25 Commits

Author SHA1 Message Date
Yuri Victorovich
3fad843b18 biology/py-bx-python: update 0.10.0 → 0.11.0
Reported by:	portscout
2024-02-12 15:07:35 -08:00
Ruslan Makhmatkhanov
3dae35c0aa biology/py-bx-python: update to 0.10.0
Update to 0.10.0. This release adds support for python 3.11

Changes: https://github.com/bxlab/bx-python/releases/tag/v0.10.0

PR:		276683
PR:     275494
Approved by:	yuri (maintainer)
2024-01-29 01:08:29 +03:00
Rene Ladan
3d9a815d9c 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>
2023-06-27 21:34:34 +02:00
Gerald Pfeifer
8d3e020ed0 *: Bump PORTREVISIONs for math/mpc update to 1.3.1 2023-04-23 09:09:58 +00:00
Dmitry Marakasov
77d68471ad */*: rename CHEESESHOP to PYPI in MASTER_SITES
PR:			267994
Differential revision:	D37518
Approved by:		bapt
2023-01-11 18:58:34 +03:00
Stefan Eßer
fb16dfecae 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)
2022-09-07 23:58:51 +02:00
Stefan Eßer
b7f05445c0 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)
2022-09-07 23:10:59 +02:00
Tobias C. Berner
37526bbd4e 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
2022-07-20 16:20:57 +02:00
Yuri Victorovich
7697bf311c biology/py-bx-python: Update 0.8.11-6 -> 0.8.13
Reported by:	portscout
2021-12-21 01:03:57 -08:00
Yuri Victorovich
640855add1 biology/py-bx-python: Update 0.8.10 -> 0.8.11-6 2021-08-17 12:10:45 -07:00
Mathieu Arnold
305f148f48
Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
Yuri Victorovich
a030f455ea biology/py-bx-python: Update 0.8.9 -> 0.8.10 2021-02-27 03:55:36 +00:00
Antoine Brodin
aa7a6c429e Drop python 2.7 support from a few ports
With hat:	portmgr
2020-12-28 23:02:12 +00:00
Yuri Victorovich
bfb73bae45 biology/py-bx-python: Update 0.8.8 -> 0.8.9
Reported by:	portscout
2020-06-26 04:17:11 +00:00
Yuri Victorovich
faad29a703 biology/py-bx-python: Update 0.8.6 -> 0.8.8
Reported by:	portscout
2020-02-15 20:08:30 +00:00
Yuri Victorovich
10cb022e32 biology/py-bx-python: Update 0.8.4 -> 0.8.6
Reported by:	portscout
2019-11-23 05:53:50 +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
Yuri Victorovich
f04a95e391 biology/py-bx-python: Update 0.8.2 -> 0.8.4
Reported by:	pirtscout
2019-06-19 08:08:31 +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
Yuri Victorovich
1ea7750d81 biology/py-bx-python: Update 0.8.1 -> 0.8.2
Reported by:	portscout
2018-08-26 09:50:41 +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
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
Yuri Victorovich
25ee2af46d biology/py-bx-python: Update to 0.8.1
Additional port changes:
* Changed to DISTVERSION.
* Added USE_PYTHON=cython.
* Added stripping.
* Updated maintainer e-mail.

Reported compiler warnings to the upstream.

Reported by:	portscout
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D14283
2018-02-10 00:09:56 +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
Martin Wilke
177c8291a7 bx-python is a python library and associated set of scripts to allow for rapid
implementation of genome scale analyses. The library contains a variety of
useful modules, but the particular strengths are:

Classes for reading and working with genome-scale multiple local alignments
(in MAF, AXT, and LAV formats). Generic data structure for indexing on disk
files that contain blocks of data associated with intervals on various
sequences (used, for example, to provide random access to individual
alignments in huge files; optomized for use over network filesystems).
Data structures for working with intervals on sequences:
 * "Binned bitsets" which act just like chromosome sized bit arrays,
   but lazily allocate regions and allow large blocks of all set or
   all unset bits to be stored compactly
 * "Intersecter" for performing fast intersection tests that preserve
   both query and target intervals and associated annotation

WWW: https://github.com/bxlab/bx-python

PR:		218757
Submitted by:	Yuri Victorovich <yuri@rawbw.com>
2017-05-06 06:07:03 +00:00