default load_namespaces=True

CHANGELOG.md

@@ -5,6 +5,7 @@
 ### Enhancements and minor changes
 - Add `TimeSeries.get_timestamps()`. @bendichter [#1741](https://github.com/NeurodataWithoutBorders/pynwb/pull/1741)
 - Add `TimeSeries.get_data_in_units()`. @bendichter [#1745](https://github.com/NeurodataWithoutBorders/pynwb/pull/1745)
+- For `NWBHDF5IO()`, change the default of arg `load_namespaces` from `False` to `True`. @bendichter [#1748](https://github.com/NeurodataWithoutBorders/pynwb/pull/1748)
 - Updated `ExternalResources` name change to `HERD`, along with HDMF 3.9.0 being the new minimum. @mavaylon1 [#1754](https://github.com/NeurodataWithoutBorders/pynwb/pull/1754)
 
 ### Documentation and tutorial enhancements

docs/gallery/advanced_io/linking_data.py

@@ -6,57 +6,50 @@
 
 PyNWB supports linking between files using external links.
 
-"""
+Example Use Case: Integrating data from multiple files
+---------------------------------------------------------
 
-####################
-# Example Use Case: Integrating data from multiple files
-# ---------------------------------------------------------
-#
-# NBWContainer classes (e.g., :py:class:`~pynwb.base.TimeSeries`) support the integration of data stored in external
-# HDF5 files with NWB data files via external links. To make things more concrete, let's look at the following use
-# case. We want to simultaneously record multiple data streams during data acquisition. Using the concept of external
-# links allows us to save each data stream to an external HDF5 files during data acquisition and to
-# afterwards link the data into a single NWB:N file. In this case, each recording becomes represented by a
-# separate file-system object that can be set as read-only once the experiment is done.  In the following
-# we are using :py:meth:`~pynwb.base.TimeSeries` as an example, but the same approach works for other
-# NWBContainers as well.
-#
+NBWContainer classes (e.g., :py:class:`~pynwb.base.TimeSeries`) support the integration of data stored in external
+HDF5 files with NWB data files via external links. To make things more concrete, let's look at the following use
+case. We want to simultaneously record multiple data streams during data acquisition. Using the concept of external
+links allows us to save each data stream to an external HDF5 files during data acquisition and to
+afterwards link the data into a single NWB:N file. In this case, each recording becomes represented by a
+separate file-system object that can be set as read-only once the experiment is done.  In the following
+we are using :py:meth:`~pynwb.base.TimeSeries` as an example, but the same approach works for other
+NWBContainers as well.
 
-####################
-# .. tip::
-#
-#    The same strategies we use here for creating External Links also apply to Soft Links.
-#    The main difference between soft and external links is that soft links point to other
-#    objects within the same file while external links point to objects in external files.
-#
+.. tip::
 
-####################
-# .. tip::
-#
-#    In the case of :py:meth:`~pynwb.base.TimeSeries`, the uncorrected timestamps generated by the acquisition
-#    system can be stored (or linked) in the *sync* group. In the NWB:N format, hardware-recorded time data
-#    must then be corrected to a common time base (e.g., timestamps from all hardware sources aligned) before
-#    it can be included in the *timestamps* of the *TimeSeries*. This means, in the case
-#    of :py:meth:`~pynwb.base.TimeSeries` we need to be careful that we are not including data with incompatible
-#    timestamps in the same file when using external links.
-#
+    The same strategies we use here for creating External Links also apply to Soft Links.
+    The main difference between soft and external links is that soft links point to other
+    objects within the same file while external links point to objects in external files.
 
-####################
-# .. warning::
-#
-#    External links can become stale/break. Since external links are pointing to data in other files
-#    external links may become invalid any time files are modified on the file system, e.g., renamed,
-#    moved or access permissions are changed.
-#
+ .. tip::
 
-####################
-# Creating test data
-# ---------------------------
-#
-# In the following we are creating two :py:meth:`~pynwb.base.TimeSeries` each written to a separate file.
-# We then show how we can integrate these files into a single NWBFile.
+    In the case of :py:meth:`~pynwb.base.TimeSeries`, the uncorrected timestamps generated by the acquisition
+    system can be stored (or linked) in the *sync* group. In the NWB:N format, hardware-recorded time data
+    must then be corrected to a common time base (e.g., timestamps from all hardware sources aligned) before
+    it can be included in the *timestamps* of the *TimeSeries*. This means, in the case
+    of :py:meth:`~pynwb.base.TimeSeries` we need to be careful that we are not including data with incompatible
+    timestamps in the same file when using external links.
+
+
+.. warning::
+
+    External links can become stale/break. Since external links are pointing to data in other files
+    external links may become invalid any time files are modified on the file system, e.g., renamed,
+    moved or access permissions are changed.
+
+
+Creating test data
+---------------------------
+
+In the following we are creating two :py:meth:`~pynwb.base.TimeSeries` each written to a separate file.
+We then show how we can integrate these files into a single NWBFile.
+"""
 
 # sphinx_gallery_thumbnail_path = 'figures/gallery_thumbnails_linking_data.png'
+
 from datetime import datetime
 from uuid import uuid4
 

docs/gallery/general/extensions.py

@@ -254,7 +254,7 @@ def __init__(self, **kwargs):
 # 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", load_namespaces=True) as io:
+with NWBHDF5IO("cache_spec_example.nwb", mode="r") as io:
     nwbfile = io.read()
 
 ####################

src/pynwb/__init__.py

@@ -4,7 +4,6 @@
 import os.path
 from pathlib import Path
 from copy import deepcopy
-from warnings import warn
 import h5py
 
 from hdmf.spec import NamespaceCatalog
@@ -206,8 +205,9 @@ class NWBHDF5IO(_HDF5IO):
              'doc': 'the mode to open the HDF5 file with, one of ("w", "r", "r+", "a", "w-", "x")',
              'default': 'r'},
             {'name': 'load_namespaces', 'type': bool,
-             'doc': 'whether or not to load cached namespaces from given path - not applicable in write mode',
-             'default': False},
+             'doc': ('whether or not to load cached namespaces from given path - not applicable in write mode '
+                     'or when `manager` is not None or when `extensions` is not None'),
+             'default': True},
             {'name': 'manager', 'type': BuildManager, 'doc': 'the BuildManager to use for I/O', 'default': None},
             {'name': 'extensions', 'type': (str, TypeMap, list),
              'doc': 'a path to a namespace, a TypeMap, or a list consisting paths to namespaces and TypeMaps',
@@ -223,14 +223,10 @@ def __init__(self, **kwargs):
             popargs('path', 'mode', 'manager', 'extensions', 'load_namespaces',
                     'file', 'comm', 'driver', 'herd_path', kwargs)
         # Define the BuildManager to use
+        if mode in 'wx' or manager is not None or extensions is not None:
+            load_namespaces = False
+
         if load_namespaces:
-            if manager is not None:
-                warn("loading namespaces from file - ignoring 'manager'")
-            if extensions is not None:
-                warn("loading namespaces from file - ignoring 'extensions' argument")
-            # namespaces are not loaded when creating an NWBHDF5IO object in write mode
-            if 'w' in mode or mode == 'x':
-                raise ValueError("cannot load namespaces from file when writing to it")
 
             tm = get_type_map()
             super().load_namespaces(tm, path, file=file_obj, driver=driver)

tests/back_compat/test_import_structure.py

@@ -82,7 +82,6 @@ def test_outer_import_structure(self):
             "spec",
             "testing",
             "validate",
-            "warn",
         ]
         for member in expected_structure:
             self.assertIn(member=member, container=current_structure)

tests/back_compat/test_read.py

@@ -43,7 +43,7 @@ def test_read(self):
             with self.subTest(file=f.name):
                 with warnings.catch_warnings(record=True) as warnings_on_read:
                     warnings.simplefilter("always")
-                    with NWBHDF5IO(str(f), 'r', load_namespaces=True) as io:
+                    with NWBHDF5IO(str(f), 'r') as io:
                         errors = validate(io)
                         io.read()
                         for w in warnings_on_read:

tests/integration/hdf5/test_ecephys.py

@@ -116,8 +116,9 @@ def setUpTwoElectricalSeries(self):
         data2 = list(zip(reversed(range(10)), reversed(range(10, 20))))
         timestamps = list(map(lambda x: x/10., range(10)))
         es1 = ElectricalSeries(name='test_eS1', data=data1, electrodes=region1, timestamps=timestamps)
-        es2 = ElectricalSeries(name='test_eS2', data=data2, electrodes=region2, channel_conversion=[4., .4],
-                               timestamps=timestamps)
+        es2 = ElectricalSeries(
+            name='test_eS2', data=data2, electrodes=region2, channel_conversion=[4., .4], timestamps=timestamps
+        )
         return es1, es2
 
     def addContainer(self, nwbfile):

tests/read_dandi/test_read_dandi.py

@@ -41,7 +41,7 @@ def test_read_first_nwb_asset(self):
             s3_url = first_asset.get_content_url(follow_redirects=1, strip_query=True)
 
             try:
-                with NWBHDF5IO(path=s3_url, load_namespaces=True, driver="ros3") as io:
+                with NWBHDF5IO(path=s3_url, driver="ros3") as io:
                     io.read()
             except Exception as e:
                 print(traceback.format_exc())

tests/unit/test_file.py

@@ -542,7 +542,7 @@ def test_simple(self):
                           lab='Chang Lab')
         with NWBHDF5IO(self.path, 'w') as io:
             io.write(nwbfile)
-        with NWBHDF5IO(self.path, 'r', load_namespaces=True) as reader:
+        with NWBHDF5IO(self.path, 'r') as reader:
             nwbfile = reader.read()
 
 
@@ -563,9 +563,8 @@ def test_simple(self):
         with NWBHDF5IO(self.path, 'w') as io:
             io.write(nwbfile, cache_spec=False)
 
-        with self.assertWarnsWith(UserWarning, "No cached namespaces found in %s" % self.path):
-            with NWBHDF5IO(self.path, 'r', load_namespaces=True) as reader:
-                nwbfile = reader.read()
+        with NWBHDF5IO(self.path, 'r') as reader:
+            nwbfile = reader.read()
 
 
 class TestTimestampsRefDefault(TestCase):

tests/validation/test_validate.py

@@ -222,13 +222,13 @@ def test_validate_io_cached(self):
 
     def test_validate_io_cached_extension(self):
         """Test that validating a file with cached spec against its cached namespaces succeeds."""
-        with NWBHDF5IO('tests/back_compat/2.1.0_nwbfile_with_extension.nwb', 'r', load_namespaces=True) as io:
+        with NWBHDF5IO('tests/back_compat/2.1.0_nwbfile_with_extension.nwb', 'r') as io:
             errors = validate(io)
             self.assertEqual(errors, [])
 
     def test_validate_io_cached_extension_pass_ns(self):
         """Test that validating a file with cached extension spec against the extension namespace succeeds."""
-        with NWBHDF5IO('tests/back_compat/2.1.0_nwbfile_with_extension.nwb', 'r', load_namespaces=True) as io:
+        with NWBHDF5IO('tests/back_compat/2.1.0_nwbfile_with_extension.nwb', 'r') as io:
             errors = validate(io, 'ndx-testextension')
             self.assertEqual(errors, [])
 
@@ -237,9 +237,7 @@ def test_validate_io_cached_core_with_io(self):
         For back-compatability, test that validating a file with cached extension spec against the core
         namespace succeeds when using the `io` + `namespace` keywords.
         """
-        with NWBHDF5IO(
-            path='tests/back_compat/2.1.0_nwbfile_with_extension.nwb', mode='r', load_namespaces=True
-        ) as io:
+        with NWBHDF5IO(path='tests/back_compat/2.1.0_nwbfile_with_extension.nwb', mode='r') as io:
             results = validate(io=io, namespace="core")
             self.assertEqual(results, [])