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* The outdated dependency: print/py-reportlab1 instead of the modern version 3.X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.