platforms. The motivation for this project is that a simulator should
not only save the time of processors, but also the time of scientists.
Brian is easy to learn and use, highly flexible and easily extensible.
The Brian package itself and simulations using it are all written in
the Python programming language, which is an easy, concise and highly
developed language with many advanced features and development tools,
excellent documentation and a large community of users providing support
and extension packages.
WWW: http://www.briansimulator.org/
PR: ports/132155
Submitted by: Wen Heping <wenheping@gmail.com>
in Python (A real and free alternative to Matlab). PsychoPy combines
the graphical strengths of OpenGL with the easy Python syntax to give
psychophysics a free and simple stimulus presentation and control
package.
The goal is to provide, for the busy scientist (including me!), tools
to control timing and windowing and a simple set of pre-packaged
stimuli and methods. The code is platform independent, using Python
and C libraries that are widely available.
WWW: http://www.psychopy.org/
PR: ports/132156
Submitted by: wenheping at gmail.com
library and is implemented on top of HDF5. This module can read and
write files in both the new netCDF 4 and the old netCDF 3 format, and
can create files that are readable by HDF5 clients. The API modelled
after Scientific.IO.NetCDF, and should be familiar to users of that
module.
Many new features of netCDF 4 are implemented, such as multiple
unlimited dimensions, groups and zlib data compression. All the new
primitive data types (such as 64 bit and unsigned integer types) are
implemented, except variable-length strings (NC_STRING). User defined
data types (compound, vlen, enum etc.) are not supported.
WWW: http://code.google.com/p/netcdf4-python/
PR: ports/131866
Submitted by: wenheping at gmail.com
- Bump PORTREVISION for all ports depending on libglut since the shlib
version number went from 4 to 3.
- Bump PORTREVISION for all ports depending on libXaw as libXaw.so.8 isn't
installed anymore.
- Couple of ports fixes (mostly missing xorg components added to USE_XORG).
made for inspecting and modifying DICOM files in an easy "pythonic"
way. The modifications can be written again to a new file. As a pure
python package, it should run anywhere python runs without any other
requirements.
WWW: http://code.google.com/p/pydicom/
PR: ports/130492
Submitted by: Wen Heping <wenheping at gmail.com>
- Hide the regression-test under a MAINTAINER_MODE since skipped checks appear as failures
PR: 128447
Submitted by: "Pedro F. Giffuni" <giffunip at tutopia dot com> (maintainer)
- This is in order to prepare for the update (which currently fails some regression tests).
- No functional change.
PR: ports/127099
Submitted by: Pedro F. Giffuni <giffunip@tutopia.com> (maintainer)
agglomerative clustering. Its features include
* generating hierarchical clusters from distance matrices
* computing distance matrices from observation vectors
* computing statistics on clusters
* cutting linkages to generate flat clusters
* and visualizing clusters with dendrograms.
The interface is very similar to MATLAB's Statistics
Toolbox API to make code easier to port from MATLAB to
Python/Numpy. The core implementation of this library
is in C for efficiency.
WWW: http://code.google.com/p/scipy-cluster/
PR: ports/127515
Submitted by: Wen Heping <wenheping at gmail.com>
- Remove BROKEN for Metis option: it builds fine
- Remove BROKENness for 4.x, we don't check that anymore.
PR: 126696
Submitted by: Pedro Giffuni <pfgshield-freebsd at yahoo dot com>
Specifically, newer autoconf (> 2.13) has different semantic of the
configure target. In short, one should use --build=CONFIGURE_TARGET
instead of CONFIGURE_TARGET directly. Otherwise, you will get a warning
and the old semantic may be removed in later autoconf releases.
To workaround this issue, many ports hack the CONFIGURE_TARGET variable
so that it contains the ``--build='' prefix.
To solve this issue, under the fact that some ports still have
configure script generated by the old autoconf, we use runtime detection
in the do-configure target so that the proper argument can be used.
Changes to Mk/*:
- Add runtime detection magic in bsd.port.mk
- Remove CONFIGURE_TARGET hack in various bsd.*.mk
- USE_GNOME=gnometarget is now an no-op
Changes to individual ports, other than removing the CONFIGURE_TARGET hack:
= pkg-plist changed (due to the ugly CONFIGURE_TARGET prefix in * executables)
- comms/gnuradio
- science/abinit
- science/elmer-fem
- science/elmer-matc
- science/elmer-meshgen2d
- science/elmerfront
- science/elmerpost
= use x86_64 as ARCH
- devel/g-wrap
= other changes
- print/magicfilter
GNU_CONFIGURE -> HAS_CONFIGURE since it's not generated by autoconf
Total # of ports modified: 1,027
Total # of ports affected: ~7,000 (set GNU_CONFIGURE to yes)
PR: 126524 (obsoletes 52917)
Submitted by: rafan
Tested on: two pointyhat 7-amd64 exp runs (by pav)
Approved by: portmgr (pav)
- This port is unrelated with x11/silo so I suppose
NO_LATEST_LINK is relevant.
- While here, remove the unnecessary $LOCALBASE includes
in CPPFLAGS/LDFLAGS for the configure environment.
PR: ports/126614
Submitted by: "Pedro F. Giffuni" <giffunip@tutopia.com>
- It's off by default as it doesn't seem to be required by any port.
- No functional change.
PR: ports/125915
Submitted by: Pedro F. Giffuni <pfgshield-freebsd@yahoo.com>
Approved by: maintainer timeout (>2 Weeks)
- While here, rename the BROWSER option to SILEXB to avoid confusion.
- No version bump since no package has been built.
PR: ports/125846
Submitted by: Pedro F. Giffuni <giffunip@tutopia.com> (maintainer)
Reported by: pointyhat via erwin
A mesh and field I/O library and scientific database
Silo is a library for reading and writing a wide variety of scientific
data to binary, disk files. The files Silo produces and the data within
them can be easily shared and exchanged between wholly independently
developed applications running on disparate computing platforms.
Consequently, Silo facilitates the development of general purpose tools
for processing scientific data. One of the more popular tools that process
Silo data files is the VisIt visualization tool.
Silo supports gridless (point) meshes, structured meshes, unstructured-zoo
and unstructured-arbitrary-polyhedral meshes, block structured AMR meshes,
constructive solid geometry (CSG) meshes, piecewise-constant (e.g.
zone-centered) and piecewise-linear (e.g. node-centered) variables defined
on the node, edge, face or volume elements of meshes as well as the
decomposition of meshes into arbitrary subset hierarchies including
materials and mixing materials. In addition, Silo supports a wide variety
of other useful objects to address various scientific computing
application needs.Although the Silo library is a serial library, it has
some key features which enable it to be applied quite effectively and
scalably in parallel.
PR: ports/125725
Submitted by: Pedro F. Giffuni <giffunip at tutopia.com>
