biology/py-cutadapt5.2

biology/py-cutadapt: update to 5.2

Changelog: https://github.com/marcelm/cutadapt/blob/main/CHANGES.rst#v52-2025-10-23

biology/py-cutadapt: update to 5.1

python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal

Any missed ports, feel free to bump.

Any ports that need setuptools at runtime can have the devel/py-setuptools
manually added back to RUN_DEPENDS, but understand that this practice
is deprecated; see CHANGES for details.

biology/py-cutadapt: Update to 5.0

biology/py-cutadapt: update to 4.9

changelog: https://cutadapt.readthedocs.io/en/stable/changes.html#v4-9-2024-06-19

biology/py-cutadapt: update to 4.8

While here, take maintainership

biology/py-cutadapt: Release to ports@

Focusing on fastq-trim from now on

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

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

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

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>

*/*: rename CHEESESHOP to PYPI in MASTER_SITES

PR:			267994
Differential revision:	D37518
Approved by:		bapt

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)

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)

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

Approved by:	portmgr blanket

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

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

Remove # $FreeBSD$ from Makefiles.

Unbreak INDEX

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)

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

biology/py-cutadapt: Upgrade to 2.7

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

Reported by:    portscout

biology/py-cutadapt: Upgrade to 2.5

Add pigz run depend for parallel gzip/gunzip

biology/py-cutadapt: Upgrade to 2.3

Numerous bugfixes and enhancements since 2.1

Bump a few PORTREVISIONs after r498529

With hat:	portmgr

biology/py-cutadapt: Upgrade to 2.1

Add do-test target

Unbreak

biology/py-cutadapt: Upgrade to 1.18

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

Use PY_FLAVOR for dependencies.

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

Sponsored by:	Absolight

Switch all pypi.python.org WWWs to a new PyPi home pypi.org where they now redirect to anyway. All new urls checked to return 200, I've fixed a couple of them in the process.

Approved by:	portmgr blanket, mat

Canonicalize PyPi WWWs: - Switch to https:// - Remove trailing slashes

Approved by:	portmgr blanket

Fix packaging with python3

biology/py-cutadapt: Remove MASTER_SITE_SUBDIR per mentor comment

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

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

[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