Number of commits found: 480 (showing only 100 on this page)

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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

New port: science/coordgenlibs: Schrodinger-developed 2D coordinate generation

New port: science/maeparser: Parser for Schrodinger Maestro files

New port: science/molsketch: 2D molecule editor

New port: science/erkale: Quantum chemistry program to solve the electronic
structure of atoms

New port: science/py-avogadrolibs: Python bindings for Avogadro2 chemistry
libraries

New port: science/mmtf: C++ implementation of the MMTF API, decoder and encoder

New port: science/avogadro2: Chemical editor and visualization application

New port: science/avogadrolibs: Avogadro2 libraries for chemical editor and
visualization applications

New port: science/libmsym: Molecular point group symmetry library

New port: science/wxmacmolplt: Graphical user interface principally for the
GAMESS program

Re-add port: science/gamess-us: General Atomic and Molecular Electronic
Structure System (US)

It used to be in science/gamess and was removed in 2014.

New port: science/simint: Obara-Saika (OS) method of calculating electron
repulsion integrals

New port: science/molgif: Tool to create GIF animations of molecules

biology/tinker: Update 7.1.3 -> 8.4.4; Move to science/

Port changes:
* Take maintainership
* Implement the 'benchmarks' target, and stop installing benchmarks
* Add USES=gmake
* Update license
* Change MASTER_SITES and WWW to https
* Silence some commands

New port: science/bagel: Brilliantly Advanced General Electronic-structure
Library

New port: science/elk: All-electron full-potential linearised
augmented-planewave code

New port: science/py-PyFR: Framework for solving advection-diffusion type
problems

New port: science/py-chempy: Package useful useful for solving problems in
chemistry

New port: science/luscus: Molecular editor and viewer

New port: science/py-phono3py: Software to calculate phonon-phonon interaction
and related properties

New port: science/py-phonopy: Package for phonon calculations at harmonic and
quasi-harmonic levels

New port: science/py-molmod: Collection of molecular modelling tools for python

New port: science/dftbplus: Package for performing fast atomistic simulations

New port: science/openmx: Nanoscale material simulations using density
functional theories (DFT)

New port: science/msms: Program to efficiently compute molecular surfaces

New port: science/lm: Software for sampling trajectories of the
reaction-diffusion equations

New port: science/namd: Computer software for molecular dynamics simulation

New port: science/lammps: Classical molecular dynamics code with a focus on
materials modeling

New port: science/mdynamix: General purpose molecular dynamics code

New port: science/cp2k: Quantum chemistry and solid state physics software
package

New port: science/atom: Program for DFT calculations in atoms

New port: science/libgridxc: Library to compute the exchange and correlation
energy and potentials

Remove science/mpqc-mpich: Enable MPI option in science/mpqc by default

* MPICH option in science/mpqc is renamed to MPI, because MPI exists in many
other
  ports and there's MPI_DESC predefined for it.
* MPI option in science/mpqc is made default.

New port: science/siesta: Program to perform efficient electronic structure
calculations

New port: science/wannier90: Maximally-localized Wannier functions (MLWFs) and
Wannier90

New port: science/fleur: FLAPW code for atomic computations in quantum chemistry
and physics

New port: science/dalton: Powerful molecular electronic structure program for
quantum chemistry

New port: science/teem: Libraries for representing, processing and visualizing
scientific data

Number of commits found: 480 (showing only 100 on this page)

1 | 2 | 3 | 4 | 5  »  

4 vulnerabilities affecting 12 ports have been reported in the past 14 days

^* - modified, not new

All vulnerabilities

Last updated:
2019-10-19 10:52:46