Fix packaging with python3*, PYTHON_PYOEXTENSION and py3kplist should not
be used together

PR:		220986
With hat:	portmgr

Don't add the distfile twice.

This fixes a fetch error:

  => numpy-numpy-v1.13.1_GH0.tar.gz doesn't seem to exist in
  /portdistfiles/.
  => Attempting to fetch
 
https://codeload.github.com/numpy/numpy/tar.gz/v1.13.1?dummy=/numpy-numpy-v1.13.1_GH0.tar.gz
  fetch: 4336552: No such file or directory
  numpy-numpy-v1.13.1_GH0.tar.gz                           0  B    0  Bps
  => Attempting to fetch
  http://distcache.FreeBSD.org/ports-distfiles/numpy-numpy-v1.13.1_GH0.tar.gz
  fetch: 4336552: No such file or directory
  => Couldn't fetch it - please try to retrieve this
  => port manually into /portdistfiles/ and try again.

Sponsored by:	Absolight

- Update MASTER_SITES, now get source from github and doc from docs.scipy.org
  (Based on PR/181285)

- Update to 1.13.1

PR:		220986
Submitted by:	wen@(myself)
Exp-run by:	antoine@

Bump PORTREVISIONs for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some
circumstances such as versions of FreeBSD or platforms).

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

PR:		216707

- Remove dependency on math/openblas if other blas lib is selected

PR:		215764
Submitted by:	riggs@

Bump PORTREVISIONS for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some
circumstances such as versions of FreeBSD or platforms), part II.

The first part covered  ports with USE_GCC=yes, USE_GCC=any, or one of
gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang,
c++11-lang, c++0x, c11 requested via USES=compiler.

This adds ports with USES=fortran and ports using Mk/bsd.octave.mk
which in turn has USES=fortran.

PR:		214965
Reported by:	thierry

Update to 1.11.2

Changes:
https://github.com/numpy/numpy/blob/v1.11.2/doc/release/1.11.2-notes.rst

- Update to 1.11.1
- Adjust dependencies, 'numpy/core/multiarray.so' is also linked to
math/openblas (reported by QA script)
- Add patches in order to detect 'sys/endian.h' header

Remove ${PORTSDIR}/ from dependencies, categories m, n, o, and p.

With hat:	portmgr
Sponsored by:	Absolight

Update to 1.11.0

Changes: https://github.com/numpy/numpy/blob/master/doc/release/1.11.0-notes.rst

- Update to 1.10.4
- Remove DOCVERSION (use SF host to fetch PDF documentation, more up-to-date
than SciPy.org)

Changes: https://github.com/numpy/numpy/blob/master/doc/release/1.10.4-notes.rst

- Update to 1.10.2
- Reintroduce DOCVERSION variable, PDF documentation is not synchronized with
release
- Add missing dependency [1] for NETLIB option

PR:		203638 [1]
Submitted by:	John Hein [1]

- Update to 1.10.1
- Add SF to MASTER_SITES
- Add LICENSE_FILE
- Remove DOCVERSION

Changes:	https://github.com/numpy/numpy/blob/master/doc/release/1.10.1-notes.rst

- Update MASTER_SITES
- Update documentation to 1.10.0
- Bump PORTREVISION for package change

Unbreak build on FreeBSD 9

Reported by:	pkg-fallout, <soralx@cydem.org> (private email)

Update to 1.10.0

- Convert to new options target helper
- Cosmetic change

Depend on a particual file, not an executable so it picks up a correct
python version.

PR:		198989
Submitted by:	John W. O'Brien <john@saltant.com>

Allow to use OpenBLAS implementation of BLAS.
Based on the work done by Eijiro Shibusawa <phd_kimberlite@yahoo.co.jp>,
OpenBLAS port maintainer.

Hide py-nose dependency under new TESTS option.
Convert to USES=blaslapack.

Differential Revision:	D2060
Reviewed by:	koobs, thierry

Update to version 1.9.2.
This is minor bugfix release, see notes at
http://sourceforge.net/projects/numpy/files/NumPy/1.9.2/

- Tiny fix to f2py2e.py to allow it to deal with -fstack-protector flag
  as without this fix, f2py will attempt to compile -fstack-protector

Submitted by:	db
Reviewed by:	wg
Approved by:	wg

Update to version 1.9.1

Phabric:	D998

Fix
ImportError: /lib/libgcc_s.so.1: version GCC_4.6.0 required by
/usr/local/lib/gcc48/libgfortran.so.3 not found
error when importing numpy module.

PR:		188114
Patch by Thierry Thomas <thierry@FreeBSD.org>

Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)

- Add DOCS to OPTIONS_DEFINE
- Convert to new options helper

- Convert USE_PYTHON to USES=python
- Enable math/py-numpy to be installed for different Python versions
  concurrently

Phabric:	D599
Reviewed by:	db
With hat:	python@

math/py-numpy: Use INSTALLS_EGGINFO, fixes pkg_resources detection

Python packages installs .egg-info metadata directories when
--single-version-externally managed is specified, as the Python ports
framework does currently for all ports when USE_PYDISTUTILS is defined.

In this case the py-numpy port does *not* currently define
PYDISTUTILS_AUTOPLIST nor INSTALLS_EGGINFO, which precludes the contents of
the add-plist-egginfo: target from being executed.

This results in an .egg-info metadata directory being built, and staged, but
not installed.

Correctly specify INSTALLS_EGGINFO to compensate.

Additionally add an "Open" Goal Wiki entry [1] to look at automatically
detecting the
presence of .egg-info metadata directories, since all ports leveraging
USE_PYDISTUTILS also use the --record mechanism for generating installed
file lists, and potentially deprecating INSTALLS_EGGINFO and related variables.

[1] https://wiki.freebsd.org/Python#Goals

PR:		191865
Submitted by:	 John W. O'Brien <john at saltant dot com>

Update to version 1.8.1.

- Fix compiler now that -Wl,B has been added to fortran link args

Submitted by:	me

Replace TABs with spaces, otherwise it breaks with python-3.

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)

Fix path.

Respect FFLAGS.

Submitted by:	wg
Tested by:	gerald

- this change sneaked in by accident. Reverting that.

- clean-up WITH_FIXED_FENV conditional, because it is only used for
  versions of FreeBSD, we not support anymore.
- remove LATEST_LINK. There is PYTHON_PKGNAMEPREFIX set and in future
  we may have this package built against different python versions.

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)

- update to 1.8.0
- clarify LICENSE (BSD3C)
- suppor staging

while here:
- utilize PYTHON_PY3K_PLIST_HACK
- install docs uncoditionally into stage area
- convert LIB_DEPENDS to the new notation
- sort packing list

PR:		186677
Submitted by:	Johannes Jost Meixner <xmj@chaot.net>

Reset maintainer for llwang@infor.org

Reset maintainership for llwang@infor.org due to multiple timeouts and email
address permanent failure. Return all ports to the free pool except
py-numpy, which is taken under the wing of the python@ team.

We thank you for your contribution to the FreeBSD project

Approved by:	portmgr

math/py-numpy: Remove Atlas WITH_STATIC notification using ECHO_MSG

Shell commands can't be used in a Makefile without a target. Remove the atlas
WITH_STATIC messaging until a more suitable mechanism can be found.

PR:		ports/184775
Reported by:	Roland Smith <rsmith@xs4all.nl>

math/py-numpy: Add missing ending quotation to ECHO_MSG

Add a missing ending quotation from the last ECHO_MSG command added in r336423.

PR:		ports/184775
Reported by:	Roland Smith <rsmith@xs4all.nl>

math/py-numpy: Fix static library check that assumes atlas is installed

- Use BUILD_DEPENDS to check for the atlas static library at pre-build
  time instead of checking if the file exists (False if atlas is not
  installed)

- Replace IGNORE with a message to the user notifying them that
  an atlas install WITH_STATIC is needed, and provide clues as possible
  actions without being too prescriptive.

As discussed with eadler@, a correct resolution to "ports depending on other
ports with specific OPTIONS" is either an atlas slave port
(ie: atlas-static), or to modify atlas to install both shared and static
libraries.

This change is a net gain on the existing broken behaviour, by fixing
the check, while retaining the user notification.

PR:		ports/178094
Reviewed by:	jhibbits, eadler
Approved by:	maintainer timeout (7+ months)

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:
math)

Add missing files to plist;
Fix plist (hopefully) so it fits both python33 and python2.

Fix DISTFILES for docs.

Noted by:	Rainer Hurling <rhurlin@gwdg.de>

Update to version 1.7.0 (and unbreak with python-3.3).

PR:		178256
Submitted by:	Roland Smith <rsmith@xs4all.nl>
Approved by:	maintainer

- Fix all cases of 'No newline at end of file' in ports tree

Approved by: portmgr (bapt)

- Remove automatic dependency to SuiteSparse; use OPTIONS instead
- Change to new OPTIONS style

PR:		ports/171349
Submitted by:	Li-Lun Wang <llwang@infor.org> (maintainer)
Reported by:	A.J. Kehoe IV (Nanoman)

- Restore distinfo of fenv.c/fenv.h for older FreeBSD which were removed in the
commit of 1.6.2 update

PR:		ports/170224
Submitted by:	Li-Lun Wang <llwang@infor.org>

- Update to 1.6.2
- Add LICENSE

PR:             169162
Submitted by:   koobs <koobs.freebsd@gmail.com>
Approved by:    maintainer

- Support for -Wl,rpath= in f2py, now passed by bsd.gcc.mk
- Fix build for comms/wsjt

PR:             ports/164479
Submitted by:   maintainer
Approved by:    gabor (mentor)

- Update to 1.6.1

PR:             162894
Submitted by:   Gereon Kaiping <kta1c10!gereon@linta.de>
Approved by:    "Li-Lun Leland Wang" <llwang@infor.org> (maintainer)
Feature safe:   yes

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

- Update math/py-numpy to reflect changes in math/atlas
- Bump PORTREVISION
- Fix build for science/py-scipy

PR:             ports/161400
Submitted by:   Li-Lun Wang <llwang at infor.org> (maintainer)

- Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS)
- Fix all ports that add {CPP,LD}FLAGS to *_ENV to modify flags instead

PR:             157936
Submitted by:   myself
Exp-runs by:    pav
Approved by:    pav

- Slightly simplify the fenv fix, and note that FreeBSD
7.3 and 7.4 no longer need the fix after the MFC of r203441 on
17 February 2010

- While here, remove MD5 checksums in distinfo

PR:             154742
Approved by:    makc, miwi (mentors, implicit)
                Li-Lun Wang (maintainer)

Update to 1.5.1
Fix doc checksum mismatch

PR:             ports/152715
Submitted by:   Li-Lun Wang (llwang@infor.org) (maintainer)
Approved by:    itetcu (mentor) (implicit)

- Update to 1.5.0

PR:             ports/151234
Submitted by:   Li-Lun Wang (Leland Wang) <llwang@infor.org> (maintainer)

- Update to 1.4.1

PR:             ports/146007
Submitted by:   Wen Heping (myself)
Approved by:    maintainer

Unbreak.

PR:             143529
Patch from:     MAINTAINER ("Li-Lun Wang (Leland Wang)" <llwang@infor.org>)

- Mark BROKEN: does not build

Reported by:    pointyhat
Feature safe:   yes

- Update to 1.4.0

PR:             ports/142116
Submitted by:   wen
Approved by:    "Li-Lun Wang (Leland Wang)" <llwang AT infor.org> (maintainer)

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

Approved by:    portmgr

- Switch SourceForge ports to the new File Release System: categories starting
with M

* Fix build of science/py-scipy when math/suitesparse is installed, by
  correctly detect and depend on it in math/py-numpy
* Replace the old numpy documentation with the new numpy book
* Explicitly tell the distutil to use gnu95 fortran compiler
* Use ${PYTHONPREFIX_SITELIBDIR} rather than ${PYTHON_SITELIBDIR} when
  generating the packing list for science/py-scipy
* Bump PORTREVISIONs, for packing lists are changed

PR:             ports/136058
Submitted by:   Li-Lun Wang (Leland Wang) <llwang AT infor.org> (maintainer)

- Update to  1.3.0

PR:             134221
Submitted by:   Wen Heping <wenheping@gmail.com>
Approved by:    maintainer timeout

- Update to 1.2.1

PR:             ports/129581
Submitted by:   Wen Heping <wenheping@gmail.com>
Approved by:    Li-Lun "Leland" Wang" <llwang@infor.org> (maintainer)

Remove run-time dependency on lang/gcc42 which is now transparently
handled by USE_FORTRAN.  Tweak various aspects of configuration.

Submitted by:   Li-Lun "Leland" Wang <llwang@infor.org> (maintainer)

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

- Update to 1.2.0

PR:             127865
Submitted by:   Wen heping <wenheping@gmail.com>
Approved by:    maintainer

- Fix installation while WITH_ATLAS is specified [1]
- Fix plist

PR:             ports/126960 [1]
Submitted by:   Arjan Gijsberts <arjan AT liralab.it>
Approved by:    maintainer
Approved by:    portmgr (erwin)

Restore PORTEPOCH that got lost in the previous revision.

Update to 1.1.1

- Add lang/gcc42 into RUN_DEPENDS
- Remove ${PYTHON_REL} < 200 old stuff
- Remove definitions that already include in bsd.gcc.mk

Approved by:    maintainer via IRC

- Update to 1.0.4

PR:             ports/122492
Submitted by:   dikshie <dikshie at lapi.itb.ac.id>
Approved by:    Li-Lun "Leland" Wang <llwang at infor.org> (maintainer)

- Remove CONFLICT, lang/f2py removed

Approved by:    miwi (co-mentor)

- I added -fPIC to compile_switch to work around build of fftpack in scipy
  on amd64.
  A better fix would be to set pic_flags instead, and have scipy build a
  shared object for dfftpack instead a static archive, but I didn't figure
  out how. [1]
- Pass maintainership to llwang@infor.org

PR:             ports/112429 [1]
Submitted by:   Li-Lun "Leland" Wang <llwang@infor.org> (new maintainer)

- USE_FORTRAN=yes to use FORTRAN compiler.

Notified by:    maho
Approved by:    ehaupt (mentor)

- Forgotten files for 1.0.2 commit

Approved by:    ehaupt (mentor)

Update distinfo, was forgotten by the last commit.

Notified by:    bf <bf2006a@yahoo.com>

- Remove support for 4.x
- Fix glitch with gfortran attempting to use libg2c instead of libgfortran [1]
- math/py-numpy incorrect post-patch for site-cfg [2]
- Update version to 1.0.2

Notified by:    kris (via pointyhat) [1]
PR:             ports/112429 [2]
Approved by:    ehaupt (mentor)

- maho wants WANT_FORTRAN knob in gfortran ports

Submitted by:   maho
Approved by:    ehaupt (mentor)

- finish g77 to gfortran conversion
- change maintainer address to FreeBSD.org one
- fold in changes suggested by [1]

PR:             107022, 108807 (based on) [1]
Submitted by:   thinker@heaven.branda.to [1]
Approved by: ehaupt (mentor)

(Forgot to commit)
* Migrate to gfortran.
* Bump port revision.

* Migrate to gfortran.
* Bump port revision.

Approved by:  portmgr(kris)

- Update to 1.0.1

PR:             ports/107729
Submitted by:   clsung
Approved by:    maintainer (Diane Bruce)

Fix a run time error, don't append python version to the name of the
executable.

Submitted by:   Diane Bruce (maintainer)
Approved by:    tmclaught (implicit)

Update to version 1.0
Change maintainer

PR:             106551
Submitted by:   Diane Bruce <db@db.net>
Approved by:    tmclaugh (implicit)

Reassign maintainership to db@db.net who has been been awaiting maintainer-
timeouts with the PRs she has submitted.

Hat:            portmgr

- Update to 1.0rc1
- Add options for ATLAS
- Fix ATLAS detection
- Use feclearexcept(3) rather than fpsetsticky(3) on 5.3+
- Add CONFLICTS for f2py. Both ports install bin/f2py

PR:             ports/103827
Submitted by:   Li-Lun Wang
Approved by:    maintainer timeout (6 weeks)

- Mark BROKEN on FreeBSD 4.X: does not compile

Reported by:    krismail

The fundamental package needed for scientific computing with Python is
called NumPy.  This package contains:

    * a powerful N-dimensional array object
    * sophisticated (broadcasting) functions
    * basic linear algebra functions
    * basic Fourier transforms
    * sophisticated random number capabilities
    * tools for integrating Fortran code.

NumPy derives from the old Numeric code base and can be used as a
replacement for Numeric.   It also adds the features introduced by numarray
and can also be used to replace numarray.

Note:   Development for Numeric has ceased, and users should transisition to
        NumPy as quickly as possible.

WWW: http://numpy.scipy.org/

PR:             ports/102458
Submitted by:   Tony Maher <anthony.maher@uts.edu.au>