science/{,py-}avogadrolibs: update 1.97.0 → 1.99.0

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>

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

science/py-avogadrolibs: Simplify patch

science/{,py-}avogadrolibs: Update 1.95.1 -> 1.97.0

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.

science/py-avogadrolibs: Update 1.94.0 -> 1.95.1

science/py-avogadrolibs: Update 1.93.0 -> 1.94.0

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

Remove # $FreeBSD$ from Makefiles.

Mark BROKEN

CMake Error at /usr/local/share/cmake/pybind11/pybind11NewTools.cmake:184
(python3_add_library):
  Unknown CMake command "python3_add_library".

Reported by:	pkg-fallout

- Upgrade math/eigen3 to 3.3.8;

- Add some dependencies which might be detected by Find_Package but not
registered;

- Bump PORTREVISION of consumers.

PR:		250833
Submitted by:	/me
Approved by:	tcberner@ (KDE / maintainer) + exp-run

science/py-avogadrolib: Update 1.91.0-107 -> 1.93.0

Reported by:	portscout

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

Fix Qt5 symbol version scripts to put the catch-all clause first.  When
a symbol matches multiple clauses the last one takes precedence.  If the
catch-all is last it captures everything.  In the case of Qt5 libraries
this caused all symbols to have a Qt_5 label while some should have
Qt_5_PRIVATE_API.  This only affects lld because GNU ld always gives the
catch-all lowest priority.

Older versions of Qt5Webengine exported some memory allocation symbols from
the bundled Chromium.  Version 5.9 stopped exporting these [1] but the
symbols were kept as weak wrappers for the standard allocation functions to
maintain binary compatibility. [2][3]  The problem is that the call to the
standard function in these weak wrappers is only resolved to the standard
function if there's a call to this standard function in other parts of
Qt5Webengine, because only then is there a non-weak symbol that takes
precedence over the weak one.  If there's no such non-weak symbol the call

Update math/eigen3 to 3.3.7

- http://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.6
- http://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.7

Change cmake default behaviour to outsource.

Ports that build out of source now simply can use "USES=cmake"
instead of "USES=cmake:outsource". Ports that fail to build
out of source now need to specify "USES=cmake:insource".

I tried to only set insource where explictely needed.

PR:		232038
Exp-run by:	antoine

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

New port: science/py-avogadrolibs: Python bindings for Avogadro2 chemistry
libraries