biology/py-scikit-bio: Update 0.5.8 → 0.5.9

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>

www/py-cachecontrol: Fix port

- Use lowercase PORTNAME
- Fix WWW
- Fix LICENSE
- Fix FILECACHE and REDIS options: add missing RUN_DEPENDS
- Bump PORTREVISION for package change

PR:		266640
Approved by:	maintainer (timeout, 3+ months)

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

biology/py-scikit-bio: Update 0.5.7 → 0.5.8

Reported by:	portscout

biology/py-scikit-bio: Update 0.5.7 → 0.5.7

Reported by:	portscout

*/*: 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.

biology/py-scikit-bio: Broken on aarch64

Reported by:	fallout

biology/py-scikit-bio: drop unnecessary USE_GCC on powerpc64

biology/py-scikit-bio: build with clang on powerpc64le

biology/py-scikit-bio: Update 0.5.6 -> 0.5.7

Reported by:	portscout

Update CONFLICTS definitions in categories a* to c*

Update the CONFLICTS definitions of ports in the following categories:

- accessibility
- archivers
- audio
- benchmarks
- biology
- cad
- chinese
- comms
- converters

An attempt has been made to use generic conflicts patterns that do not
have to be updated whenever a new version of a conflicting port is
added to the ports system.

There is a misunderstanding that the port being built/installed has to
be omitted from the conflicts pattern. This is not true - the port
being built is implicitly non-conflicting due to logic in bsd.port.mk.

Approved by:	portmgr (implicit)

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

Remove # $FreeBSD$ from Makefiles.

biology/py-scikit-bio: fix build on powerpc64

GCC is also necessary on powerpc64:
In file included from skbio/alignment/_ssw_wrapper.c:626:
In file included from skbio/alignment/_lib/ssw.h:17:
In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13:
/usr/lib/clang/11.0.1/include/mmintrin.h:50:12: error: invalid conversion
between vector type '__m64' (vector of 1 'long long' value) and integer type
'int' of different size
    return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);

biology/py-scikit-bio: fix build on powerpc64le

Use GCC:
In file included from skbio/alignment/_ssw_wrapper.c:626:
In file included from skbio/alignment/_lib/ssw.h:17:
In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13:
/usr/lib/clang/11.0.1/include/mmintrin.h:50:12: error: invalid conversion
between vector type '__m64' (vector of 1 'long long' value) and integer type
'int' of different size
    return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);

Add education virtual category

PR:		248402
Submitted by:	PauAmma

biology/py-scikit-bio: Fix build on the i386 architecture

Reported by:	fallout
MFH:		2020Q3

devel/ipython: Update to 7.17.0

IPython 7.17+ supports Python 3.7 and above, following NEP 29.
Update consumers to use Python >= 3.7 (avoid break bulk -a).

Changelog:	https://ipython.readthedocs.io/en/latest/whatsnew/version7.html?highlight=7.17#ipython-7-17

Approved by:	dbaio (python, maintainer)

biology/py-scikit-bio: Fix license

biology/py-scikit-bio: Remove bogus lines

New port: biology/py-scikit-bio: Data structures, algorithms, educational
resources for bioinformatics