biology/py-dna-features-viewer3.1.5

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-dna-features-viewer: Update to 3.1.5

Code modernization and clean up
Changes: https://github.com/Edinburgh-Genome-Foundry/\
    DnaFeaturesViewer/releases

Reported by:    portscout

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.

Multiple biology ports: Replace pypi homepage with github

portscout apparently can't work with PYPI homepages

biology/py-dna-features-viewer: Update to 3.1.3

Latest biopython and matplotlib compatibility
Changes:
https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/releases

Reported by:    portscout

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

biology/py-dna-features-viewer: Update to 3.1.2

Fixes compatibility with biophython 1.80

*/*: 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-dna-features-viewer: Update to 3.1.1

python 3.9 compatibility

Changes: https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/tags

Reported by:    portscout

biology/py-dna-features-viewer: Add missing dependency

py-packaging not mentioned in setup.py, but runtime errors thrown
without it.

biology/py-dna-features-viewer: Add py-bcbio-gff dep

Needed to automatically extract features from GFF files

biology/py-dna-features-viewer: Python lib to visualize DNA features

DNA Features Viewer is a Python library to visualize DNA features, e.g.
from GenBank or Gff files.

DNA Features Viewer can plot sequence maps linearly or circularly, with
or without nucleotide sequence and amino-acid sequences. The plotter
automatically produces clear plots even for sequences with many
overlapping features and long labels. The library plays well with
Matplotlib and Biopython, and the figures can be saved in different
formats (PNG, JPEG, SVG, PDF), e.g. for report generation or LIMS
interfaces.