science/py-pyteomics 5.0.1

science/py-pyteomics: Update to 5.0.1

- Add PROFORMA option

Changes:	https://github.com/levitsky/pyteomics/releases
		https://pyteomics.readthedocs.io/en/latest/changelog.html

*/py-*: Update version requirement of *_DEPENDS

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

*/*: Switch to NumPy 2.x

PR:		294328
Exp-run:	antoine

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

...and bump PORTREVISIONs of consumers with hard RUN_DEPENDS

PR: 281470

*/*: switch dependency from devel/py-lxml5 to devel/py-lxml

Currently, there are two versions of python XML processing library
which conflict each other in the ports tree, namely:
- devel/py-lxml5 (now at version 5.4.0)
- devel/py-lxml  (now at version 6.0.1)

To avoid the situation that some ports depend on py-lxml5 and some
others do on py-lxml (by switching dependencies individually), this
commit switches the dependencies from py-lxml5 to py-lxml at once.

Additional note: There are still two ports (textproc/py-rdflib and
www/py-draftjs-exporter) depending on py-lxml5 since they limit upper
version to less than 6.

PR:		289491
Approved by:	Michiel van Baak Jansen <michiel@vanbaak.eu>, arrowd,
		crees, madpilot, delphij, marcus, nivit, kai,
		skreuzer, fluffy, bofh, thierry, stephen, sunpoet,
		0mp, Eric Camachat <eric@camachat.org>

all: bump PORTREVISION after updating graphics/libyuv

Using the Tools/scripts/bump_revision.pl script

*/*: update dependency on devel/py-lxml to devel/py-lxml5 (2nd attempt)

This is a follow up to the commit 230fb2661c78, which updated some
ports' dependencies on devel/py-lxml to devel/py-lxml5. It was an
attempt to follow the dependency change of
www/py-beautifulsoup. However, the switch was incomplete and broke
some other ports.

It has turned out that the ports depending on devel/py-lxml (at
version 4.9.3) does not limit their dependencies' upper bound to 4.x
except for one (devel/py-pymaven-patch). So updating them to
devel/py-lxml5 (at version 5.4.0) should cause no harm.

This commit switch dependencies of all the ports (except
devel/py-pymaven-patch) to devel/py-lxml5 avoid potential conflicts.

Co-authored-by: Daniel Engberg <diizzy@FreeBSD.org>

PR:		287144, 288047
Reported by:	makc (via ports-committers),
		vvd (PR 288047),
		diizzy (PR 287144)
Approved by:	portmgr (chase dependency change, unbreak build)
Fixes:		230fb2661c78 (*/*: update dependency on devel/py-lxml to devel/py-lxml5)

science/py-pyteomics: Update to 4.7.5

Changes:	https://github.com/levitsky/pyteomics/releases
		https://pyteomics.readthedocs.io/en/latest/changelog.html

science/py-pyteomics: Update to 4.7.4

Changes:	https://github.com/levitsky/pyteomics/releases
		https://pyteomics.readthedocs.io/en/latest/changelog.html

science/py-pyteomics: Update to 4.7.3

Changes:	https://github.com/levitsky/pyteomics/releases
		https://pyteomics.readthedocs.io/en/latest/changelog.html

science/py-pyteomics: Update to 4.7.2

Changes:	https://github.com/levitsky/pyteomics/releases
		https://pyteomics.readthedocs.io/en/latest/changelog.html

science/py-pyteomics: Convert to USE_PYTHON=pep517

- Bump PORTREVISION for package change

science/py-pyteomics: update to 4.7.1

PR:		277087
Approved by:	maintainer timeout

science/py-pyteomics: Update to 4.7

- Update WWW and clean up pkg-descr

Changes:	https://github.com/levitsky/pyteomics/releases
		https://pyteomics.readthedocs.io/en/latest/changelog.html

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>

science/py-pyteomics: Update to 4.6

Changes:	https://github.com/levitsky/pyteomics/releases
		https://pyteomics.readthedocs.io/en/latest/changelog.html

*: 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

science/py-pyteomics: Update to 4.5.6

Changes:	https://github.com/levitsky/pyteomics/releases
		https://pyteomics.readthedocs.io/en/latest/changelog.html

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)

science/py-pyteomics: Update to 4.5.5

Changes:	https://github.com/levitsky/pyteomics/releases
		https://pyteomics.readthedocs.io/en/latest/changelog.html

science/py-pyteomics: Update to 4.5.4

Changes:	https://github.com/levitsky/pyteomics/releases
		https://pyteomics.readthedocs.io/en/latest/changelog.html

science/py-pyteomics: Update to 4.5.3

Changes:	https://github.com/levitsky/pyteomics/releases
		https://pyteomics.readthedocs.io/en/latest/changelog.html

science/py-pyteomics: Update to 4.5.2

Changes:	https://github.com/levitsky/pyteomics/releases
		https://pyteomics.readthedocs.io/en/latest/changelog.html

science/py-pyteomics: Update to 4.5

Changes:	https://github.com/levitsky/pyteomics/releases
		https://pyteomics.readthedocs.io/en/latest/changelog.html

science/py-pyteomics: Change RUN_DEPENDS from py-sqlalchemy13 to py-sqlalchemy14

- Bump PORTREVISION for dependency change

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

science/py-pyteomics: Remove PYNUMPY

science/py-pyteomics: Update to 4.4.2

Changes:	https://github.com/levitsky/pyteomics/releases
		https://pyteomics.readthedocs.io/en/latest/changelog.html

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

Remove # $FreeBSD$ from Makefiles.

Update to 4.4.1

Changes:	https://github.com/levitsky/pyteomics/releases
		https://pyteomics.readthedocs.io/en/latest/changelog.html

Update to 4.4.0

Changes:	https://github.com/levitsky/pyteomics/releases
		https://pyteomics.readthedocs.io/en/latest/changelog.html

Update to 4.3.3

Changes:	https://github.com/levitsky/pyteomics/releases
		https://pyteomics.readthedocs.io/en/latest/changelog.html

Unbreak bulk -a

Update version requirement of RUN_DEPENDS

Add DF, GRAPHICS, TDA, UNIMOD and XML options

Update to 4.3.2

- Update WWW

Changes:	https://github.com/levitsky/pyteomics/releases
		https://pyteomics.readthedocs.io/en/latest/changelog.html

Update to 4.2

Changes:	https://bitbucket.org/levitsky/pyteomics/src/default/CHANGELOG
		https://pyteomics.readthedocs.io/en/latest/changelog.html

Bump PORTREVISION for ports depending on the canonical version of GCC as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3 to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330

Update to 4.1.2

Changes:	https://bitbucket.org/levitsky/pyteomics/src/default/CHANGELOG
		https://pyteomics.readthedocs.io/en/latest/changelog.html

Update to 4.1.1

Changes:	https://pyteomics.readthedocs.io/en/latest/changelog.html

Update to 4.1

- Update pkg-descr
- Update WWW
- Take maintainership

Changes:	https://pyteomics.readthedocs.io/en/latest/changelog.html

Bump PORTREVISION for ports depending on the canonical version of GCC defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590

science/py-pyteomics: - Update to 3.5.1 and enable for all Python versions

Use PY_FLAVOR for dependencies.

FLAVOR is the current port's flavor, it should not be used outside of
this scope.

Sponsored by:	Absolight

Switch all pypi.python.org WWWs to a new PyPi home pypi.org where they now redirect to anyway. All new urls checked to return 200, I've fixed a couple of them in the process.

Approved by:	portmgr blanket, mat

Bump PORTREVISIONs of all users of math/mpc that we just updated to version 1.1.0 (via revision 464079).