science/abinit: Update 9.4.2 -> 9.6.2

science/hdf5: bump PORTREVISION of consumers

The SO-version increased in the update to 1.12.2 in
a43418b81530f7e897abfbe18dd59f44265a1a0f .

Reported by:	VVD <vvd@unislabs.com>

science: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Andreas Fehlner <fehlner@gmx.de>
  *  Brad Huntting <huntting@glarp.com>
  *  Chao Shin <quakelee@cn.FreeBSD.org>
  *  Cheng-Lung Sung <clsung@FreeBSD.org>
  *  Chia-Hsing Yu <me@davidyu.org>
  *  Chris Rees <utisoft@gmail.com>
  *  David Naylor <dbn@FreeBSD.org>
  *  Dmitry Sivachenko <demon@FreeBSD.org>
  *  Ed Schouten <ed@FreeBSD.org>
  *  Eric Freeman <freebsdports@chillibear.com>
  *  Erik B Knudsen

science/abinit: Fix build with HDF5 1.12.0+

*/*: Replace science/szip with science/libaec

- Bump PORTREVISION of dependent ports for dependency change

szip does not allow redistribution in binary form without proper commercial
license. Its LICENSE_PERMS should be set to no-auto-accept which blocks building
this port, therefore building dependent ports are also blocked. Switch all
dependent ports to science/libaec to avoid conflicts and license issue.

PR:		228743, 246097, 250165

textproc/libxml2: bump all LIB_DEPENDS consumers

This is a separate commit to facilitate easier cherry-picking for
quarterly.

PR: 262853, 262940, 262877, 263126
Approved by: fluffy (mentor)

textproc/libxml2: bump all dependencies

This should make sure that all dependent ports will pick
up the new version commited with a13ec21cd733f67a9fc0dc00ab45268bdc236246

science/netcdf-fortran: Update to 4.5.4

- Update MASTER_SITES
- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://github.com/Unidata/netcdf-fortran/releases

science/abinit: Remove PY_PYGMENTS

With hat:	python

science/abinit: Update 9.4.1 -> 9.4.2

Reported by:	portscout

Remove # $FreeBSD$ from Makefiles.

science/abinit: Update 9.4.0 -> 9.4.1

Reported by:	portscout

science/abinit: Update 9.2.2 -> 9.4.0

Reported by:	portscout

Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+

PR:		250103

Bump PORTREVISION for science/netcdf shlib change

science/abinit: enable on powerpc64le

science/abinit: enable on powerpc64

science/abinit: Update 8.10.3 -> 9.2.2

PR:		252221
Submitted by:	thierry

Mark BROKEN: fails to build

m_polynomial_coeff.F90:2883:67:

 2800 |    do icoeff1=icoeff,ncoeff+nstr
      |                                2
......
 2883 | &                                    
index_coeff,list_combination,icoeff1,max_power_strain,&
      |                                                                   1
Error: Variable 'icoeff1' at (1) not definable inside loop beginning at (2) as
INTENT(INOUT) argument to subroutine 'computecombinationfromlist'
m_polynomial_coeff.F90:2643:26:

 2553 |    do icoeff1=icoeff,ncoeff+nstr
      |                                2
......
 2643 | &                        
icoeff1,icoeff_tot,natom,ncoeff,nstr,ncoeff_out,nrpt,nsym,power_disp+1,&
      |                          1
Error: Variable 'icoeff1' at (1) not definable inside loop beginning at (2) as
INTENT(INOUT) argument to subroutine 'computenorder'

Reported by:	pkg-fallout

Re-add port: science/abinit: Full-featured atomic-scale first-principles
simulation software

The taball for the 8.10.3 version was replaced on the upstream website with
significant updates in it.
The new tarball doesn't compile.
I preserved the previous 8.10.3 version tarball so that the package can build.
The new, 9.x version is upcoming.

Remove expired ports:

Adjusted for ports rescued since r534032

2020-05-05 audio/festvox-czech: Broken for more than 6 months
2020-05-05 audio/gkrellmvolume2: Broken for more than 6 months
2020-05-05 audio/mixmos: Broken for more than 6 months
2020-05-05 audio/mma: Broken for more than 6 months
2020-05-05 audio/pd-cyclone: Broken for more than 6 months
2020-05-05 audio/shorten: Broken for more than 6 months
2020-05-05 audio/taglib-sharp: Broken for more than 6 months
2020-05-05 audio/xhippo: Broken for more than 6 months
2020-05-05 biology/consed: Broken for more than 6 months
2020-05-05 biology/plinkseq: Broken for more than 6 months
2020-05-05 biology/seqtools: Broken for more than 6 months

Deprecate ports broken for more than 6 months

Drop dependency on devel/openmp

- Drop if devel/llvm* was used as a substitute

Approved by:	yuri, rene (earlier version)
Differential Revision:	https://reviews.freebsd.org/D23020

Mark a few ports BROKEN (unfetchable)

devel/openmp: update to 9.0.0

- Connect tests to the framework to help QA remaining patches
- Force rebuild all consumers after https://reviews.llvm.org/D59783

Changes:	http://llvm.org/viewvc/llvm-project/openmp/tags/RELEASE_900/final/?view=log
ABI:		https://abi-laboratory.pro/tracker/timeline/llvm_openmp/

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

science/abinit: Fix libomp.so in LDFLAGS (this also might fix the breakage on
13)

Reported by:	fallout

devel/openmp: phase out

- Expire after the last version without /usr/lib/libomp.so
- Drop SOVERSION for seamless transition (i.e., avoid conditionals)

PR:		236907
Approved by:	bapt (maintainer)
Differential Revision:	https://reviews.freebsd.org/D19767

Related to revision 499061 bump ports with USES=fortran to have them
benefit from the improved situation where libgcc_s is only used when
absolutely necessary.

Suggested by:	tijl

science/abinit: Broken on i386

Reported by:	fallout

science/abinit: Add the 'test' target

science/abinit: Add OPENMP and MPI options

science/abinit: Update 8.10.2 -> 8.10.3

Reported by:	portscout

science/abinit: Update 8.8.4 -> 8.10.2

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

Bump PORTREVISION for ports depending on the canonical version of GCC
in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which
has now moved from GCC 6 to GCC 7 by default.

This includes ports
 - featuring USE_GCC=yes or USE_GCC=any,
 - featuring USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and those
 - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
   c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.

PR:		222542

science/abinit: Update 8.8.3 -> 8.8.4

Reported by:	portscout

science/abinit: Update 8.8.2 -> 8.8.3

Reported by:	portscout

Re-add port: science/abinit: Full-featured atomic-scale first-principles
simulation software

I couldn't make MPI work, created a bug report.
Will add DOCS and EXAMPLES options later.

PR:		219025

Remove non staged ports without pending PR from s*

math/gsl:
- Add USES=libtool and bump dependent ports
- Add USES=pathfix and INSTALL_TARGET=install-strip

Approved by:	portmgr (implicit, bump unstage port)

- Update to 4.4.0
- Bump PORTREVISION for science/netcdf-fortran shlib change [1]

Changes:	https://github.com/Unidata/netcdf-fortran/blob/master/RELEASE_NOTES.md
Approved by:	portmgr (implicit, unstaged port) [1]

Reset maintainership for ports not staged with no pending PR

With hat:	portmgr

Fix LIB_DEPENDS

With hat:	portmgr

Fix some non default LIB_DEPENDS

With hat:	portmgr

Convert GMAKE to MAKE_CMD
Please note that lots of invocation of MAKE_CMD here are wrong as they do not
properly respect MAKE_ENV and friends

With hat:	portmgr

- Bump PORTREVISION for dependency change from science/netcdf-ftn and
  science/netcdf3-ftn to science/netcdf-fortran

Approved by:	portmgr (bapt)

Update the default version of GCC used in the Ports Collection from
GCC 4.6.4 to GCC 4.7.3.  This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.

Part II, Bump PORTREVISIONs.

PR:		182136
Supported by:	Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by:	bdrewery (two -exp runs)

Convert all USE_FORTRAN=yes to "USES=fortran, USE_GCC=yes".  In most cases
USE_GCC=yes has been omitted though.

Remove USE_FORTRAN handling from bsd.port.mk and bsd.gcc.mk.

Minor cleanups in some ports like USE_GMAKE, NOPORTDOCS,...

Exp-run:	bdrewery
Approved by:	portmgr (bdrewery)

science/abinit: depends explicitly on "python"

Reported by:	exp-run (PR 184591)
Approved by:	portmgr (blanket)

Update to libmpc version 1.0.1 which brings the following fixes:

 - Switched to automake 1.11.6, see CVE-2012-3386.
 - #14669: Fixed extraction of CC from gmp.h.
 - Fixed case of intermediate zero real or imaginary part in mpc_fma,
   found by hydra with GMP_CHECK_RANDOMIZE=1346362345.

This is on top of the following changes from version 1.0

 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
   invariant sections) for the documentation.
 - 100% of all lines are covered by tests
 - Renamed functions
   . mpc_mul_2exp to mpc_mul_2ui
   . mpc_div_2exp to mpc_div_2ui

Add NO_STAGE all over the place in preparation for the staging support (cat:
science)

- convert to the new perl5 framework
- convert USE_GMAKE to Uses

Approved by:	portmgr (bapt@, blanket)

Update math/gsl to 1.16 and adjust some dependent ports

Rectify USE_TEX to support both of teTeX and TeXLive.

TEX_DEFAULT:
	A knob to choose teTeX or TeXLive.  One can specify in /etc/make.conf.

USE_TEX:
	A knob for port developers.  Valid keywords are listed in
	bsd.tex.mk.

Remove *_DEPENDS from ports which depend on teTeX and add USE_TEX=tetex
instead to make migration to TeXLive easier.

- update png to 1.5.10

adjust linking and comments in dependent ports after the math/atlas update;
math/atlas-devel will be updated to use the same constructs at a later date

PR:             162706
Approved by:    miwi (portmgr)
Feature safe:   yes

 - remove MD5

Update math/gsl to 1.15, and adjust PORTREVISION
and LIB_DEPENDS of dependent ports

Sync to new bsd.autotools.mk

Punt autoconf267->autoconf268

Round one migration of ports from automake{19,110} to automake111

Autotools update.   Read ports/UPDATING 20100915 for details.

Approved by:    portmgr (for Mk/bsd.port.mk part)
Tested by:      Multiple -exp runs

Don't build packages for this on the Tier-2 archs; we simply don't
have enough power on the nodes, and this winds up slowing down our
builds.

Hat:            portmgr

- Fix build, abinit builds with science/netcdf3-ftn

Submitted by:   Sunpoet Po-Chuan Hsieh <sunpoet AT sunpoet.net>
Approved by:    maho
Notified by:    pav

- Bump PORTREVISION to chase the update of math/gsl

- update to 1.4.1
Reviewed by:    exp8 run on pointyhat
Supported by:   miwi

- update to jpeg-8

Chase math/gsl update,
bump PORTREVISION

Bump PORTREVISION for everything that sets USE_FORTRAN=yes which now
implies lang/gcc44 up from lang/gcc43.

Approved by:    portmgr

- bump all port that indirectly depends on libjpeg and have not yet been bumped
or updated
Requested by:   edwin

Fix build with NOPORTDOCS, NOPORTEXAMPLES.

Submitted by:   QAT

Fix build on amd64.

Spotted by: QAT and pav.

- Upgrade to 5.7.3
        Release notes at
        <http://www.abinit.org/Infos_v5.7/release_notes/release_notes.html>

- enable bindings to get the headers
        This requires makemake and GSL.

Approved by:    Maho (maintainer)

- Upgrade to 5.6.5;

- Install libabinit;

- Handle NOPORTDOCS and NOPORTEXAMPLES;

- s/test/regression-test/;

- Don't install under a versionned $PREFIX.

Approved by:    maho (maintainer)

Remove CONFIGURE_ENV

Submitted by:   gerald@

Bump PORTREVISION due to change of USE_FORTRAN=yes to GCC 4.3.

Update CONFIGURE_ARGS for how we pass CONFIGURE_TARGET to configure script.
Specifically, newer autoconf (> 2.13) has different semantic of the
configure target. In short, one should use --build=CONFIGURE_TARGET
instead of CONFIGURE_TARGET directly. Otherwise, you will get a warning
and the old semantic may be removed in later autoconf releases.

To workaround this issue, many ports hack the CONFIGURE_TARGET variable
so that it contains the ``--build='' prefix.

To solve this issue, under the fact that some ports still have
configure script generated by the old autoconf, we use runtime detection
in the do-configure target so that the proper argument can be used.

Changes to Mk/*:
 - Add runtime detection magic in bsd.port.mk

Conversion from (now defunct) autoconf-2.61 to autoconf-2.62

Tested by:      exp build run (erwin)

Switch autoconf dependencies from 2.53 or 2.59 to 2.61.

PR:             ports/116639
Submitted by:   aDe

Now we use USE_FORTRAN=yes to use FORTRAN compiler.

Temporary place distfile at maho/public_distdir.

Submitted by:   kris

Better support of CPU optimization. This should also fixes
the builds for amd64/ia64, sparc64 and some i[3-6]86 platforms.
However, flags may not be a very optimized ones.

A possible fix for fenner's distfile survey.

Submitted by:   fenner

Fix pkg-plist.

Submitted by:   pav.

* Update to 5.2.4
* make fetchable (fenner)
* Migrate to gfortran.
* Use gfortran compiled atlas/blas/lapack.

Remove USE_REINPLACE from all categories starting with S

Update to 4.6.5

Notified by: fenner, kris, and edwin

update to 4.4.5, and make fetchable

Submitted by:   kris, linimon, fenner

Update to 4.4.4 (preferred production version, robust)

Submitted by:   edwin

Add abinit, calculates total energy, charge density
and electronic structure of systems.