04:05 Charlie Li (vishwin) 

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.

    06a08e6

13:04 Jason W. Bacon (jwb) 

Multiple biology ports: Replace pypi homepage with github

portscout apparently can't work with PYPI homepages

    d758b1c

08:11 Ruslan Makhmatkhanov (rm) 

biology/py-pywgsim: fix build

cython dependency not available at post-patch stage. Use post-configure instead

Approved by:	portmgr (blanket approval)

    de4b547

11:55 Ruslan Makhmatkhanov (rm) 

biology/py-pywgsim: unbreak with python3.11

make it recreate the source with newer cython

PR:		275494
Approved by:	portmgr (blanket approval)

    91e7916

12:18 Antoine Brodin (antoine) 

biology/py-pywgsim: unbreak bulk -a

    f1e51f1

11:41 Jason W. Bacon (jwb) 

biology/py-pywgsim: Limit to python 3.10

Nontrivial changes needed for python 3.11
Abandoned upstream

Reported by:    pkg-fallout

    155267d

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

12:55 Jason W. Bacon (jwb) 

biology/py-pywgsim: Modified wgsim genomic data simulator

pywgsim is a modified version of the wgsim short read simulator.  The
code for wgsim has been modified to allow visualizing the simulated
mutations as a GFF file.

    c085af1