netCDF4 1.2.1__tar.gz → 1.2.3__tar.gz

{netCDF4-1.2.1 → netCDF4-1.2.3.1}/Changelog

@@ -1,3 +1,57 @@
+ 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,

{netCDF4-1.2.1/netCDF4.egg-info → netCDF4-1.2.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.1
 Name: netCDF4
-Version: 1.2.1
+Version: 1.2.3.1
 Summary: Provides an object-oriented python interface to the netCDF version 4 library.
 Home-page: http://github.com/Unidata/netcdf4-python
 Author: Jeff Whitaker

{netCDF4-1.2.1 → netCDF4-1.2.3.1}/README.md

@@ -7,6 +7,25 @@
 ## News
 For the latest updates, see the [Changelog](https://github.com/Unidata/netcdf4-python/blob/master/Changelog).
 
+3/10/2016: Version [1.2.3](https://pypi.python.org/pypi/netCDF4/1.2.3) released. Various bug fixes.
+All text attributes in ``NETCDF4`` formatted files are now written as type ``NC_CHAR``, unless they contain unicode characters that
+cannot be encoded in ascii, in which case they are written as ``NC_STRING``.  Previously,
+all unicode strings were written as ``NC_STRING``. This change preserves compatibility
+with clients, like Matlab, that can't deal with ``NC_STRING`` attributes. 
+A ``setncattr_string`` method was added to force attributes to be written as ``NC_STRING``.
+
+1/1/2016: Version [1.2.2](https://pypi.python.org/pypi/netCDF4/1.2.2) released. Mostly bugfixes, but with two new features.
+
+* support for the new ``NETCDF3_64BIT_DATA`` format introduced in netcdf-c 4.4.0.
+Similar to ``NETCDF3_64BIT`` (now ``NETCDF3_64BIT_OFFSET``), but includes
+64 bit dimension sizes (> 2 billion), plus unsigned and 64 bit integer data types.
+Uses the classic (netcdf-3) data model, and does not use HDF5 as the underlying storage format.
+
+* Dimension objects now have a ``size`` attribute, which is the current length
+of the dimension (same as invoking ``len`` on the Dimension instance).
+
+The minimum required python version has now been increased from 2.5 to 2.6.
+
 10/15/2015: Version [1.2.1](https://pypi.python.org/pypi/netCDF4/1.2.1) released. Adds the ability
 to slice Variables with unsorted integer sequences, and integer sequences with duplicates.
 
@@ -50,7 +69,7 @@ instead of relying exclusively on the nc-config utility.
 * Clone GitHub repository (`git clone https://github.com/Unidata/netcdf4-python.git`), or get source tarball from [PyPI](https://pypi.python.org/pypi/netCDF4). Links to Windows and OS X precompiled binary packages are also available on [PyPI](https://pypi.python.org/pypi/netCDF4).
 
 * Make sure [numpy](http://www.numpy.org/) (required) and [Cython](http://cython.org/) (recommended) are
-  installed and you have [Python](https://www.python.org) 2.5 or newer.
+  installed and you have [Python](https://www.python.org) 2.6 or newer.
 
 * Make sure [HDF5](http://www.h5py.org/) and netcdf-4 are installed, and the `nc-config` utility
   is in your Unix PATH. If `setup.cfg` does not exist, copy `setup.cfg.template`

{netCDF4-1.2.1 → netCDF4-1.2.3.1}/docs/netCDF4/index.html

@@ -4,7 +4,7 @@
   <meta name="viewport" content="width=device-width, initial-scale=1, minimum-scale=1" />
 
     <title>netCDF4 API documentation</title>
-    <meta name="description" content="Version 1.2.1
+    <meta name="description" content="Version 1.2.3
 -------------
 - - - 
 
@@ -1096,6 +1096,7 @@ table {
     <li class="mono"><a href="#netCDF4.Dataset.set_fill_off">set_fill_off</a></li>
     <li class="mono"><a href="#netCDF4.Dataset.set_fill_on">set_fill_on</a></li>
     <li class="mono"><a href="#netCDF4.Dataset.setncattr">setncattr</a></li>
+    <li class="mono"><a href="#netCDF4.Dataset.setncattr_string">setncattr_string</a></li>
     <li class="mono"><a href="#netCDF4.Dataset.setncatts">setncatts</a></li>
     <li class="mono"><a href="#netCDF4.Dataset.sync">sync</a></li>
   </ul>
@@ -1150,6 +1151,7 @@ table {
     <li class="mono"><a href="#netCDF4.Group.set_fill_off">set_fill_off</a></li>
     <li class="mono"><a href="#netCDF4.Group.set_fill_on">set_fill_on</a></li>
     <li class="mono"><a href="#netCDF4.Group.setncattr">setncattr</a></li>
+    <li class="mono"><a href="#netCDF4.Group.setncattr_string">setncattr_string</a></li>
     <li class="mono"><a href="#netCDF4.Group.setncatts">setncatts</a></li>
     <li class="mono"><a href="#netCDF4.Group.sync">sync</a></li>
   </ul>
@@ -1181,6 +1183,7 @@ table {
     <li class="mono"><a href="#netCDF4.MFDataset.set_fill_off">set_fill_off</a></li>
     <li class="mono"><a href="#netCDF4.MFDataset.set_fill_on">set_fill_on</a></li>
     <li class="mono"><a href="#netCDF4.MFDataset.setncattr">setncattr</a></li>
+    <li class="mono"><a href="#netCDF4.MFDataset.setncattr_string">setncattr_string</a></li>
     <li class="mono"><a href="#netCDF4.MFDataset.setncatts">setncatts</a></li>
     <li class="mono"><a href="#netCDF4.MFDataset.sync">sync</a></li>
     <li class="mono"><a href="#netCDF4.MFDataset.__init__">__init__</a></li>
@@ -1232,6 +1235,7 @@ table {
     <li class="mono"><a href="#netCDF4.Variable.set_auto_scale">set_auto_scale</a></li>
     <li class="mono"><a href="#netCDF4.Variable.set_var_chunk_cache">set_var_chunk_cache</a></li>
     <li class="mono"><a href="#netCDF4.Variable.setncattr">setncattr</a></li>
+    <li class="mono"><a href="#netCDF4.Variable.setncattr_string">setncattr_string</a></li>
     <li class="mono"><a href="#netCDF4.Variable.setncatts">setncatts</a></li>
   </ul>
 
@@ -1251,7 +1255,7 @@ table {
 
   <header id="section-intro">
   <h1 class="title"><span class="name">netCDF4</span> module</h1>
-  <h2>Version 1.2.1</h2>
+  <h2>Version 1.2.3</h2>
 <hr />
 <h1>Introduction</h1>
 <p>netcdf4-python is a Python interface to the netCDF C library.  </p>
@@ -1279,7 +1283,7 @@ types) are not supported.</p>
 </ul>
 <h1>Requires</h1>
 <ul>
-<li>Python 2.5 or later (python 3 works too).</li>
+<li>Python 2.6 or later (python 3 works too).</li>
 <li><a href="http://numpy.scipy.org">numpy array module</a>, version 1.7.0 or later.</li>
 <li><a href="http://cython.org">Cython</a>, version 0.19 or later, is optional - if it is installed setup.py will
    use it to recompile the Cython source code into C, using conditional compilation
@@ -1352,10 +1356,17 @@ types) are not supported.</p>
 constructor. This is also the method used to open an existing netCDF
 file.  If the file is open for write access (<code>mode='w', 'r+'</code> or <code>'a'</code>), you may
 write any type of data including new dimensions, groups, variables and
-attributes.  netCDF files come in several flavors (<code>NETCDF3_CLASSIC,
-NETCDF3_64BIT, NETCDF4_CLASSIC</code>, and <code>NETCDF4</code>). The first two flavors
-are supported by version 3 of the netCDF library. <code>NETCDF4_CLASSIC</code>
-files use the version 4 disk format (HDF5), but do not use any features
+attributes.  netCDF files come in five flavors (<code>NETCDF3_CLASSIC,
+NETCDF3_64BIT_OFFSET, NETCDF3_64BIT_DATA, NETCDF4_CLASSIC</code>, and <code>NETCDF4</code>). 
+<code>NETCDF3_CLASSIC</code> was the original netcdf binary format, and was limited 
+to file sizes less than 2 Gb. <code>NETCDF3_64BIT_OFFSET</code> was introduced
+in version 3.6.0 of the library, and extended the original binary format
+to allow for file sizes greater than 2 Gb. 
+<code>NETCDF3_64BIT_DATA</code> is a new format that requires version 4.4.0 of
+the C library - it extends the <code>NETCDF3_64BIT_OFFSET</code> binary format to
+allow for unsigned/64 bit integer data types and 64-bit dimension sizes.
+<code>NETCDF3_64BIT</code> is an alias for <code>NETCDF3_64BIT_OFFSET</code>.
+<code>NETCDF4_CLASSIC</code> files use the version 4 disk format (HDF5), but omits features
 not found in the version 3 API. They can be read by netCDF 3 clients
 only if they have been relinked against the netCDF 4 library. They can
 also be read by HDF5 clients. <code>NETCDF4</code> files use the version 4 disk
@@ -1383,7 +1394,7 @@ OPenDAP support, via the <code>--enable-dap</code> configure option (added in
 version 4.0.1).</p>
 <h2><div id='section2'>2) Groups in a netCDF file.</h2>
 <p>netCDF version 4 added support for organizing data in hierarchical
-groups, which are analagous to directories in a filesystem. Groups serve
+groups, which are analogous to directories in a filesystem. Groups serve
 as containers for variables, dimensions and attributes, as well as other
 groups.  A <a href="#netCDF4.Dataset"><code>Dataset</code></a> defines creates a special group, called
 the 'root group', which is similar to the root directory in a unix
@@ -1499,9 +1510,9 @@ The <a href="#netCDF4.Dimension.isunlimited"><code>isunlimited</code></a> method
 can be used to determine if the dimensions is unlimited, or appendable.</p>
 <div class="codehilite"><pre><span class="o">&gt;&gt;&gt;</span> <span class="k">print</span> <span class="nb">len</span><span class="p">(</span><span class="n">lon</span><span class="p">)</span>
 <span class="mi">144</span>
-<span class="o">&gt;&gt;&gt;</span> <span class="k">print</span> <span class="nb">len</span><span class="o">.</span><span class="n">is_unlimited</span><span class="p">()</span>
+<span class="o">&gt;&gt;&gt;</span> <span class="k">print</span> <span class="nb">len</span><span class="o">.</span><span class="n">isunlimited</span><span class="p">()</span>
 <span class="bp">False</span>
-<span class="o">&gt;&gt;&gt;</span> <span class="k">print</span> <span class="n">time</span><span class="o">.</span><span class="n">is_unlimited</span><span class="p">()</span>
+<span class="o">&gt;&gt;&gt;</span> <span class="k">print</span> <span class="n">time</span><span class="o">.</span><span class="n">isunlimited</span><span class="p">()</span>
 <span class="bp">True</span>
 </pre></div>
 
@@ -1787,8 +1798,8 @@ Variables in the list of files that share the same unlimited
 dimension are aggregated together, and can be sliced across multiple
 files.  To illustrate this, let's first create a bunch of netCDF files with
 the same variable (with the same unlimited dimension).  The files
-must in be in <code>NETCDF3_64BIT</code>, <code>NETCDF3_CLASSIC</code> or
-<code>NETCDF4_CLASSIC format</code> (<code>NETCDF4</code> formatted multi-file
+must in be in <code>NETCDF3_64BIT_OFFSET</code>, <code>NETCDF3_64BIT_DATA</code>, <code>NETCDF3_CLASSIC</code> or
+<code>NETCDF4_CLASSIC</code> format (<code>NETCDF4</code> formatted multi-file
 datasets are not supported).</p>
 <div class="codehilite"><pre><span class="o">&gt;&gt;&gt;</span> <span class="k">for</span> <span class="n">nf</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">10</span><span class="p">):</span>
 <span class="o">&gt;&gt;&gt;</span>     <span class="n">f</span> <span class="o">=</span> <span class="n">Dataset</span><span class="p">(</span><span class="s">&quot;mftest</span><span class="si">%s</span><span class="s">.nc&quot;</span> <span class="o">%</span> <span class="n">nf</span><span class="p">,</span><span class="s">&quot;w&quot;</span><span class="p">)</span>
@@ -1833,7 +1844,7 @@ and <code>endian</code> keyword arguments to
 <a href="#netCDF4.Dataset.createVariable"><code>createVariable</code></a>.  These keyword arguments only
 are relevant for <code>NETCDF4</code> and <code>NETCDF4_CLASSIC</code> files (where the
 underlying file format is HDF5) and are silently ignored if the file
-format is <code>NETCDF3_CLASSIC</code> or <code>NETCDF3_64BIT</code>,</p>
+format is <code>NETCDF3_CLASSIC</code>, <code>NETCDF3_64BIT_OFFSET</code> or <code>NETCDF3_64BIT_DATA</code>.</p>
 <p>If your data only has a certain number of digits of precision (say for
 example, it is temperature data that was measured with a precision of
 0.1 degrees), you can dramatically improve zlib compression by
@@ -2420,7 +2431,7 @@ Enum types defined for the <a href="#netCDF4.Group"><code>Group</code></a> or <a
 of the <a href="#netCDF4.EnumType"><code>EnumType</code></a> class.</p>
 <p><strong><code>data_model</code></strong>: <code>data_model</code> describes the netCDF
 data model version, one of <code>NETCDF3_CLASSIC</code>, <code>NETCDF4</code>,
-<code>NETCDF4_CLASSIC</code> or <code>NETCDF3_64BIT</code>.</p>
+<code>NETCDF4_CLASSIC</code>, <code>NETCDF3_64BIT_OFFSET</code> or <code>NETCDF3_64BIT_DATA</code>.</p>
 <p><strong><code>file_format</code></strong>: same as <code>data_model</code>, retained for backwards compatibility.</p>
 <p><strong><code>disk_format</code></strong>: <code>disk_format</code> describes the underlying
 file format, one of <code>NETCDF3</code>, <code>HDF5</code>, <code>HDF4</code>,
@@ -2468,7 +2479,7 @@ compound types defined for the <a href="#netCDF4.Group"><code>Group</code></a> o
   
     <div class="desc"><p><code>data_model</code> describes the netCDF
 data model version, one of <code>NETCDF3_CLASSIC</code>, <code>NETCDF4</code>,
-<code>NETCDF4_CLASSIC</code> or <code>NETCDF3_64BIT</code>.</p></div>
+<code>NETCDF4_CLASSIC</code>, <code>NETCDF3_64BIT_OFFSET</code> or <code>NETCDF3_64BIT_DATA</code>.</p></div>
   <div class="source_cont">
 </div>
 
@@ -2614,13 +2625,15 @@ variable-length types defined for the <a href="#netCDF4.Group"><code>Group</code
     
   
     <div class="desc"><p><a href="#netCDF4.Dataset"><code>Dataset</code></a> constructor.</p>
-<p><strong><code>filename</code></strong>: Name of netCDF file to hold dataset.</p>
+<p><strong><code>filename</code></strong>: Name of netCDF file to hold dataset. Can also
+be a python 3 pathlib instance or the URL of an OpenDAP dataset.</p>
 <p><strong><code>mode</code></strong>: access mode. <code>r</code> means read-only; no data can be
 modified. <code>w</code> means write; a new file is created, an existing file with
 the same name is deleted. <code>a</code> and <code>r+</code> mean append (in analogy with
 serial files); an existing file is opened for reading and writing.
 Appending <code>s</code> to modes <code>w</code>, <code>r+</code> or <code>a</code> will enable unbuffered shared
-access to <code>NETCDF3_CLASSIC</code> or <code>NETCDF3_64BIT</code> formatted files.
+access to <code>NETCDF3_CLASSIC</code>, <code>NETCDF3_64BIT_OFFSET</code> or
+<code>NETCDF3_64BIT_DATA</code> formatted files.
 Unbuffered acesss may be useful even if you don't need shared
 access, since it may be faster for programs that don't access data
 sequentially. This option is ignored for <code>NETCDF4</code> and <code>NETCDF4_CLASSIC</code>
@@ -2629,18 +2642,22 @@ formatted files.</p>
 will clobber an existing file with the same name.  if <code>False</code>, an
 exception will be raised if a file with the same name already exists.</p>
 <p><strong><code>format</code></strong>: underlying file format (one of <code>'NETCDF4',
-'NETCDF4_CLASSIC', 'NETCDF3_CLASSIC'</code> or <code>'NETCDF3_64BIT'</code>.  Only
-relevant if <code>mode = 'w'</code> (if <code>mode = 'r','a'</code> or <code>'r+'</code> the file format
+'NETCDF4_CLASSIC', 'NETCDF3_CLASSIC'</code>, <code>'NETCDF3_64BIT_OFFSET'</code> or
+<code>'NETCDF3_64BIT_DATA'</code>.
+Only relevant if <code>mode = 'w'</code> (if <code>mode = 'r','a'</code> or <code>'r+'</code> the file format
 is automatically detected). Default <code>'NETCDF4'</code>, which means the data is
 stored in an HDF5 file, using netCDF 4 API features.  Setting
 <code>format='NETCDF4_CLASSIC'</code> will create an HDF5 file, using only netCDF 3
 compatibile API features. netCDF 3 clients must be recompiled and linked
 against the netCDF 4 library to read files in <code>NETCDF4_CLASSIC</code> format.
 <code>'NETCDF3_CLASSIC'</code> is the classic netCDF 3 file format that does not
-handle 2+ Gb files very well. <code>'NETCDF3_64BIT'</code> is the 64-bit offset
+handle 2+ Gb files. <code>'NETCDF3_64BIT_OFFSET'</code> is the 64-bit offset
 version of the netCDF 3 file format, which fully supports 2+ GB files, but
 is only compatible with clients linked against netCDF version 3.6.0 or
-later.</p>
+later. <code>'NETCDF3_64BIT_DATA'</code> is the 64-bit data version of the netCDF 3
+file format, which supports 64-bit dimension sizes plus unsigned and
+64 bit integer data types, but is only compatible with clients linked against
+netCDF version 4.4.0 or later.</p>
 <p><strong><code>diskless</code></strong>: If <code>True</code>, create diskless (in memory) file.<br />
 This is an experimental feature added to the C library after the
 netcdf-4.2 release.</p>
@@ -2753,7 +2770,7 @@ datatype.</p></div>
     <div class="desc"><p>Creates a new <a href="#netCDF4.Group"><code>Group</code></a> with the given <code>groupname</code>.</p>
 <p>If <code>groupname</code> is specified as a path, using forward slashes as in unix to
 separate components, then intermediate groups will be created as necessary 
-(analagous to <code>mkdir -p</code> in unix).  For example,
+(analogous to <code>mkdir -p</code> in unix).  For example,
 <code>createGroup('/GroupA/GroupB/GroupC')</code> will create <code>GroupA</code>,
 <code>GroupA/GroupB</code>, and <code>GroupA/GroupB/GroupC</code>, if they don't already exist.
 If the specified path describes a group that already exists, no error is
@@ -2943,7 +2960,7 @@ contain all of the matches. For example, </p>
 <div class="codehilite"><pre><span class="o">&gt;&gt;&gt;</span> <span class="c"># Get variables with x-axis attribute.</span>
 <span class="o">&gt;&gt;&gt;</span> <span class="n">vs</span> <span class="o">=</span> <span class="n">nc</span><span class="o">.</span><span class="n">get_variables_by_attributes</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="s">&#39;X&#39;</span><span class="p">)</span>
 <span class="o">&gt;&gt;&gt;</span> <span class="c"># Get variables with matching &quot;standard_name&quot; attribute</span>
-<span class="o">&gt;&gt;&gt;</span> <span class="n">nc</span><span class="o">.</span><span class="n">get_variables_by_attributes</span><span class="p">(</span><span class="n">standard_name</span><span class="o">=</span><span class="s">&#39;northward_sea_water_velocity&#39;</span><span class="p">)</span>
+<span class="o">&gt;&gt;&gt;</span> <span class="n">vs</span> <span class="o">=</span> <span class="n">nc</span><span class="o">.</span><span class="n">get_variables_by_attributes</span><span class="p">(</span><span class="n">standard_name</span><span class="o">=</span><span class="s">&#39;northward_sea_water_velocity&#39;</span><span class="p">)</span>
 </pre></div>
 
 
@@ -3188,6 +3205,23 @@ with the same name as one of the reserved python attributes.</p></div>
   </div>
   
             
+  <div class="item">
+    <div class="name def" id="netCDF4.Dataset.setncattr_string">
+    <p>def <span class="ident">setncattr_string</span>(</p><p>self,name,value)</p>
+    </div>
+    
+
+    
+  
+    <div class="desc"><p>set a netCDF dataset or group string attribute using name,value pair.
+Use if you need to ensure that of netCDF attribute is created with type
+<code>NC_STRING</code> if the file format is <code>NETCDF4</code>.</p></div>
+  <div class="source_cont">
+</div>
+
+  </div>
+  
+            
   <div class="item">
     <div class="name def" id="netCDF4.Dataset.setncatts">
     <p>def <span class="ident">setncatts</span>(</p><p>self,attdict)</p>
@@ -3235,7 +3269,9 @@ calling the python <code>len</code> function on the <a href="#netCDF4.Dimension"
 determine if the dimension is unlimited.</p>
 <p>Read-only class variables:</p>
 <p><strong><code>name</code></strong>: String name, used when creating a <a href="#netCDF4.Variable"><code>Variable</code></a> with
-<a href="#netCDF4.Dataset.createVariable"><code>createVariable</code></a>.</p></div>
+<a href="#netCDF4.Dataset.createVariable"><code>createVariable</code></a>.</p>
+<p><strong><code>size</code></strong>: Current <a href="#netCDF4.Dimension"><code>Dimension</code></a> size (same as <code>len(d)</code>, where <code>d</code> is a
+<a href="#netCDF4.Dimension"><code>Dimension</code></a> instance).</p></div>
   <div class="source_cont">
 </div>
 
@@ -3255,6 +3291,16 @@ determine if the dimension is unlimited.</p>
   
     <div class="desc"><p>A string describing the name of the <a href="#netCDF4.Dimension"><code>Dimension</code></a> - used when creating a
 <a href="#netCDF4.Variable"><code>Variable</code></a> instance with <a href="#netCDF4.Dataset.createVariable"><code>createVariable</code></a>.</p></div>
+  <div class="source_cont">
+</div>
+
+            </div>
+            <div class="item">
+            <p id="netCDF4.Dimension.size" class="name">var <span class="ident">size</span></p>
+            
+
+            
+  
   <div class="source_cont">
 </div>
 
@@ -3402,7 +3448,7 @@ method of a <a href="#netCDF4.Dataset"><code>Dataset</code></a> or <a href="#net
       
   
     <div class="desc"><p>Groups define a hierarchical namespace within a netCDF file. They are
-analagous to directories in a unix filesystem. Each <a href="#netCDF4.Group"><code>Group</code></a> behaves like
+analogous to directories in a unix filesystem. Each <a href="#netCDF4.Group"><code>Group</code></a> behaves like
 a <a href="#netCDF4.Dataset"><code>Dataset</code></a> within a Dataset, and can contain it's own variables,
 dimensions and attributes (and other Groups). See <a href="#netCDF4.Group.__init__"><code>__init__</code></a>
 for more details.</p>
@@ -3452,7 +3498,7 @@ compound types defined for the <a href="#netCDF4.Group"><code>Group</code></a> o
   
     <div class="desc inherited"><p><code>data_model</code> describes the netCDF
 data model version, one of <code>NETCDF3_CLASSIC</code>, <code>NETCDF4</code>,
-<code>NETCDF4_CLASSIC</code> or <code>NETCDF3_64BIT</code>.</p></div>
+<code>NETCDF4_CLASSIC</code>, <code>NETCDF3_64BIT_OFFSET</code> or <code>NETCDF3_64BIT_DATA</code>.</p></div>
   <div class="source_cont">
 </div>
 
@@ -3775,7 +3821,7 @@ datatype.</p></div>
     <div class="desc inherited"><p>Creates a new <a href="#netCDF4.Group"><code>Group</code></a> with the given <code>groupname</code>.</p>
 <p>If <code>groupname</code> is specified as a path, using forward slashes as in unix to
 separate components, then intermediate groups will be created as necessary 
-(analagous to <code>mkdir -p</code> in unix).  For example,
+(analogous to <code>mkdir -p</code> in unix).  For example,
 <code>createGroup('/GroupA/GroupB/GroupC')</code> will create <code>GroupA</code>,
 <code>GroupA/GroupB</code>, and <code>GroupA/GroupB/GroupC</code>, if they don't already exist.
 If the specified path describes a group that already exists, no error is
@@ -3985,7 +4031,7 @@ contain all of the matches. For example, </p>
 <div class="codehilite"><pre><span class="o">&gt;&gt;&gt;</span> <span class="c"># Get variables with x-axis attribute.</span>
 <span class="o">&gt;&gt;&gt;</span> <span class="n">vs</span> <span class="o">=</span> <span class="n">nc</span><span class="o">.</span><span class="n">get_variables_by_attributes</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="s">&#39;X&#39;</span><span class="p">)</span>
 <span class="o">&gt;&gt;&gt;</span> <span class="c"># Get variables with matching &quot;standard_name&quot; attribute</span>
-<span class="o">&gt;&gt;&gt;</span> <span class="n">nc</span><span class="o">.</span><span class="n">get_variables_by_attributes</span><span class="p">(</span><span class="n">standard_name</span><span class="o">=</span><span class="s">&#39;northward_sea_water_velocity&#39;</span><span class="p">)</span>
+<span class="o">&gt;&gt;&gt;</span> <span class="n">vs</span> <span class="o">=</span> <span class="n">nc</span><span class="o">.</span><span class="n">get_variables_by_attributes</span><span class="p">(</span><span class="n">standard_name</span><span class="o">=</span><span class="s">&#39;northward_sea_water_velocity&#39;</span><span class="p">)</span>
 </pre></div>
 
 
@@ -4282,6 +4328,27 @@ with the same name as one of the reserved python attributes.</p></div>
   </div>
   
             
+  <div class="item">
+    <div class="name def" id="netCDF4.Group.setncattr_string">
+    <p>def <span class="ident">setncattr_string</span>(</p><p>self,name,value)</p>
+    </div>
+    
+    <p class="inheritance">
+     <strong>Inheritance:</strong>
+       <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.setncattr_string">setncattr_string</a></code>
+    </p>
+
+    
+  
+    <div class="desc inherited"><p>set a netCDF dataset or group string attribute using name,value pair.
+Use if you need to ensure that of netCDF attribute is created with type
+<code>NC_STRING</code> if the file format is <code>NETCDF4</code>.</p></div>
+  <div class="source_cont">
+</div>
+
+  </div>
+  
+            
   <div class="item">
     <div class="name def" id="netCDF4.Group.setncatts">
     <p>def <span class="ident">setncatts</span>(</p><p>self,attdict)</p>
@@ -4331,8 +4398,8 @@ each attribute</p></div>
   
     <div class="desc"><p>Class for reading multi-file netCDF Datasets, making variables
 spanning multiple files appear as if they were in one file.
-Datasets must be in <code>NETCDF4_CLASSIC, NETCDF3_CLASSIC or NETCDF3_64BIT</code>
-format (<code>NETCDF4</code> Datasets won't work).</p>
+Datasets must be in <code>NETCDF4_CLASSIC, NETCDF3_CLASSIC, NETCDF3_64BIT_OFFSET
+or NETCDF3_64BIT_DATA</code> format (<code>NETCDF4</code> Datasets won't work).</p>
 <p>Adapted from <a href="http://pysclint.sourceforge.net/pycdf">pycdf</a> by Andre Gosselin.</p>
 <p>Example usage (See <a href="#netCDF4.MFDataset.__init__"><code>__init__</code></a> for more details):</p>
 <div class="codehilite"><pre><span class="o">&gt;&gt;&gt;</span> <span class="kn">import</span> <span class="nn">numpy</span>
@@ -4393,7 +4460,7 @@ compound types defined for the <a href="#netCDF4.Group"><code>Group</code></a> o
   
     <div class="desc inherited"><p><code>data_model</code> describes the netCDF
 data model version, one of <code>NETCDF3_CLASSIC</code>, <code>NETCDF4</code>,
-<code>NETCDF4_CLASSIC</code> or <code>NETCDF3_64BIT</code>.</p></div>
+<code>NETCDF4_CLASSIC</code>, <code>NETCDF3_64BIT_OFFSET</code> or <code>NETCDF3_64BIT_DATA</code>.</p></div>
   <div class="source_cont">
 </div>
 
@@ -4660,7 +4727,7 @@ datatype.</p></div>
     <div class="desc inherited"><p>Creates a new <a href="#netCDF4.Group"><code>Group</code></a> with the given <code>groupname</code>.</p>
 <p>If <code>groupname</code> is specified as a path, using forward slashes as in unix to
 separate components, then intermediate groups will be created as necessary 
-(analagous to <code>mkdir -p</code> in unix).  For example,
+(analogous to <code>mkdir -p</code> in unix).  For example,
 <code>createGroup('/GroupA/GroupB/GroupC')</code> will create <code>GroupA</code>,
 <code>GroupA/GroupB</code>, and <code>GroupA/GroupB/GroupC</code>, if they don't already exist.
 If the specified path describes a group that already exists, no error is
@@ -4870,7 +4937,7 @@ contain all of the matches. For example, </p>
 <div class="codehilite"><pre><span class="o">&gt;&gt;&gt;</span> <span class="c"># Get variables with x-axis attribute.</span>
 <span class="o">&gt;&gt;&gt;</span> <span class="n">vs</span> <span class="o">=</span> <span class="n">nc</span><span class="o">.</span><span class="n">get_variables_by_attributes</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="s">&#39;X&#39;</span><span class="p">)</span>
 <span class="o">&gt;&gt;&gt;</span> <span class="c"># Get variables with matching &quot;standard_name&quot; attribute</span>
-<span class="o">&gt;&gt;&gt;</span> <span class="n">nc</span><span class="o">.</span><span class="n">get_variables_by_attributes</span><span class="p">(</span><span class="n">standard_name</span><span class="o">=</span><span class="s">&#39;northward_sea_water_velocity&#39;</span><span class="p">)</span>
+<span class="o">&gt;&gt;&gt;</span> <span class="n">vs</span> <span class="o">=</span> <span class="n">nc</span><span class="o">.</span><span class="n">get_variables_by_attributes</span><span class="p">(</span><span class="n">standard_name</span><span class="o">=</span><span class="s">&#39;northward_sea_water_velocity&#39;</span><span class="p">)</span>
 </pre></div>
 
 
@@ -5148,6 +5215,27 @@ with the same name as one of the reserved python attributes.</p></div>
   </div>
   
             
+  <div class="item">
+    <div class="name def" id="netCDF4.MFDataset.setncattr_string">
+    <p>def <span class="ident">setncattr_string</span>(</p><p>self,name,value)</p>
+    </div>
+    
+    <p class="inheritance">
+     <strong>Inheritance:</strong>
+       <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.setncattr_string">setncattr_string</a></code>
+    </p>
+
+    
+  
+    <div class="desc inherited"><p>set a netCDF dataset or group string attribute using name,value pair.
+Use if you need to ensure that of netCDF attribute is created with type
+<code>NC_STRING</code> if the file format is <code>NETCDF4</code>.</p></div>
+  <div class="source_cont">
+</div>
+
+  </div>
+  
+            
   <div class="item">
     <div class="name def" id="netCDF4.MFDataset.setncatts">
     <p>def <span class="ident">setncatts</span>(</p><p>self,attdict)</p>
@@ -5453,7 +5541,7 @@ method of a <a href="#netCDF4.Dataset"><code>Dataset</code></a> or <a href="#net
       
   
     <div class="desc"><p>A netCDF <a href="#netCDF4.Variable"><code>Variable</code></a> is used to read and write netCDF data.  They are
-analagous to numpy array objects. See <a href="#netCDF4.Variable.__init__"><code>__init__</code></a> for more
+analogous to numpy array objects. See <a href="#netCDF4.Variable.__init__"><code>__init__</code></a> for more
 details.</p>
 <p>A list of attribute names corresponding to netCDF attributes defined for
 the variable can be obtained with the <a href="#netCDF4.Variable.ncattrs"><code>ncattrs</code></a> method. These
@@ -5884,7 +5972,9 @@ is set to the missing_value attribute (if it exists), otherwise
 the netCDF _FillValue attribute (which has a default value
 for each data type).  When data is written to a variable, the masked
 array is converted back to a regular numpy array by replacing all the
-masked values by the fill_value of the masked array.</p>
+masked values by the missing_value attribute of the variable (if it
+exists).  If the variable has no missing_value attribute, the _FillValue
+is used instead.</p>
 <p>The default value of <code>mask</code> is <code>True</code>
 (automatic conversions are performed).</p></div>
   <div class="source_cont">
@@ -5912,7 +6002,9 @@ is set to the missing_value attribute (if it exists), otherwise
 the netCDF _FillValue attribute (which has a default value
 for each data type).  When data is written to a variable, the masked
 array is converted back to a regular numpy array by replacing all the
-masked values by the fill_value of the masked array.</p>
+masked values by the missing_value attribute of the variable (if it
+exists).  If the variable has no missing_value attribute, the _FillValue
+is used instead.</p>
 <p>If <code>maskandscale</code> is set to <code>True</code>, and the variable has a
 <code>scale_factor</code> or an <code>add_offset</code> attribute, then data read
 from that variable is unpacked using::</p>
@@ -6009,6 +6101,23 @@ attributes.</p></div>
   </div>
   
             
+  <div class="item">
+    <div class="name def" id="netCDF4.Variable.setncattr_string">
+    <p>def <span class="ident">setncattr_string</span>(</p><p>self,name,value)</p>
+    </div>
+    
+
+    
+  
+    <div class="desc"><p>set a netCDF variable string attribute using name,value pair.
+Use if you need to ensure that of netCDF attribute is created with type
+<code>NC_STRING</code> if the file format is <code>NETCDF4</code>.</p></div>
+  <div class="source_cont">
+</div>
+
+  </div>
+  
+            
   <div class="item">
     <div class="name def" id="netCDF4.Variable.setncatts">
     <p>def <span class="ident">setncatts</span>(</p><p>self,attdict)</p>
@@ -6036,7 +6145,7 @@ each attribute</p></div>
   <footer id="footer">
     <p>
       Documentation generated by
-      <a href="https://github.com/BurntSushi/pdoc">pdoc 0.3.1</a>
+      <a href="https://github.com/BurntSushi/pdoc">pdoc 0.3.2.dev16</a>
     </p>
 
     <p>pdoc is in the public domain with the

{netCDF4-1.2.1 → netCDF4-1.2.3.1}/examples/bench_compress.py

@@ -13,7 +13,7 @@ n4dim = 144
 ntrials = 10
 sys.stdout.write('reading and writing a %s by %s by %s by %s random array ..\n'%(n1dim,n2dim,n3dim,n4dim))
 sys.stdout.write('(average of %s trials)\n' % ntrials)
-array = netCDF4._quantize(uniform(size=(n1dim,n2dim,n3dim,n4dim)),4)
+array = netCDF4.utils._quantize(uniform(size=(n1dim,n2dim,n3dim,n4dim)),4)
 
 
 def write_netcdf(filename,zlib=False,shuffle=False,complevel=6):

{netCDF4-1.2.1 → netCDF4-1.2.3.1}/examples/bench_compress2.py

@@ -12,22 +12,20 @@ n3dim = 73
 n4dim = 144
 ntrials = 10
 sys.stdout.write('reading and writing a %s by %s by %s by %s random array ..\n'%(n1dim,n2dim,n3dim,n4dim))
-sys.stdout.write('(average of %s trials)\n' % ntrials)
-lsd = 4
-if lsd is not None:
-    array = netCDF4._quantize(uniform(size=(n1dim,n2dim,n3dim,n4dim)),4)
-else:
-    array = uniform(size=(n1dim,n2dim,n3dim,n4dim))
+sys.stdout.write('(average of %s trials)\n\n' % ntrials)
+array = uniform(size=(n1dim,n2dim,n3dim,n4dim))
 
 
-def write_netcdf(filename,complevel):
+def write_netcdf(filename,complevel,lsd):
     file = netCDF4.Dataset(filename,'w',format='NETCDF4')
     file.createDimension('n1', n1dim)
     file.createDimension('n2', n2dim)
     file.createDimension('n3', n3dim)
     file.createDimension('n4', n4dim)
     foo = file.createVariable('data',\
-                              'f8',('n1','n2','n3','n4'),zlib=True,shuffle=True,complevel=complevel)
+                              'f8',('n1','n2','n3','n4'),\
+                              zlib=True,shuffle=True,complevel=complevel,\
+                              least_significant_digit=lsd)
     foo[:] = array
     file.close()
 
@@ -36,10 +34,27 @@ def read_netcdf(filename):
     data = file.variables['data'][:]
     file.close()
 
-for complevel in range(0,10):
+lsd = None
+sys.stdout.write('using least_significant_digit %s\n\n' % lsd)
+for complevel in range(0,10,2):
     sys.stdout.write('testing compression with complevel %s...\n' % complevel)
     # writing.
-    t = Timer("write_netcdf('test.nc',%s)" % complevel,"from __main__ import write_netcdf")
+    t = Timer("write_netcdf('test.nc',%s,%s)" % (complevel,lsd),"from __main__ import write_netcdf")
+    sys.stdout.write('writing took %s seconds\n' %\
+            repr(sum(t.repeat(ntrials,1))/ntrials))
+    # test reading.
+    t = Timer("read_netcdf('test.nc')","from __main__ import read_netcdf")
+    sys.stdout.write('reading took %s seconds\n' %
+            repr(sum(t.repeat(ntrials,1))/ntrials))
+    # print out size of resulting files.
+    sys.stdout.write('size of test.nc = %s\n'%repr(os.stat('test.nc').st_size))
+
+complevel = 4
+sys.stdout.write('\nusing complevel %s\n\n' % complevel)
+for lsd in range(1,6):
+    sys.stdout.write('testing compression with least_significant_digit %s...\n' % lsd)
+    # writing.
+    t = Timer("write_netcdf('test.nc',%s,%s)" % (complevel,lsd),"from __main__ import write_netcdf")
     sys.stdout.write('writing took %s seconds\n' %\
             repr(sum(t.repeat(ntrials,1))/ntrials))
     # test reading.