02:19 yuri 

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

 

06:36 yuri 

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

 

06:24 yuri 

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

 

06:20 yuri 

New port: science/py-paramz: Parameterization framework

 

02:58 yuri 

New port: science/drawxtl: Crystal structure visualization tool

 

13:02 rene 

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
2018-12-10 graphics/gx: GNOME 2 application
2018-12-10 graphics/amide: GNOME 2 application
2018-12-10 graphics/cbrpager: GNOME 2 application
2018-12-10 www/gurlchecker: GNOME 2 application
2018-12-10 security/gpass: GNOME 2 application
2018-12-10 security/libgnomesu: GNOME 2 application
2018-12-10 security/gnome-gpg: GNOME 2 application
2018-12-10 devel/gnome-vfs-monikers: GNOME 2 application
2018-12-10 ftp/gwget: GNOME 2 application
2018-12-10 print/gribouy: GNOME 2 application
2018-12-10 print/gnomephotoprinter: GNOME 2 application
2018-12-10 print/ggv: GNOME 2 application
2018-12-10 print/gnome-cups-manager: GNOME 2 application
2018-12-10 editors/conglomerate: GNOME 2 application
2018-12-10 misc/gregexp: GNOME 2 application
2018-12-10 science/linsmith: GNOME 2 application
2018-12-10 games/grhino: GNOME 2 application
2018-12-10 games/gnono: GNOME 2 application
2018-12-10 games/gnomekiss: GNOME 2 application
2018-12-10 games/gtktetcolor: GNOME 2 application
2018-12-10 games/gturing: GNOME 2 application
2018-12-10 games/gtetrinet: GNOME 2 application
2018-12-10 games/gdado: GNOME 2 application
2018-12-10 games/monkeybubble: GNOME 2 application
2018-12-10 games/teg: GNOME 2 application
2018-12-10 games/gnomeattacks: GNOME 2 application
2018-12-10 games/gnomebreakout: GNOME 2 application
2018-12-10 x11-clocks/gtubeclock: GNOME 2 application
2018-12-10 x11-clocks/sanduhr: GNOME 2 application
2018-12-10 audio/grip: GNOME 2 application
2018-12-10 audio/jack-rack: GNOME 2 application
2018-12-10 math/gdcalc: GNOME 2 application
2018-12-10 x11/brightside: GNOME 2 application
2018-12-10 x11-fm/gnome-commander2: GNOME 2 application
2018-12-10 multimedia/quark: GNOME 2 application
2018-12-10 astro/celestia-gnome: GNOME 2 application
2018-12-10 comms/gmfsk: GNOME 2 application
2018-12-10 comms/ge-x2212: GNOME 2 application
2018-12-10 comms/efax-gtk: GNOME 2 application
2018-12-10 sysutils/gnome-pkgview: GNOME 2 application
2018-12-10 sysutils/fusefs-gnome-vfs: GNOME 2 application
2018-12-10 sysutils/gai-leds: GNOME 2 application
2018-12-10 sysutils/gnome-device-manager: GNOME 2 application
2018-12-10 sysutils/battfink: GNOME 2 application
2018-12-10 sysutils/cog: GNOME 2 application
2018-12-10 sysutils/gcdmaster: GNOME 2 application

 

20:30 sunpoet 

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

 

08:15 yuri 

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

 

22:34 yuri 

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

 

21:56 yuri 

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

Only a serial version for now.

 

02:55 yuri 

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

 

06:40 yuri 

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

 

18:35 rm 

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

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

 

03:02 yuri 

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

 

05:16 yuri 

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

 

17:18 thierry 

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

 

08:24 yuri 

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

 

23:05 yuri 

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

 

04:36 yuri 

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

 

07:36 yuri 

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

 

07:24 yuri 

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

 

05:36 yuri 

New port: science/molsketch: 2D molecule editor

 

17:56 yuri 

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

 

17:52 yuri 

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

 

21:21 yuri 

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

 

01:04 yuri 

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

 

01:02 yuri 

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

 

22:58 yuri 

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

 

23:15 yuri 

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

 

03:18 yuri 

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.

 

07:52 yuri 

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

 

21:54 yuri 

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

 

00:19 yuri 

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

 

18:11 yuri 

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

 

08:43 yuri 

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

 

07:11 yuri 

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

 

21:33 yuri 

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

 

07:44 yuri 

New port: science/luscus: Molecular editor and viewer

 

05:37 yuri 

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

 

05:01 yuri 

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

 

03:10 yuri 

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

 

22:25 yuri 

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

 

03:00 yuri 

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

 

05:53 yuri 

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

 

20:57 yuri 

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

 

23:28 yuri 

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

 

06:31 yuri 

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

 

05:14 yuri 

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

 

21:28 yuri 

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

 

15:05 yuri 

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

 

15:03 yuri 

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

 

06:07 yuri 

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.

 

17:51 yuri 

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

 

04:09 yuri 

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

 

21:10 yuri 

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

 

07:49 yuri 

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

 

06:43 yuri 

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

 

18:31 yuri 

New port: science/py-gpaw:  DFT and beyond within the projector-augmented wave
method in chemistry

 

18:17 yuri 

New port: science/py-ase: Atomic simulation environment

 

06:30 yuri 

New port: science/jdftx: Software for joint density functional theory in
chemistry

 

06:45 yuri 

New port: science/qbox: First-principles molecular dynamics code

 

00:57 yuri 

New port: science/libint2: Evaluate the integrals in modern atomic and molecular
theory

Repocopy of science/libint.
science/libint is at version 1.X, is incompatible, and is used by several other
packages.

 

07:56 yuri 

New port: science/madness: Multiresolution adaptive numeric environment for
scientific simulation

 

06:15 yuri 

New port: science/datawarrior: Chemistry-aware multi-purpose data visualization
and analysis program

 

19:04 yuri 

New port: science/multiwfn: Multifunctional wavefunction analysis for quantum
chemistry

 

18:08 yuri 

New port: science/gabedit: Graphical user interface for several chemistry
software packages

 

17:54 yuri 

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

 

22:00 yuri 

New port: science/nwchem: High-performance computational chemistry sotware

 

04:31 yuri 

New port: science/qwalk: Quantum Monte Carlo package for quantum chemistry
computations

 

07:44 yuri 

New port: science/qmcpack: Many-body ab initio Quantum Monte Carlo code for
quantum chemstry

 

23:16 yuri 

New port: science/chrono: C++ library for multi-physics simulation

 

08:13 yuri 

Re-add port: science/xdrawchem: Two-dimensional molecule drawing program

 

19:09 brooks 

Remove broken and expired port which also depends on clang38 (on 10).

 

19:19 yuri 

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

 

21:47 yuri 

New port: science/quantum-espresso: Package for research in electronic
structure, simulation, optimization

 

04:41 yuri 

New port: science/openstructure: Molecular modelling and visualization
environment

 

04:45 yuri 

New port: science/coot: Crystallographic Object-Oriented Toolkit

 

01:27 yuri 

New port: science/clipper: Libraries for the organisation of crystallographic
data

 

00:39 yuri 

New port: science/libssm: C++ toolkit for superposition of macromolecules

 

00:24 yuri 

New port: science/libccp4: Protein X-ray crystallography toolkit

 

23:32 yuri 

New port: science/mmdb2: C++ toolkit for working with macromolecular coordinate
files

 

05:22 yuri 

New port: science/py-rmf: Library to support reading and writing of Rich
Molecular Format files

 

09:04 yuri 

New port: science/rmf: Library to support reading and writing of Rich Molecular
Format files

 

08:34 yuri 

New port: science/py-ScientificPython: Various Python modules for scientific
computing

 

21:18 sunpoet 

Add eccodes 2.8.0

ecCodes is a package developed by ECMWF which provides an application
programming interface and a set of tools for decoding and encoding messages in
the following formats:
- WMO FM-92 GRIB edition 1 and edition 2
- WMO FM-94 BUFR edition 3 and edition 4
- WMO GTS abbreviated header (only decoding).

A useful set of command line tools provide quick access to the messages. C,
Fortran 90 and Python interfaces provide access to the main ecCodes
functionality.

ecCodes is an evolution of GRIB-API. It is designed to provide the user with a
simple set of functions to access data from several formats with a key/value
approach.

For GRIB encoding and decoding, the GRIB-API functionality is provided fully in
ecCodes with only minor interface and behaviour changes. Interfaces for C,
Fortran 90 and Python are all maintained as in GRIB-API. However, the GRIB-API
Fortran 77 interface is no longer available.

WWW: https://software.ecmwf.int/wiki/display/ECC

 

20:05 sunpoet 

Add py-kinematics 0.0.7

kinematics is Python package to perform attitude kinematics. It is written
completely in Python and only requires numpy as a runtime dependency.

WWW: https://github.com/skulumani/kinematics

 

02:34 yuri 

New port: science/py-SimpleSpectral: Simplified scipy.signal.spectral module
with only pyFFTW support

 

21:25 yuri 

science/Makefile: Fix sortedness

 

21:24 yuri 

New port: science/py-PyQuante: Quantum chemistry in Python

 

02:42 yuri 

New port: science/dft_tools: Interface to DFT codes in TRIQS

 

23:24 yuri 

New port: science/triqs: Toolbox for Research on Interacting Quantum Systems

 

00:37 yuri 

New port: science/py-abipy: Library for analyzing the results produced by ABINIT

 

23:49 yuri 

New port: science/py-pymatgen: Python Materials Genomics is a robust materials
analysis code

 

22:28 yuri 

New port: science/py-spglib: Library for finding and handling crystal symmetries

 

17:42 yuri 

New port: science/spglib: C library for finding and handling crystal symmetries

 

05:52 yuri 

New port: science/atompaw: Tool for projector augmented wave functions for
molecular simulations

 

05:49 yuri 

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

I couldn't make MPI work, created a bug report.
Will add DOCS and EXAMPLES options later.

PR:		219025

 

00:40 rene 

Remove science/orthanc and dependent ports, it has expired

 

21:44 tcberner 

Update lang/ghc 8.4.2 and the hs-* ports the newer versions

* Update lang/ghc to 8.4.2
* Update the boostrap compiler to 8.4.1
* Update the many hs-* ports
* Bump the rest

Thanks a lot to arrowd for doing all the heavy lifting :)

PR:		227968
Exp-run by:	antoine
Submitted by:	arrowd
Differential Revision:	https://reviews.freebsd.org/D15005

 

00:16 yuri 

New port: science/py-MDAnalysisTests: Test code and the trajectory data for test
cases of MDAnalysis