Merge branch 'dev' into streaming_add_remfile2

NeurodataWithoutBorders · Nov 29, 2023 · b3591ed · b3591ed
2 parents 2a70ca9 + 5e8ddc2
commit b3591ed
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Showing 3 changed files with 9 additions and 14 deletions.
diff --git a/docs/gallery/advanced_io/streaming.py b/docs/gallery/advanced_io/streaming.py
@@ -69,7 +69,7 @@
 # next, open the file
 with fs.open(s3_url, "rb") as f:
     with h5py.File(f) as file:
-        with pynwb.NWBHDF5IO(file=file, load_namespaces=True) as io:
+        with pynwb.NWBHDF5IO(file=file) as io:
             nwbfile = io.read()
             print(nwbfile.acquisition['lick_times'].time_series['lick_left_times'].data[:])
 
@@ -99,7 +99,7 @@
 
 from pynwb import NWBHDF5IO
 
-with NWBHDF5IO(s3_url, mode='r', load_namespaces=True, driver='ros3') as io:
+with NWBHDF5IO(s3_url, mode='r', driver='ros3') as io:
     nwbfile = io.read()
     print(nwbfile)
     print(nwbfile.acquisition['lick_times'].time_series['lick_left_times'].data[:])

diff --git a/docs/gallery/general/extensions.py b/docs/gallery/general/extensions.py
@@ -248,16 +248,11 @@ def __init__(self, **kwargs):
 # .. note::
 #
 #     For more information on writing NWB files, see :ref:`basic_writing`.
-
-####################
-# By default, PyNWB does not use the namespaces cached in a file--you must
-# explicitly specify this. This behavior is enabled by the *load_namespaces*
-# argument to the :py:class:`~pynwb.NWBHDF5IO` constructor.
-
-with NWBHDF5IO("cache_spec_example.nwb", mode="r") as io:
-    nwbfile = io.read()
-
-####################
+#
+# By default, if a namespace is not already loaded, PyNWB loads the namespace cached in
+# the file. To disable this, set ``load_namespaces=False`` in the
+# :py:class:`~pynwb.NWBHDF5IO` constructor.
+#
 # .. _MultiContainerInterface:
 #
 # Creating and using a custom MultiContainerInterface

diff --git a/docs/gallery/general/plot_read_basics.py b/docs/gallery/general/plot_read_basics.py
@@ -104,14 +104,14 @@
 
 filepath = "sub-P11HMH_ses-20061101_ecephys+image.nwb"
 # Open the file in read mode "r",
-io = NWBHDF5IO(filepath, mode="r", load_namespaces=True)
+io = NWBHDF5IO(filepath, mode="r")
 nwbfile = io.read()
 nwbfile
 
 #######################################
 # :py:class:`~pynwb.NWBHDF5IO` can also be used as a context manager:
 
-with NWBHDF5IO(filepath, mode="r", load_namespaces=True) as io2:
+with NWBHDF5IO(filepath, mode="r") as io2:
     nwbfile2 = io2.read()
 
     # data accessible here