biology/py-biopython: Update to 1.83

PR:		277979
Reported by:	wen@
Approved by:	maintainer

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>

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

biology/py-biopython: Update to 1.81

PR:		269995
Reported by:	wen@
Approved by:	maintainer

biology/py-biopython: Update to 1.80

PR:		268106
Reported by:	wen@
Approved by:	maintainer

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.

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>

biology/py-biopython: Update to 1.79

PR:		259046
Reported by:	wen@
Approved by:	maintainer

Remove # $FreeBSD$ from Makefiles.

biology/py-biopython: Upgrade to 1.78

Eliminates Bio.Alphabet
Other minor improvements

PR:             ports/250324
Submitted by:   Mauricio Herrera Cuadra

biology/py-biopython: Set python requirement to 3.6+

New requirement for v1.77 overlooked during upgrade

biology/py-biopython: Upgrade to 1.77

Upstream support for python 3

PR:             ports/246763
Submitted by:   Mauricio Herrera Cuadra <mauricio@arareko.net>

Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330

- Update WWW

Approved by:	portmgr blanket

- Update to 1.73

PR:		234154
Submitted by:	wenheping2000@hotmail.com(myself)
Approved by:	maintainer

Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590

- Update to 1.72

PR:		230723
Submitted by:	wen@(myself)
Approved by:	maintainer

Use PY_FLAVOR for dependencies.

FLAVOR is the current port's flavor, it should not be used outside of
this scope.

Sponsored by:	Absolight

biology/py-biopython: Unbreak on python3; Add license

Two items prevented python3 compatibility:
* Breakage of ASCII codec due to non-ascii characters in README:
https://github.com/biopython/biopython/issues/1649
* The outdated dependency: print/py-reportlab1 instead of the modern version 3.X
print/py-reportlab

Port changes:
* USES=python:2.7 -> USES=python
* Add pre-configure that clears the README file
* Add LICENSE/LICENSE_FILE

Testing:
* Ran the tutorial testcase
http://biopython.org/DIST/docs/tutorial/Tutorial.html,
  particularly pdf writing through print/py-reportlab worked fine.

Asked the upstream to clarify the acceptable dependency version:
https://github.com/biopython/biopython/issues/1650

Approved by:	portmgr blanket (unbreak for python3; add license)

- Update to 1.71

Approved by:	mauricio@arareko.net(maintainer, via email)

Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).

Reduce dependency on the python2 metaport

PR:		225752
Submitted by:	Yasuhiro KIMURA

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

- update to 1.70

PR:		221443
Submitted by:	wen@(myself)
Approved by:	maintainer

- Update to 1.69

PR:		218903
Submitted by:	wen@
Approved by:	maintainer

- Update to 1.68

PR:		212874
Submitted by:	wen@(myself)
Approved by:	maintainer

- Update to 1.66

PR:		208825
Submitted by:	wen@
Approved by:	maintainer

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

With hat:	portmgr
Sponsored by:	Absolight

Update to 1.65.

PR:		201888
Submitted by:	brueffer
Approved by:	maintainer
Sponsored by:	Absolight

biology/py-biopython:
- Convert to options framework

Approved by:	portmgr blanket

- Convert ports from benchmarks/ and biology/ to new USES=python

Approved by:	portmgr (implicit)

Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)

- Stage
- Drop easy_install
- Use auto pkg-plist
- Delete pkg-plist

PR:		ports/188818
Submitted by:	Bartek Rutkowski <ports@robakdesign.com>
Approved by:	portmgr@ (blanket)

Update the default version of GCC used in the Ports Collection from
GCC 4.6.4 to GCC 4.7.3.  This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.

Part II, Bump PORTREVISIONs.

PR:		182136
Supported by:	Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by:	bdrewery (two -exp runs)

- Repocopy print/py-reportlab to print/py-reportlab1
  to preserve version 1.x and to update to 3.0

  print/py-reportlab:
    - Update print/py-reportlab to 3.0 based on print/py-reportlab2
    - Support STAGEDIR
    - Use PYDISTUTILS_AUTOPLIST
      * Remove pkg-plist, accordingly
    - Set CONFLICTS
    - Add PORTSCOUT
    - Replace tab with a single space after WWW: in pkg-descr

  print/py-reportlab1:
    - Support STAGEDIR
    - Add PKGNAMESUFFIX not to duplicate ports with the same name

Python cleanup:
- USE_PYTHON* = 2.X -> USE_PYTHON* = 2
- USE_PYTHON* = 2.X+ -> USE_PYTHON* = yes
Reviewed by:	python (mva, rm)
Approved by:	portmgr-lurkers (mat)

Update to libmpc version 1.0.1 which brings the following fixes:

 - Switched to automake 1.11.6, see CVE-2012-3386.
 - #14669: Fixed extraction of CC from gmp.h.
 - Fixed case of intermediate zero real or imaginary part in mpc_fma,
   found by hydra with GMP_CHECK_RANDOMIZE=1346362345.

This is on top of the following changes from version 1.0

 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
   invariant sections) for the documentation.
 - 100% of all lines are covered by tests
 - Renamed functions
   . mpc_mul_2exp to mpc_mul_2ui
   . mpc_div_2exp to mpc_div_2ui

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

- update to 1.60

while here:
- convert Makefile header into two-line format
- update COMMENT (indefinite article removed)
- change USE_PYTHON to just -2.7
- remove py-reportlab from BUILD_DEPENDS and kick PYTHON_SITELIBDIR from there
- tab -> space change in pkg-descr:WWW

PR:		171115
Submitted by:	wen
Approved by:	Mauricio Herrera Cuadra <mauricio at arareko dot net> (maintainer)

- Update to 1.59

PR:             ports/165582
Submitted by:   wen@ (myself)
Approved by:    Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer, via
email)

- remove maintainer tags from pkg-descr

Approved by:    portmgr
Approved by:    bapt (mentor)

- Update to 1.57

PR:             ports/156329
Submitted by:   Wen Heping (myself)
Approved by:    maintainer

- Move over to python2.5 or higher
- While here kick md5

- Update to 1.54

PR:             ports/148274
Submitted by:   Ju Pengfei <jupengfei@gmail.com>
Approved by:    maintainer
Feature safe:   yes

- Update to 1.53

PR:             ports/142221
Submitted by:   Wen Heping (myself)
Approved by:    maintainer

- Update to 138038

PR:             138038
Submitted by:   Wen Heping <wenheping@gmail.com>
Approved by:    maintainer

- Update to 1.48

PR:             127776
Submitted by:   Wen heping <wenheping@gmail.com>
Approved by:    maintainer

- Update to 1.47

PR:             125912
Submitted by:   Wen heping <wenheping@gmail.com>
Approved by:    maintainer timeout

- Update to 1.45

PR:             ports/125134
Submitted by:   Wen heping <wenheping@gmail.com>
Approved by:    Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer)

- Fix typos.

Reported by:    stas@

- Update to 1.43

PR:             111817
Submitted by:   "P.BandieraPaiva" <paiva@unifesp.br>
Approved by:    maintainer

- Update to 1.42

PR:             ports/104635
Submitted by:   Thomas Abthorpe <thomas@goodking.ca>
Approved by:    maintainer

Update to 1.41
Take MAINTAINER
Add SHA256

PR:             88792
Submitted by:   Mauricio Herrera Cuadra <mauricio@arareko.net>

Fix build on Python 2.4

Spotted by:     kris

With portmgr hat on, reset inactive maintainer.  These ports are now up
for adoption.

- Fix build on amd64 (crude hack to pass -fPIC to c++ compiles)

Reported by:    pointyhat via kris
Tested on:      arved's box

- Update to 1.30

PR:             ports/71400
Submitted by:   Stefan Walter <sw@gegenunendlich.de>
Approved by:    maintainer timeout (2 months)

BROKEN: Does not build

SIZEify (maintainer timeout)

Upgrade to 1.23.

Approved by:    maintainer timeout

Define USE_PERL5_BUILD, not erroneous USE_PERL.

Submitted by:   Oliver Eikemeier

Define USE_PERL to make Perl available for (mostly deprecated)
"perl -pi -e" construction.

Use the FIND and XARGS macros introduced in bsd.port.mk 1.391.

Cosmetic fix: use %%DOCSDIR%% macro.
No functionally changes.

Submitted by:   Oleg Karachevtsev <ok@etrust.ru>
A part of PR:   57992

Fix python version detection routines to cope with python 2.3's
boolean representation.

Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.

Use $PYNUMERIC in the dependencies.

- Update to version 1.00a4    

- Update the included (optional) Biopython-CORBA pacakge to version 0.3.0   - If
CORBA support is included, the default ORB has changed from omniORB to     ORBit
  - PORTREVISION bump    

- Update to version 1.00.a3   - Use pkg-req to check the installed version of
Python    

Update to version 1.00.a2    

Use $FILESDIR rather than hard-coded path.    

Update to 1.00.a1; change MAINTAINER to my new address.   Many changes to port,
including addition of CORBA functionality.    

math/numpy was renamed to math/py-numeric.    

Convert category biology to new layout.  

Update to 0.90.d03    

Don't break package building on Satoshi's cluster. Explicitly depend   on
python1.5:lang/python15.    

Upgrade to 0.90.d02.    

Add py-biopython, is a collection of Python packages and modules created   by
the Biopython Project, intended to provide the basis for building  
bioinformatics applications in the Python language.