[Git][debian-gis-team/netcdf4-python][master] 4 commits: New upstream version 1.5.0
Bas Couwenberg
gitlab at salsa.debian.org
Sun Mar 24 07:29:14 GMT 2019
Bas Couwenberg pushed to branch master at Debian GIS Project / netcdf4-python
Commits:
14339366 by Bas Couwenberg at 2019-03-24T06:57:43Z
New upstream version 1.5.0
- - - - -
1e6ca436 by Bas Couwenberg at 2019-03-24T06:57:45Z
Merge tag 'upstream/1.5.0'
Upstream version 1.5.0
- - - - -
6e4a3651 by Bas Couwenberg at 2019-03-24T06:58:31Z
New upstream release.
- - - - -
0faa545a by Bas Couwenberg at 2019-03-24T06:59:32Z
Set distribution to experimental.
- - - - -
14 changed files:
- .travis.yml
- Changelog
- PKG-INFO
- README.md
- ci/travis/build-parallel-netcdf.sh
- debian/changelog
- + docs/index.html
- docs/netCDF4/index.html
- examples/mpi_example.py
- include/netCDF4.pxi
- netCDF4/__init__.py
- netCDF4/_netCDF4.pyx
- setup.py
- test/run_all.py
Changes:
=====================================
.travis.yml
=====================================
@@ -44,7 +44,24 @@ matrix:
- MPI=1
- CC=mpicc.mpich
- DEPENDS="numpy>=1.9.0 cython>=0.21 setuptools>=18.0 mpi4py>=1.3.1 cftime"
- - NETCDF_VERSION=4.6.2
+ - NETCDF_VERSION=4.6.3
+ - NETCDF_DIR=$HOME
+ - PATH=${NETCDF_DIR}/bin:${PATH} # pick up nc-config here
+ addons:
+ apt:
+ packages:
+ - mpich
+ - libmpich-dev
+ - libhdf5-mpich-dev
+ # test MPI with latest released version
+ - python: 3.7
+ dist: xenial
+ env:
+ - MPI=1
+ - CC=mpicc.mpich
+ - DEPENDS="numpy>=1.9.0 cython>=0.21 setuptools>=18.0 mpi4py>=1.3.1 cftime"
+ - NETCDF_VERSION=4.6.3
+ - PNETCDF_VERSION=1.11.0
- NETCDF_DIR=$HOME
- PATH=${NETCDF_DIR}/bin:${PATH} # pick up nc-config here
addons:
@@ -86,6 +103,8 @@ script:
- cd test
- python run_all.py
- |
+ echo "MPI = ${MPI}"
+ echo "PNETCDF_VERSION = ${PNETCDF_VERSION}"
if [ $MPI -eq 1 ] ; then
cd ../examples
mpirun.mpich -np 4 python mpi_example.py
@@ -94,6 +113,14 @@ script:
exit 1
else
echo "mpi test passed!"
- exit 0
+ fi
+ if [ -n "${PNETCDF_VERSION}" ] ; then
+ mpirun.mpich -np 4 python mpi_example.py NETCDF3_64BIT_DATA
+ if [ $? -ne 0 ] ; then
+ echo "PnetCDF mpi test failed!"
+ exit 1
+ else
+ echo "PnetCDF mpi test passed!"
+ fi
fi
fi
=====================================
Changelog
=====================================
@@ -1,9 +1,14 @@
- version 1.4.3.2 (tag v1.4.3.2rel)
-==================================
+ version 1.5.0 (tag v1.5.0rel)
+===============================
+ * added support for parallel IO in the classic netcdf-3 formats through the
+ pnetcdf library (pull request #897).
+
+ version 1.4.3.2 (tag v1.4.3.2)
+===============================
* include missing membuf.pyx file in release source tarball.
version 1.4.3.1 (tag v1.4.3.1)
-===================================
+===============================
* fix bug in implementation of NETCDF4_CLASSIC support for parallel IO
in v1.4.3 release.
=====================================
PKG-INFO
=====================================
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: netCDF4
-Version: 1.4.3.1
+Version: 1.5.0
Author: Jeff Whitaker
Author-email: jeffrey s whitaker at noaa gov
Home-page: https://github.com/Unidata/netcdf4-python
=====================================
README.md
=====================================
@@ -5,12 +5,17 @@
[](https://ci.appveyor.com/project/jswhit/netcdf4-python/branch/master)
[](http://python.org/pypi/netCDF4)
[](https://anaconda.org/conda-forge/netCDF4)
+[](https://doi.org/10.5281/zenodo.2592291)
## News
For details on the latest updates, see the [Changelog](https://github.com/Unidata/netcdf4-python/blob/master/Changelog).
+03/24/2019: Version [1.5.0](https://pypi.python.org/pypi/netCDF4/1.5.0) released. Parallel IO support for classic
+file formats added using the pnetcdf library (contribution from Lars Pastewka, [pull request #897](https://github.com/Unidata/netcdf4-python/pull/897)).
+
03/08/2019: Version [1.4.3.2](https://pypi.python.org/pypi/netCDF4/1.4.3.2) released.
-Include missing membuf.pyx file in source tarball.
+Include missing membuf.pyx file in source tarball. No need to update if you installed
+1.4.3.1 from a binary wheel.
03/07/2019: Version [1.4.3.1](https://pypi.python.org/pypi/netCDF4/1.4.3.1) released.
Fixes bug in implementation of NETCDF4_CLASSIC parallel IO support in 1.4.3.
=====================================
ci/travis/build-parallel-netcdf.sh
=====================================
@@ -2,8 +2,19 @@
set -e
-echo "Using downloaded netCDF version ${NETCDF_VERSION} with parallel capabilities enabled"
pushd /tmp
+if [ -n "${PNETCDF_VERSION}" ]; then
+ echo "Using downloaded PnetCDF version ${PNETCDF_VERSION}"
+ wget https://parallel-netcdf.github.io/Release/pnetcdf-${PNETCDF_VERSION}.tar.gz
+ tar -xzf pnetcdf-${PNETCDF_VERSION}.tar.gz
+ pushd pnetcdf-${PNETCDF_VERSION}
+ ./configure --prefix $NETCDF_DIR --enable-shared --disable-fortran --disable-cxx
+ NETCDF_EXTRA_CONFIG="--enable-pnetcdf"
+ make -j 2
+ make install
+ popd
+fi
+echo "Using downloaded netCDF version ${NETCDF_VERSION} with parallel capabilities enabled"
if [ ${NETCDF_VERSION} == "GITMASTER" ]; then
git clone http://github.com/Unidata/netcdf-c netcdf-c
pushd netcdf-c
@@ -14,9 +25,10 @@ else
pushd netcdf-c-${NETCDF_VERSION}
fi
# for Ubuntu xenial
-export CPPFLAGS="-I/usr/include/hdf5/mpich"
+export CPPFLAGS="-I/usr/include/hdf5/mpich -I${NETCDF_DIR}/include"
+export LDFLAGS="-L${NETCDF_DIR}/lib"
export LIBS="-lhdf5_mpich_hl -lhdf5_mpich -lm -lz"
-./configure --prefix $NETCDF_DIR --enable-netcdf-4 --enable-shared --disable-dap --enable-parallel
+./configure --prefix $NETCDF_DIR --enable-netcdf-4 --enable-shared --disable-dap --enable-parallel4 $NETCDF_EXTRA_CONFIG
make -j 2
make install
popd
=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+netcdf4-python (1.5.0-1~exp1) experimental; urgency=medium
+
+ * New upstream release.
+
+ -- Bas Couwenberg <sebastic at debian.org> Sun, 24 Mar 2019 07:59:15 +0100
+
netcdf4-python (1.4.3.2-1~exp1) experimental; urgency=medium
* New upstream release.
=====================================
docs/index.html
=====================================
@@ -0,0 +1 @@
+<meta http-equiv="refresh" content="0; url=./netCDF4/index.html" />
=====================================
docs/netCDF4/index.html
=====================================
@@ -1174,6 +1174,8 @@ table {
<ul>
+ <li class="mono"><a href="#netCDF4.MFDataset.__init__">__init__</a></li>
+ <li class="mono"><a href="#netCDF4.MFDataset.close">close</a></li>
<li class="mono"><a href="#netCDF4.MFDataset.createCompoundType">createCompoundType</a></li>
<li class="mono"><a href="#netCDF4.MFDataset.createDimension">createDimension</a></li>
<li class="mono"><a href="#netCDF4.MFDataset.createEnumType">createEnumType</a></li>
@@ -1185,6 +1187,7 @@ table {
<li class="mono"><a href="#netCDF4.MFDataset.get_variables_by_attributes">get_variables_by_attributes</a></li>
<li class="mono"><a href="#netCDF4.MFDataset.getncattr">getncattr</a></li>
<li class="mono"><a href="#netCDF4.MFDataset.isopen">isopen</a></li>
+ <li class="mono"><a href="#netCDF4.MFDataset.ncattrs">ncattrs</a></li>
<li class="mono"><a href="#netCDF4.MFDataset.renameAttribute">renameAttribute</a></li>
<li class="mono"><a href="#netCDF4.MFDataset.renameDimension">renameDimension</a></li>
<li class="mono"><a href="#netCDF4.MFDataset.renameGroup">renameGroup</a></li>
@@ -1201,9 +1204,6 @@ table {
<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>
- <li class="mono"><a href="#netCDF4.MFDataset.close">close</a></li>
- <li class="mono"><a href="#netCDF4.MFDataset.ncattrs">ncattrs</a></li>
</ul>
</li>
@@ -1335,9 +1335,10 @@ types) are not supported.</p>
If you want <a href="http://opendap.org">OPeNDAP</a> support, add <code>--enable-dap</code>.
If you want HDF4 SD support, add <code>--enable-hdf4</code> and add
the location of the HDF4 headers and library to <code>$CPPFLAGS</code> and <code>$LDFLAGS</code>.</li>
-<li>for MPI parallel IO support, MPI-enabled versions of the HDF5 and netcdf
- libraries are required, as is the <a href="http://mpi4py.scipy.org">mpi4py</a> python
- module.</li>
+<li>for MPI parallel IO support, an MPI-enabled versions of the netcdf library
+ is required, as is the <a href="http://mpi4py.scipy.org">mpi4py</a> python module.
+ Parallel IO further depends on the existence of MPI-enabled HDF5 or the
+ <a href="https://parallel-netcdf.github.io/">PnetCDF</a> library.</li>
</ul>
<h1>Install</h1>
<ul>
@@ -2151,13 +2152,14 @@ specified names.</p>
<h2><div id='section13'>13) Parallel IO.</h2>
-<p>If MPI parallel enabled versions of netcdf and hdf5 are detected, and
-<a href="https://mpi4py.scipy.org">mpi4py</a> is installed, netcdf4-python will
-be built with parallel IO capabilities enabled. Since parallel IO
-uses features of HDF5, it can only be used with NETCDF4 or
-NETCDF4_CLASSIC formatted files. To use parallel IO,
-your program must be running in an MPI environment using
-<a href="https://mpi4py.scipy.org">mpi4py</a>.</p>
+<p>If MPI parallel enabled versions of netcdf and hdf5 or pnetcdf are detected,
+and <a href="https://mpi4py.scipy.org">mpi4py</a> is installed, netcdf4-python will
+be built with parallel IO capabilities enabled. Parallel IO of NETCDF4 or
+NETCDF4_CLASSIC formatted files is only available if the MPI parallel HDF5
+library is available. Parallel IO of classic netcdf-3 file formats is only
+available if the <a href="https://parallel-netcdf.github.io/">PnetCDF</a> library is
+available. To use parallel IO, your program must be running in an MPI
+environment using <a href="https://mpi4py.scipy.org">mpi4py</a>.</p>
<div class="codehilite"><pre><span></span><span class="o">>>></span> <span class="kn">from</span> <span class="nn">mpi4py</span> <span class="kn">import</span> <span class="n">MPI</span>
<span class="o">>>></span> <span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
<span class="o">>>></span> <span class="kn">from</span> <span class="nn">netCDF4</span> <span class="kn">import</span> <span class="n">Dataset</span>
@@ -2204,9 +2206,12 @@ participate in doing IO. To toggle back and forth between
the two types of IO, use the <a href="#netCDF4.Variable.set_collective"><code>set_collective</code></a>
<a href="#netCDF4.Variable"><code>Variable</code></a>method. All metadata
operations (such as creation of groups, types, variables, dimensions, or attributes)
-are collective. There are a couple of important limitatons of parallel IO:</p>
+are collective. There are a couple of important limitations of parallel IO:</p>
<ul>
-<li>only works with NETCDF4 or NETCDF4_CLASSIC formatted files.</li>
+<li>parallel IO for NETCDF4 or NETCDF4_CLASSIC formatted files is only available
+ if the netcdf library was compiled with MPI enabled HDF5.</li>
+<li>parallel IO for all classic netcdf-3 file formats is only available if the
+ netcdf library was compiled with PnetCDF.</li>
<li>If a variable has an unlimited dimension, appending data must be done in collective mode.
If the write is done in independent mode, the operation will fail with a
a generic "HDF Error".</li>
@@ -2616,7 +2621,7 @@ the user.</p></div>
<h3>Ancestors (in MRO)</h3>
<ul class="class_list">
<li><a href="#netCDF4.CompoundType">CompoundType</a></li>
- <li>__builtin__.object</li>
+ <li>builtins.object</li>
</ul>
<h3>Class variables</h3>
<div class="item">
@@ -2747,7 +2752,7 @@ strings.</p></div>
<h3>Ancestors (in MRO)</h3>
<ul class="class_list">
<li><a href="#netCDF4.Dataset">Dataset</a></li>
- <li>__builtin__.object</li>
+ <li>builtins.object</li>
</ul>
<h3>Class variables</h3>
<div class="item">
@@ -3669,7 +3674,7 @@ determine if the dimension is unlimited.</p>
<h3>Ancestors (in MRO)</h3>
<ul class="class_list">
<li><a href="#netCDF4.Dimension">Dimension</a></li>
- <li>__builtin__.object</li>
+ <li>builtins.object</li>
</ul>
<h3>Class variables</h3>
<div class="item">
@@ -3767,7 +3772,7 @@ the user.</p></div>
<h3>Ancestors (in MRO)</h3>
<ul class="class_list">
<li><a href="#netCDF4.EnumType">EnumType</a></li>
- <li>__builtin__.object</li>
+ <li>builtins.object</li>
</ul>
<h3>Class variables</h3>
<div class="item">
@@ -3855,22 +3860,15 @@ to a <a href="#netCDF4.Group"><code>Group</code></a> instance (except the <code>
<ul class="class_list">
<li><a href="#netCDF4.Group">Group</a></li>
<li><a href="#netCDF4.Dataset">Dataset</a></li>
- <li>__builtin__.object</li>
+ <li>builtins.object</li>
</ul>
<h3>Class variables</h3>
<div class="item">
<p id="netCDF4.Group.cmptypes" class="name">var <span class="ident">cmptypes</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.cmptypes">cmptypes</a></code>
- </p>
- <div class="desc inherited"><p>The <code>cmptypes</code> dictionary maps the names of
-compound types defined for the <a href="#netCDF4.Group"><code>Group</code></a> or <a href="#netCDF4.Dataset"><code>Dataset</code></a> to instances of the
-<a href="#netCDF4.CompoundType"><code>CompoundType</code></a> class.</p></div>
<div class="source_cont">
</div>
@@ -3878,16 +3876,9 @@ compound types defined for the <a href="#netCDF4.Group"><code>Group</code></a> o
<div class="item">
<p id="netCDF4.Group.data_model" class="name">var <span class="ident">data_model</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.data_model">data_model</a></code>
- </p>
- <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>, <code>NETCDF3_64BIT_OFFSET</code> or <code>NETCDF3_64BIT_DATA</code>.</p></div>
<div class="source_cont">
</div>
@@ -3895,16 +3886,9 @@ data model version, one of <code>NETCDF3_CLASSIC</code>, <code>NETCDF4</code>,
<div class="item">
<p id="netCDF4.Group.dimensions" class="name">var <span class="ident">dimensions</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.dimensions">dimensions</a></code>
- </p>
- <div class="desc inherited"><p>The <code>dimensions</code> dictionary maps the names of
-dimensions defined for the <a href="#netCDF4.Group"><code>Group</code></a> or <a href="#netCDF4.Dataset"><code>Dataset</code></a> to instances of the
-<a href="#netCDF4.Dimension"><code>Dimension</code></a> class.</p></div>
<div class="source_cont">
</div>
@@ -3912,18 +3896,9 @@ dimensions defined for the <a href="#netCDF4.Group"><code>Group</code></a> or <a
<div class="item">
<p id="netCDF4.Group.disk_format" class="name">var <span class="ident">disk_format</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.disk_format">disk_format</a></code>
- </p>
- <div class="desc inherited"><p><code>disk_format</code> describes the underlying
-file format, one of <code>NETCDF3</code>, <code>HDF5</code>, <code>HDF4</code>,
-<code>PNETCDF</code>, <code>DAP2</code>, <code>DAP4</code> or <code>UNDEFINED</code>. Only available if using
-netcdf C library version >= 4.3.1, otherwise will always return
-<code>UNDEFINED</code>.</p></div>
<div class="source_cont">
</div>
@@ -3931,16 +3906,9 @@ netcdf C library version >= 4.3.1, otherwise will always return
<div class="item">
<p id="netCDF4.Group.enumtypes" class="name">var <span class="ident">enumtypes</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.enumtypes">enumtypes</a></code>
- </p>
- <div class="desc inherited"><p>The <code>enumtypes</code> dictionary maps the names of
-Enum types defined for the <a href="#netCDF4.Group"><code>Group</code></a> or <a href="#netCDF4.Dataset"><code>Dataset</code></a> to instances of the
-<a href="#netCDF4.EnumType"><code>EnumType</code></a> class.</p></div>
<div class="source_cont">
</div>
@@ -3948,14 +3916,9 @@ Enum types defined for the <a href="#netCDF4.Group"><code>Group</code></a> or <a
<div class="item">
<p id="netCDF4.Group.file_format" class="name">var <span class="ident">file_format</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.file_format">file_format</a></code>
- </p>
- <div class="desc inherited"><p>same as <code>data_model</code>, retained for backwards compatibility.</p></div>
<div class="source_cont">
</div>
@@ -3963,17 +3926,9 @@ Enum types defined for the <a href="#netCDF4.Group"><code>Group</code></a> or <a
<div class="item">
<p id="netCDF4.Group.groups" class="name">var <span class="ident">groups</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.groups">groups</a></code>
- </p>
- <div class="desc inherited"><p>The groups dictionary maps the names of groups created for
-this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or <a href="#netCDF4.Group"><code>Group</code></a> to instances of the <a href="#netCDF4.Group"><code>Group</code></a> class (the
-<a href="#netCDF4.Dataset"><code>Dataset</code></a> class is simply a special case of the <a href="#netCDF4.Group"><code>Group</code></a> class which
-describes the root group in the netCDF4 file).</p></div>
<div class="source_cont">
</div>
@@ -3981,15 +3936,9 @@ describes the root group in the netCDF4 file).</p></div>
<div class="item">
<p id="netCDF4.Group.keepweakref" class="name">var <span class="ident">keepweakref</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.keepweakref">keepweakref</a></code>
- </p>
- <div class="desc inherited"><p>If <code>True</code>, child Dimension and Variables objects only keep weak references to
-the parent Dataset or Group.</p></div>
<div class="source_cont">
</div>
@@ -4008,15 +3957,9 @@ the parent Dataset or Group.</p></div>
<div class="item">
<p id="netCDF4.Group.parent" class="name">var <span class="ident">parent</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.parent">parent</a></code>
- </p>
- <div class="desc inherited"><p><code>parent</code> is a reference to the parent
-<a href="#netCDF4.Group"><code>Group</code></a> instance. <code>None</code> for the root group or <a href="#netCDF4.Dataset"><code>Dataset</code></a> instance</p></div>
<div class="source_cont">
</div>
@@ -4024,17 +3967,9 @@ the parent Dataset or Group.</p></div>
<div class="item">
<p id="netCDF4.Group.path" class="name">var <span class="ident">path</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.path">path</a></code>
- </p>
- <div class="desc inherited"><p><code>path</code> shows the location of the <a href="#netCDF4.Group"><code>Group</code></a> in
-the <a href="#netCDF4.Dataset"><code>Dataset</code></a> in a unix directory format (the names of groups in the
-hierarchy separated by backslashes). A <a href="#netCDF4.Dataset"><code>Dataset</code></a> instance is the root
-group, so the path is simply <code>'/'</code>.</p></div>
<div class="source_cont">
</div>
@@ -4042,16 +3977,9 @@ group, so the path is simply <code>'/'</code>.</p></div>
<div class="item">
<p id="netCDF4.Group.variables" class="name">var <span class="ident">variables</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.variables">variables</a></code>
- </p>
- <div class="desc inherited"><p>The <code>variables</code> dictionary maps the names of variables
-defined for this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or <a href="#netCDF4.Group"><code>Group</code></a> to instances of the <a href="#netCDF4.Variable"><code>Variable</code></a>
-class.</p></div>
<div class="source_cont">
</div>
@@ -4059,16 +3987,9 @@ class.</p></div>
<div class="item">
<p id="netCDF4.Group.vltypes" class="name">var <span class="ident">vltypes</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.vltypes">vltypes</a></code>
- </p>
- <div class="desc inherited"><p>The <code>vltypes</code> dictionary maps the names of
-variable-length types defined for the <a href="#netCDF4.Group"><code>Group</code></a> or <a href="#netCDF4.Dataset"><code>Dataset</code></a> to instances of the
-<a href="#netCDF4.VLType"><code>VLType</code></a> class.</p></div>
<div class="source_cont">
</div>
@@ -4105,10 +4026,6 @@ another <a href="#netCDF4.Group"><code>Group</code></a> instance, not using this
<p>def <span class="ident">close</span>(</p><p>self)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.close">close</a></code>
- </p>
@@ -4125,14 +4042,10 @@ instances, raises IOError.</p></div>
<p>def <span class="ident">createCompoundType</span>(</p><p>self, datatype, datatype_name)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.createCompoundType">createCompoundType</a></code>
- </p>
- <div class="desc inherited"><p>Creates a new compound data type named <code>datatype_name</code> from the numpy
+ <div class="desc"><p>Creates a new compound data type named <code>datatype_name</code> from the numpy
dtype object <code>datatype</code>.</p>
<p><strong><em>Note</em></strong>: If the new compound data type contains other compound data types
(i.e. it is a 'nested' compound type, where not all of the elements
@@ -4151,14 +4064,10 @@ datatype.</p></div>
<p>def <span class="ident">createDimension</span>(</p><p>self, dimname, size=None)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.createDimension">createDimension</a></code>
- </p>
- <div class="desc inherited"><p>Creates a new dimension with the given <code>dimname</code> and <code>size</code>.</p>
+ <div class="desc"><p>Creates a new dimension with the given <code>dimname</code> and <code>size</code>.</p>
<p><code>size</code> must be a positive integer or <code>None</code>, which stands for
"unlimited" (default is <code>None</code>). Specifying a size of 0 also
results in an unlimited dimension. The return value is the <a href="#netCDF4.Dimension"><code>Dimension</code></a>
@@ -4177,14 +4086,10 @@ instance. To determine if a dimension is 'unlimited', use the
<p>def <span class="ident">createEnumType</span>(</p><p>self, datatype, datatype_name, enum_dict)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.createEnumType">createEnumType</a></code>
- </p>
- <div class="desc inherited"><p>Creates a new Enum data type named <code>datatype_name</code> from a numpy
+ <div class="desc"><p>Creates a new Enum data type named <code>datatype_name</code> from a numpy
integer dtype object <code>datatype</code>, and a python dictionary
defining the enum fields and values.</p>
<p>The return value is the <a href="#netCDF4.EnumType"><code>EnumType</code></a> class instance describing the new
@@ -4200,14 +4105,10 @@ datatype.</p></div>
<p>def <span class="ident">createGroup</span>(</p><p>self, groupname)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.createGroup">createGroup</a></code>
- </p>
- <div class="desc inherited"><p>Creates a new <a href="#netCDF4.Group"><code>Group</code></a> with the given <code>groupname</code>.</p>
+ <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
(analogous to <code>mkdir -p</code> in unix). For example,
@@ -4227,14 +4128,10 @@ raised.</p>
<p>def <span class="ident">createVLType</span>(</p><p>self, datatype, datatype_name)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.createVLType">createVLType</a></code>
- </p>
- <div class="desc inherited"><p>Creates a new VLEN data type named <code>datatype_name</code> from a numpy
+ <div class="desc"><p>Creates a new VLEN data type named <code>datatype_name</code> from a numpy
dtype object <code>datatype</code>.</p>
<p>The return value is the <a href="#netCDF4.VLType"><code>VLType</code></a> class instance describing the new
datatype.</p></div>
@@ -4249,14 +4146,10 @@ datatype.</p></div>
<p>def <span class="ident">createVariable</span>(</p><p>self, varname, datatype, dimensions=(), zlib=False, complevel=4, shuffle=True, fletcher32=False, contiguous=False, chunksizes=None, endian='native', least_significant_digit=None, fill_value=None)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.createVariable">createVariable</a></code>
- </p>
- <div class="desc inherited"><p>Creates a new variable with the given <code>varname</code>, <code>datatype</code>, and
+ <div class="desc"><p>Creates a new variable with the given <code>varname</code>, <code>datatype</code>, and
<code>dimensions</code>. If dimensions are not given, the variable is assumed to be
a scalar.</p>
<p>If <code>varname</code> is specified as a path, using forward slashes as in unix to
@@ -4366,14 +4259,10 @@ is the number of variable dimensions.</p></div>
<p>def <span class="ident">delncattr</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.delncattr">delncattr</a></code>
- </p>
- <div class="desc inherited"><p>delete a netCDF dataset or group attribute. Use if you need to delete a
+ <div class="desc"><p>delete a netCDF dataset or group attribute. Use if you need to delete a
netCDF attribute with the same name as one of the reserved python
attributes.</p></div>
<div class="source_cont">
@@ -4387,14 +4276,10 @@ attributes.</p></div>
<p>def <span class="ident">filepath</span>(</p><p>self,encoding=None)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.filepath">filepath</a></code>
- </p>
- <div class="desc inherited"><p>Get the file system path (or the opendap URL) which was used to
+ <div class="desc"><p>Get the file system path (or the opendap URL) which was used to
open/create the Dataset. Requires netcdf >= 4.1.2. The path
is decoded into a string using <code>sys.getfilesystemencoding()</code> by default, this can be
changed using the <code>encoding</code> kwarg.</p></div>
@@ -4409,14 +4294,10 @@ changed using the <code>encoding</code> kwarg.</p></div>
<p>def <span class="ident">get_variables_by_attributes</span>(</p><p>...)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.get_variables_by_attributes">get_variables_by_attributes</a></code>
- </p>
- <div class="desc inherited"><p>Returns a list of variables that match specific conditions.</p>
+ <div class="desc"><p>Returns a list of variables that match specific conditions.</p>
<p>Can pass in key=value parameters and variables are returned that
contain all of the matches. For example,</p>
<div class="codehilite"><pre><span></span><span class="o">>>></span> <span class="c1"># Get variables with x-axis attribute.</span>
@@ -4448,14 +4329,10 @@ attribute does not exist on the variable. For example,</p>
<p>def <span class="ident">getncattr</span>(</p><p>self,name)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.getncattr">getncattr</a></code>
- </p>
- <div class="desc inherited"><p>retrieve a netCDF dataset or group attribute.
+ <div class="desc"><p>retrieve a netCDF dataset or group attribute.
Use if you need to get a netCDF attribute with the same
name as one of the reserved python attributes.</p>
<p>option kwarg <code>encoding</code> can be used to specify the
@@ -4471,14 +4348,10 @@ character encoding of a string attribute (default is <code>utf-8</code>).</p></d
<p>def <span class="ident">isopen</span>(</p><p>...)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.isopen">isopen</a></code>
- </p>
- <div class="desc inherited"><p>is the Dataset open or closed?</p></div>
+ <div class="desc"><p>is the Dataset open or closed?</p></div>
<div class="source_cont">
</div>
@@ -4490,14 +4363,10 @@ character encoding of a string attribute (default is <code>utf-8</code>).</p></d
<p>def <span class="ident">ncattrs</span>(</p><p>self)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.ncattrs">ncattrs</a></code>
- </p>
- <div class="desc inherited"><p>return netCDF global attribute names for this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or <a href="#netCDF4.Group"><code>Group</code></a> in a list.</p></div>
+ <div class="desc"><p>return netCDF global attribute names for this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or <a href="#netCDF4.Group"><code>Group</code></a> in a list.</p></div>
<div class="source_cont">
</div>
@@ -4509,14 +4378,10 @@ character encoding of a string attribute (default is <code>utf-8</code>).</p></d
<p>def <span class="ident">renameAttribute</span>(</p><p>self, oldname, newname)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.renameAttribute">renameAttribute</a></code>
- </p>
- <div class="desc inherited"><p>rename a <a href="#netCDF4.Dataset"><code>Dataset</code></a> or <a href="#netCDF4.Group"><code>Group</code></a> attribute named <code>oldname</code> to <code>newname</code>.</p></div>
+ <div class="desc"><p>rename a <a href="#netCDF4.Dataset"><code>Dataset</code></a> or <a href="#netCDF4.Group"><code>Group</code></a> attribute named <code>oldname</code> to <code>newname</code>.</p></div>
<div class="source_cont">
</div>
@@ -4528,14 +4393,10 @@ character encoding of a string attribute (default is <code>utf-8</code>).</p></d
<p>def <span class="ident">renameDimension</span>(</p><p>self, oldname, newname)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.renameDimension">renameDimension</a></code>
- </p>
- <div class="desc inherited"><p>rename a <a href="#netCDF4.Dimension"><code>Dimension</code></a> named <code>oldname</code> to <code>newname</code>.</p></div>
+ <div class="desc"><p>rename a <a href="#netCDF4.Dimension"><code>Dimension</code></a> named <code>oldname</code> to <code>newname</code>.</p></div>
<div class="source_cont">
</div>
@@ -4547,14 +4408,10 @@ character encoding of a string attribute (default is <code>utf-8</code>).</p></d
<p>def <span class="ident">renameGroup</span>(</p><p>self, oldname, newname)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.renameGroup">renameGroup</a></code>
- </p>
- <div class="desc inherited"><p>rename a <a href="#netCDF4.Group"><code>Group</code></a> named <code>oldname</code> to <code>newname</code> (requires netcdf >= 4.3.1).</p></div>
+ <div class="desc"><p>rename a <a href="#netCDF4.Group"><code>Group</code></a> named <code>oldname</code> to <code>newname</code> (requires netcdf >= 4.3.1).</p></div>
<div class="source_cont">
</div>
@@ -4566,14 +4423,10 @@ character encoding of a string attribute (default is <code>utf-8</code>).</p></d
<p>def <span class="ident">renameVariable</span>(</p><p>self, oldname, newname)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.renameVariable">renameVariable</a></code>
- </p>
- <div class="desc inherited"><p>rename a <a href="#netCDF4.Variable"><code>Variable</code></a> named <code>oldname</code> to <code>newname</code></p></div>
+ <div class="desc"><p>rename a <a href="#netCDF4.Variable"><code>Variable</code></a> named <code>oldname</code> to <code>newname</code></p></div>
<div class="source_cont">
</div>
@@ -4585,14 +4438,10 @@ character encoding of a string attribute (default is <code>utf-8</code>).</p></d
<p>def <span class="ident">set_always_mask</span>(</p><p>self, True_or_False)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.set_always_mask">set_always_mask</a></code>
- </p>
- <div class="desc inherited"><p>Call <a href="#netCDF4.Variable.set_always_mask"><code>set_always_mask</code></a> for all variables contained in
+ <div class="desc"><p>Call <a href="#netCDF4.Variable.set_always_mask"><code>set_always_mask</code></a> for all variables contained in
this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or <a href="#netCDF4.Group"><code>Group</code></a>, as well as for all
variables in all its subgroups.</p>
<p><strong><code>True_or_False</code></strong>: Boolean determining if automatic conversion of
@@ -4612,14 +4461,10 @@ the default behaviour.</p></div>
<p>def <span class="ident">set_auto_chartostring</span>(</p><p>self, True_or_False)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.set_auto_chartostring">set_auto_chartostring</a></code>
- </p>
- <div class="desc inherited"><p>Call <a href="#netCDF4.Variable.set_auto_chartostring"><code>set_auto_chartostring</code></a> for all variables contained in this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or
+ <div class="desc"><p>Call <a href="#netCDF4.Variable.set_auto_chartostring"><code>set_auto_chartostring</code></a> for all variables contained in this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or
<a href="#netCDF4.Group"><code>Group</code></a>, as well as for all variables in all its subgroups.</p>
<p><strong><code>True_or_False</code></strong>: Boolean determining if automatic conversion of
all character arrays <--> string arrays should be performed for
@@ -4638,14 +4483,10 @@ after calling this function will follow the default behaviour.</p></div>
<p>def <span class="ident">set_auto_mask</span>(</p><p>self, True_or_False)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.set_auto_mask">set_auto_mask</a></code>
- </p>
- <div class="desc inherited"><p>Call <a href="#netCDF4.Variable.set_auto_mask"><code>set_auto_mask</code></a> for all variables contained in this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or
+ <div class="desc"><p>Call <a href="#netCDF4.Variable.set_auto_mask"><code>set_auto_mask</code></a> for all variables contained in this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or
<a href="#netCDF4.Group"><code>Group</code></a>, as well as for all variables in all its subgroups.</p>
<p><strong><code>True_or_False</code></strong>: Boolean determining if automatic conversion to masked arrays
shall be applied for all variables.</p>
@@ -4662,14 +4503,10 @@ after calling this function will follow the default behaviour.</p></div>
<p>def <span class="ident">set_auto_maskandscale</span>(</p><p>self, True_or_False)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.set_auto_maskandscale">set_auto_maskandscale</a></code>
- </p>
- <div class="desc inherited"><p>Call <a href="#netCDF4.Variable.set_auto_maskandscale"><code>set_auto_maskandscale</code></a> for all variables contained in this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or
+ <div class="desc"><p>Call <a href="#netCDF4.Variable.set_auto_maskandscale"><code>set_auto_maskandscale</code></a> for all variables contained in this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or
<a href="#netCDF4.Group"><code>Group</code></a>, as well as for all variables in all its subgroups.</p>
<p><strong><code>True_or_False</code></strong>: Boolean determining if automatic conversion to masked arrays
and variable scaling shall be applied for all variables.</p>
@@ -4686,14 +4523,10 @@ after calling this function will follow the default behaviour.</p></div>
<p>def <span class="ident">set_auto_scale</span>(</p><p>self, True_or_False)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.set_auto_scale">set_auto_scale</a></code>
- </p>
- <div class="desc inherited"><p>Call <a href="#netCDF4.Variable.set_auto_scale"><code>set_auto_scale</code></a> for all variables contained in this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or
+ <div class="desc"><p>Call <a href="#netCDF4.Variable.set_auto_scale"><code>set_auto_scale</code></a> for all variables contained in this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or
<a href="#netCDF4.Group"><code>Group</code></a>, as well as for all variables in all its subgroups.</p>
<p><strong><code>True_or_False</code></strong>: Boolean determining if automatic variable scaling
shall be applied for all variables.</p>
@@ -4710,14 +4543,10 @@ after calling this function will follow the default behaviour.</p></div>
<p>def <span class="ident">set_fill_off</span>(</p><p>self)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.set_fill_off">set_fill_off</a></code>
- </p>
- <div class="desc inherited"><p>Sets the fill mode for a <a href="#netCDF4.Dataset"><code>Dataset</code></a> open for writing to <code>off</code>.</p>
+ <div class="desc"><p>Sets the fill mode for a <a href="#netCDF4.Dataset"><code>Dataset</code></a> open for writing to <code>off</code>.</p>
<p>This will prevent the data from being pre-filled with fill values, which
may result in some performance improvements. However, you must then make
sure the data is actually written before being read.</p></div>
@@ -4732,14 +4561,10 @@ sure the data is actually written before being read.</p></div>
<p>def <span class="ident">set_fill_on</span>(</p><p>self)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.set_fill_on">set_fill_on</a></code>
- </p>
- <div class="desc inherited"><p>Sets the fill mode for a <a href="#netCDF4.Dataset"><code>Dataset</code></a> open for writing to <code>on</code>.</p>
+ <div class="desc"><p>Sets the fill mode for a <a href="#netCDF4.Dataset"><code>Dataset</code></a> open for writing to <code>on</code>.</p>
<p>This causes data to be pre-filled with fill values. The fill values can be
controlled by the variable's <code>_Fill_Value</code> attribute, but is usually
sufficient to the use the netCDF default <code>_Fill_Value</code> (defined
@@ -4758,14 +4583,10 @@ to.</p></div>
<p>def <span class="ident">set_ncstring_attrs</span>(</p><p>self, True_or_False)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.set_ncstring_attrs">set_ncstring_attrs</a></code>
- </p>
- <div class="desc inherited"><p>Call <a href="#netCDF4.Variable.set_ncstring_attrs"><code>set_ncstring_attrs</code></a> for all variables contained in
+ <div class="desc"><p>Call <a href="#netCDF4.Variable.set_ncstring_attrs"><code>set_ncstring_attrs</code></a> for all variables contained in
this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or <a href="#netCDF4.Group"><code>Group</code></a>, as well as for all its
subgroups and their variables.</p>
<p><strong><code>True_or_False</code></strong>: Boolean determining if all string attributes are
@@ -4784,14 +4605,10 @@ of existing (sub-) groups and their variables.</p></div>
<p>def <span class="ident">setncattr</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">setncattr</a></code>
- </p>
- <div class="desc inherited"><p>set a netCDF dataset or group attribute using name,value pair.
+ <div class="desc"><p>set a netCDF dataset or group attribute using name,value pair.
Use if you need to set a netCDF attribute with the
with the same name as one of the reserved python attributes.</p></div>
<div class="source_cont">
@@ -4805,14 +4622,10 @@ with the same name as one of the reserved python attributes.</p></div>
<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.
+ <div class="desc"><p>set a netCDF dataset or group string attribute using name,value pair.
Use if you need to ensure that a netCDF attribute is created with type
<code>NC_STRING</code> if the file format is <code>NETCDF4</code>.</p></div>
<div class="source_cont">
@@ -4826,14 +4639,10 @@ Use if you need to ensure that a netCDF attribute is created with type
<p>def <span class="ident">setncatts</span>(</p><p>self,attdict)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.setncatts">setncatts</a></code>
- </p>
- <div class="desc inherited"><p>set a bunch of netCDF dataset or group attributes at once using a python dictionary.
+ <div class="desc"><p>set a bunch of netCDF dataset or group attributes at once using a python dictionary.
This may be faster when setting a lot of attributes for a <code>NETCDF3</code>
formatted file, since nc_redef/nc_enddef is not called in between setting
each attribute</p></div>
@@ -4848,14 +4657,10 @@ each attribute</p></div>
<p>def <span class="ident">sync</span>(</p><p>self)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.sync">sync</a></code>
- </p>
- <div class="desc inherited"><p>Writes all buffered data in the <a href="#netCDF4.Dataset"><code>Dataset</code></a> to the disk file.</p></div>
+ <div class="desc"><p>Writes all buffered data in the <a href="#netCDF4.Dataset"><code>Dataset</code></a> to the disk file.</p></div>
<div class="source_cont">
</div>
@@ -4900,22 +4705,15 @@ or NETCDF3_64BIT_DATA</code> format (<code>NETCDF4</code> Datasets won't work).<
<ul class="class_list">
<li><a href="#netCDF4.MFDataset">MFDataset</a></li>
<li><a href="#netCDF4.Dataset">Dataset</a></li>
- <li>__builtin__.object</li>
+ <li>builtins.object</li>
</ul>
<h3>Class variables</h3>
<div class="item">
<p id="netCDF4.MFDataset.cmptypes" class="name">var <span class="ident">cmptypes</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.cmptypes">cmptypes</a></code>
- </p>
- <div class="desc inherited"><p>The <code>cmptypes</code> dictionary maps the names of
-compound types defined for the <a href="#netCDF4.Group"><code>Group</code></a> or <a href="#netCDF4.Dataset"><code>Dataset</code></a> to instances of the
-<a href="#netCDF4.CompoundType"><code>CompoundType</code></a> class.</p></div>
<div class="source_cont">
</div>
@@ -4923,16 +4721,9 @@ compound types defined for the <a href="#netCDF4.Group"><code>Group</code></a> o
<div class="item">
<p id="netCDF4.MFDataset.data_model" class="name">var <span class="ident">data_model</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.data_model">data_model</a></code>
- </p>
- <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>, <code>NETCDF3_64BIT_OFFSET</code> or <code>NETCDF3_64BIT_DATA</code>.</p></div>
<div class="source_cont">
</div>
@@ -4940,16 +4731,9 @@ data model version, one of <code>NETCDF3_CLASSIC</code>, <code>NETCDF4</code>,
<div class="item">
<p id="netCDF4.MFDataset.dimensions" class="name">var <span class="ident">dimensions</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.dimensions">dimensions</a></code>
- </p>
- <div class="desc inherited"><p>The <code>dimensions</code> dictionary maps the names of
-dimensions defined for the <a href="#netCDF4.Group"><code>Group</code></a> or <a href="#netCDF4.Dataset"><code>Dataset</code></a> to instances of the
-<a href="#netCDF4.Dimension"><code>Dimension</code></a> class.</p></div>
<div class="source_cont">
</div>
@@ -4957,18 +4741,9 @@ dimensions defined for the <a href="#netCDF4.Group"><code>Group</code></a> or <a
<div class="item">
<p id="netCDF4.MFDataset.disk_format" class="name">var <span class="ident">disk_format</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.disk_format">disk_format</a></code>
- </p>
- <div class="desc inherited"><p><code>disk_format</code> describes the underlying
-file format, one of <code>NETCDF3</code>, <code>HDF5</code>, <code>HDF4</code>,
-<code>PNETCDF</code>, <code>DAP2</code>, <code>DAP4</code> or <code>UNDEFINED</code>. Only available if using
-netcdf C library version >= 4.3.1, otherwise will always return
-<code>UNDEFINED</code>.</p></div>
<div class="source_cont">
</div>
@@ -4976,16 +4751,9 @@ netcdf C library version >= 4.3.1, otherwise will always return
<div class="item">
<p id="netCDF4.MFDataset.enumtypes" class="name">var <span class="ident">enumtypes</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.enumtypes">enumtypes</a></code>
- </p>
- <div class="desc inherited"><p>The <code>enumtypes</code> dictionary maps the names of
-Enum types defined for the <a href="#netCDF4.Group"><code>Group</code></a> or <a href="#netCDF4.Dataset"><code>Dataset</code></a> to instances of the
-<a href="#netCDF4.EnumType"><code>EnumType</code></a> class.</p></div>
<div class="source_cont">
</div>
@@ -4993,14 +4761,9 @@ Enum types defined for the <a href="#netCDF4.Group"><code>Group</code></a> or <a
<div class="item">
<p id="netCDF4.MFDataset.file_format" class="name">var <span class="ident">file_format</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.file_format">file_format</a></code>
- </p>
- <div class="desc inherited"><p>same as <code>data_model</code>, retained for backwards compatibility.</p></div>
<div class="source_cont">
</div>
@@ -5008,17 +4771,9 @@ Enum types defined for the <a href="#netCDF4.Group"><code>Group</code></a> or <a
<div class="item">
<p id="netCDF4.MFDataset.groups" class="name">var <span class="ident">groups</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.groups">groups</a></code>
- </p>
- <div class="desc inherited"><p>The groups dictionary maps the names of groups created for
-this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or <a href="#netCDF4.Group"><code>Group</code></a> to instances of the <a href="#netCDF4.Group"><code>Group</code></a> class (the
-<a href="#netCDF4.Dataset"><code>Dataset</code></a> class is simply a special case of the <a href="#netCDF4.Group"><code>Group</code></a> class which
-describes the root group in the netCDF4 file).</p></div>
<div class="source_cont">
</div>
@@ -5026,15 +4781,9 @@ describes the root group in the netCDF4 file).</p></div>
<div class="item">
<p id="netCDF4.MFDataset.keepweakref" class="name">var <span class="ident">keepweakref</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.keepweakref">keepweakref</a></code>
- </p>
- <div class="desc inherited"><p>If <code>True</code>, child Dimension and Variables objects only keep weak references to
-the parent Dataset or Group.</p></div>
<div class="source_cont">
</div>
@@ -5042,15 +4791,9 @@ the parent Dataset or Group.</p></div>
<div class="item">
<p id="netCDF4.MFDataset.parent" class="name">var <span class="ident">parent</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.parent">parent</a></code>
- </p>
- <div class="desc inherited"><p><code>parent</code> is a reference to the parent
-<a href="#netCDF4.Group"><code>Group</code></a> instance. <code>None</code> for the root group or <a href="#netCDF4.Dataset"><code>Dataset</code></a> instance</p></div>
<div class="source_cont">
</div>
@@ -5058,17 +4801,9 @@ the parent Dataset or Group.</p></div>
<div class="item">
<p id="netCDF4.MFDataset.path" class="name">var <span class="ident">path</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.path">path</a></code>
- </p>
- <div class="desc inherited"><p><code>path</code> shows the location of the <a href="#netCDF4.Group"><code>Group</code></a> in
-the <a href="#netCDF4.Dataset"><code>Dataset</code></a> in a unix directory format (the names of groups in the
-hierarchy separated by backslashes). A <a href="#netCDF4.Dataset"><code>Dataset</code></a> instance is the root
-group, so the path is simply <code>'/'</code>.</p></div>
<div class="source_cont">
</div>
@@ -5076,16 +4811,9 @@ group, so the path is simply <code>'/'</code>.</p></div>
<div class="item">
<p id="netCDF4.MFDataset.variables" class="name">var <span class="ident">variables</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.variables">variables</a></code>
- </p>
- <div class="desc inherited"><p>The <code>variables</code> dictionary maps the names of variables
-defined for this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or <a href="#netCDF4.Group"><code>Group</code></a> to instances of the <a href="#netCDF4.Variable"><code>Variable</code></a>
-class.</p></div>
<div class="source_cont">
</div>
@@ -5093,16 +4821,9 @@ class.</p></div>
<div class="item">
<p id="netCDF4.MFDataset.vltypes" class="name">var <span class="ident">vltypes</span></p>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.vltypes">vltypes</a></code>
- </p>
- <div class="desc inherited"><p>The <code>vltypes</code> dictionary maps the names of
-variable-length types defined for the <a href="#netCDF4.Group"><code>Group</code></a> or <a href="#netCDF4.Dataset"><code>Dataset</code></a> to instances of the
-<a href="#netCDF4.VLType"><code>VLType</code></a> class.</p></div>
<div class="source_cont">
</div>
@@ -5110,18 +4831,74 @@ variable-length types defined for the <a href="#netCDF4.Group"><code>Group</code
<h3>Static methods</h3>
<div class="item">
- <div class="name def" id="netCDF4.MFDataset.createCompoundType">
- <p>def <span class="ident">createCompoundType</span>(</p><p>self, datatype, datatype_name)</p>
+ <div class="name def" id="netCDF4.MFDataset.__init__">
+ <p>def <span class="ident">__init__</span>(</p><p>self, files, check=False, aggdim=None, exclude=[], master_file=None)</p>
</div>
<p class="inheritance">
<strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.createCompoundType">createCompoundType</a></code>
+ <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.__init__">__init__</a></code>
</p>
- <div class="desc inherited"><p>Creates a new compound data type named <code>datatype_name</code> from the numpy
+ <div class="desc"><p><strong><code>__init__(self, files, check=False, aggdim=None, exclude=[],
+master_file=None)</code></strong></p>
+<p>Open a Dataset spanning multiple files, making it look as if it was a
+single file. Variables in the list of files that share the same
+dimension (specified with the keyword <code>aggdim</code>) are aggregated. If
+<code>aggdim</code> is not specified, the unlimited is aggregated. Currently,
+<code>aggdim</code> must be the leftmost (slowest varying) dimension of each
+of the variables to be aggregated.</p>
+<p><strong><code>files</code></strong>: either a sequence of netCDF files or a string with a
+wildcard (converted to a sorted list of files using glob) If
+the <code>master_file</code> kwarg is not specified, the first file
+in the list will become the "master" file, defining all the
+variables with an aggregation dimension which may span
+subsequent files. Attribute access returns attributes only from "master"
+file. The files are always opened in read-only mode.</p>
+<p><strong><code>check</code></strong>: True if you want to do consistency checking to ensure the
+correct variables structure for all of the netcdf files. Checking makes
+the initialization of the MFDataset instance much slower. Default is
+False.</p>
+<p><strong><code>aggdim</code></strong>: The name of the dimension to aggregate over (must
+be the leftmost dimension of each of the variables to be aggregated).
+If None (default), aggregate over the unlimited dimension.</p>
+<p><strong><code>exclude</code></strong>: A list of variable names to exclude from aggregation.
+Default is an empty list.</p>
+<p><strong><code>master_file</code></strong>: file to use as "master file", defining all the
+variables with an aggregation dimension and all global attributes.</p></div>
+ <div class="source_cont">
+</div>
+
+ </div>
+
+
+ <div class="item">
+ <div class="name def" id="netCDF4.MFDataset.close">
+ <p>def <span class="ident">close</span>(</p><p>self)</p>
+ </div>
+
+
+
+
+ <div class="desc"><p><strong><code>close(self)</code></strong></p>
+<p>close all the open files.</p></div>
+ <div class="source_cont">
+</div>
+
+ </div>
+
+
+ <div class="item">
+ <div class="name def" id="netCDF4.MFDataset.createCompoundType">
+ <p>def <span class="ident">createCompoundType</span>(</p><p>self, datatype, datatype_name)</p>
+ </div>
+
+
+
+
+ <div class="desc"><p>Creates a new compound data type named <code>datatype_name</code> from the numpy
dtype object <code>datatype</code>.</p>
<p><strong><em>Note</em></strong>: If the new compound data type contains other compound data types
(i.e. it is a 'nested' compound type, where not all of the elements
@@ -5140,14 +4917,10 @@ datatype.</p></div>
<p>def <span class="ident">createDimension</span>(</p><p>self, dimname, size=None)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.createDimension">createDimension</a></code>
- </p>
- <div class="desc inherited"><p>Creates a new dimension with the given <code>dimname</code> and <code>size</code>.</p>
+ <div class="desc"><p>Creates a new dimension with the given <code>dimname</code> and <code>size</code>.</p>
<p><code>size</code> must be a positive integer or <code>None</code>, which stands for
"unlimited" (default is <code>None</code>). Specifying a size of 0 also
results in an unlimited dimension. The return value is the <a href="#netCDF4.Dimension"><code>Dimension</code></a>
@@ -5166,14 +4939,10 @@ instance. To determine if a dimension is 'unlimited', use the
<p>def <span class="ident">createEnumType</span>(</p><p>self, datatype, datatype_name, enum_dict)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.createEnumType">createEnumType</a></code>
- </p>
- <div class="desc inherited"><p>Creates a new Enum data type named <code>datatype_name</code> from a numpy
+ <div class="desc"><p>Creates a new Enum data type named <code>datatype_name</code> from a numpy
integer dtype object <code>datatype</code>, and a python dictionary
defining the enum fields and values.</p>
<p>The return value is the <a href="#netCDF4.EnumType"><code>EnumType</code></a> class instance describing the new
@@ -5189,14 +4958,10 @@ datatype.</p></div>
<p>def <span class="ident">createGroup</span>(</p><p>self, groupname)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.createGroup">createGroup</a></code>
- </p>
- <div class="desc inherited"><p>Creates a new <a href="#netCDF4.Group"><code>Group</code></a> with the given <code>groupname</code>.</p>
+ <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
(analogous to <code>mkdir -p</code> in unix). For example,
@@ -5216,14 +4981,10 @@ raised.</p>
<p>def <span class="ident">createVLType</span>(</p><p>self, datatype, datatype_name)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.createVLType">createVLType</a></code>
- </p>
- <div class="desc inherited"><p>Creates a new VLEN data type named <code>datatype_name</code> from a numpy
+ <div class="desc"><p>Creates a new VLEN data type named <code>datatype_name</code> from a numpy
dtype object <code>datatype</code>.</p>
<p>The return value is the <a href="#netCDF4.VLType"><code>VLType</code></a> class instance describing the new
datatype.</p></div>
@@ -5238,14 +4999,10 @@ datatype.</p></div>
<p>def <span class="ident">createVariable</span>(</p><p>self, varname, datatype, dimensions=(), zlib=False, complevel=4, shuffle=True, fletcher32=False, contiguous=False, chunksizes=None, endian='native', least_significant_digit=None, fill_value=None)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.createVariable">createVariable</a></code>
- </p>
- <div class="desc inherited"><p>Creates a new variable with the given <code>varname</code>, <code>datatype</code>, and
+ <div class="desc"><p>Creates a new variable with the given <code>varname</code>, <code>datatype</code>, and
<code>dimensions</code>. If dimensions are not given, the variable is assumed to be
a scalar.</p>
<p>If <code>varname</code> is specified as a path, using forward slashes as in unix to
@@ -5355,14 +5112,10 @@ is the number of variable dimensions.</p></div>
<p>def <span class="ident">delncattr</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.delncattr">delncattr</a></code>
- </p>
- <div class="desc inherited"><p>delete a netCDF dataset or group attribute. Use if you need to delete a
+ <div class="desc"><p>delete a netCDF dataset or group attribute. Use if you need to delete a
netCDF attribute with the same name as one of the reserved python
attributes.</p></div>
<div class="source_cont">
@@ -5376,14 +5129,10 @@ attributes.</p></div>
<p>def <span class="ident">filepath</span>(</p><p>self,encoding=None)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.filepath">filepath</a></code>
- </p>
- <div class="desc inherited"><p>Get the file system path (or the opendap URL) which was used to
+ <div class="desc"><p>Get the file system path (or the opendap URL) which was used to
open/create the Dataset. Requires netcdf >= 4.1.2. The path
is decoded into a string using <code>sys.getfilesystemencoding()</code> by default, this can be
changed using the <code>encoding</code> kwarg.</p></div>
@@ -5398,14 +5147,10 @@ changed using the <code>encoding</code> kwarg.</p></div>
<p>def <span class="ident">get_variables_by_attributes</span>(</p><p>...)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.get_variables_by_attributes">get_variables_by_attributes</a></code>
- </p>
- <div class="desc inherited"><p>Returns a list of variables that match specific conditions.</p>
+ <div class="desc"><p>Returns a list of variables that match specific conditions.</p>
<p>Can pass in key=value parameters and variables are returned that
contain all of the matches. For example,</p>
<div class="codehilite"><pre><span></span><span class="o">>>></span> <span class="c1"># Get variables with x-axis attribute.</span>
@@ -5437,14 +5182,10 @@ attribute does not exist on the variable. For example,</p>
<p>def <span class="ident">getncattr</span>(</p><p>self,name)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.getncattr">getncattr</a></code>
- </p>
- <div class="desc inherited"><p>retrieve a netCDF dataset or group attribute.
+ <div class="desc"><p>retrieve a netCDF dataset or group attribute.
Use if you need to get a netCDF attribute with the same
name as one of the reserved python attributes.</p>
<p>option kwarg <code>encoding</code> can be used to specify the
@@ -5460,14 +5201,26 @@ character encoding of a string attribute (default is <code>utf-8</code>).</p></d
<p>def <span class="ident">isopen</span>(</p><p>...)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.isopen">isopen</a></code>
- </p>
- <div class="desc inherited"><p>is the Dataset open or closed?</p></div>
+ <div class="desc"><p>is the Dataset open or closed?</p></div>
+ <div class="source_cont">
+</div>
+
+ </div>
+
+
+ <div class="item">
+ <div class="name def" id="netCDF4.MFDataset.ncattrs">
+ <p>def <span class="ident">ncattrs</span>(</p><p>self)</p>
+ </div>
+
+
+
+
+ <div class="desc"><p><strong><code>ncattrs(self)</code></strong></p>
+<p>return the netcdf attribute names from the master file.</p></div>
<div class="source_cont">
</div>
@@ -5479,14 +5232,10 @@ character encoding of a string attribute (default is <code>utf-8</code>).</p></d
<p>def <span class="ident">renameAttribute</span>(</p><p>self, oldname, newname)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.renameAttribute">renameAttribute</a></code>
- </p>
- <div class="desc inherited"><p>rename a <a href="#netCDF4.Dataset"><code>Dataset</code></a> or <a href="#netCDF4.Group"><code>Group</code></a> attribute named <code>oldname</code> to <code>newname</code>.</p></div>
+ <div class="desc"><p>rename a <a href="#netCDF4.Dataset"><code>Dataset</code></a> or <a href="#netCDF4.Group"><code>Group</code></a> attribute named <code>oldname</code> to <code>newname</code>.</p></div>
<div class="source_cont">
</div>
@@ -5498,14 +5247,10 @@ character encoding of a string attribute (default is <code>utf-8</code>).</p></d
<p>def <span class="ident">renameDimension</span>(</p><p>self, oldname, newname)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.renameDimension">renameDimension</a></code>
- </p>
- <div class="desc inherited"><p>rename a <a href="#netCDF4.Dimension"><code>Dimension</code></a> named <code>oldname</code> to <code>newname</code>.</p></div>
+ <div class="desc"><p>rename a <a href="#netCDF4.Dimension"><code>Dimension</code></a> named <code>oldname</code> to <code>newname</code>.</p></div>
<div class="source_cont">
</div>
@@ -5517,14 +5262,10 @@ character encoding of a string attribute (default is <code>utf-8</code>).</p></d
<p>def <span class="ident">renameGroup</span>(</p><p>self, oldname, newname)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.renameGroup">renameGroup</a></code>
- </p>
- <div class="desc inherited"><p>rename a <a href="#netCDF4.Group"><code>Group</code></a> named <code>oldname</code> to <code>newname</code> (requires netcdf >= 4.3.1).</p></div>
+ <div class="desc"><p>rename a <a href="#netCDF4.Group"><code>Group</code></a> named <code>oldname</code> to <code>newname</code> (requires netcdf >= 4.3.1).</p></div>
<div class="source_cont">
</div>
@@ -5536,14 +5277,10 @@ character encoding of a string attribute (default is <code>utf-8</code>).</p></d
<p>def <span class="ident">renameVariable</span>(</p><p>self, oldname, newname)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.renameVariable">renameVariable</a></code>
- </p>
- <div class="desc inherited"><p>rename a <a href="#netCDF4.Variable"><code>Variable</code></a> named <code>oldname</code> to <code>newname</code></p></div>
+ <div class="desc"><p>rename a <a href="#netCDF4.Variable"><code>Variable</code></a> named <code>oldname</code> to <code>newname</code></p></div>
<div class="source_cont">
</div>
@@ -5555,14 +5292,10 @@ character encoding of a string attribute (default is <code>utf-8</code>).</p></d
<p>def <span class="ident">set_always_mask</span>(</p><p>self, True_or_False)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.set_always_mask">set_always_mask</a></code>
- </p>
- <div class="desc inherited"><p>Call <a href="#netCDF4.Variable.set_always_mask"><code>set_always_mask</code></a> for all variables contained in
+ <div class="desc"><p>Call <a href="#netCDF4.Variable.set_always_mask"><code>set_always_mask</code></a> for all variables contained in
this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or <a href="#netCDF4.Group"><code>Group</code></a>, as well as for all
variables in all its subgroups.</p>
<p><strong><code>True_or_False</code></strong>: Boolean determining if automatic conversion of
@@ -5582,14 +5315,10 @@ the default behaviour.</p></div>
<p>def <span class="ident">set_auto_chartostring</span>(</p><p>self, True_or_False)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.set_auto_chartostring">set_auto_chartostring</a></code>
- </p>
- <div class="desc inherited"><p>Call <a href="#netCDF4.Variable.set_auto_chartostring"><code>set_auto_chartostring</code></a> for all variables contained in this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or
+ <div class="desc"><p>Call <a href="#netCDF4.Variable.set_auto_chartostring"><code>set_auto_chartostring</code></a> for all variables contained in this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or
<a href="#netCDF4.Group"><code>Group</code></a>, as well as for all variables in all its subgroups.</p>
<p><strong><code>True_or_False</code></strong>: Boolean determining if automatic conversion of
all character arrays <--> string arrays should be performed for
@@ -5608,14 +5337,10 @@ after calling this function will follow the default behaviour.</p></div>
<p>def <span class="ident">set_auto_mask</span>(</p><p>self, True_or_False)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.set_auto_mask">set_auto_mask</a></code>
- </p>
- <div class="desc inherited"><p>Call <a href="#netCDF4.Variable.set_auto_mask"><code>set_auto_mask</code></a> for all variables contained in this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or
+ <div class="desc"><p>Call <a href="#netCDF4.Variable.set_auto_mask"><code>set_auto_mask</code></a> for all variables contained in this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or
<a href="#netCDF4.Group"><code>Group</code></a>, as well as for all variables in all its subgroups.</p>
<p><strong><code>True_or_False</code></strong>: Boolean determining if automatic conversion to masked arrays
shall be applied for all variables.</p>
@@ -5632,14 +5357,10 @@ after calling this function will follow the default behaviour.</p></div>
<p>def <span class="ident">set_auto_maskandscale</span>(</p><p>self, True_or_False)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.set_auto_maskandscale">set_auto_maskandscale</a></code>
- </p>
- <div class="desc inherited"><p>Call <a href="#netCDF4.Variable.set_auto_maskandscale"><code>set_auto_maskandscale</code></a> for all variables contained in this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or
+ <div class="desc"><p>Call <a href="#netCDF4.Variable.set_auto_maskandscale"><code>set_auto_maskandscale</code></a> for all variables contained in this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or
<a href="#netCDF4.Group"><code>Group</code></a>, as well as for all variables in all its subgroups.</p>
<p><strong><code>True_or_False</code></strong>: Boolean determining if automatic conversion to masked arrays
and variable scaling shall be applied for all variables.</p>
@@ -5656,14 +5377,10 @@ after calling this function will follow the default behaviour.</p></div>
<p>def <span class="ident">set_auto_scale</span>(</p><p>self, True_or_False)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.set_auto_scale">set_auto_scale</a></code>
- </p>
- <div class="desc inherited"><p>Call <a href="#netCDF4.Variable.set_auto_scale"><code>set_auto_scale</code></a> for all variables contained in this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or
+ <div class="desc"><p>Call <a href="#netCDF4.Variable.set_auto_scale"><code>set_auto_scale</code></a> for all variables contained in this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or
<a href="#netCDF4.Group"><code>Group</code></a>, as well as for all variables in all its subgroups.</p>
<p><strong><code>True_or_False</code></strong>: Boolean determining if automatic variable scaling
shall be applied for all variables.</p>
@@ -5680,14 +5397,10 @@ after calling this function will follow the default behaviour.</p></div>
<p>def <span class="ident">set_fill_off</span>(</p><p>self)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.set_fill_off">set_fill_off</a></code>
- </p>
- <div class="desc inherited"><p>Sets the fill mode for a <a href="#netCDF4.Dataset"><code>Dataset</code></a> open for writing to <code>off</code>.</p>
+ <div class="desc"><p>Sets the fill mode for a <a href="#netCDF4.Dataset"><code>Dataset</code></a> open for writing to <code>off</code>.</p>
<p>This will prevent the data from being pre-filled with fill values, which
may result in some performance improvements. However, you must then make
sure the data is actually written before being read.</p></div>
@@ -5702,14 +5415,10 @@ sure the data is actually written before being read.</p></div>
<p>def <span class="ident">set_fill_on</span>(</p><p>self)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.set_fill_on">set_fill_on</a></code>
- </p>
- <div class="desc inherited"><p>Sets the fill mode for a <a href="#netCDF4.Dataset"><code>Dataset</code></a> open for writing to <code>on</code>.</p>
+ <div class="desc"><p>Sets the fill mode for a <a href="#netCDF4.Dataset"><code>Dataset</code></a> open for writing to <code>on</code>.</p>
<p>This causes data to be pre-filled with fill values. The fill values can be
controlled by the variable's <code>_Fill_Value</code> attribute, but is usually
sufficient to the use the netCDF default <code>_Fill_Value</code> (defined
@@ -5728,14 +5437,10 @@ to.</p></div>
<p>def <span class="ident">set_ncstring_attrs</span>(</p><p>self, True_or_False)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.set_ncstring_attrs">set_ncstring_attrs</a></code>
- </p>
- <div class="desc inherited"><p>Call <a href="#netCDF4.Variable.set_ncstring_attrs"><code>set_ncstring_attrs</code></a> for all variables contained in
+ <div class="desc"><p>Call <a href="#netCDF4.Variable.set_ncstring_attrs"><code>set_ncstring_attrs</code></a> for all variables contained in
this <a href="#netCDF4.Dataset"><code>Dataset</code></a> or <a href="#netCDF4.Group"><code>Group</code></a>, as well as for all its
subgroups and their variables.</p>
<p><strong><code>True_or_False</code></strong>: Boolean determining if all string attributes are
@@ -5754,14 +5459,10 @@ of existing (sub-) groups and their variables.</p></div>
<p>def <span class="ident">setncattr</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">setncattr</a></code>
- </p>
- <div class="desc inherited"><p>set a netCDF dataset or group attribute using name,value pair.
+ <div class="desc"><p>set a netCDF dataset or group attribute using name,value pair.
Use if you need to set a netCDF attribute with the
with the same name as one of the reserved python attributes.</p></div>
<div class="source_cont">
@@ -5775,14 +5476,10 @@ with the same name as one of the reserved python attributes.</p></div>
<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.
+ <div class="desc"><p>set a netCDF dataset or group string attribute using name,value pair.
Use if you need to ensure that a netCDF attribute is created with type
<code>NC_STRING</code> if the file format is <code>NETCDF4</code>.</p></div>
<div class="source_cont">
@@ -5796,14 +5493,10 @@ Use if you need to ensure that a netCDF attribute is created with type
<p>def <span class="ident">setncatts</span>(</p><p>self,attdict)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.setncatts">setncatts</a></code>
- </p>
- <div class="desc inherited"><p>set a bunch of netCDF dataset or group attributes at once using a python dictionary.
+ <div class="desc"><p>set a bunch of netCDF dataset or group attributes at once using a python dictionary.
This may be faster when setting a lot of attributes for a <code>NETCDF3</code>
formatted file, since nc_redef/nc_enddef is not called in between setting
each attribute</p></div>
@@ -5818,95 +5511,10 @@ each attribute</p></div>
<p>def <span class="ident">sync</span>(</p><p>self)</p>
</div>
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.sync">sync</a></code>
- </p>
- <div class="desc inherited"><p>Writes all buffered data in the <a href="#netCDF4.Dataset"><code>Dataset</code></a> to the disk file.</p></div>
- <div class="source_cont">
-</div>
-
- </div>
-
- <h3>Methods</h3>
-
- <div class="item">
- <div class="name def" id="netCDF4.MFDataset.__init__">
- <p>def <span class="ident">__init__</span>(</p><p>self, files, check=False, aggdim=None, exclude=[], master_file=None)</p>
- </div>
-
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.__init__">__init__</a></code>
- </p>
-
-
-
- <div class="desc"><p>Open a Dataset spanning multiple files, making it look as if it was a
-single file. Variables in the list of files that share the same
-dimension (specified with the keyword <code>aggdim</code>) are aggregated. If
-<code>aggdim</code> is not specified, the unlimited is aggregated. Currently,
-<code>aggdim</code> must be the leftmost (slowest varying) dimension of each
-of the variables to be aggregated.</p>
-<p><strong><code>files</code></strong>: either a sequence of netCDF files or a string with a
-wildcard (converted to a sorted list of files using glob) If
-the <code>master_file</code> kwarg is not specified, the first file
-in the list will become the "master" file, defining all the
-variables with an aggregation dimension which may span
-subsequent files. Attribute access returns attributes only from "master"
-file. The files are always opened in read-only mode.</p>
-<p><strong><code>check</code></strong>: True if you want to do consistency checking to ensure the
-correct variables structure for all of the netcdf files. Checking makes
-the initialization of the MFDataset instance much slower. Default is
-False.</p>
-<p><strong><code>aggdim</code></strong>: The name of the dimension to aggregate over (must
-be the leftmost dimension of each of the variables to be aggregated).
-If None (default), aggregate over the unlimited dimension.</p>
-<p><strong><code>exclude</code></strong>: A list of variable names to exclude from aggregation.
-Default is an empty list.</p>
-<p><strong><code>master_file</code></strong>: file to use as "master file", defining all the
-variables with an aggregation dimension and all global attributes.</p></div>
- <div class="source_cont">
-</div>
-
- </div>
-
-
- <div class="item">
- <div class="name def" id="netCDF4.MFDataset.close">
- <p>def <span class="ident">close</span>(</p><p>self)</p>
- </div>
-
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.close">close</a></code>
- </p>
-
-
-
- <div class="desc"><p>close all the open files.</p></div>
- <div class="source_cont">
-</div>
-
- </div>
-
-
- <div class="item">
- <div class="name def" id="netCDF4.MFDataset.ncattrs">
- <p>def <span class="ident">ncattrs</span>(</p><p>self)</p>
- </div>
-
- <p class="inheritance">
- <strong>Inheritance:</strong>
- <code><a href="#netCDF4.Dataset">Dataset</a></code>.<code><a href="#netCDF4.Dataset.ncattrs">ncattrs</a></code>
- </p>
-
-
-
- <div class="desc"><p>return the netcdf attribute names from the master file.</p></div>
+ <div class="desc"><p>Writes all buffered data in the <a href="#netCDF4.Dataset"><code>Dataset</code></a> to the disk file.</p></div>
<div class="source_cont">
</div>
@@ -5957,9 +5565,9 @@ time unit and/or calendar to all files.</p>
<ul class="class_list">
<li><a href="#netCDF4.MFTime">MFTime</a></li>
<li>netCDF4._netCDF4._Variable</li>
- <li>__builtin__.object</li>
+ <li>builtins.object</li>
</ul>
- <h3>Methods</h3>
+ <h3>Static methods</h3>
<div class="item">
<div class="name def" id="netCDF4.MFTime.__init__">
@@ -5969,7 +5577,8 @@ time unit and/or calendar to all files.</p>
- <div class="desc"><p>Create a time Variable with units consistent across a multifile
+ <div class="desc"><p><strong><code>__init__(self, time, units=None, calendar=None)</code></strong></p>
+<p>Create a time Variable with units consistent across a multifile
dataset.</p>
<p><strong><code>time</code></strong>: Time variable from a <a href="#netCDF4.MFDataset"><code>MFDataset</code></a>.</p>
<p><strong><code>units</code></strong>: Time units, for example, <code>'days since 1979-01-01'</code>. If <code>None</code>,
@@ -5986,7 +5595,7 @@ is present on each variable and values are unique across files raising a
<div class="item">
<div class="name def" id="netCDF4.MFTime.ncattrs">
- <p>def <span class="ident">ncattrs</span>(</p><p>...)</p>
+ <p>def <span class="ident">ncattrs</span>(</p><p>self)</p>
</div>
@@ -6000,7 +5609,7 @@ is present on each variable and values are unique across files raising a
<div class="item">
<div class="name def" id="netCDF4.MFTime.set_always_mask">
- <p>def <span class="ident">set_always_mask</span>(</p><p>...)</p>
+ <p>def <span class="ident">set_always_mask</span>(</p><p>self, val)</p>
</div>
@@ -6014,7 +5623,7 @@ is present on each variable and values are unique across files raising a
<div class="item">
<div class="name def" id="netCDF4.MFTime.set_auto_chartostring">
- <p>def <span class="ident">set_auto_chartostring</span>(</p><p>...)</p>
+ <p>def <span class="ident">set_auto_chartostring</span>(</p><p>self, val)</p>
</div>
@@ -6028,7 +5637,7 @@ is present on each variable and values are unique across files raising a
<div class="item">
<div class="name def" id="netCDF4.MFTime.set_auto_mask">
- <p>def <span class="ident">set_auto_mask</span>(</p><p>...)</p>
+ <p>def <span class="ident">set_auto_mask</span>(</p><p>self, val)</p>
</div>
@@ -6042,7 +5651,7 @@ is present on each variable and values are unique across files raising a
<div class="item">
<div class="name def" id="netCDF4.MFTime.set_auto_maskandscale">
- <p>def <span class="ident">set_auto_maskandscale</span>(</p><p>...)</p>
+ <p>def <span class="ident">set_auto_maskandscale</span>(</p><p>self, val)</p>
</div>
@@ -6056,7 +5665,7 @@ is present on each variable and values are unique across files raising a
<div class="item">
<div class="name def" id="netCDF4.MFTime.set_auto_scale">
- <p>def <span class="ident">set_auto_scale</span>(</p><p>...)</p>
+ <p>def <span class="ident">set_auto_scale</span>(</p><p>self, val)</p>
</div>
@@ -6070,7 +5679,7 @@ is present on each variable and values are unique across files raising a
<div class="item">
<div class="name def" id="netCDF4.MFTime.typecode">
- <p>def <span class="ident">typecode</span>(</p><p>...)</p>
+ <p>def <span class="ident">typecode</span>(</p><p>self)</p>
</div>
@@ -6102,7 +5711,7 @@ the user.</p></div>
<h3>Ancestors (in MRO)</h3>
<ul class="class_list">
<li><a href="#netCDF4.VLType">VLType</a></li>
- <li>__builtin__.object</li>
+ <li>builtins.object</li>
</ul>
<h3>Class variables</h3>
<div class="item">
@@ -6207,7 +5816,7 @@ behavior is similar to Fortran or Matlab, but different than numpy.</p>
<h3>Ancestors (in MRO)</h3>
<ul class="class_list">
<li><a href="#netCDF4.Variable">Variable</a></li>
- <li>__builtin__.object</li>
+ <li>builtins.object</li>
</ul>
<h3>Class variables</h3>
<div class="item">
@@ -6936,7 +6545,7 @@ slower than multiple calls to the unstrided read routine <code>nc_get_vara</code
<footer id="footer">
<p>
Documentation generated by
- <a href="https://github.com/BurntSushi/pdoc">pdoc 0.3.2.dev16</a>
+ <a href="https://github.com/BurntSushi/pdoc">pdoc 0.3.2.dev29</a>
</p>
<p>pdoc is in the public domain with the
=====================================
examples/mpi_example.py
=====================================
@@ -1,10 +1,17 @@
# to run: mpirun -np 4 python mpi_example.py
+import sys
from mpi4py import MPI
import numpy as np
from netCDF4 import Dataset
+if len(sys.argv) == 2:
+ format = sys.argv[1]
+else:
+ format = 'NETCDF4_CLASSIC'
rank = MPI.COMM_WORLD.rank # The process ID (integer 0-3 for 4-process run)
+if rank == 0:
+ print('Creating file with format {}'.format(format))
nc = Dataset('parallel_test.nc', 'w', parallel=True, comm=MPI.COMM_WORLD,
- info=MPI.Info(),format='NETCDF4_CLASSIC')
+ info=MPI.Info(),format=format)
# below should work also - MPI_COMM_WORLD and MPI_INFO_NULL will be used.
#nc = Dataset('parallel_test.nc', 'w', parallel=True)
d = nc.createDimension('dim',4)
=====================================
include/netCDF4.pxi
=====================================
@@ -51,6 +51,7 @@ cdef extern from "netcdf.h":
NC_CLOBBER
NC_NOCLOBBER # Don't destroy existing file on create
NC_64BIT_OFFSET # Use large (64-bit) file offsets
+ NC_64BIT_DATA # Use cdf-5 format
NC_NETCDF4 # Use netCDF-4/HDF5 format
NC_CLASSIC_MODEL # Enforce strict netcdf-3 rules.
# Use these 'mode' flags for both nc_create and nc_open.
@@ -703,7 +704,7 @@ IF HAS_NC_CREATE_MEM:
int flags
int nc_close_memio(int ncid, NC_memio* info);
-IF HAS_NC_PAR:
+IF HAS_PARALLEL4_SUPPORT or HAS_PNETCDF_SUPPORT:
cdef extern from "mpi-compat.h": pass
cdef extern from "netcdf_par.h":
ctypedef int MPI_Comm
=====================================
netCDF4/__init__.py
=====================================
@@ -6,6 +6,7 @@ from ._netCDF4 import __doc__, __pdoc__
from ._netCDF4 import (__version__, __netcdf4libversion__, __hdf5libversion__,
__has_rename_grp__, __has_nc_inq_path__,
__has_nc_inq_format_extended__, __has_nc_open_mem__,
- __has_nc_create_mem__,__has_cdf5_format__,__has_nc_par__)
+ __has_nc_create_mem__, __has_cdf5_format__,
+ __has_parallel4_support__, __has_pnetcdf_support__)
__all__ =\
['Dataset','Variable','Dimension','Group','MFDataset','MFTime','CompoundType','VLType','date2num','num2date','date2index','stringtochar','chartostring','stringtoarr','getlibversion','EnumType']
=====================================
netCDF4/_netCDF4.pyx
=====================================
@@ -63,9 +63,10 @@ Requires
If you want [OPeNDAP](http://opendap.org) support, add `--enable-dap`.
If you want HDF4 SD support, add `--enable-hdf4` and add
the location of the HDF4 headers and library to `$CPPFLAGS` and `$LDFLAGS`.
- - for MPI parallel IO support, MPI-enabled versions of the HDF5 and netcdf
- libraries are required, as is the [mpi4py](http://mpi4py.scipy.org) python
- module.
+ - for MPI parallel IO support, an MPI-enabled versions of the netcdf library
+ is required, as is the [mpi4py](http://mpi4py.scipy.org) python module.
+ Parallel IO further depends on the existence of MPI-enabled HDF5 or the
+ [PnetCDF](https://parallel-netcdf.github.io/) library.
Install
@@ -918,13 +919,14 @@ specified names.
## <div id='section13'>13) Parallel IO.
-If MPI parallel enabled versions of netcdf and hdf5 are detected, and
-[mpi4py](https://mpi4py.scipy.org) is installed, netcdf4-python will
-be built with parallel IO capabilities enabled. Since parallel IO
-uses features of HDF5, it can only be used with NETCDF4 or
-NETCDF4_CLASSIC formatted files. To use parallel IO,
-your program must be running in an MPI environment using
-[mpi4py](https://mpi4py.scipy.org).
+If MPI parallel enabled versions of netcdf and hdf5 or pnetcdf are detected,
+and [mpi4py](https://mpi4py.scipy.org) is installed, netcdf4-python will
+be built with parallel IO capabilities enabled. Parallel IO of NETCDF4 or
+NETCDF4_CLASSIC formatted files is only available if the MPI parallel HDF5
+library is available. Parallel IO of classic netcdf-3 file formats is only
+available if the [PnetCDF](https://parallel-netcdf.github.io/) library is
+available. To use parallel IO, your program must be running in an MPI
+environment using [mpi4py](https://mpi4py.scipy.org).
:::python
>>> from mpi4py import MPI
@@ -971,9 +973,12 @@ participate in doing IO. To toggle back and forth between
the two types of IO, use the `netCDF4.Variable.set_collective`
`netCDF4.Variable`method. All metadata
operations (such as creation of groups, types, variables, dimensions, or attributes)
-are collective. There are a couple of important limitatons of parallel IO:
+are collective. There are a couple of important limitations of parallel IO:
- - only works with NETCDF4 or NETCDF4_CLASSIC formatted files.
+ - parallel IO for NETCDF4 or NETCDF4_CLASSIC formatted files is only available
+ if the netcdf library was compiled with MPI enabled HDF5.
+ - parallel IO for all classic netcdf-3 file formats is only available if the
+ netcdf library was compiled with PnetCDF.
- If a variable has an unlimited dimension, appending data must be done in collective mode.
If the write is done in independent mode, the operation will fail with a
a generic "HDF Error".
@@ -1185,7 +1190,7 @@ except ImportError:
# python3: zip is already python2's itertools.izip
pass
-__version__ = "1.4.3.2"
+__version__ = "1.5.0"
# Initialize numpy
import posixpath
@@ -1202,7 +1207,7 @@ import_array()
include "constants.pyx"
include "membuf.pyx"
include "netCDF4.pxi"
-IF HAS_NC_PAR:
+IF HAS_PARALLEL4_SUPPORT or HAS_PNETCDF_SUPPORT:
cimport mpi4py.MPI as MPI
from mpi4py.libmpi cimport MPI_Comm, MPI_Info, MPI_Comm_dup, MPI_Info_dup, \
MPI_Comm_free, MPI_Info_free, MPI_INFO_NULL,\
@@ -1240,7 +1245,8 @@ __has_nc_inq_format_extended__ = HAS_NC_INQ_FORMAT_EXTENDED
__has_cdf5_format__ = HAS_CDF5_FORMAT
__has_nc_open_mem__ = HAS_NC_OPEN_MEM
__has_nc_create_mem__ = HAS_NC_CREATE_MEM
-__has_nc_par__ = HAS_NC_PAR
+__has_parallel4_support__ = HAS_PARALLEL4_SUPPORT
+__has_pnetcdf_support__ = HAS_PNETCDF_SUPPORT
_needsworkaround_issue485 = __netcdf4libversion__ < "4.4.0" or \
(__netcdf4libversion__.startswith("4.4.0") and \
"-development" in __netcdf4libversion__)
@@ -1282,20 +1288,29 @@ _intnptonctype = {'i1' : NC_BYTE,
_format_dict = {'NETCDF3_CLASSIC' : NC_FORMAT_CLASSIC,
'NETCDF4_CLASSIC' : NC_FORMAT_NETCDF4_CLASSIC,
'NETCDF4' : NC_FORMAT_NETCDF4}
+# create dictionary mapping string identifiers to netcdf create format codes
+_cmode_dict = {'NETCDF3_CLASSIC' : NC_CLASSIC_MODEL,
+ 'NETCDF4_CLASSIC' : NC_CLASSIC_MODEL | NC_NETCDF4,
+ 'NETCDF4' : NC_NETCDF4}
IF HAS_CDF5_FORMAT:
# NETCDF3_64BIT deprecated, saved for compatibility.
# use NETCDF3_64BIT_OFFSET instead.
_format_dict['NETCDF3_64BIT_OFFSET'] = NC_FORMAT_64BIT_OFFSET
_format_dict['NETCDF3_64BIT_DATA'] = NC_FORMAT_64BIT_DATA
+ _cmode_dict['NETCDF3_64BIT_OFFSET'] = NC_64BIT_OFFSET
+ _cmode_dict['NETCDF3_64BIT_DATA'] = NC_64BIT_DATA
ELSE:
_format_dict['NETCDF3_64BIT'] = NC_FORMAT_64BIT
+ _cmode_dict['NETCDF3_64BIT'] = NC_64BIT_OFFSET
# invert dictionary mapping
_reverse_format_dict = dict((v, k) for k, v in _format_dict.iteritems())
# add duplicate entry (NETCDF3_64BIT == NETCDF3_64BIT_OFFSET)
IF HAS_CDF5_FORMAT:
_format_dict['NETCDF3_64BIT'] = NC_FORMAT_64BIT_OFFSET
+ _cmode_dict['NETCDF3_64BIT'] = NC_64BIT_OFFSET
ELSE:
_format_dict['NETCDF3_64BIT_OFFSET'] = NC_FORMAT_64BIT
+ _cmode_dict['NETCDF3_64BIT_OFFSET'] = NC_64BIT_OFFSET
# default fill_value to numpy datatype mapping.
default_fillvals = {#'S1':NC_FILL_CHAR,
@@ -2084,7 +2099,7 @@ strings.
cdef char *path
cdef char namstring[NC_MAX_NAME+1]
cdef int cmode
- IF HAS_NC_PAR:
+ IF HAS_PARALLEL4_SUPPORT or HAS_PNETCDF_SUPPORT:
cdef MPI_Comm mpicomm
cdef MPI_Info mpiinfo
@@ -2107,12 +2122,20 @@ strings.
raise ValueError(msg)
if parallel:
- IF HAS_NC_PAR != 1:
+ IF HAS_PARALLEL4_SUPPORT != 1 and HAS_PNETCDF_SUPPORT != 1:
msg='parallel mode requires MPI enabled netcdf-c'
raise ValueError(msg)
ELSE:
- if format not in ['NETCDF4','NETCDF4_CLASSIC']:
- msg='parallel mode only works with format=NETCDF4 or NETCDF4_CLASSIC'
+ parallel_formats = []
+ IF HAS_PARALLEL4_SUPPORT:
+ parallel_formats += ['NETCDF4','NETCDF4_CLASSIC']
+ IF HAS_PNETCDF_SUPPORT:
+ parallel_formats += ['NETCDF3_CLASSIC',
+ 'NETCDF3_64BIT_OFFSET',
+ 'NETCDF3_64BIT_DATA',
+ 'NETCDF3_64BIT']
+ if format not in parallel_formats:
+ msg='parallel mode only works with the following formats: ' + ' '.join(parallel_formats)
raise ValueError(msg)
if comm is not None:
mpicomm = comm.ob_mpi
@@ -2122,9 +2145,7 @@ strings.
mpiinfo = info.ob_mpi
else:
mpiinfo = MPI_INFO_NULL
- cmode = NC_MPIIO | NC_NETCDF4
- if format == 'NETCDF4_CLASSIC':
- cmode = cmode | NC_CLASSIC_MODEL
+ cmode = NC_MPIIO | _cmode_dict[format]
self._inmemory = False
if mode == 'w':
@@ -2144,7 +2165,7 @@ strings.
else:
if clobber:
if parallel:
- IF HAS_NC_PAR:
+ IF HAS_PARALLEL4_SUPPORT or HAS_PNETCDF_SUPPORT:
ierr = nc_create_par(path, NC_CLOBBER | cmode, \
mpicomm, mpiinfo, &grpid)
ELSE:
@@ -2159,7 +2180,7 @@ strings.
ierr = nc_create(path, NC_CLOBBER, &grpid)
else:
if parallel:
- IF HAS_NC_PAR:
+ IF HAS_PARALLEL4_SUPPORT or HAS_PNETCDF_SUPPORT:
ierr = nc_create_par(path, NC_NOCLOBBER | cmode, \
mpicomm, mpiinfo, &grpid)
ELSE:
@@ -2194,7 +2215,7 @@ strings.
version 4.4.1 or higher of the netcdf C lib, and rebuild netcdf4-python."""
raise ValueError(msg)
elif parallel:
- IF HAS_NC_PAR:
+ IF HAS_PARALLEL4_SUPPORT or HAS_PNETCDF_SUPPORT:
ierr = nc_open_par(path, NC_NOWRITE | NC_MPIIO, \
mpicomm, mpiinfo, &grpid)
ELSE:
@@ -2205,7 +2226,7 @@ strings.
ierr = nc_open(path, NC_NOWRITE, &grpid)
elif mode == 'r+' or mode == 'a':
if parallel:
- IF HAS_NC_PAR:
+ IF HAS_PARALLEL4_SUPPORT or HAS_PNETCDF_SUPPORT:
ierr = nc_open_par(path, NC_WRITE | NC_MPIIO, \
mpicomm, mpiinfo, &grpid)
ELSE:
@@ -2217,7 +2238,7 @@ strings.
elif mode == 'as' or mode == 'r+s':
if parallel:
# NC_SHARE ignored
- IF HAS_NC_PAR:
+ IF HAS_PARALLEL4_SUPPORT or HAS_PNETCDF_SUPPORT:
ierr = nc_open_par(path, NC_WRITE | NC_MPIIO, \
mpicomm, mpiinfo, &grpid)
ELSE:
@@ -2231,7 +2252,7 @@ strings.
if clobber:
if parallel:
# NC_SHARE ignored
- IF HAS_NC_PAR:
+ IF HAS_PARALLEL4_SUPPORT or HAS_PNETCDF_SUPPORT:
ierr = nc_create_par(path, NC_CLOBBER | cmode, \
mpicomm, mpiinfo, &grpid)
ELSE:
@@ -2246,7 +2267,7 @@ strings.
else:
if parallel:
# NC_SHARE ignored
- IF HAS_NC_PAR:
+ IF HAS_PARALLEL4_SUPPORT or HAS_PNETCDF_SUPPORT:
ierr = nc_create_par(path, NC_NOCLOBBER | cmode, \
mpicomm, mpiinfo, &grpid)
ELSE:
@@ -5345,7 +5366,7 @@ NC_CHAR).
turn on or off collective parallel IO access. Ignored if file is not
open for parallel access.
"""
- IF HAS_NC_PAR:
+ IF HAS_PARALLEL4_SUPPORT or HAS_PNETCDF_SUPPORT:
# set collective MPI IO mode on or off
if value:
ierr = nc_var_par_access(self._grpid, self._varid,
@@ -6099,6 +6120,10 @@ Example usage (See `netCDF4.MFDataset.__init__` for more details):
else:
files = sorted(glob(files))
+ if not files:
+ msg='no files specified (file list is empty)'
+ raise IOError(msg)
+
if master_file is not None:
if master_file not in files:
raise ValueError('master_file not in files list')
=====================================
setup.py
=====================================
@@ -56,7 +56,8 @@ def check_api(inc_dirs):
has_cdf5_format = False
has_nc_open_mem = False
has_nc_create_mem = False
- has_nc_par = False
+ has_parallel4_support = False
+ has_pnetcdf_support = False
for d in inc_dirs:
try:
@@ -65,7 +66,6 @@ def check_api(inc_dirs):
continue
has_nc_open_mem = os.path.exists(os.path.join(d, 'netcdf_mem.h'))
- has_nc_par = os.path.exists(os.path.join(d, 'netcdf_par.h'))
for line in f:
if line.startswith('nc_rename_grp'):
@@ -91,10 +91,15 @@ def check_api(inc_dirs):
for line in open(ncmetapath):
if line.startswith('#define NC_HAS_CDF5'):
has_cdf5_format = bool(int(line.split()[2]))
+ elif line.startswith('#define NC_HAS_PARALLEL4'):
+ has_parallel4_support = bool(int(line.split()[2]))
+ elif line.startswith('#define NC_HAS_PNETCDF'):
+ has_pnetcdf_support = bool(int(line.split()[2]))
break
return has_rename_grp, has_nc_inq_path, has_nc_inq_format_extended, \
- has_cdf5_format, has_nc_open_mem, has_nc_create_mem, has_nc_par
+ has_cdf5_format, has_nc_open_mem, has_nc_create_mem, \
+ has_parallel4_support, has_pnetcdf_support
def getnetcdfvers(libdirs):
@@ -488,7 +493,8 @@ if 'sdist' not in sys.argv[1:] and 'clean' not in sys.argv[1:]:
os.remove(netcdf4_src_c)
# this determines whether renameGroup and filepath methods will work.
has_rename_grp, has_nc_inq_path, has_nc_inq_format_extended, \
- has_cdf5_format, has_nc_open_mem, has_nc_create_mem, has_nc_par = check_api(inc_dirs)
+ has_cdf5_format, has_nc_open_mem, has_nc_create_mem, \
+ has_parallel4_support, has_pnetcdf_support = check_api(inc_dirs)
# for netcdf 4.4.x CDF5 format is always enabled.
if netcdf_lib_version is not None and\
(netcdf_lib_version > "4.4" and netcdf_lib_version < "4.5"):
@@ -498,7 +504,8 @@ if 'sdist' not in sys.argv[1:] and 'clean' not in sys.argv[1:]:
try:
import mpi4py
except ImportError:
- has_nc_par = False
+ has_parallel4_support = False
+ has_pnetcdf_support = False
f = open(osp.join('include', 'constants.pyx'), 'w')
if has_rename_grp:
@@ -544,16 +551,23 @@ if 'sdist' not in sys.argv[1:] and 'clean' not in sys.argv[1:]:
sys.stdout.write('netcdf lib does not have cdf-5 format capability\n')
f.write('DEF HAS_CDF5_FORMAT = 0\n')
- if has_nc_par:
+ if has_parallel4_support:
sys.stdout.write('netcdf lib has netcdf4 parallel functions\n')
- f.write('DEF HAS_NC_PAR = 1\n')
+ f.write('DEF HAS_PARALLEL4_SUPPORT = 1\n')
else:
sys.stdout.write('netcdf lib does not have netcdf4 parallel functions\n')
- f.write('DEF HAS_NC_PAR = 0\n')
+ f.write('DEF HAS_PARALLEL4_SUPPORT = 0\n')
+
+ if has_pnetcdf_support:
+ sys.stdout.write('netcdf lib has pnetcdf parallel functions\n')
+ f.write('DEF HAS_PNETCDF_SUPPORT = 1\n')
+ else:
+ sys.stdout.write('netcdf lib does not have pnetcdf parallel functions\n')
+ f.write('DEF HAS_PNETCDF_SUPPORT = 0\n')
f.close()
- if has_nc_par:
+ if has_parallel4_support or has_pnetcdf_support:
inc_dirs.append(mpi4py.get_include())
# mpi_incdir should not be needed if using nc-config
# (should be included in nc-config --cflags)
@@ -570,7 +584,7 @@ else:
setup(name="netCDF4",
cmdclass=cmdclass,
- version="1.4.3.2",
+ version="1.5.0",
long_description="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.\n\nThis project is hosted on a `GitHub repository <https://github.com/Unidata/netcdf4-python>`_ where you may access the most up-to-date source.",
author="Jeff Whitaker",
author_email="jeffrey.s.whitaker at noaa.gov",
=====================================
test/run_all.py
=====================================
@@ -1,7 +1,7 @@
import glob, os, sys, unittest, struct
from netCDF4 import getlibversion,__hdf5libversion__,__netcdf4libversion__,__version__
-from netCDF4 import __has_cdf5_format__, __has_nc_inq_path__, __has_nc_par__,\
- __has_nc_create_mem__
+from netCDF4 import __has_cdf5_format__, __has_nc_inq_path__, __has_nc_create_mem__, \
+ __has_parallel4_support__, __has_pnetcdf_support__
# can also just run
# python -m unittest discover . 'tst*py'
@@ -16,7 +16,7 @@ if python3:
else:
test_files.remove('tst_unicode3.py')
sys.stdout.write('not running tst_unicode3.py ...\n')
-if __netcdf4libversion__ < '4.2.1' or __has_nc_par__:
+if __netcdf4libversion__ < '4.2.1' or __has_parallel4_support__ or __has_pnetcdf_support__:
test_files.remove('tst_diskless.py')
sys.stdout.write('not running tst_diskless.py ...\n')
if not __has_nc_inq_path__:
View it on GitLab: https://salsa.debian.org/debian-gis-team/netcdf4-python/compare/5c836b569af81e659f7b4af05c6ae777b9add589...0faa545acca617229935dc69b56bfa56c6b8502c
--
View it on GitLab: https://salsa.debian.org/debian-gis-team/netcdf4-python/compare/5c836b569af81e659f7b4af05c6ae777b9add589...0faa545acca617229935dc69b56bfa56c6b8502c
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