biology/libsbml 5.21.2

biology/libsbml: Update to 5.21.2

Changes:	https://github.com/sbmlteam/libsbml/releases

biology/libsbml: Remove unnecessary substitution

- Cosmetic change

biology/*: Add CPE info

biology/libsbml: Update to 5.21.0

Changes:	https://github.com/sbmlteam/libsbml/releases

biology/*: remove useless USES=pathfix

libxml2: chase libxml soversion bump

biology/libsbml: Update to 5.20.5

Changes:	https://github.com/sbmlteam/libsbml/releases

textproc/xerces-c3: Update to 3.3.0

- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://issues.apache.org/jira/secure/ReleaseNote.jspa?projectId=10510&version=12355023

biology/libsbml: Update to 5.20.4

Changes:	https://github.com/sbmlteam/libsbml/releases

biology/libsbml: Fix build with libxml2 2.12.0+

PR:		279752
Obtained from:	https://github.com/sbmlteam/libsbml/commit/a3e217851f18d3c5e8e2b0082fb98176738491e8

biology/libsbml: Update to 5.20.2

Changes:	https://github.com/sbmlteam/libsbml/releases

all: remove explicit versions in USES=python for "3.x+"

The logic in USES=python will automatically convert this to 3.8+ by
itself.

Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.

finance/quickfix: mark BROKEN with PYTHON

libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++ -DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable -Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi -Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings -Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x -MT _quickfix_la-QuickfixPython.lo -MD -MP -MF .deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp  -fPIC -DPIC -o .libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean '-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
          ^~~~~~~~~~
1 warning and 1 error generated.

Reviewed by:	portmgr, vishwin, yuri
Differential Revision:	<https://reviews.freebsd.org/D40568>

biology/libsbml: Update to 5.20.0

- Update MASTER_SITES
- Update WWW
- Sort PLIST

Changes:	https://github.com/sbmlteam/libsbml/releases

biology/libsbml: Update WWW and clean up pkg-descr

biology/libsbml: unbreak build after 18c6e1827669 (+)

Changes in framework need adjustment for declared options.

*_USE=ruby now became as *_USES=ruby

Approved by:	portmgr blanket

Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)

Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.

This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.

There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.

The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.

Approved by:		portmgr (tcberner)

biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
  *  Johann Visagie <johann@egenetics.com>
  *  Johann Visagie <wjv@FreeBSD.org>
  *  Mauricio Herrera Cuadra <mauricio@arareko.net>
  *  Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
  *  Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@niid.go.jp>
  *  Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Razi Khaja <razi@genet.sickkids.on.ca>
  *  Reed A. Cartwright <cartwright@asu.edu>
  *  Ryo MIYAMOTO
  *  Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
  *  Sangwoo Shim <sangwoos@gmail.com>
  *  Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Tassilo Philipp <tphilipp@potion-studios.com>
  *  Tony Maher
  *  Tony Maher <tonym@biolateral.com.au>
  *  Wen Heping <wen@FreeBSD.org>
  *  Wen Heping <wenheping@gmail.com>
  *  Yonatan <onatan@gmail.com>
  *  Yuri Victorovich <yuri@rawbw.com>
  *  ballen
  *  barnhart@genetics.wustl.edu
  *  camson@bilateral.com.au
  *  chuynh@biolateral.com.au
  *  dbader@eece.unm.edu
  *  frankch@waru.life.nthu.edu.tw
  *  h2
  *  lentferj
  *  maho@FreeBSD.org
  *  mzaki@biol.s.u-tokyo.ac.jp
  *  tonym
  *  wen@FreeBSD.org

With hat:	portmgr

textproc/libxml2: bump all LIB_DEPENDS consumers

This is a separate commit to facilitate easier cherry-picking for
quarterly.

PR: 262853, 262940, 262877, 263126
Approved by: fluffy (mentor)

textproc/libxml2: bump all dependencies

This should make sure that all dependent ports will pick
up the new version commited with a13ec21cd733f67a9fc0dc00ab45268bdc236246

biology/libsbml: Update WWW

biology/libsbml: Fix build with Python 3.10

Obtained from:	https://github.com/sbmlteam/libsbml/commit/4f01a15fde1d8afa9eaffb4c13dfc83a3404f183 (based on)

biology/libsbml: limit supported python versions

File "/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.19.0/src/bindings/python/doc-converter/rewrite_pydoc.py", line 121, in <module>
    from formatter import NullWriter, AbstractFormatter
ModuleNotFoundError: No module named 'formatter'

Approved by:	portmgr blanket

biology/libsbml: Rename LIBXML option to LIBXML2

Remove # $FreeBSD$ from Makefiles.

Set CMAKE options explicitly

Add EXPAT, LIBXML and XERCES options

It allows choosing XML parser library.

Update to 5.19.0

Changes:	https://github.com/sbmlteam/libsbml/releases

Convert REINPLACE_CMD to patch file

Update PYTHON option to use Python 3

Move devel/swig30 to devel/swig and update to 4.0.1

- Do not silence installation message
- Update dependent ports:
  - Fix build with swig 4.0.1
  - Update *_DEPENDS
  - Remove BINARY_ALIAS

Changes:	http://www.swig.org/news.php
PR:		246613
Exp-run by:	antoine

Clean up Makefile

Use USES=pathfix

- Add USES=gnome
- Use = instead of += for PLIST_SUB
- Use CMAKE_BOOL
- Cosmetic change
- Take maintainership

- Update to 5.18.0

Change cmake default behaviour to outsource.

Ports that build out of source now simply can use "USES=cmake"
instead of "USES=cmake:outsource". Ports that fail to build
out of source now need to specify "USES=cmake:insource".

I tried to only set insource where explictely needed.

PR:		232038
Exp-run by:	antoine

biology/libsbml: Fix build with Clang 6

In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/Model.cpp:41:
In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBMLDocument.h:298:
In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBMLTransforms.h:48:
In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/FunctionDefinition.h:129:
In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBO.h:207:
/usr/include/c++/v1/map:629:15: error: object of type 'std::__1::pair<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>' cannot be assigned because its copy assignment operator is implicitly deleted
        {__nc = __v.__cc; return *this;}
              ^

http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/libsbml-5.17.0.log

Mark as broken with clang6 after r473289.

- Update to 5.17.0

- Update to 5.16.0

Switch from swig 2.0 to swig 3.0

Convert Python ports to FLAVORS.

Ports using USE_PYTHON=distutils are now flavored.  They will
  automatically get flavors (py27, py34, py35, py36) depending on what
  versions they support.

  There is also a USE_PYTHON=flavors for ports that do not use distutils
  but need FLAVORS to be set.  A USE_PYTHON=noflavors can be set if
  using distutils but flavors are not wanted.

  A new USE_PYTHON=optsuffix that will add PYTHON_PKGNAMESUFFIX has been
  added to cope with Python ports that did not have the Python
  PKGNAMEPREFIX but are flavored.

  USES=python now also exports a PY_FLAVOR variable that contains the
  current python flavor.  It can be used in dependency lines when the
  port itself is not python flavored.  For example, deskutils/calibre.

  By default, all the flavors are generated.  To only generate flavors
  for the versions in PYTHON2_DEFAULT and PYTHON3_DEFAULT, define
  BUILD_DEFAULT_PYTHON_FLAVORS in your make.conf.

  In all the ports with Python dependencies, the *_DEPENDS entries MUST
  end with the flavor so that the framework knows which to build/use.
  This is done by appending '@${PY_FLAVOR}' after the origin (or
  @${FLAVOR} if in a Python module with Python flavors, as the content
  will be the same).  For example:

    RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR}

PR:		223071
Reviewed by:	portmgr, python
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D12464

- Update to 5.15.0

Cleanup no longer needed CHMOD usage after r424898.

PR:		213743
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight

Upgrade from 5.12.0 to 5.13.0. Release-announcement available here:

https://groups.google.com/forum/#!topic/sbml-discuss/OEq_49c_X78

Notified by:	portscout

Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight

- Update to 5.12.0

- Add LICENSE_FILE - Switch to options helpers

Switch to USES=iconv:build.

The port does not use iconv on its own, the only dependency comes via
libxml2, which has one header that includes iconv.h.

- Update to 5.11.4

- Convert USE_PYTHON -> USES leftovers missed in the previous commits

Spotted by:	antoine
With hat:	python