py-netcdf4: revert most changes in previous commit, and finish update to 1.2.4

[Thomas Klausner <wiz%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Thomas Klausner <wiz%NetBSD.org@localhost>
Pushed By:	wiz
Date:		Thu Sep 29 15:35:47 2016 +0200
Changeset:	74c1b7d954c2761cb4a4ae7b64fedca3a671e53c

Modified Files:
	py-netcdf4/DESCR
	py-netcdf4/Makefile
	py-netcdf4/PLIST

Log Message:
py-netcdf4: revert most changes in previous commit, and finish update to 1.2.4

Changes to 1.1.8:

 version 1.2.4 (tag v1.2.4rel)
==============================
 * Fix for issue #554.  It is now ensured that data is in native endian
   byte order before passing to netcdf-c library.  Data read from variable
   with non-native byte order is also byte-swapped, so that dtype remains
   consistent with netcdf variable.  Behavior now consistent with h5py.
 * raise warning for HDF5 1.10.x (issue #549), since backwards
   incompatible files may be created.
 * raise AttributeError instead of RuntimeError when attribute operation
   fails.  raise IOError instead of RuntimeError when nc_create or
   nc_open fails (issue #546).
 * Use NamedTemporaryFile instead of deprecated mktemp in tests
   (pull request #543).
 * add AppVeyor automated windows tests (pull request #540).

 version 1.2.3.1 (tag v1.2.3.1rel)
==================================
 * fix bug in setup.py (pull request #539, introduced in issue #518).

 version 1.2.3 (tag v1.2.3rel)
==============================
 * try to avoid writing NC_STRING attributes if possible, by
   trying to convert unicode strings to ascii and write as NC_CHAR (issue
   #529).  This preserves compatibility with clients (like Matlab) that
   can't deal with NC_STRING attributes. A 'setncattr_string' method
   was added for Dataset and Variable to that users can force attributes
   to be written as NC_STRING if necessary.
 * fix failing tests with numpy 1.11 (issues #521 and #522).
 * fix indentation bug in nc4tonc3 utility (issue #519).
 * add the capability in setup.py to use pkg-config instead of
   nc-config (pull request #518).
 * make sure slices which return scalar masked arrays
   are consistent with numpy.ma (issue #515).
 * add test/tst_cdf5.py and test/tst_filepath.py (to test new
   NETCDF3_64BIT_DATA format and filepath Dataset method).
 * expose netcdftime.__version__ (issue #504).
 * fix potential memory leak in Dataset.filepath in attempt to fix
   mysterious segfaults on CentOS6 (issue #506). Segfaults
   can apparently still occur on systems like CentOS6 with old versions of glibc.

 version 1.2.2 (tag v1.2.2rel)
 =============================
 * fix failing tests on python 2.6 (issue #497). Change minimum required
   python from 2.5 to 2.6.
 * Potential memory leaks fixed by freeing string pointers internally allocated
   in netcdf-c using nc_free_string. Also use nc_free_vlens to free space allocated
   for vlens inside netcdf-c (issue #495).
 * invoke str on filename argument to Dataset constructor, so pathlib
   instances can be used (issue #489).
 * don't use hardwired NC_MAX_DIMS or NC_MAX_VARS internally to allocate space
   for dimension or variable ids.  Instead, find out the number of dims
   and vars and use malloc.  NC_MAX_NAME is still used to allocate space
   for attribute and variable names, since there is no obvious way to
   determine the length of these names.
 * if trying to write a unicode attribute, check to see if it exists
   first and is NC_CHAR, and if so, delete it and recreate it.  Workaround for C
   lib bug discovered in issue #485.
 * support for NETCDF3_64BIT_DATA format supported in netcdf-c 4.4.0.
   Similar to NETCDF3_64BIT (now NETCDF3_64BIT_OFFSET), but includes
   64 bit dimensions and sizes, plus unsigned and 64 bit integer
   data types.
 * make sure chunksize does not exceed dimension size
   (for non-unlimited dimensions) on variable creation (issue #480).
 * add 'size' attribute to Dimension (same as len(d), where
   d is a Dimension instance, issue #477).
 * fix bug in nc3tonc4 with --unpackshort=1 (issue #474).
 * dates do not have to be contiguous, i.e. can be before and after the
   missing dates in Gregorian calendar (pull request #476).

 version 1.2.1 (tag v1.2.1rel)
 =============================
 * add the capability to slice variables with unsorted integer sequences,
   or integer sequences with duplicates (issue #467). This was done
   by converting boolean array slices to integer array slices internally,
   instead of the other way around.
 * raise TypeError if masked array assigned to a VLEN str variable slice
   (issue #464).
 * Ellipsis now can be used with scalar VLEN str variables (issue #458).
   Slicing of scalar VLEN (non-str) variables now works.
 * Allow non-positive reference years in non-real-world calendars
   (issue #442).

 version 1.2.0 (tag v1.2.0rel)
 =============================
 * Fixes to setup.py for building on windows (issue #460).
 * warnings now issued if file being read contains unsupported
   variables or data types (they were previously being silently
   skipped).
 * added 'get_variables_by_attributes' method (issue #454).
 * check for 'units' attribute in date2index (issue #453).
 * added support for enum types (issue #452).
 * added 'isopen' Dataset method (issue #450).
 * raise ValueError if year 0 or negative year used in time units string.
   The year 0 does not exist in the Julian and Gregorian
   calendars (issue #442).

 version 1.1.9 (tag v1.1.9rel)
 =============================
 * fix for issue #391 (data is already byte-swapped to native
   endian format by the HDF4 library).
 * fix for issue #415 (copy.deepcopy does not work on
   netcdftime datetime object).
 * fix for issue #420 - len(v) where v is a scalar variable returned
   unexpected IndexError, now returns "TypeError: len() on unsized object"
   (same as numpy does for len() on a scalar array).
 * translate docstrings from epydoc markup to markdown, so
   pdoc can be used (epydoc is dead).
 * add small offset in conversion to Julian date for numerical
   stability (more accurate round trip calculations). This offset is removed
   in back conversion only from microseconds. Pull request #433.
 * add detection of unsigned integers to handling of automatic
   packing (set_auto_scale and set_auto_maskandscale) when writing.
   Pull request #435.
 * use USE_SETUPCFG env var to over-ride use of setup.cfg. If USE_SETUPCFG
   evaluates to false, setup.cfg will not be used and all configuration
   variables can be set from environment variables.  Useful when using 'pip
   install' and nc-config is broken (issue #438).
 * fix for integer overflow in date2index (issue #444).

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=74c1b7d954c2761cb4a4ae7b64fedca3a671e53c

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 py-netcdf4/DESCR    |  6 ++++++
 py-netcdf4/Makefile | 11 ++++-------
 py-netcdf4/PLIST    | 23 +++++++++++++++++++++++
 3 files changed, 33 insertions(+), 7 deletions(-)

diffs:
diff --git a/py-netcdf4/DESCR b/py-netcdf4/DESCR
index e69de29..5c64ae1 100644
--- a/py-netcdf4/DESCR
+++ b/py-netcdf4/DESCR
@@ -0,0 +1,6 @@
+netCDF version 4 has many features not found in earlier versions of the library,
+such as hierarchical groups, zlib compression, multiple unlimited dimensions,
+and new data types.  It is implemented on top of HDF5.  This module implements
+most of the new features, and can read and write netCDF files compatible with
+older versions of the library.  The API is modelled after Scientific.IO.NetCDF,
+and should be familiar to users of that module.
diff --git a/py-netcdf4/Makefile b/py-netcdf4/Makefile
index 3c26b44..3249c8f 100644
--- a/py-netcdf4/Makefile
+++ b/py-netcdf4/Makefile
@@ -3,16 +3,14 @@
 DISTNAME=	netCDF4-1.2.4
 PKGNAME=	${PYPKGPREFIX}-${DISTNAME:tl}
 CATEGORIES=	devel python
-MASTER_SITES=	https://pypi.python.org/packages/b2/a3/8ddc328fd9067e98f03884fb7de5900c43cbe609eb75b3fd516c211a1012/
+MASTER_SITES=	${MASTER_SITE_PYPI:=n/netCDF4/}
 
 MAINTAINER=	jihbed.research%gmail.com@localhost
 HOMEPAGE=	http://code.google.com/p/netcdf4-python/
 COMMENT=	Python/numpy interface to netCDF library (versions 3 and 4)
-#LICENSE=	# TODO: (see mk/license.mk)
+LICENSE=	mit
 
-WRKSRC=	${WRKDIR}/netCDF4-1.2.4
-
-USE_TOOLS+= pkg-config
+USE_TOOLS+=	pkg-config
 
 SUBST_CLASSES+=		paths
 SUBST_STAGE.paths=	pre-configure
@@ -23,9 +21,8 @@ SUBST_MESSAGE.paths=	Fixing header search paths.
 do-test:
 	${RUN} cd ${WRKSRC}/test; ${SETENV} ${TEST_ENV} ${PYTHONBIN} run_all.py
 
-
-
 .include "../../devel/hdf5/buildlink3.mk"
+.include "../../devel/netcdf/buildlink3.mk"
 .include "../../devel/py-cython/buildlink3.mk"
 .include "../../lang/python/egg.mk"
 .include "../../math/py-numpy/buildlink3.mk"
diff --git a/py-netcdf4/PLIST b/py-netcdf4/PLIST
index 48d96a5..ff51b28 100644
--- a/py-netcdf4/PLIST
+++ b/py-netcdf4/PLIST
@@ -1 +1,24 @@
 @comment $NetBSD$
+bin/nc3tonc4
+bin/nc4tonc3
+bin/ncinfo
+${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
+${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
+${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
+${PYSITELIB}/${EGG_INFODIR}/entry_points.txt
+${PYSITELIB}/${EGG_INFODIR}/requires.txt
+${PYSITELIB}/${EGG_INFODIR}/top_level.txt
+${PYSITELIB}/netCDF4/__init__.py
+${PYSITELIB}/netCDF4/__init__.pyo
+${PYSITELIB}/netCDF4/__init__.pyc
+${PYSITELIB}/netCDF4/utils.pyo
+${PYSITELIB}/netCDF4/utils.pyc
+${PYSITELIB}/netCDF4/_netCDF4.so
+${PYSITELIB}/netCDF4/utils.py
+${PYSITELIB}/netcdftime/__init__.py
+${PYSITELIB}/netcdftime/__init__.pyo
+${PYSITELIB}/netcdftime/__init__.pyc
+${PYSITELIB}/netcdftime/netcdftime.pyo
+${PYSITELIB}/netcdftime/netcdftime.pyc
+${PYSITELIB}/netcdftime/_datetime.so
+${PYSITELIB}/netcdftime/netcdftime.py