biology/libsbml 5.21.2

- Update to 5.11.0

PR:		196377
Submitted by:	koue@chaosophia.net

Cleanup plist

- Update to 5.10.2

PR:		192198
Submitted by:	tkato432@yahoo.com

Convert the Python framework bits to USES=python.

Please use USES=python instead of USE_PYTHON.

  USE_PYTHON=yes becomes USES=python
  USE_PYTHON=2.7+ becomes USES=python:2.7+
  USE_PYTHON_BUILD=3.3 becomes USES=python:3.3,build
  ...

A new PYTHON_FEATURES variable was added, which enables certain features for a
port and replaces some knobs at the same time;

  PYTHON_FEATURES=distutils replaces USE_PYDISTUTILS
  PYTHON_FEATURES=autoplist replaces PYDISTUTILS_AUTOPLIST
  PYTHON_FEATURES=py3kplist replaces PYTHON_PY3K_PLIST_HACK
  PYTHON_FEATURES=noegginfo replaces PYDISTUTILS_NOEGGINFO
  PYTHON_FEATURES=concurrent replaces PYTHON_CONCURRENT_INSTALL
  PYTHON_FEATURES=pythonprefix replaces USE_PYTHON_PREFIX

Some knobs have been deprecated and are to be removed in the near future:

  PYTHON_MASTER_SITES - use MASTER_SITE_PYTHON instead
  PYTHON_PKGNAMESUFFIX - use PYTHON_PKGNAMEPREFIX instead
  PYDISTUTILS_INSTALLNOSINGLE - deprecated without replacement

Some knobs have been removed completely:

  PYTHON_MASTER_SITE_SUBDIR
  PYTHON_DISTNAME
  PYTHON_WRKSRC

Several variables specific to the Python framework are no longer passed to the
build environment to avoid polluting dependency builds.

  PYTHON_VERSION is not passed to .MAKEFLAGS anymore
  PYTHON_DEFAULT_VERSION,
  PYTHON_DEFAULT_PORTVERSION and
  PYTHONBASE are not passed to the make environment anymore

The conversion required a couple of ports to be updated to fit the changes and
new requirements. Those included "bsd.python.mk" directly or contained checks
in places, for which the USES framework would fail to provide correct values.

Python modules directly using the upstream Python package (such as py-tkinter
or py-sqlite3) were updated to avoid using the now unnecessary and remmoved
knobs from "bsd.python.mk".

Phabric:	D399
exp-run:	167368 192357
PR:		167368 192357
Reviewed by:	antoine, wg
Exp-run award:	antoine
With hat:	python@
Approved by:	portmgr

- Update to 5.10.0

- Update to 5.9.0 [1] - Stage support [1] - Add LICENSE [1] - Reset maintainer to port@

PR:		188554 [1]
Submitted by:	Muhammad Moinur Rahman <5u623l20@gmail.com> [1]

The FreeBSD x11@ and graphics team proudly presents a zeising, kwm production, with help from dumbbell, bdrewery:

NEW XORG ON FREEBSD 9-STABLE AND 10-STABLE

This update switches over to use the new xorg stack by default on FreeBSD 9
and 10 stable, on osversions where vt(9) is available.
It is still possible to use the old stack by specifying WITHOUT_NEW_XORG in
/etc/make.conf .
FreeBSD 8-STABLE and released versions of FreeBSD still use
the old version.
A package repository with binary packages for new xorg will
be available soon.

This patch also contains updates of libxcb and related ports, pixman, as well
as some drivers and utilities.

Bump portrevisions for xf86-* ports, as well as virtualbox-ose-additions due
to xserver version change.

Apart from these updates, the way shared libraries are handled has been
changed for all xorg ports, as well as libxml2 and freetype, which means
ltverhack is gone and as a consequence shared libraries have been bumped.
The plan is that this change will make library bumps less likely in the
future.
All affected ports have had their portrevisions bumped as a consequence of
this.

Fix some issues where WITH_NEW_XORG weren't detected properly on CURRENT.

Update instructions, hardware support, and more notes can be found on
https://wiki.freebsd.org/Graphics

Thanks to:	all testers, bdrewery and the FreeBSD x11@ team
exp-run by:	bdrewery [1]
PR:		ports/187602 [1]
Approved by:	portmgr (bdrewery), core (jhb)

Convert b* to USES=zip

Reduce over inclusion of bsd.port.mk

In preparation for making libtool generate libraries with a sane name, fix all LIB_DEPENDS in biology

- Fix build on head

- Switch to build with lang/ruby19 - No PORTREVISION bump, option is off by default

With hat:	portmgr

Add NO_STAGE all over the place in preparation for the staging support (cat: biology)

- adoption of optionsNG - trim historical header - tighten COMMENT

Approved by:	portmgr (miwi)

- Get Rid MD5 support

- Update to 4.2.0

- Update to 4.1.0

- Update to 4.0.1

- Mark MAKE_JOBS_UNSAFE

Reported by:	pointyhat

- Update to 4.0.0 - Update my mail address to FreeBSD

PR:		ports/137652
Submitted by:	wenheping@gmail.com(myself)
Approved by:	miwi(mentor)
Feature safe:	yes

- Switch SourceForge ports to the new File Release System: categories starting with B,C

LibSBML is an open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. It is not an application itself (though it does come with example programs), but rather a library you can embed in your own applications.

LibSBML understands all Levels and Versions of SBML, as well as the
SBML Layout proposal by Gauges, Rost, Sahle and Wegner. It's written in
ISO C and C++ but can be used from all the languages listed in the
right-hand box.

WWW: http://www.sbml.org/

PR:		ports/135022
Submitted by:	Wen Heping <wenheping at gmail.com>