Fix various documentation build warnings and broken links

docs/gallery/advanced_io/h5dataio.py

@@ -109,9 +109,9 @@
 # .. note::
 #
 #    Chunking can help improve data read/write performance by allowing us to align chunks with common
-#    read/write operations. The following blog post provides an example
-#    `http://geology.beer/2015/02/10/hdf-for-large-arrays/ <http://geology.beer/2015/02/10/hdf-for-large-arrays/>`__.
-#    for this. But you should also know that, with great power comes great responsibility! I.e., if you choose a
+#    read/write operations. You can find a discussion on how chunking can help in the
+#    `Python and HDF5 book  <https://www.oreilly.com/library/view/python-and-hdf5/9781491944981/ch04.html>`__.
+#    by Andrew Collette. But you should also know that, with great power comes great responsibility! I.e., if you choose a
 #    bad chunk size e.g., too small chunks that don't align with our read/write operations, then chunking can
 #    also harm I/O performance.
 
@@ -208,7 +208,7 @@
 # how ``h5py.Dataset`` objects should be handled on write by the PyNWBs HDF5 backend via the ``link_data``
 # parameter. If ``link_data`` is set to ``True`` then a ``SoftLink`` or ``ExternalLink`` will be created to
 # point to the HDF5 dataset On the other hand, if ``link_data`` is set to ``False`` then the dataset
-# be copied using `h5py.Group.copy <http://docs.h5py.org/en/latest/high/group.html#Group.copy>`__
+# be copied using `h5py.Group.copy <https://docs.h5py.org/en/latest/high/group.html#h5py.Group.copy>`__
 # **without copying attributes** and **without expanding soft links, external links, or references**.
 #
 # .. note::

docs/gallery/domain/ecephys.py

@@ -286,7 +286,7 @@
 #
 # As mentioned above, :py:class:`~pynwb.ecephys.ElectricalSeries` objects
 # are meant for storing specific types of extracellular recordings. In addition to this
-# :py:class:`~pynwb.base.TimeSeries` class, NWB provides some :ref:`basic_data_interfaces`
+# :py:class:`~pynwb.base.TimeSeries` class, NWB provides some :ref:`modules_overview`
 # for designating the type of data you are storing. We will briefly discuss them here, and refer the reader to
 # :py:mod:`API documentation <pynwb.ecephys>` and :ref:`basics` for more details on
 # using these objects.

docs/gallery/domain/plot_behavior.py

@@ -15,7 +15,7 @@
 * create an object:
 
   * :py:class:`~pynwb.base.TimeSeries` for continuous time series data,
-  * :py:class:`~pynwb.base.SpatialSeries` for continuous spatial data (e.g. position, direction relative to some reference frame),
+  * :py:class:`~pynwb.behavior.SpatialSeries` for continuous spatial data (e.g. position, direction relative to some reference frame),
   * :py:class:`~pynwb.misc.IntervalSeries` or :py:class:`~pynwb.epoch.TimeIntervals` for time intervals
 
 * store that object inside a behavior interface object:
@@ -239,7 +239,7 @@
 ####################
 # Storing only the timestamps of the events is possible with the `ndx-events <https://pypi.org/project/ndx-events/>`_
 # NWB extension. You can also add labels associated with the events with this extension.
-# You can find information about installation and example usage `here <https://github.com/rly/ndx-events#ndx-events-extension-for-nwb>`_.
+# You can find information about installation and example usage `here <https://github.com/nwb-extensions/ndx-events-record>`_.
 #
 # .. seealso::
 #    You can learn more about using extensions in the :ref:`tutorial-extending-nwb` tutorial.
@@ -284,7 +284,7 @@
 ####################
 # Using :py:class:`~pynwb.epoch.TimeIntervals` representing time intervals
 # is often preferred over :py:class:`~pynwb.behavior.BehavioralEpochs` and :py:class:`~pynwb.misc.IntervalSeries`.
-# :py:class:`~pynwb.epoch.TimeIntervals` is a subclass of :py:class:`~pynwb.core.DynamicTable` which offers
+# :py:class:`~pynwb.epoch.TimeIntervals` is a subclass of :py:class:`~hdmf.common.table.DynamicTable` which offers
 # flexibility for tabular data by allowing the addition of optional columns which are not defined in the standard.
 #
 # Create a :py:class:`~pynwb.epoch.TimeIntervals` object that represents the time

docs/gallery/general/extensions.py

@@ -7,11 +7,16 @@
 The NWB format was designed to be easily extendable. Here we discuss some of the basic functionality
 in PyNWB for creating  Neurodata Extensions (NDX).
 
-.. note::
+.. seealso::
 
     For a more in-depth, step-by-step guide on how to create, document, and publish NWB extensions, we highly
-    recommend visiting the :nwb-overview:`extension tutorial <extensions_tutorial/6_documenting_extension.html>`
-    on the :nwb-overview:`nwb overview <>` website.
+    recommend visiting the :nwb_overview:`extension tutorial <extensions_tutorial/6_documenting_extension.html>`
+    on the :nwb_overview:`nwb overview <>` website.
+
+.. seealso::
+
+   For more information on available tools for creating extensions, see
+   :nwb_overview:`here <core_tools/core_tools_home.html#svg-version-1-1-width-1-5em-height-1-5em-class-sd-octicon-sd-octicon-diff-added-viewbox-0-0-16-16-aria-hidden-true-path-fill-rule-evenodd-d-m13-25-2-5h2-75a-25-25-0-00-25-25v10-5c0-138-112-25-25-25h10-5a-25-25-0-00-25-25v2-75a-25-25-0-00-25-25zm2-75-1h10-5c-966-0-1-75-784-1-75-1-75v10-5a1-75-1-75-0-0113-25-15h2-75a1-75-1-75-0-011-13-25v2-75c1-1-784-1-784-1-2-75-1zm8-4a-75-75-0-01-75-75v2-5h2-5a-75-75-0-010-1-5h-2-5v2-5a-75-75-0-01-1-5-0v-2-5h-2-5a-75-75-0-010-1-5h2-5v-2-5a-75-75-0-018-4z-path-svg-extending-nwb>`.
 
 '''
 
@@ -24,8 +29,6 @@
 # Extensions should be defined separately from the code that uses the extensions. This design decision is
 # based on the assumption that the extension will be written once, and read or used multiple times. Here, we
 # provide an example of how to create an extension for subsequent use.
-# (For more information on the available tools for creating extensions, see :ref:`extending-nwb`).
-#
 #
 # The following block of code demonstrates how to create a new namespace, and then add a new `neurodata_type`
 # to this namespace. Finally,