biology/py-macs33.0.5

Release numerous ports to ports@

I've been retired for a few years, and it is unlikely I will be doing
any more scientific computing support in the future.  I have continued
to maintain ~160 ports to the best of my ability, mainly as a favor to
the community, but I can no longer justify the time and effort
required.  I am therefore releasing most of my scientific ports, along
with a few others, to ports@.  I will continue to maintain ports I am
actively using and those for which I am upstream.

biology/py-macs3: Update to 3.0.5

A few fixes and enhancements
Changes: https://github.com/macs3-project/MACS/releases

Reported by:    portscout

biology/py-macs3: Fix USE_PYTHON=cython usage

Approved by:	portmgr (blanket)
With hat:	python

*/*: bump PORTREVISION after switching to NumPy 2.x

*/*: Switch to NumPy 2.x

PR:		294328
Exp-run:	antoine

python.mk: retire ${PYNUMPY}

With both math/py-numpy (2) and math/py-numpy1, the variable stopped
making sense. Also remove the upper version bound.

biology/py-macs3: Update to 3.0.4

A few fixes and enhancements
Changes: https://github.com/macs3-project/MACS/releases

Reported by:    portscout

Mk/Uses/python.mk: Remove USE_PYTHON=cython3{,_run,_test}

- Convert all cython3 occurrence to USE_PYTHON=cython*
- Bump PORTREVISION dependent ports of USE_PYTHON=cython_run for dependency change

PR:		291778

Mk/Uses/python.mk: Introduce USE_PYTHON=cython3{,_run,_test}

- Update USE_PYTHON=cython{,_run,_test}
- Convert all cython3 occurrence to USE_PYTHON=cython3*
- While I'm here, fix incorrect usage of combining cython3 in BUILD_DEPENDS and USE_PYTHON=cython

It is added to simplify the future transition from Cython 0.29 to 3.

The minimal version is set to 3.0.12 because it is required by devel/py-propcache.
The upper bound of version is set to 3.1 because it is limited by multiple ports.

biology/py-macs3: Unbreak package build

pep57 -> distutils
Port passed poudriere before, but spontaneously broke due to
other changes

Reported by:    pkg-fallout

biology/py-macs3: Update to 3.0.3

A few new features and bug fixes
Changes: https://github.com/macs3-project/MACS/releases

Reported by:    portscout

biology/py-macs3: Update to 3.0.2

Some minor enhancements and improved docs
Changes: https://github.com/macs3-project/MACS/releases

Reported by:    portscout

all: drop support for FreeBSD 13.2 which reached EOL today

Thanks again to jbeich for noticing various things I overlooked.

Reviewed by:	acm, ashish, eduardo, ehaupt, eugen, jbeich, martymac, mat, nobukata, sunpoet, tagattie, yuri, arrowd, kde
Differential Revision:	https://reviews.freebsd.org/D45141

*/*: Add ${PY_SETUPTOOLS} to BUILD_DEPENDS

Fix build when setuptools is removed from RUN_DEPENDS in
Mk/Uses/python.mk.

PR:		270510
Approved by:	portmgr (blanket)

biology/py-macs3: Mark not for i386

SIMDE does not support _Float16
Nobody does bioinformatics on 32-bit processors anyway, as many
applications have huge memory requirements

biology/py-macs3: Update to 3.0.1

Minor bug fix release
Changes: https://github.com/macs3-project/MACS/releases

biology/py-macs3: Peak caller for TF binding sites

MACS (Model-based Analysis of ChIP-Seq) is a tool for identifying
transcription factor (TF) binding sites.   Such sites are generated
by CHiP-Seq (CHromatin immuno-Precipitation sequencing) and ATAC-Seq
(Assay for Transposase Accessible Chromatin Sequencing).  MACS
identifies "peaks" in the genome sequence, which are areas enriched
in bound TFs or accessible chromatin.