14:52 Yuri Victorovich (yuri) 

biology/py-pysam: update 0.22.0 → 0.22.1

Reported by:	portscout

    c76da4a

11:51 Ruslan Makhmatkhanov (rm) 

biology/py-pysam: relax python version requirement

According to [1] pysam support Python 3.11 since version 0.21.0

[1] https://github.com/pysam-developers/pysam/releases/tag/v0.21.0

PR:		275494
Approved by:	portmgr (blanket)

    aefceb7

10:09 Yuri Victorovich (yuri) 

biology/py-pysam: update 0.21.0 → 0.22.0

Reported by:	portscout

    45df857

19:34 Rene Ladan (rene) 

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>

    3d9a815

21:46 Yuri Victorovich (yuri) 

biology/py-pysam: Update 0.20.0 → 0.21.0

Reported by:	portscout

    67a7336

09:39 Robert Clausecker (fuz) 

biology/py-pysam: unbundle biology/htslib

This fixes the build on armv7 by picking up our custom fixed libhts
over the bundled unfixed version.  The CFLAGS workaround is now no
longer required either.

Approved by:	yuri (maintainer)
Differential Revision: https://reviews.freebsd.org/D40251

    41cce74

15:58 Dmitry Marakasov (amdmi3) 

*/*: rename CHEESESHOP to PYPI in MASTER_SITES

PR:			267994
Differential revision:	D37518
Approved by:		bapt

    77d6847

17:36 Yuri Victorovich (yuri) 

biology/py-pysam: Update 0.19.1 -> 0.20.0

Reported by:	portscout

    db3783a

21:10 Stefan Eßer (se) 

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)

    b7f0544

15:51 Yuri Victorovich (yuri) 

biology/py-pysam: Remove BROKEN lines

    978fbbf

15:51 Yuri Victorovich (yuri) 

biology/py-pysam: Fix on aarch64, riscv6 by backporting of symbols failure fix

    8e9198d

02:09 Yuri Victorovich (yuri) 

biology/py-pysam: Correct BROKEN line; Add comment

    09d9d82

02:45 Yuri Victorovich (yuri) 

biology/py-pysam: Broken on arm64 and riscv64

Reported by:	fallout

    2f374bc

00:23 Yuri Victorovich (yuri) 

biology/py-pysam: Update 0.19.0 -> 0.19.1

Reported by:	portscout

    e8c0b45

17:38 Yuri Victorovich (yuri) 

biology/py-pysam: Update 0.18.0 -> 0.19.0

Reported by:	portscout

    84de620

07:48 Yuri Victorovich (yuri)  Author: Wen Heping

biology/py-pysam: Update 0.16.0.1 -> 0.18.0

PR:		260556

    876147e

13:59 Dmitry Marakasov (amdmi3) 

biology/py-pysam: limit supported python versions

pysam/libchtslib.c:1269:15: error: no member named 'use_tracing' in 'struct _ts'
      tstate->use_tracing = 0;

Approved by:	portmgr blanket

    f924135

08:09 Mathieu Arnold (mat) 

One more small cleanup, forgotten yesterday.
Reported by:	lwhsu

    cf118cc

14:31 Mathieu Arnold (mat) 

Remove # $FreeBSD$ from Makefiles.

    305f148

23:02 antoine 

Drop python 2.7 support from a few ports

With hat:	portmgr

 

19:26 yuri 

biology/py-pysam: Update 0.16.0 -> 0.16.0.1

 

05:03 yuri 

biology/py-pysam: Update 0.15.4 -> 0.16.0

Reported by:	potscout

 

02:53 yuri 

biology/py-pysam: Update 0.15.3 -> 0.15.4

Reported by:	portscout

 

15:49 yuri 

biology/py-pysam: Update 0.15.2 -> 0.15.3

Reported by:	portscout

 

04:15 yuri 

biology/py-pysam: Update 0.15.1 -> 0.15.2

Reported by:	portscout

 

17:40 yuri 

biology/py-pysam: Update 0.15.0 -> 0.15.1

Reported by:	portscout

 

19:47 yuri 

biology/py-pysam: Update 0.14.1 -> 0.15.0

Port changes:
* Remove stripping: done by the project now
* Update WWW

Reported by:	portscout

 

08:12 yuri 

biology/py-pysam: Update to 0.14.1

Also silenced STRIP_CMD.

Reported by:	portscout

 

23:01 yuri 

biology/py-pysam: Update to 0.14

Changelog:
https://github.com/pysam-developers/pysam/releases/tag/v0.14

Reported by:	portscout
Approved by:	tcberner (mentor, implicit)

 

15:50 mat 

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

 

19:12 yuri 

biology/py-pysam: Update to 0.13

Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D12967

 

05:30 tcberner 

Update biology/py-pysam to 0.12.0.1

PR:		223254
Submitted by:	Yuri Victorovich <yuri@rawbw.com> (maintainer)

 

02:03 wen 

- Update to 0.11.2.2

PR:		219892
Submitted by:	yuri@rawbw.com(maintainer)

 

22:04 joneum 

- Update to 0.11.2.1

PR:	219396
Submitted by:	Yuri Victorovich (Maintainer) <yuri@rawbw.com>
Approved by:	rene (mentor)
Differential Revision:	https://reviews.freebsd.org/D10856

 

16:06 miwi 

- Update to 0.11.1

PR:		219122
Submitted by:	maintainer

 

06:05 miwi 

pysam is a lightweight wrapper of the htslib C-API and provides facilities to
read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access
to the command line functionality of the samtools and bcftools packages. The
module supports compression and random access through indexing.

This module provides a low-level wrapper around the htslib C-API as using
cython and a high-level API for convenient access to the data within standard
genomic file formats.

WWW: https://pypi.python.org/pypi/pysam

PR:		218745
Submitted by:	Yuri Victorovich <yuri@rawbw.com>