From c25c53d5dca620c2db78f88fb90fccb9f9dfa25b Mon Sep 17 00:00:00 2001 From: Jeff Whitaker Date: Sun, 20 Jun 2021 13:11:25 -0600 Subject: [PATCH 1/3] update Changelog and docs/index.html --- Changelog | 4 ++-- docs/index.html | 19 ++++++++++--------- 2 files changed, 12 insertions(+), 11 deletions(-) diff --git a/Changelog b/Changelog index 2b129986b..efa2121a0 100644 --- a/Changelog +++ b/Changelog @@ -1,5 +1,5 @@ - version 1.5.7 (not yet released) -================================= + version 1.5.7 (tag v1.5.7rel) +============================== * don't try to mask vlens with default _FillValue, since vlens don't have a default _FillValue. This gets rid of numpy DeprecationWarning (issue #1099). * update docs to reflect the fact that a variable must be in collective mode before writing diff --git a/docs/index.html b/docs/index.html index 154907fa4..149208924 100644 --- a/docs/index.html +++ b/docs/index.html @@ -641,11 +641,9 @@

Groups in a netCDF file

object yields summary information about it's contents.

>>> def walktree(top):
-...     values = top.groups.values()
-...     yield values
+...     yield top.groups.values()
 ...     for value in top.groups.values():
-...         for children in walktree(value):
-...             yield children
+...         yield from walktree(value)
 >>> print(rootgrp)
 <class 'netCDF4._netCDF4.Dataset'>
 root group (NETCDF4 data model, file format HDF5):
@@ -987,8 +985,9 @@ 
Writing data
 The result will be a numpy scalar array.

 
 
By default, netcdf4-python returns numpy masked arrays with values equal to the
-missing_value or _FillValue variable attributes masked.  The
-Dataset.set_auto_mask Dataset and Variable methods
+missing_value or _FillValue variable attributes masked for primitive and
+enum data types.
+The Dataset.set_auto_mask Dataset and Variable methods
 can be used to disable this feature so that
 numpy arrays are always returned, with the missing values included. Prior to
 version 1.4.0 the default behavior was to only return masked arrays when the
@@ -1596,7 +1595,7 @@ 
In-memory (diskless) Datasets

 the parallel IO example, which is in examples/mpi_example.py.
 Unit tests are in the test directory.

 
-
contact: Jeffrey Whitaker jeffrey.s.whitaker@noaa.gov

+
contact: Jeffrey Whitaker jeffrey.s.whitaker@noaa.gov

 
 
copyright: 2008 by Jeffrey Whitaker.

 
@@ -2403,7 +2402,8 @@ 
In-memory (diskless) Datasets

             
set_auto_mask(self, True_or_False)

 
 
Call Variable.set_auto_mask for all variables contained in this Dataset or
-Group, as well as for all variables in all its subgroups.

+Group, as well as for all variables in all its subgroups. Only affects
+Variables with primitive or enum types (not compound or vlen Variables).

 
 
True_or_False: Boolean determining if automatic conversion to masked arrays
 shall be applied for all variables.

@@ -2744,7 +2744,8 @@ 
In-memory (diskless) Datasets

 
mask: If True, data is automatically converted to/from masked
 arrays when missing values or fill values are present. Default is True, can be
 reset using Variable.set_auto_mask and Variable.set_auto_maskandscale
-methods.

+methods. Only relevant for Variables with primitive or enum types (ignored
+for compound and vlen Variables).

 
 
chartostring: If True, data is automatically converted to/from character
 arrays to string arrays when the _Encoding variable attribute is set.

From e5eb3fa062516398895cef2a16558bbaef6d00d8 Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Sun, 20 Jun 2021 15:59:19 -0600
Subject: [PATCH 2/3] fix test so it doesn't fail on 32 bit machines

---
 test/tst_slicing.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/test/tst_slicing.py b/test/tst_slicing.py
index 7d56f54c6..1b5c0bde2 100644
--- a/test/tst_slicing.py
+++ b/test/tst_slicing.py
@@ -2,7 +2,7 @@
 from numpy.random import seed, randint
 from numpy.testing import assert_array_equal, assert_equal,\
 assert_array_almost_equal
-import tempfile, unittest, os, random
+import tempfile, unittest, os, random, sys
 import numpy as np
 
 file_name = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
@@ -35,8 +35,8 @@ def setUp(self):
         vu[:,::-1,:] = data
 
         v1[:] = data[:, 0, 0]
-        #v2[0:2**31] = 1 # issue 1112 (overflow on windows)
-        v2[2**31] = 1 # issue 1112 (overflow on windows)
+        if sys.maxsize > 2**32:
+            v2[2**31] = 1 # issue 1112 (overflow on windows)
         f.close()
 
     def tearDown(self):
@@ -82,8 +82,8 @@ def test_1d(self):
         v2 = f.variables['data1dx']
         d = data[:,0,0]
         assert_equal(v1[:], d)
-        #assert_equal(v2[:], np.ones(2**31,dtype=np.uint8))
-        assert_equal(v2[2**31], 1)
+        if sys.maxsize > 2**32:
+            assert_equal(v2[2**31], 1)
         assert_equal(v1[4:], d[4:])
         # test return of array scalar.
         assert_equal(v1[0].shape, ())

From 26761d0826de4bb695074fe7be43973dd2a0f206 Mon Sep 17 00:00:00 2001
From: Jeff Whitaker 
Date: Sun, 20 Jun 2021 20:26:41 -0600
Subject: [PATCH 3/3] update

---
 README.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/README.md b/README.md
index 268179b08..cebdc014c 100644
--- a/README.md
+++ b/README.md
@@ -10,6 +10,10 @@
 ## News
 For details on the latest updates, see the [Changelog](https://github.com/Unidata/netcdf4-python/blob/master/Changelog).
 
+6/22/2021:  Version [1.5.7](https://pypi.python.org/pypi/netCDF4/1.5.7) released.
+Fixed OverflowError on Windows when reading data with dimension sizes greater than 2**32-1.
+Masked arrays no longer returned for vlens.
+
 2/15/2021:  Version [1.5.6](https://pypi.python.org/pypi/netCDF4/1.5.6) released. Added `Dataset.fromcdl` and `Dataset.tocdl`, which require `ncdump` and `ncgen` utilities to be in `$PATH`. Removed python 2.7 support.
 
 12/20/2020: Version [1.5.5.1](https://pypi.python.org/pypi/netCDF4/1.5.5.1) released.