Merge branch 'dev' into update-versioning-from-VCS

CHANGELOG.md

@@ -7,6 +7,10 @@
 - Add `NWBHDF5IO.can_read()`. @bendichter [#1703](https://github.com/NeurodataWithoutBorders/pynwb/pull/1703)
 - Add `pynwb.get_nwbfile_version()`. @bendichter [#1703](https://github.com/NeurodataWithoutBorders/pynwb/pull/1703)
 - Updated timeseries data checks to warn instead of error when reading invalid files. @stephprince [#1793](https://github.com/NeurodataWithoutBorders/pynwb/pull/1793)
+- Expose the offset, conversion and channel conversion parameters in `mock_ElectricalSeries`. @h-mayorquin [#1796](https://github.com/NeurodataWithoutBorders/pynwb/pull/1796)
+
+### Bug fixes
+- Fix bug where namespaces were loaded in "w-" mode. @h-mayorquin [#1795](https://github.com/NeurodataWithoutBorders/pynwb/pull/1795)
 
 ## PyNWB 2.5.0 (August 18, 2023)
 

src/pynwb/__init__.py

@@ -261,7 +261,8 @@ 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:
+        io_modes_that_create_file = ['w', 'w-', 'x']
+        if mode in io_modes_that_create_file or manager is not None or extensions is not None:
             load_namespaces = False
 
         if load_namespaces:

src/pynwb/testing/mock/ecephys.py

@@ -73,7 +73,10 @@ def mock_ElectricalSeries(
     timestamps=None,
     electrodes: Optional[DynamicTableRegion] = None,
     filtering: str = "filtering",
-    nwbfile: Optional[NWBFile] = None
+    nwbfile: Optional[NWBFile] = None,
+    channel_conversion: Optional[np.ndarray] = None,
+    conversion: float = 1.0,
+    offset: float = 0.,
 ) -> ElectricalSeries:
     electrical_series = ElectricalSeries(
         name=name or name_generator("ElectricalSeries"),
@@ -83,6 +86,9 @@ def mock_ElectricalSeries(
         timestamps=timestamps,
         electrodes=electrodes or mock_electrodes(nwbfile=nwbfile),
         filtering=filtering,
+        conversion=conversion,
+        offset=offset,
+        channel_conversion=channel_conversion,
     )
 
     if nwbfile is not None:

tests/integration/hdf5/test_io.py

@@ -3,6 +3,7 @@
 import numpy as np
 from h5py import File
 from pathlib import Path
+import tempfile
 
 from pynwb import NWBFile, TimeSeries, get_manager, NWBHDF5IO, validate
 
@@ -14,6 +15,7 @@
 from pynwb.spec import NWBGroupSpec, NWBDatasetSpec, NWBNamespace
 from pynwb.ecephys import ElectricalSeries, LFP
 from pynwb.testing import remove_test_file, TestCase
+from pynwb.testing.mock.file import mock_NWBFile
 
 
 class TestHDF5Writer(TestCase):
@@ -122,6 +124,19 @@ def test_write_no_cache_spec(self):
         with File(self.path, 'r') as f:
             self.assertNotIn('specifications', f)
 
+    def test_file_creation_io_modes(self):
+        io_modes_that_create_file = ["w", "w-", "x"]
+
+        with tempfile.TemporaryDirectory() as temp_dir:
+            temp_dir = Path(temp_dir)
+            for io_mode in io_modes_that_create_file:
+                file_path = temp_dir / f"test_io_mode={io_mode}.nwb"
+
+                # Test file creation
+                nwbfile = mock_NWBFile()
+                with NWBHDF5IO(str(file_path), io_mode) as io:
+                    io.write(nwbfile)
+
 
 class TestHDF5WriterWithInjectedFile(TestCase):