CVS commit: pkgsrc/math/py-netCDF4

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/math/py-netCDF4
From: "Adam Ciarcinski" <adam%netbsd.org@localhost>
Date: Mon, 5 Aug 2024 18:58:55 +0000

Module Name:    pkgsrc
Committed By:   adam
Date:           Mon Aug  5 18:58:55 UTC 2024

Modified Files:
        pkgsrc/math/py-netCDF4: Makefile PLIST distinfo
Added Files:
        pkgsrc/math/py-netCDF4: ALTERNATIVES

Log Message:
py-netCDF4: updated to 1.7.1.post1

ersion 1.7.1 (tag v1.7.1rel)

* include nc_complex source code from v0.2.0 tag (instead of using submodule).
* add aarch64 wheels.

version 1.7.0 (tag v1.7.0rel)

* add support for complex numbers via `auto_complex` keyword to `Dataset`
* fix for deprecated Cython `DEF` and `IF` statements using compatibility header
  with shims for unavailable functionality
* use `szip` as the library name on Windows
* add support for MS-MPI `MPI_Message` detection
* fix for issue 1306 - surprising result when indexing vlen str with non-contiguous
  indices.
* Fix bug in set_collective introduced in PR 1277 (collective mode was
  always set).

version 1.6.5 (tag v1.6.5rel)

* fix for issue 1271 (mask ignored if bool MA assinged to uint8 var)
* include information on specific object when reporting errors from netcdf-c
* python 3.12 wheels added, support for python 3.7 removed.

version 1.6.4 (tag v1.6.4rel)

* set path to SSL certificates internally, so https DAP URLs work with wheels
  Added certifi as a dependency.
* Added `isopen` method to `MFDataset` object to check if underlying files are open.

version 1.6.3 (tag v1.6.3rel)

* Use ``nc_put_vars`` for strided writes for netcdf-c >= 4.6.2
* _Unsigned="false" should be same as not having _Unsigned set
  _Unsigned now must be set to "true" or "True" for variable to be interpreted
  as unsigned, instead of just having _Unsigned be set (to anything).
* pypi wheels built with netcdf-c 4.9.1.

version 1.6.2 (tag v1.6.2rel)

* Added ``netCDF4.__has_set_alignment__`` property to help identify if the
  underlying netcdf4 supports setting the HDF5 alignment.
* Slicing multi-dimensional variables with an all False boolean index array
  now returns an empty numpy array (instead of raising an exception).
  Behavior now consistent with numpy slicing.
* fix problem with compiling using netcdf-c < 4.9.0
* pypi wheels build with netcdf-c 4.9.0.

version 1.6.1 (tag v1.6.1rel)

* add Dataset methods has_<name>_filter (where <name>=zstd,blosc,bzip2,szip)
  to check for availability of extra compression filters.
* release GIL for all C-lib calls
* Add support for nc_set_alignment and nc_get_alignment to control alignment
  of data within HDF5 files.

version 1.6.0 (tag v1.6.0rel)

* add support for new quantization functionality in netcdf-c 4.9.0 via "signficant_digits"
  and "quantize_mode" kwargs in Dataset.createVariable. Default quantization_mode is "BitGroom",
  but alternate methods "BitRound" and GranularBitRound" also supported.
* opening a Dataset in append mode (mode = 'a' or 'r+') creates a Dataset
  if one does not already exist (similar to python open builtin).
  Added a mode='x' option (as in python open) which is the same as mode='w' with
  clobber=False.
* allow createVariable to accept either Dimension instances or Dimension
  names in "dimensions" tuple kwarg
* remove all vestiges of python 2 in _netCDF4.pyx and set cython language_level
  directive to 3 in setup.py.
* add 'compression' kwarg to createVariable to enable new compression
  functionality in netcdf-c 4.9.0.  'None','zlib','szip','zstd','bzip2'
  'blosc_lz','blosc_lz4','blosc_lz4hc','blosc_zlib' and 'blosc_zstd'
  are currently supported. 'blosc_shuffle',
  'szip_mask' and 'szip_pixels_per_block' kwargs also added.
  compression='zlib' is equivalent to (the now deprecated) zlib=True.
  If the environment variable NETCDF_PLUGIN_DIR is set to point to the
  directory with the compression plugin lib__nc* files, then the compression plugins will
  be installed within the package and be automatically available (the binary
  wheels have this).  Otherwise, the environment variable HDF5_PLUGIN_PATH
  needs to be set at runtime  to point to plugins in order to use the new compression
  options.
* MFDataset did not aggregate 'name' variable attribute
* issue warning instead of raising an exception if missing_value or
  _FillValue can't be cast to the variable type when creating a
  masked array
* Define MPI_Session for compatibility with current mpi4py


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/math/py-netCDF4/ALTERNATIVES
cvs rdiff -u -r1.28 -r1.29 pkgsrc/math/py-netCDF4/Makefile
cvs rdiff -u -r1.1 -r1.2 pkgsrc/math/py-netCDF4/PLIST
cvs rdiff -u -r1.6 -r1.7 pkgsrc/math/py-netCDF4/distinfo

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

Modified files:

Index: pkgsrc/math/py-netCDF4/Makefile
diff -u pkgsrc/math/py-netCDF4/Makefile:1.28 pkgsrc/math/py-netCDF4/Makefile:1.29
--- pkgsrc/math/py-netCDF4/Makefile:1.28        Wed May 29 16:33:28 2024
+++ pkgsrc/math/py-netCDF4/Makefile     Mon Aug  5 18:58:55 2024
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.28 2024/05/29 16:33:28 adam Exp $
+# $NetBSD: Makefile,v 1.29 2024/08/05 18:58:55 adam Exp $
 
-DISTNAME=      netCDF4-1.5.8
-PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
-PKGREVISION=   8
+DISTNAME=      netcdf4-1.7.1.post1
+PKGNAME=       ${PYPKGPREFIX}-${DISTNAME:S/cdf/CDF/}
 CATEGORIES=    math python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=n/netCDF4/}
 
@@ -11,6 +10,11 @@ HOMEPAGE=    https://github.com/Unidata/net
 COMMENT=       Object-oriented python interface to netCDF version 4
 LICENSE=       mit
 
+WHEEL_NAME=    netCDF4-${PKGVERSION_NOREV}
+
+TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools>=61:../../devel/py-setuptools
+TOOL_DEPENDS+= ${PYPKGPREFIX}-wheel-[0-9]*:../../devel/py-wheel
+DEPENDS+=      ${PYPKGPREFIX}-certifi-[0-9]*:../../security/py-certifi
 DEPENDS+=      ${PYPKGPREFIX}-cftime-[0-9]*:../../time/py-cftime
 
 USE_TOOLS+=    pkg-config
@@ -21,9 +25,13 @@ SUBST_SED.paths+=    -e 's,/usr/local,${PRE
 SUBST_FILES.paths+=    setup.py
 SUBST_MESSAGE.paths=   Fixing header search paths.
 
-PYTHON_VERSIONS_INCOMPATIBLE+= 27 38
+PYTHON_VERSIONS_INCOMPATIBLE=  27 38
 
-USE_PKG_RESOURCES=     yes
+post-install:
+.for bin in nc3tonc4 nc4tonc3 ncinfo
+       cd ${DESTDIR}${PREFIX}/bin && \
+       ${MV} ${bin} ${bin}-${PYVERSSUFFIX} || ${TRUE}
+.endfor
 
 do-test:
        cd ${WRKSRC}/test && ${SETENV} ${TEST_ENV} ${PYTHONBIN} run_all.py
@@ -31,6 +39,6 @@ do-test:
 .include "../../devel/hdf5/buildlink3.mk"
 .include "../../devel/netcdf/buildlink3.mk"
 .include "../../devel/py-cython/buildlink3.mk"
-.include "../../lang/python/egg.mk"
+.include "../../lang/python/wheel.mk"
 .include "../../math/py-numpy/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"

Index: pkgsrc/math/py-netCDF4/PLIST
diff -u pkgsrc/math/py-netCDF4/PLIST:1.1 pkgsrc/math/py-netCDF4/PLIST:1.2
--- pkgsrc/math/py-netCDF4/PLIST:1.1    Wed Oct  2 21:14:42 2019
+++ pkgsrc/math/py-netCDF4/PLIST        Mon Aug  5 18:58:55 2024
@@ -1,17 +1,19 @@
-@comment $NetBSD: PLIST,v 1.1 2019/10/02 21:14:42 minskim Exp $
-${PYSITELIB}/${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
+@comment $NetBSD: PLIST,v 1.2 2024/08/05 18:58:55 adam Exp $
+bin/nc3tonc4-${PYVERSSUFFIX}
+bin/nc4tonc3-${PYVERSSUFFIX}
+bin/ncinfo-${PYVERSSUFFIX}
+${PYSITELIB}/${WHEEL_INFODIR}/LICENSE
+${PYSITELIB}/${WHEEL_INFODIR}/METADATA
+${PYSITELIB}/${WHEEL_INFODIR}/RECORD
+${PYSITELIB}/${WHEEL_INFODIR}/WHEEL
+${PYSITELIB}/${WHEEL_INFODIR}/entry_points.txt
+${PYSITELIB}/${WHEEL_INFODIR}/top_level.txt
 ${PYSITELIB}/netCDF4/__init__.py
 ${PYSITELIB}/netCDF4/__init__.pyc
 ${PYSITELIB}/netCDF4/__init__.pyo
+${PYSITELIB}/netCDF4/_netCDF4.pyx
 ${PYSITELIB}/netCDF4/_netCDF4.so
+${PYSITELIB}/netCDF4/plugins/empty.txt
 ${PYSITELIB}/netCDF4/utils.py
 ${PYSITELIB}/netCDF4/utils.pyc
 ${PYSITELIB}/netCDF4/utils.pyo
-bin/nc3tonc4
-bin/nc4tonc3
-bin/ncinfo

Index: pkgsrc/math/py-netCDF4/distinfo
diff -u pkgsrc/math/py-netCDF4/distinfo:1.6 pkgsrc/math/py-netCDF4/distinfo:1.7
--- pkgsrc/math/py-netCDF4/distinfo:1.6 Thu Dec 16 09:53:28 2021
+++ pkgsrc/math/py-netCDF4/distinfo     Mon Aug  5 18:58:55 2024
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.6 2021/12/16 09:53:28 adam Exp $
+$NetBSD: distinfo,v 1.7 2024/08/05 18:58:55 adam Exp $
 
-BLAKE2s (netCDF4-1.5.8.tar.gz) = 305344f0fa526171e71e15da2e82691b6699edf53eac5577f531f988ba8c288b
-SHA512 (netCDF4-1.5.8.tar.gz) = b43e10356a60ecdd1aaa7585648242e9d610e042da8fd97f374617d7813cc9f35b4133a88ac4c10e921df12d5b2f2b1668af4fb69578b57b7c3d57a731579260
-Size (netCDF4-1.5.8.tar.gz) = 767013 bytes
+BLAKE2s (netcdf4-1.7.1.post1.tar.gz) = 2043052aad92055cd2d8bfc26c15054639fd0991bc0f976e91d215a93c0f3787
+SHA512 (netcdf4-1.7.1.post1.tar.gz) = 34c5a7295b9860ad74a14444272e5db964e8684c48216eeff1ccebcb86a3fccba842ceac61849f74b2be0da12ea1a794938c9856f1c3ed76160e1093d8b3f710
+Size (netcdf4-1.7.1.post1.tar.gz) = 827730 bytes

Added files:

Index: pkgsrc/math/py-netCDF4/ALTERNATIVES
diff -u /dev/null pkgsrc/math/py-netCDF4/ALTERNATIVES:1.1
--- /dev/null   Mon Aug  5 18:58:55 2024
+++ pkgsrc/math/py-netCDF4/ALTERNATIVES Mon Aug  5 18:58:55 2024
@@ -0,0 +1,3 @@
+bin/nc3tonc4 @PREFIX@/bin/nc3tonc4-@PYVERSSUFFIX@
+bin/nc4tonc3 @PREFIX@/bin/nc4tonc3-@PYVERSSUFFIX@
+bin/ncinfo @PREFIX@/bin/ncinfo-@PYVERSSUFFIX@

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