Merge pull request #951 from apdavison/remove_hdf5io

Remove NeoHdf5IO

Author: samuelgarcia

doc/source/developers_guide.rst

@@ -45,7 +45,7 @@ Requirements
     * Sphinx_ (for building documentation)
     * (optional) coverage_ >= 2.85 (for measuring test coverage)
     * (optional) scipy >= 0.12 (for MatlabIO)
-    * (optional) h5py >= 2.5 (for KwikIO, NeoHdf5IO)
+    * (optional) h5py >= 2.5 (for KwikIO)
     * (optional) nixio (for NixIO)
     * (optional) pillow (for TiffIO)
 

doc/source/install.rst

@@ -23,7 +23,7 @@ Certain IO modules have additional dependencies. If these are not satisfied,
 Neo will still install but the IO module that uses them will fail on loading:
 
    * scipy >= 1.0.0 for NeoMatlabIO
-   * h5py >= 2.5 for Hdf5IO, KwikIO
+   * h5py >= 2.5 for KwikIO
    * klusta for KwikIO
    * igor >= 0.2 for IgorIO
    * nixio >= 1.5 for NixIO
@@ -33,15 +33,14 @@ Neo will still install but the IO module that uses them will fail on loading:
 These dependencies can be installed by specifying a comma-separated list with the
 ``pip install`` command::
 
-    $ pip install neo[hdf5io,tiffio]
+    $ pip install neo[nixio,tiffio]
 
 Or when installing a specific version of neo::
 
-    $ pip install neo[hdf5io,tiffio]==0.9.0
+    $ pip install neo[nixio,tiffio]==0.9.0
 
 These additional dependencies for IO modules are available::
 
-  * hdf5io
   * igorproio
   * kwikio
   * neomatlabio

doc/source/io.rst

@@ -224,7 +224,7 @@ Logging
 
 :mod:`neo` uses the standard Python :mod:`logging` module for logging.
 All :mod:`neo.io` classes have logging set up by default, although not all classes produce log messages.
-The logger name is the same as the full qualified class name, e.g. :class:`neo.io.hdf5io.NeoHdf5IO`.
+The logger name is the same as the full qualified class name, e.g. :class:`neo.io.nixio.NixIO`.
 By default, only log messages that are critically important for users are displayed, so users should not disable log messages unless they are sure they know what they are doing.
 However, if you wish to disable the messages, you can do so::
 
@@ -264,22 +264,22 @@ This can also be done for individual IO classes::
 
     >>> import logging
     >>>
-    >>> logger = logging.getLogger('neo.io.hdf5io.NeoHdf5IO')
+    >>> logger = logging.getLogger('neo.io.nixio.NixIO')
     >>> handler = logging.FileHandler('filename.log')
     >>> logger.addHandler(handler)
 
 Individual IO classes can have their loggers disabled as well::
 
     >>> import logging
     >>>
-    >>> logger = logging.getLogger('neo.io.hdf5io.NeoHdf5IO')
+    >>> logger = logging.getLogger('neo.io.nixio.NixIO')
     >>> logger.setLevel(100)
 
 And more detailed logging messages can be enabled for individual IO classes::
 
     >>> import logging
     >>>
-    >>> logger = logging.getLogger('neo.io.hdf5io.NeoHdf5IO')
+    >>> logger = logging.getLogger('neo.io.nixio.NixIO')
     >>> logger.setLevel(logging.INFO)
 
 The default handler, which is used to print logs to the command line, is stored in :attr:`neo.logging_handler`.

doc/source/io_developers_guide.rst

@@ -71,7 +71,7 @@ Logging
 =======
 
 All IO classes by default have logging using the standard :mod:`logging` module: already set up.
-The logger name is the same as the fully qualified class name, e.g. :class:`neo.io.hdf5io.NeoHdf5IO`.
+The logger name is the same as the fully qualified class name, e.g. :class:`neo.io.nixio.NixIO`.
 The :attr:`class.logger` attribute holds the logger for easy access.
 
 There are generally 3 types of situations in which an IO class should use a logger

neo/io/__init__.py

@@ -34,7 +34,6 @@
 * :attr:`KlustaKwikIO`
 * :attr:`KwikIO`
 * :attr:`MicromedIO`
-* :attr:`NeoHdf5IO`
 * :attr:`NeoMatlabIO`
 * :attr:`NestIO`
 * :attr:`NeuralynxIO`
@@ -141,10 +140,6 @@
 
     .. autoattribute:: extensions
 
-.. autoclass:: neo.io.NeoHdf5IO
-
-    .. autoattribute:: extensions
-
 .. autoclass:: neo.io.NeoMatlabIO
 
     .. autoattribute:: extensions
@@ -267,7 +262,6 @@
 from neo.io.kwikio import KwikIO
 from neo.io.mearecio import MEArecIO
 from neo.io.micromedio import MicromedIO
-from neo.io.hdf5io import NeoHdf5IO
 from neo.io.neomatlabio import NeoMatlabIO
 from neo.io.nestio import NestIO
 from neo.io.neuralynxio import NeuralynxIO
@@ -312,8 +306,7 @@
     KwikIO,
     MEArecIO,
     MicromedIO,
-    NixIO,  # place NixIO before NeoHdf5IO to make it the default for .h5 files
-    NeoHdf5IO,
+    NixIO,  # place NixIO before other IOs that use HDF5 to make it the default for .h5 files
     NeoMatlabIO,
     NestIO,
     NeuralynxIO,