: Unfetchable, unmaintained
2019-10-16 audio/maplay: Unfetchable, unmaintained

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science/packmol: Pack molecules in defined regions of space

PACKMOL creates an initial point for molecular dynamics simulations by packing
molecules in defined regions of space. The packing guarantees that short range
repulsive interactions do not disrupt the simulations.

Sort SUBDIRs

Move science/py-onnx -> math/py-onnx

math is a more appropriate category, but neural networks is really
an emerging field in itself and it probably deserves the category
of its own.

New port: science/py-tensorflow-estimator: TensorFlow Estimator, an API to
simplify machine learning programming

Dependencies are unusual for science/py-tensorflow-estimator:
science/py-tensorflow imports science/py-tensorflow-estimator in its python
code,
but science/py-tensorflow-estimator is a separate project that depends on
science/py-tensorflow
in order to build.

PR:		226400
Submitted by:	Anthony <amzo1337@gmail.com>

New port: science/py-chainer-chemistry: Library for deep learning in biology and
chemistry

New port: science/py-chainer: Deep learning framework

New port: science/py-onnx: Open Neural Network eXchange

Re-add science/py-tensorflow: Computation using data flow graphs for scalable
machine learning

Many thanks to Anthony who was highly persistent and skillful in getting the
Tensorflow build on FreeBSD!

PR:		226400
Submitted by:	Anthony <amzo1337@gmail.com>

Hook up science/openkim-models to build.

New port: science/ncnn: High-performance neural network inference framework

New port: science/wwplot: Plotting tool for experimental physics classes

New port: science/kim-api: Framework for reliable, reproducible, portable
molecular simulations

New port: science/py-ruffus

The Ruffus module is a lightweight way to add support for running
computational pipelines.

Computational pipelines are often conceptually quite simple, especially if
we breakdown the process into simple stages, or separate tasks.

Each stage or task in a computational pipeline is represented by a Python
function. Each Python function can be called in parallel to run multiple
jobs.

Ruffus was originally designed for use in bioinformatics to analyse multiple
genome data sets.

WWW: http://www.ruffus.org.uk

Remove dupplicate port.

Pointy hat:	yuri

New port: science/molden: Program for molecular and electronic structure
visualization

New port: science/smoldyn: Biochemical simulator for molecular diffusion,
surface interactions

New port: science/opensph: Library and graphical tools for running SPH and
N-body simulations

Add py-eccodes-python 0.9.0

Python 3 interface to encode and decode GRIB and BUFR files via the ECMWF
ecCodes library.

Features:
- reads and writes GRIB 1 and 2 files,
- reads and writes BUFR 3 and 4 files,
- supports all modern versions of Python 3.7, 3.6, 3.5 and PyPy3,
- works on most Linux distributions and MacOS, the ecCodes C-library is the only
  system dependency,
- PyPI package with no install time build (binds with CFFI ABI level, in-line
  mode),
- supports writing the index of a GRIB file to disk, to save a full-file scan on
  open.

WWW: https://github.com/ecmwf/eccodes-python

New port: science/libvdwxc: Van der Waals density functional (DFT) library

New port: science/simgrid: Simulator of the behavior of large-scale distributed
systems

New port: science/nest: Simulator for spiking neural network models

New port: science/apbs: Electrostatic and solvation properties for complex
molecules

New port: science/pagmo2: Platform to perform parallel computations of
optimization tasks

New port: science/cp2k-data: Data for cp2k quantum chemistry package

New port: science/py-qcengine: Quantum chemistry program executor and IO
standardizer (QCSchema)

New port: science/py-qcelemental: Essentials for quantum chemistry

Re-add science/py-veusz: the latest version builds with Qt5

Add py-geometer 0.1.2

Geometer is a geometry library for Python 3 that uses projective geometry and
numpy for fast geometric computation. In projective geometry every point in 2D
is represented by a three-dimensional vector and every point in 3D is
represented by a four-dimensional vector. This has the following advantages:

There are points at infinity that can be treated just like normal points.
- Projective transformations are described by matrices but they can also
  represent affine transformations i.e. also translations.
- Every two lines have a unique point of intersection if they lie in the same
  plane. Parallel lines have a point of intersection at infinity.
- Points of intersection, planes or lines through given points can be calculated
  using simple cross products or tensor diagrams.
- Special complex points at infinity and cross ratios can be used to calculate
  angles and to construct perpendicular geometric structures.
- Most of the computation in the library done via tensor diagrams (using
  numpy.einsum).

WWW: https://github.com/jan-mue/geometer

Qt4 deprecation: Remove Qt4 and its consumes.

2019-03-15 accessibility/qt4-accessible: Qt4 has been EOL since december 2015
2019-03-15 astro/qlandkartegt: Qt4 has been EOL since december 2015
2019-03-15 astro/stellarium-qt4: Qt4 has been EOL since december 2015
2019-03-15 astro/xglobe: Qt4 has been EOL since december 2015
2019-03-15 audio/acoustid-fingerprinter: Qt4 has been EOL since december 2015
2019-03-15 audio/cueplayer: Qt4 has been EOL since december 2015
2019-03-15 audio/esperanza: Qt4 has been EOL since december 2015
2019-03-15 audio/lastfm-desktop: Qt4 has been EOL since december 2015
2019-03-15 audio/minitunes: Qt4 has been EOL since december 2015
2019-03-15 audio/mixxx20: Qt4 has been EOL since december 2015
2019-03-15 audio/mumble: Qt4 has been EOL since december 2015
2019-03-15 audio/murmur: Qt4 has been EOL since december 2015
2019-03-15 audio/puddletag: Qt4 has been EOL since december 2015

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Remove expired ports:
2019-03-05 devel/elixir-lager_logger: Broken for more than 6 months
2019-03-05 devel/gpsim: Broken for more than 6 months
2019-03-05 devel/hgview: Broken for more than 6 months
2019-03-05 games/mudmagic: Broken for more than 6 months
2019-03-05 math/mumps-mpich: Broken for more than 6 months
2019-03-05 math/sdpara: Broken for more than 6 months
2019-03-05 net/tn5250j: Broken for more than 6 months
2019-03-05 net-im/pidgin-skype: Broken for more than 6 months
2019-03-05 net-im/skype: Broken for more than 6 months
2019-03-05 net-im/skype-devel: Broken for more than 6 months
2019-03-05 science/dft_tools: Broken for more than 6 months
2019-03-05 science/triqs: Broken for more than 6 months
2019-03-05 security/hamachi: Broken for more than 6 months
2019-03-05 textproc/elixir-ex_doc: Broken for more than 6 months
2019-03-05 x11/altyo: Broken for more than 6 months
2019-03-05 x11/pantheon-terminal: Broken for more than 6 months
2019-03-05 x11-wm/e-module-everything-websearch: Broken for more than 6 months

New port: science/dvc: Git for data scientists: manage code and data together

Move: science/mmtf -> science/mmtf-cpp

Also update its COMMENT to be more descriptive

New port: science/opsin: Open Parser for Systematic IUPAC Nomenclature of
chemical names

Re-add: science/jmol: Java 3D viewer for chemical structures

New port: science/molscript: Display 3D molecules in schematic and detailed
representations

New port: science/py-oddt: Open Drug Discovery Toolkit

New port: science/healpix: Software for pixelization, visualization, etc of data
on the sphere

Approved by:	portmgr
Differential Revision:	D18548

New port: science/nwchem-data: Data for NWChem, the computational chemistry
software

Split out data from science/nwchem to facilitate flavor creation there.

Sort categories Makefiles.

New port: science/py-rmsd: Calculate root-mean-square deviation (RMSD) between
coordinate sets

Add py-asdf 2.3.1

The Advanced Scientific Data Format (ASDF) is a next-generation interchange
format for scientific data. This package contains the Python implementation of
the ASDF Standard.

The ASDF format has the following features:
- A hierarchical, human-readable metadata format (implemented using YAML)
- Numerical arrays are stored as binary data blocks which can be memory mapped.
  Data blocks can optionally be compressed.
- The structure of the data can be automatically validated using schemas
  (implemented using JSON Schema)
- Native Python data types (numerical types, strings, dicts, lists) are
  serialized automatically
- ASDF can be extended to serialize custom data types

WWW: https://github.com/spacetelescope/asdf

New port: science/erkale-pseudopotentials: Pseudopotentials for Erkale, the
quantum chemistry program

Remove KDE4, part 5
2018-12-31 korean/kde4-l10n: KDE4 is EOL upstream
2018-12-31 net/kget-kde4: KDE4 is EOL upstream
2018-12-31 net/kdenetwork-strigi-analyzers-kde4: KDE4 is EOL upstream
2018-12-31 net/zeroconf-ioslave-kde4: KDE4 is EOL upstream
2018-12-31 net/libkfbapi: Qt4 has been EOL since december 2015
2018-12-31 net/kdenetwork-kde4: KDE4 is EOL upstream
2018-12-31 net/kwooty: Qt4 has been EOL since december 2015
2018-12-31 net/kdenetwork-filesharing-kde4: KDE4 is EOL upstream
2018-12-31 net/libmediawiki-kde4: KDE4 is EOL upstream
2018-12-31 net/kio-upnp-ms: Qt4 has been EOL since december 2015
2018-12-31 net/libkvkontakte-kde4: KDE4 is EOL upstream
2018-12-31 net/krfb-kde4: KDE4 is EOL upstream
2018-12-31 net/smb4k-kde4: Qt4 has been EOL since december 2015
2018-12-31 net/krdc-kde4: KDE4 is EOL upstream

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Add new port science/scidavis:

Cross-platform program for data analysis and visualization.

WWW: http://scidavis.sourceforge.net

New port: science/vipster: Crystalline and molecular structure visualisation
program

New port: science/agrum: Graphical modeler for Bayesian networks, influence
diagrams, etc

New port: science/h5z-zfp: Registered ZFP compression plugin for HDF5

New port: science/py-GPyOpt: Bayesian optimization toolbox based on GPy

New port: science/py-GPy: Gaussian process toolbox

New port: science/py-paramz: Parameterization framework

New port: science/drawxtl: Crystal structure visualization tool

Remove expired ports:
2018-12-10 net/g2ipmsg: GNOME 2 application
2018-12-10 net/grdesktop: GNOME 2 application
2018-12-10 textproc/gnome-spell: GNOME 2 application
2018-12-10 textproc/sagasu: GNOME 2 application
2018-12-10 deskutils/planner: GNOME 2 application
2018-12-10 deskutils/multisync: GNOME 2 application
2018-12-10 deskutils/drivel: GNOME 2 application
2018-12-10 deskutils/notecase: GNOME 2 application
2018-12-10 deskutils/gtodo: GNOME 2 application
2018-12-10 deskutils/gtweakui: GNOME 2 application
2018-12-10 deskutils/gnotime: GNOME 2 application
2018-12-10 deskutils/gruler: GNOME 2 application
2018-12-10 japanese/gjiten: GNOME 2 application
2018-12-10 graphics/truevision: GNOME 2 application

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Add py-pygeodesy 18.11.12

PyGeodesy is a pure Python implementation of geodesy tools for various
ellipsoidal and spherical earth models using precision trigonometric,
vector-based and approximate methods for geodetic (lat-/longitude) and
geocentric cartesian (x/y/z) coordinates.

WWW: https://github.com/mrJean1/PyGeodesy

New port: science/yoda: Particle physics package with classes for data analysis,
histogramming

New port: science/quantum-espresso-pseudopotentials: Pseudopotentials for use
with Quantum Espresso

New port: science/berkeleygw: Scientific program aimed at the ab initio virtual
experimentation

Only a serial version for now.

New port: science/opensim-core: Software for modeling of musculoskeletal
structures

New port: science/simbody: Multibody dynamics library for (bio)mechanical
systems simulation

Survival analysis in Python, including Kaplan Meier, Nelson Aalen and regression

WWW: https://github.com/CamDavidsonPilon/lifelines/

New port: science/sparta: Gas simulator: SPARTA DSMC software package

New port: science/esys-particle: Particle-based numerical modelling software

bft, ecs, fvm, mei and ncs have been merged to code_saturne.

New port: science/liggghts: Discrete element method particle simulation software

New port: science/latte: Quantum chemistry: Density functional tight binding
molecular dynamics

New port: science/gpaw-setups: Setups (data files) for py-gpaw, the DFT quantum
chemistry software

Number of commits found XX: 518 (showing only 100 on this page)

1 | 2 | 3 | 4 | 5 | 6  »  

18 vulnerabilities affecting 82 ports have been reported in the past 14 days

^* - modified, not new

All vulnerabilities

Last updated:
2020-07-10 06:33:27