Commit Graph

368 Commits

Author SHA1 Message Date
Yuri Victorovich
402a69a5d4 New port: science/py-rmf: Library to support reading and writing of Rich Molecular Format files 2018-07-01 05:22:27 +00:00
Yuri Victorovich
c9d2c4b709 New port: science/rmf: Library to support reading and writing of Rich Molecular Format files 2018-06-29 09:04:22 +00:00
Yuri Victorovich
9674ab63a6 New port: science/py-ScientificPython: Various Python modules for scientific computing 2018-06-29 08:34:18 +00:00
Sunpoet Po-Chuan Hsieh
a61692dd4c 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
2018-06-28 21:18:03 +00:00
Sunpoet Po-Chuan Hsieh
cdc3df02d1 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
2018-06-24 20:05:42 +00:00
Yuri Victorovich
9502930cb1 New port: science/py-SimpleSpectral: Simplified scipy.signal.spectral module with only pyFFTW support 2018-06-18 02:34:02 +00:00
Yuri Victorovich
d5d1488a3d science/Makefile: Fix sortedness 2018-06-17 21:25:26 +00:00
Yuri Victorovich
075dd77083 New port: science/py-PyQuante: Quantum chemistry in Python 2018-06-17 21:24:03 +00:00
Yuri Victorovich
12356f2652 New port: science/dft_tools: Interface to DFT codes in TRIQS 2018-06-17 02:42:52 +00:00
Yuri Victorovich
933be6c634 New port: science/triqs: Toolbox for Research on Interacting Quantum Systems 2018-06-16 23:24:58 +00:00
Yuri Victorovich
53cdab2eb4 New port: science/py-abipy: Library for analyzing the results produced by ABINIT 2018-06-16 00:37:35 +00:00
Yuri Victorovich
e80a83df0a New port: science/py-pymatgen: Python Materials Genomics is a robust materials analysis code 2018-06-15 23:49:36 +00:00
Yuri Victorovich
f823ddc829 New port: science/py-spglib: Library for finding and handling crystal symmetries 2018-06-15 22:28:20 +00:00
Yuri Victorovich
eda32fd6c3 New port: science/spglib: C library for finding and handling crystal symmetries 2018-06-15 17:42:24 +00:00
Yuri Victorovich
fe44dbecc9 New port: science/atompaw: Tool for projector augmented wave functions for molecular simulations 2018-06-14 05:52:57 +00:00
Yuri Victorovich
2e455aebc4 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
2018-06-14 05:49:39 +00:00
Rene Ladan
4d67bc624a Remove science/orthanc and dependent ports, it has expired 2018-06-07 00:40:35 +00:00
Tobias C. Berner
fff1aa535b 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
2018-05-25 21:44:12 +00:00
Yuri Victorovich
d9244ccb72 New port: science/py-MDAnalysisTests: Test code and the trajectory data for test cases of MDAnalysis 2018-05-14 00:16:52 +00:00
Yuri Victorovich
31bf24f627 New port: science/py-MDAnalysis: Python library to analyze molecular dynamics trajectories 2018-05-14 00:15:31 +00:00
Yuri Victorovich
a0d8c948c6 New port: science/py-gsd: GSD (General Simulation Data) file format for Python 2018-05-13 20:32:41 +00:00
Yuri Victorovich
653f628147 New port: science/py-mmtf-python: MMTF (Macromolecular Transmission Format) Python API 2018-05-13 17:14:13 +00:00
Kurt Jaeger
4d96ff4654 New port: science/mcxtrace-comps
McXtrace - Monte Carlo ray tracing simulations of X-ray experiments.

McXtrace is a tool for simulating X-ray instrumentation and experiments
using a ray-tracing formalism. Currently the main use of McXtrace
is in the field of synchrotron beamline instrumentation design, but
various other uses have been found, for instance for designing X-ray
telescopes or for laboratory sources.

This port contains the McXtrace component library.

WWW: http://www.mcxtrace.org

PR:		206506
Submitted by:	Erik B. Knudsen <erkn@fysik.dtu.dk>
2018-05-07 19:36:58 +00:00
Adriaan de Groot
35fbbebe34 New ports science/dlib-cpp and science/py-dlib (Python bindings for the former)
Changed from the reviewed form:
 - fixed typo's
 - added support for suffixed Boost::Python
 - removed commented-out lines from patch

Submitted by:	arrowsvc (6yearold@gmail.com, new maintainer)
Reviewed by:	tcberner, adridg
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D14798
2018-04-26 20:39:16 +00:00
Yuri Victorovich
74524d88c7 New port: science/antioch: C++ Chemical Kinetics, Thermodynaimics, and Transport Library 2018-04-18 06:51:47 +00:00
Yuri Victorovich
07b50b05da New port: science/metaphysicl: Metaprogramming, operator-overloaded classes for numerical simulations 2018-04-18 04:59:15 +00:00
Jason W. Bacon
1dfb1d6004 fsom: Tiny C library for managing SOM (Self-Organizing Maps) neural networks
Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15103
2018-04-16 18:15:30 +00:00
Tobias C. Berner
d5f25d5b15 New port: science/step, science/kalzium
This is the current version of KDE Applications <foo>.
Note that users of KDE SC4 should stick with <foo>-kde4.
2018-04-09 18:32:24 +00:00
Sunpoet Po-Chuan Hsieh
70b56fdc2c Add rubygem-rgeo-shapefile 1.0.0
RGeo::Shapefile is an optional module for RGeo for reading geospatial data from
ESRI shapefiles.

WWW: https://github.com/rgeo/rgeo-shapefile
2018-04-07 16:33:40 +00:00
Sunpoet Po-Chuan Hsieh
8019a81868 Add rubygem-rgeo-proj4 1.0.0
RGeo::Proj4 contains proj.4 extensions to the RGeo gem.

WWW: https://github.com/rgeo/rgeo-proj4
2018-04-07 16:33:14 +00:00
Sunpoet Po-Chuan Hsieh
f0e475bd6f Add rubygem-rgeo-geojson 2.0.0
RGeo::GeoJSON is an extension to the RGeo gem that provides GeoJSON encoding and
decoding.

WWW: https://github.com/rgeo/rgeo-geojson
2018-04-07 16:32:45 +00:00
Sunpoet Po-Chuan Hsieh
bb0fe16f32 Add rubygem-rgeo 1.0.0
RGeo is a geospatial data library for Ruby.

RGeo is a key component for writing location-aware applications in the Ruby
programming language. At its core is an implementation of the industry standard
OGC Simple Features Specification, which provides data representations of
geometric objects such as points, lines, and polygons, along with a set of
geometric analysis operations. This makes it ideal for modeling geolocation
data. It also supports a suite of optional add-on modules that provide various
geolocation-related services.

Use the core rgeo gem to:
- Represent spatial and geolocation data objects such as points, lines, and
  polygons in your Ruby application.
- Perform standard spatial analysis operations such as finding intersections,
  creating buffers, and computing lengths and areas.
- Correctly handle spherical geometry, and compute geographic projections for
  map display and data analysis.
- Read and write location data in the WKT and WKB representations used by
  spatial databases.

WWW: https://github.com/rgeo/rgeo
2018-04-07 16:32:18 +00:00
Max Brazhnikov
53f46b075b Add new port science/py-openpiv:
Python module for Particle Image Velocimetry (PIV) image analysis
and post-processing.

WWW: http://www.openpiv.net/
2018-04-02 08:43:54 +00:00
Yuri Victorovich
2ba5005caa New port: science/py-quantities: Support for physical quantities with units, based on numpy 2018-03-29 20:37:39 +00:00
Yuri Victorovich
89e7355c19 New port: science/libcint: General GTO integrals for quantum chemistry 2018-03-26 23:13:45 +00:00
Yuri Victorovich
f28f234b25 New port: science/py-OpenFermion: Electronic structure package for quantum computers 2018-03-26 09:39:42 +00:00
Yuri Victorovich
2c432ea8ff science/siril: Move to astro/siril; Mark broken on i386; Add OPENMP category 2018-03-26 09:04:18 +00:00
Yuri Victorovich
fcedcd5e27 New port: science/py-pyosf: Python lib for synching with OpenScienceFramework projects 2018-03-24 06:38:46 +00:00
Yuri Victorovich
a067889d03 New port: science/rdkit: Collection of cheminformatics and machine-learning software 2018-03-22 08:23:57 +00:00
Yuri Victorovich
90e129ca89 science/veusz: Unbroke; Renamed to science/py-veusz.
It was breaking because of wrong python shebang.

This port is a python port, renamed per section 6.17.

Unbroke:
* Added USES=shebangfix and SHEBANG_FILES
* Added stripping (post-install)

Additional changes:
* Added USE_QT4
* Added USE_PYTHON=concurrent

Approved by:	tcberner (mentor, implicit)
Approved by:	portmgr (port compliance, infrastructure)
2018-03-01 11:29:58 +00:00
Tobias C. Berner
a4a7daf069 Give the KDE SC4 applications ports a -kde4 suffix
In order to make room for the up-to-date version of the KDE Desktop and its
applications move the KDE Application ports based on Qt4.

PR:		225992
Exp-run by:	antoine
Reviewed by:	rakuco, adridg
Differential Revision:	https://reviews.freebsd.org/D14413
2018-02-22 19:03:17 +00:00
Yuri Victorovich
b172dcc89b New port: science/siril: Astronomical image processing software
See details here: https://free-astro.org/index.php/Siril

Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D14190
2018-02-04 19:00:27 +00:00
Yuri Victorovich
a03c50d808 Re-added port: science/py-pymol: OpenGL based molecular visualization system (existed 2002/08/13-2014/09/01, deleted in r366862)
Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D12902
2017-12-19 19:49:17 +00:00
Yuri Victorovich
e51eda6b05 New port: science/MOOSE-neural-simulator: Multiphysics Object Oriented Simulation Environment
Multiphysics Object Oriented Simulation Environment

MOOSE-neural-simulator allows to simulate
- chemical and biochemical reactions
- networks of neurons
- neural networks

This project is commonly referred to as MOOSE, in the capitalized form.
There is another science project called MOOSE, completely unrelated to this one, which will also be ported.
MOOSE-neural-simulator is a candidate for the future 'chemistry' category in case it will be approved.

Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D13539
2017-12-19 16:04:34 +00:00
Yuri Victorovich
97f90d255e New port: science/PETSc: Suite of data structures and routines from Argonne National Laboratory
Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D13527
2017-12-19 00:03:01 +00:00
David Naylor
e007fca186 science/R-cran-fastICA: FastICA Algorithms to Perform ICA and Projection Pursuit
Generated by:	portcran (0.1.7)
2017-12-18 12:31:46 +00:00
Yuri Victorovich
9e8cc175a0 New port: science/mcxtrace: Monte Carlo X-ray tracing package
PR:		206505
Submitted by:	Erik B Knudsen <erkn@fysik.dtu.dk>
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13216
2017-12-05 19:15:49 +00:00
Rodrigo Osorio
1b363765bd Add new port science/aircraft-datcom
aircraft-datcom is a modified version of USAF Aircraft DATCOM
The goal of the project is to update the code and make it more usable by the end users

PR:		207928
Submitted by:	Michael Danilov <mike.d.ft402@gmail.com>
2017-12-03 21:26:18 +00:00
Yuri Victorovich
0026e03cbb New port: science/ALPSCore: Generic algorithms and utilities for condensed matter physics
PR:		223850
Submitted by:	Michael Danilov <mike.d.ft402@gmail.com>
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13237
2017-12-03 19:29:13 +00:00
Yuri Victorovich
4fb7bfbe5a New port: science/chemps2: Spin-adapted implementation of DMRG for ab initio quantum chemistry
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13100
2017-11-23 05:58:51 +00:00