biology/py-multiqc 1.35

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-multiqc: Update to 1.35

Many fixes and new features since 1.25.2
Changes: https://github.com/MultiQC/MultiQC/releases

Reported by:    portscout

*/*: 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.

math/py-numpy: switch all consumers to math/py-numpy1

...and bump PORTREVISIONs of consumers with hard RUN_DEPENDS

PR: 281470

all: bump PORTREVISION after updating graphics/libyuv

Using the Tools/scripts/bump_revision.pl script

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-multiqc: Add missing py-natsort RUN_DEPEND

biology/py-multiqc: Update to 1.25.2

Numerous fixes and a few new features
Changes: https://github.com/MultiQC/MultiQC/releases

Reported by:    portscout

biology/py-multiqc: Update to 1.25.1

Numerous fixes and enhancements since 1.15
(Update blocked by py-plotly)
Changes: https://github.com/MultiQC/MultiQC/releases

devel/py-pyyaml: Move devel/py-yaml to devel/py-pyyaml

- Bump PORTREVISION of dependent ports for dependency change

biology/py-multiqc: Update to 1.15

Major performance boost for file search
New "Librarian" module
Numerous enhancements and module updates
Changes: https://github.com/ewels/MultiQC/releases

Reported by:    portscout

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>

biology/py-multiqc: Update to 1.14

Numerous new features, enhancements and bug fixes

Changes: https://github.com/ewels/MultiQC/releases

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

*/*: 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)

math/py-matplotlib: chase minimum Python version in dependent ports

Since the previous update changed USES=python from 3.6+ to 3.7+, all
dependent ports must have USES=python:3.7+ as well, otherwise it breaks
the @py36 flavor.

PR:		255347
Reported by:	sunpoet

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

Remove # $FreeBSD$ from Makefiles.

biology/py-multiqc: Update to 1.10

Numerous new features, a few bug fixes since 1.9

Reported by:    portscout

biology/py-multiqc: Update to 1.9

Fix runtime error due to incompatibility of 1.8 with latest matplotlib
Drop python2 support
Numerous new features and bug fixes

Unbreak bulk -a

biology/py-multiqc: Upgrade to 1.8

Major enhancements including 6 new modules and improvements to existing modules
Numerous minor fixes and enhancements

Reported by:    portscout

biology/py-multiqc: Aggregate bioinformatics analysis reports

MultiQC searches a given directory for analysis logs and compiles an HTML
report. It's a general use tool, perfect for summarising the output from
numerous bioinformatics tools.