science/rdkit: update 2025_09_2 → 2026.03.6

also:
- fixed many tests and upstreamed fixes (their testsuite is in a disarray,
  we shouldn't really be fixing people's tests, but anyways)
- discovered and fixed wrong clang detection in the code, reported
  upstream
- fixed wrongfully excluded code that caused plist issues
- fixed compiler crash on 16 (by using llvm:23)

*/*: update boost consumers after boost-1.92

*/*: bump consumers after devel/boost update

science/rdkit: correction

science/rdkit: Broken on 16 arm64

Reported by:	fallout

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

*/*: Switch to NumPy 2.x

PR:		294328
Exp-run:	antoine

python.mk: retire ${PYNUMPY}

With both math/py-numpy (2) and math/py-numpy1, the variable stopped
making sense. Also remove the upper version bound.

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

...and bump PORTREVISIONs of consumers with hard RUN_DEPENDS

PR: 281470

science/rdkit: update 2025_09_1 → 2025.09.2

science/rdkit: Broken on 16: clang crashes

science/rdkit: update 2025_03_1 → 2025.09.1

devel/boost: bump consumers after boost upgrade (+)

Get rid of direct dependency ob libbost_system.so, use libboost_thread.so
instead

science/rdkit: Broken on 16/amd64

Reported by:	fallout

all: bump PORTREVISION after updating graphics/libyuv

Using the Tools/scripts/bump_revision.pl script

devel/boost: bump consumers after Boost update

science/rdkit: update 2024_09_4 → 2025_03_1

devel/boost: bump consumers after Boost-1.87 update

Sponsored by:	Future Crew, LLC

science/rdkit: Broken ion 15/i386

Reported by:	fallout

science/rdkit: fix build on armv7

Only attempt to use -mpopcnt on architectures known to support it

Approved by:	portmgr (build fix blanket)
Event:		38C3

science/rdkit: update 2024_03_6 → 2024_09_4

science/rdkit: correct pkg-plist on big-endian, correct ARCH check, enable on
i386

1. powerpc64le is also little-endian.
2. There are now less big-endian architectures than little-endian, so revert
the check, now also covering powerpc64le.
3. Tested on i386, works fine on 14.2-RELEASE.

devel/boost: bump consu,ers after update Boost to 1.86 release

Sponsored by:	Future Crew, LLC

*/*: bump consumers after devel/boost* update

With hat:	office
Sponsored by:	Future Crew, LLC

science/rdkit: Fix fetch by caching unstable font distfile

PR:		281322
Reported by:	Daniel Engberg <diizzy@FreeBSD.org>

science/rdkit: update 2023_09_6 → 2024_03_6

Reported by:	portscout

science/rdkit: Broken on 15 aarch64

Reported by:	fallout

science/rdkit: Clang-17 crashes on FreeBSD 15 amd64

Reported by:	fallout

science/rdkit: update 2023_09_5 → 2023_09_6

Reported by:	portscout

science/rdkit: update 2023_09_3 → 2023_09_5

Reported by:	portscout

devel/boost: bump consumers after library update

science/rdkit: Update/add BROKEN_xx lines

science/rdkit: update 2023_09_1 → 2023_09_3

Reported by:	portscout

science/rdkit: update 2023_03_3 → 2023_09_1

Reported by:	portscout

devel/boost*: bump all consumers after 1.83.0

science/rdkit: Update 2023_03_2 → 2023_03_3

Reported by:	portscout

science/rdkit: Mark BROKEN on FreeBSD 14

Fails to compile as clang crashes with:
error: clang frontend command failed with exit code 134

Have tried to build with llvm14 and llvm15 and it builds but there are
lots of modules which are not built.

Approved by:	portmgr (blanket)
Sponsored by:	The FreeBSD Foundation

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/rdkit: Update 2022_03_5 → 2023_03_2

Reported by:	portscout

*/*: bump all direct Boost cunsumers

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

*/*:	bump libboost*.so libraries consumert after Boost upgrade

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.

*/*: bump all consumers after recent boost upgrade

science/rdkit: Update 2022.03.4 -> 2022.03.5

Reported by:	portscout

science/rdkit: Update 2022.03.3 -> 2022.03.4

Reported by:	portscout

science/rdkit: Update 2022.03.2 -> 2022.03.3

Reported by:	portscout

devel/boost-all: bump all library consumers after boost upgrade

PR:	246106

science/rdkit: Update 2022.03.1 -> 2022.03.2

Reported by:	portscout

science/rdkit: Update 2021.09.5 -> 2022.03.1

Reported by:	portscout

science/rdkit: Update 2021.09.4 -> 2021.09.5

Reported by:	portscout

science/rdkit: Broken on i386

Reported by:	fallout

science/rdkit: Update 2021.03.5 -> 2021.09.4

PR:		261223
Reported by:	diizzy@

science/coordgenlibs: Update 2.0.3 -> 3.0.0

science/rdkit: Update 2021.03.4 -> 2021.03.5

science/rdkit: Update 2021.03.3 -> 2021.03.4

Reported by:	portscout

science/rdkit: Update 2020.09.5 -> 2021.03.3

Reported by:	portscout

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

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

Remove # $FreeBSD$ from Makefiles.

science/rdkit: Add PGSQL option to build the PostgreSQL cartridge

Also fix build with DOCS=OFF

science/rdkit: Update 2020.09.4 -> 2020.09.5

Reported by:	portscout

science/rdkit: Update 2020.09.3 -> 2020.09.4

Reported by:	portscout

science/rdkit: fix packaging on powerpc64

Also switch not-working with Clang -mpopcntb with -mpopcntd (as a side effect it
also raises requirements from POWER5 to POWER7).

MFH:		2021Q1

Follow up on graphics/py-pillow6 port removal in r559976

The graphics/py-pillow6 port was removed in r559976 as it was for
Python 2.7 only and no longer referenced in the default cases.
However it was still defined in Mk/Uses/python.mk in PY_PILLOW,
leaving a dangling reference.

Remove it from Mk/Uses/python.mk, leaving only the Python 3
version of that port, graphics/py-pillow, defined and bump the
minimal verion of Python to 3.6 for affected ports.

science/rdkit: Update 2018.09.3 -> 2020.09.3

Reported by:	portscout

- 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

Convert the tree to use PY_PILLOW

With hat:	portmgr
Originally submitted by:	kai

graphics/py-pillow: Update to 7.0.0

* Repo-Copy the Pillow 6.2.2 release to graphics/py-pillow6 to retain
  backwards compatibility for Python 2 consumers as the Pillow 7.0.0 release
  dropped the support for Python 2.

* Apply conditional statements to use either Pillow 7.x or Pillow 6.x for
  consumers that can be built for Python 2 or newer.

* Exceptions are ports that can be built only for either Python 2 or
  Python 3.  For the first case, consumers are just assigned to the
  repo-copied graphics/py-pillow6.

* Also remove Pillow from BUILD_DEPENDS of math/py-PyWavelets as it is not
  listed in setup.py as a build dependency [1] and relax the version

devel/boost-*: update to 1.72.0

Changes:	http://www.boost.org/users/history/version_1_72_0.html
PR:		241449
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D22136

science/rdkit: fix build on GCC architectures

This port needs new GCC to build.

It adds -mpopcnt to *FLAGS, which breaks build on non-x86. Since it optimizes
for the host CPU, don't enable it.

Some libraries are not installed on big-endian systems.

PR:             239299
Approved by:    yuri (maintainer), mat (mentor)
Differential Revision:  https://reviews.freebsd.org/D20997

devel/boost-*: update to 1.71.0

Changes:	http://www.boost.org/users/history/version_1_71_0.html
PR:		238827
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D20774

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

devel/boost-*: update to 1.70.0

Changes:	http://www.boost.org/users/history/version_1_70_0.html
PR:		235956
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D19303

Bump a few PORTREVISIONs after r498529

With hat:	portmgr

science/rdkit: Update 2018.09.2 -> 2018.09.3

Reported by:	portscout

science/rdkit: Update 2018_09_1 -> 2018_09_2

Reported by:	portscout

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

devel/boost-*: update to 1.69.0

Changes:	http://www.boost.org/users/history/version_1_69_0.html
PR:		232525
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D17645

science/rdkit: Update 2018_03_4 -> 2018_09_1

Approved by:	portscout

science/rdkit: Update 2018_03_3 -> 2018_03_4

Reported by:	portscout

devel/boost-*: update to 1.68.0

- Switch to C++14 for libboost_system to support C++14 consumers

Changes:	http://www.boost.org/users/history/version_1_68_0.html
PR:		229569
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D16165

science/rdkit: Update 2018_03_2 -> 2018_03_3

Changelog:
https://github.com/rdkit/rdkit/releases/tag/Release_2018_03_3

science/rdkit: Update 2018_03_1 -> 2018_03_2

Reported by:	portscout

science/rdkit: Update 2017_09_3 -> 2018_03_1

Port changes:
* Add GH_TUPLE for 2 new bundled dependencies
* Add BUILD_DEPENDS and post-extract script for the new rapidjson dependency

Reported by:	portscout

devel/boost-*: update to 1.67.0

Changes:	http://www.boost.org/users/history/version_1_67_0.html
PR:		227427
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D15030

science/rdkit: Add python binding

New port: science/rdkit: Collection of cheminformatics and machine-learning
software