00:12 Jason W. Bacon (jwb) 

biology/py-cutadapt: Release to ports@

Focusing on fastq-trim from now on

    7045d13

13:31 Jason W. Bacon (jwb) 

py-cutadapt: Update to 4.7

Send error message to stderr
Add support for single-ended uBAM
Drop Python 3.7

Changes: https://cutadapt.readthedocs.io/en/stable/changes.html

Reported by:    portscout

    43e4ca8

07:18 Charlie Li (vishwin) 

devel/py-setuptools-scm: update to 8.0.4

Directory and PORTNAME changed to match normalised name in release
tarball; consumers updated to match.

Although setuptools itself is specified as a run dependency in the
Python package metadata, it is currently left out here to prevent
environment pollution until at least PR 270510 is committed.
Additionally, this version of setuptools-scm requires setuptools>=61,
which means this version is only meant for USE_PYTHON=pep517 ports
as all USE_PYTHON=distutils ports will switch to devel/py-setuptools58
also after PR 270510. science/py-emmet-core is switched to
devel/py-setuptools_scm7 accordingly, as it specifies setuptools-scm<8.
devel/py-{flit-scm,hatch-vcs} have ${PY_SETUPTOOLS} added to
RUN_DEPENDS to compensate.

Further details: https://wiki.freebsd.org/Python/setuptools

Reported by: yuri
Co-authored by: matthew
Exp-run by: antoine (earlier iteration)
Approved by: yuri (science/py-emmet-core, previous iteration)
PR: 272134
Differential Revision: https://reviews.freebsd.org/D39288

    5d4139f

12:55 Jason W. Bacon (jwb) 

biology/py-cutadapt: Update to 4.6

Numerous bug fixes and enhancements since 3.3
Changes: https://github.com/marcelm/cutadapt/tags

PR:             276814
Reported by:    wen

    7c280eb

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

15:58 Dmitry Marakasov (amdmi3) 

*/*: rename CHEESESHOP to PYPI in MASTER_SITES

PR:			267994
Differential revision:	D37518
Approved by:		bapt

    77d6847

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

18:59 Dmitry Marakasov (amdmi3) 

biology/py-cutadapt: fix tests by adding missing test depend

Approved by:	portmgr blanket

    ff5a2c3

13:20 Jason W. Bacon (jwb) 

biology/py-cutadapt: Update strict py-dnaio dep version

    ba4a552

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

21:18 antoine 

Unbreak INDEX

 

17:55 jwb 

py-cutadapt: Update to 3.3

Numerous small bug fixes and enhancements, code refactoring

py-xopen: Update to 1.1.0

Required by cutadapt 3.3
Drop python 3.5 support
Add isal support (not yet utilized in FreeBSD port)

 

20:39 jwb 

biology/py-cutadapt: Update to 3.2
biology/py-dnaio: Update to 0.5.0
archivers/py-xopen: Update to 1.0.0

Numerous bug fixes and enhancements since cutadapt 3.2

Document cutadapt dependency versions dnaio~=0.5.0 xopen~=1.0.0
Bump python dependency to 3.6+ to restrict package builds

 

14:45 jwb 

biology/py-cutadapt: Upgrade to 2.7

Numerous minor fixes and enhancements.
Upstreamed setup.py patches for dependency versions.

Reported by:    portscout

 

13:17 jwb 

biology/py-cutadapt: Upgrade to 2.5

Add pigz run depend for parallel gzip/gunzip

 

01:26 jwb 

biology/py-cutadapt: Upgrade to 2.3

Numerous bugfixes and enhancements since 2.1

 

06:18 antoine 

Bump a few PORTREVISIONs after r498529

With hat:	portmgr

 

21:20 jwb 

biology/py-cutadapt: Upgrade to 2.1

Add do-test target

 

20:28 antoine 

Unbreak

 

14:10 jwb 

biology/py-cutadapt: Upgrade to 1.18

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D17099

 

17:05 mat 

Use PY_FLAVOR for dependencies.

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

Sponsored by:	Absolight

 

06:18 antoine 

Fix packaging with python3

 

22:11 jwb 

biology/py-cutadapt: Remove MASTER_SITE_SUBDIR per mentor comment

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13303

 

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

 

22:17 jwb 

[new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, po
ly-A tails, etc
Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13294