Commit Graph

69 Commits

Author SHA1 Message Date
Jason W. Bacon 92ede5b056 biology/py-biopython: Upgrade to 1.78
Eliminates Bio.Alphabet
Other minor improvements

PR:             ports/250324
Submitted by:   Mauricio Herrera Cuadra
2020-10-16 19:12:43 +00:00
Jason W. Bacon 3fadea798f biology/py-biopython: Set python requirement to 3.6+
New requirement for v1.77 overlooked during upgrade
2020-06-13 13:42:12 +00:00
Jason W. Bacon 176e391e4b biology/py-biopython: Upgrade to 1.77
Upstream support for python 3

PR:             ports/246763
Submitted by:   Mauricio Herrera Cuadra <mauricio@arareko.net>
2020-05-29 02:03:29 +00:00
Gerald Pfeifer ea8c8ec7da 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
2019-07-26 20:46:53 +00:00
Dmitry Marakasov 8687848456 - Update WWW
Approved by:	portmgr blanket
2019-07-08 09:32:08 +00:00
Wen Heping 1534498735 - Update to 1.73
PR:		234154
Submitted by:	wenheping2000@hotmail.com(myself)
Approved by:	maintainer
2018-12-22 04:54:51 +00:00
Gerald Pfeifer a9f015d155 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
2018-12-12 01:35:33 +00:00
Wen Heping 87329c588f - Update to 1.72
PR:		230723
Submitted by:	wen@(myself)
Approved by:	maintainer
2018-08-24 00:12:38 +00:00
Mathieu Arnold 4376dbbb58 Use PY_FLAVOR for dependencies.
FLAVOR is the current port's flavor, it should not be used outside of
this scope.

Sponsored by:	Absolight
2018-06-20 17:05:41 +00:00
Yuri Victorovich 0f34b9361d 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)
2018-05-13 22:30:00 +00:00
Wen Heping 44601e138d - Update to 1.71
Approved by:	mauricio@arareko.net(maintainer, via email)
2018-04-09 06:26:18 +00:00
Gerald Pfeifer c2a92a1aea Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).
2018-03-10 17:46:04 +00:00
Antoine Brodin f7455240e3 Reduce dependency on the python2 metaport
PR:		225752
Submitted by:	Yasuhiro KIMURA
2018-02-19 11:10:43 +00:00
Mathieu Arnold 551be3c723 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
2017-11-30 15:50:30 +00:00
Wen Heping 4da10c5d1d - update to 1.70
PR:		221443
Submitted by:	wen@(myself)
Approved by:	maintainer
2017-08-18 12:57:06 +00:00
Wen Heping 41624b9113 - Update to 1.69
PR:		218903
Submitted by:	wen@
Approved by:	maintainer
2017-05-03 12:39:28 +00:00
Wen Heping ab5636ea47 - Update to 1.68
PR:		212874
Submitted by:	wen@(myself)
Approved by:	maintainer
2016-09-23 01:54:45 +00:00
Wen Heping 4c31a1cd8d - Update to 1.66
PR:		208825
Submitted by:	wen@
Approved by:	maintainer
2016-04-17 03:55:01 +00:00
Mathieu Arnold 7f4572eae4 Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
With hat:	portmgr
Sponsored by:	Absolight
2016-04-01 13:29:15 +00:00
Mathieu Arnold 53cb289f4a Update to 1.65.
PR:		201888
Submitted by:	brueffer
Approved by:	maintainer
Sponsored by:	Absolight
2015-08-05 10:32:31 +00:00
Max Brazhnikov e3e9f1f2a1 biology/py-biopython:
- Convert to options framework

Approved by:	portmgr blanket
2015-01-19 20:21:12 +00:00
Marcus von Appen 57f1865da8 - Convert ports from benchmarks/ and biology/ to new USES=python
Approved by:	portmgr (implicit)
2014-10-19 07:38:11 +00:00
Gerald Pfeifer 15945f8122 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)
2014-09-10 20:50:31 +00:00
Steve Wills 4404ec6009 - 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)
2014-04-27 01:59:47 +00:00
Gerald Pfeifer 1cd277bdce 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)
2014-03-10 20:55:20 +00:00
TAKATSU Tomonari 0cbe65e47c - 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
    - Set CONFLICTS
    - Use PYDISTUTILS_AUTOPLIST
      * Remove pkg-plist, accordingly
    - Make use of PORTDOCS
    - Set OPTIONS_DEFINE explicitly
    - Fix include statement
    - Make docs unconditional to stage
    - Replace tab with a single space after WWW: in pkg-descr

  print/py-reportlab2:
    - Update CONFLICTS
    - Set PORTSCOUT

  dependent ports:
    - Switch dependency from print/py-reportlab to print/py-reportlab1
      * biology/py-biopython
      * deskutils/gourmet
      * deskutils/griffith
      * games/pythonsudoku
      * misc/pdfmap
      * print/py-trml2pdf
      * www/py-satchmo

PR:		ports/186970
Submitted by:	tota (myself)
Approved by:	Muhammad Moinur Rahman (maintainer)
2014-02-25 12:44:10 +00:00
Rene Ladan 50f8eaece1 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)
2014-01-13 21:00:02 +00:00
Gerald Pfeifer 3be3e90f93 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
 - 0^0, which returned (NaN,NaN) previously, now returns (1,+0).
 - Removed compatibility with K&R compilers, which was untestable due
   to lack of such compilers.
 - New functions
   . mpc_log10
   . mpc_mul_2si, mpc_div_2si
 - Speed-ups
   . mpc_fma
 - Bug fixes
   . mpc_div and mpc_norm now return a value indicating the effective
     rounding direction, as the other functions.
   . mpc_mul, mpc_sqr and mpc_norm now return correct results even if
     there are over- or underflows during the computation.
   . mpc_asin, mpc_proj, mpc_sqr: Wrong result when input variable has
     infinite part and equals output variable is corrected.
   . mpc_fr_sub: Wrong return value for imaginary part is corrected.

Convert to the new LIB_DEPENDS standard and remove hard-coded
.so versions from a couple of dependent ports.

Bump PORTREVISIONS of all dependent ports.

PR:		183141
Approved by:	portmgr (bdrewery)
2013-10-26 00:52:33 +00:00
Baptiste Daroussin 7055ff02f1 Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
Ruslan Makhmatkhanov 9f67b5e7f1 - 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)
2012-09-25 08:06:42 +00:00
Wen Heping c01d2361ab - Update to 1.59
PR:		ports/165582
Submitted by:	wen@ (myself)
Approved by:	Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer, via email)
2012-03-06 06:40:50 +00:00
Eitan Adler 7e3b32fff8 - remove maintainer tags from pkg-descr
Approved by:	portmgr
Approved by:	bapt (mentor)
2011-10-22 23:50:23 +00:00
Wen Heping 5d036cfb8c - Update to 1.57
PR:		ports/156329
Submitted by:	Wen Heping (myself)
Approved by:	maintainer
2011-05-24 09:06:29 +00:00
Martin Wilke 9992960752 - Move over to python2.5 or higher
- While here kick md5
2011-02-24 23:25:54 +00:00
Wen Heping 08ad71435d - Update to 1.54
PR:		ports/148274
Submitted by:	Ju Pengfei <jupengfei@gmail.com>
Approved by:	maintainer
Feature safe:	yes
2010-07-02 02:57:19 +00:00
Wen Heping 43d8e24a17 - Update to 1.53
PR:		ports/142221
Submitted by:	Wen Heping (myself)
Approved by:	maintainer
2010-01-06 00:29:25 +00:00
Martin Wilke 2f12ae5444 - Update to 138038
PR:		138038
Submitted by:	Wen Heping <wenheping@gmail.com>
Approved by:	maintainer
2009-09-04 20:41:25 +00:00
Martin Wilke 41618ec344 - Update to 1.48
PR:		127776
Submitted by:	Wen heping <wenheping@gmail.com>
Approved by:	maintainer
2008-10-11 15:26:33 +00:00
Martin Wilke e3fe8b1b7e - Update to 1.47
PR:		125912
Submitted by:	Wen heping <wenheping@gmail.com>
Approved by:	maintainer timeout
2008-08-11 22:06:31 +00:00
Beech Rintoul 63a004d6f2 - Update to 1.45
PR:		ports/125134
Submitted by:	Wen heping <wenheping@gmail.com>
Approved by:	Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer)
2008-07-04 02:53:15 +00:00
Martin Wilke b7bc246771 - Fix typos.
Reported by:    stas@
2007-05-31 03:49:14 +00:00
Martin Wilke 884af2b045 - Update to 1.43
PR:		111817
Submitted by:	"P.BandieraPaiva" <paiva@unifesp.br>
Approved by:	maintainer
2007-05-30 06:57:20 +00:00
Martin Wilke 58c1e960b2 - Update to 1.42
PR:		ports/104635
Submitted by:	Thomas Abthorpe <thomas@goodking.ca>
Approved by:	maintainer
2006-10-31 13:25:21 +00:00
Marcus Alves Grando 23d07b2cdb Update to 1.41
Take MAINTAINER
Add SHA256

PR:		88792
Submitted by:	Mauricio Herrera Cuadra <mauricio@arareko.net>
2005-11-11 01:15:35 +00:00
Hye-Shik Chang 5a37bd265f Fix build on Python 2.4
Spotted by:	kris
2004-12-02 05:51:25 +00:00
Mark Linimon e22ed3d655 With portmgr hat on, reset inactive maintainer. These ports are now up
for adoption.
2004-11-20 08:09:49 +00:00
Pav Lucistnik 6743d66769 - Fix build on amd64 (crude hack to pass -fPIC to c++ compiles)
Reported by:	pointyhat via kris
Tested on:	arved's box
2004-11-06 23:12:14 +00:00
Pav Lucistnik 7d98b3c8b4 - Update to 1.30
PR:		ports/71400
Submitted by:	Stefan Walter <sw@gegenunendlich.de>
Approved by:	maintainer timeout (2 months)
2004-10-27 20:39:17 +00:00
Kris Kennaway 6212ab4dc6 BROKEN: Does not build 2004-07-02 08:20:02 +00:00
Trevor Johnson 8232e82f85 SIZEify (maintainer timeout) 2004-03-31 03:12:58 +00:00