Improve Zarr tutorial

docs/gallery/advanced_io/zarr_io.py → docs/gallery/advanced_io/plot_zarr_io.py

@@ -10,11 +10,10 @@
 
 Note that the Zarr native storage formats are optimized for storage in cloud storage
 (e.g., S3). For very large files, Zarr will create many files which can lead to
-issues for traditional file systems (that are not cloud object stores) due to
-limitations on the number of files per directory (this affects local disk,
-GDrive, Dropbox etc.).
+issues for traditional file system (that are not cloud object stores) due to limitations
+on the number of files per directory (this affects local disk, GDrive, Dropbox etc.).
 
-Zarr read and write is provided by the :hdmf-zarr:`hdmf-zarr package<>`. First, create an
+Zarr read and write is provided by the :hdmf-zarr:`hdmf-zarr` package. First, create an
 an NWBFile using PyNWB.
 """
 
@@ -41,8 +40,8 @@
 # Like HDF5, Zarr provides options to chunk and compress datasets. To leverage these
 # features, replace all :py:class:`~hdmf.backends.hdf5.h5_utils.H5DataIO` with the analogous
 # :py:class:`~hdmf_zarr.utils.ZarrDataIO`, which takes compressors specified by the
-# `numcodecs` library. For example, to create a :py:class:`.TimeSeries`
-# with a Zarr backend, use the following:
+# :py:mod:`numcodecs` library. For example, here is an example :py:class:`.TimeSeries`
+# where the ``data`` Dataset is compressed with a Blosc-zstd compressor:
 
 from numcodecs import Blosc
 from hdmf_zarr import ZarrDataIO
@@ -55,7 +54,7 @@
 )
 
 #######################################################################################
-# Now add it to the `NWBFile`.
+# Now add it to the :py:class:`.NWBFile`.
 
 nwbfile.add_acquisition(
     TimeSeries(
@@ -70,7 +69,7 @@
 # Writing to Zarr
 # ---------------
 # To write NWB files to Zarr, replace the :py:class:`~pynwb.NWBHDF5IO` with
-# :py:class:`hdmf_zarr.nwb.NWBZarrIO` for read/write
+# :py:class:`hdmf_zarr.nwb.NWBZarrIO`.
 
 from hdmf_zarr.nwb import NWBZarrIO
 import os
@@ -81,9 +80,10 @@
     io.write(nwbfile)
 
 #######################################################################################
-# The main reason for using the absolute_path here is for testing purposes to ensure
-# links and references work as expected. Otherwise, using the relative path here instead
-# is fine.
+# .. note::
+#   The main reason for using the ``absolute_path`` here is for testing purposes to
+#   ensure links and references work as expected. Otherwise, using the relative path
+#   here instead is fine.
 #
 # Reading from Zarr
 # -----------------
@@ -96,3 +96,4 @@
 #######################################################################################
 # .. note::
 #    For more information, see the :hdmf-zarr:`hdmf-zarr documentation<>`.
+

docs/source/conf.py

@@ -149,6 +149,7 @@ def __call__(self, filename):
     'nwbwidgets': ("https://nwb-widgets.readthedocs.io/en/latest/", None),
     'nwb-overview': ("https://nwb-overview.readthedocs.io/en/latest/", None),
     'hdmf-zarr': ("https://hdmf-zarr.readthedocs.io/en/latest/", None),
+    'numcodecs': ("https://numcodecs.readthedocs.io/en/latest/", None),
 }
 
 extlinks = {