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Merge branch 'dev' into streaming_add_remfile2
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rly authored Dec 2, 2023
2 parents b3591ed + 87a7c57 commit bae8d30
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -6,6 +6,7 @@
- For `NWBHDF5IO()`, change the default of arg `load_namespaces` from `False` to `True`. @bendichter [#1748](https://github.com/NeurodataWithoutBorders/pynwb/pull/1748)
- 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)

### Documentation and tutorial enhancements
- Add RemFile to streaming tutorial @bendichter [#1761](https://github.com/NeurodataWithoutBorders/pynwb/pull/1761)
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12 changes: 10 additions & 2 deletions src/pynwb/base.py
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Expand Up @@ -174,15 +174,23 @@ def __init__(self, **kwargs):
timestamps = args_to_process['timestamps']
if timestamps is not None:
if self.rate is not None:
raise ValueError('Specifying rate and timestamps is not supported.')
self._error_on_new_warn_on_construct(
error_msg='Specifying rate and timestamps is not supported.'
)
if self.starting_time is not None:
raise ValueError('Specifying starting_time and timestamps is not supported.')
self._error_on_new_warn_on_construct(
error_msg='Specifying starting_time and timestamps is not supported.'
)
self.fields['timestamps'] = timestamps
self.timestamps_unit = self.__time_unit
self.interval = 1
if isinstance(timestamps, TimeSeries):
timestamps.__add_link('timestamp_link', self)
elif self.rate is not None:
if self.rate <= 0:
self._error_on_new_warn_on_construct(
error_msg='Rate must be a positive value.'
)
if self.starting_time is None: # override default if rate is provided but not starting time
self.starting_time = 0.0
self.starting_time_unit = self.__time_unit
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57 changes: 57 additions & 0 deletions tests/unit/test_base.py
Original file line number Diff line number Diff line change
Expand Up @@ -405,6 +405,63 @@ def test_get_data_in_units(self):
ts = mock_TimeSeries(data=[1., 2., 3.])
assert_array_equal(ts.get_data_in_units(), [1., 2., 3.])

def test_non_positive_rate(self):
with self.assertRaisesWith(ValueError, 'Rate must be a positive value.'):
TimeSeries(name='test_ts', data=list(), unit='volts', rate=-1.0)
with self.assertRaisesWith(ValueError, 'Rate must be a positive value.'):
TimeSeries(name='test_ts1', data=list(), unit='volts', rate=0.0)

def test_file_with_non_positive_rate_in_construct_mode(self):
"""Test that UserWarning is raised when rate is 0 or negative
while being in construct mode (i.e,. on data read)."""
obj = TimeSeries.__new__(TimeSeries,
container_source=None,
parent=None,
object_id="test",
in_construct_mode=True)
with self.assertWarnsWith(warn_type=UserWarning, exc_msg='Rate must be a positive value.'):
obj.__init__(
name="test_ts",
data=list(),
unit="volts",
rate=-1.0
)

def test_file_with_rate_and_timestamps_in_construct_mode(self):
"""Test that UserWarning is raised when rate and timestamps are both specified
while being in construct mode (i.e,. on data read)."""
obj = TimeSeries.__new__(TimeSeries,
container_source=None,
parent=None,
object_id="test",
in_construct_mode=True)
with self.assertWarnsWith(warn_type=UserWarning, exc_msg='Specifying rate and timestamps is not supported.'):
obj.__init__(
name="test_ts",
data=[11, 12, 13, 14, 15],
unit="volts",
rate=1.0,
timestamps=[1, 2, 3, 4, 5]
)

def test_file_with_starting_time_and_timestamps_in_construct_mode(self):
"""Test that UserWarning is raised when starting_time and timestamps are both specified
while being in construct mode (i.e,. on data read)."""
obj = TimeSeries.__new__(TimeSeries,
container_source=None,
parent=None,
object_id="test",
in_construct_mode=True)
with self.assertWarnsWith(warn_type=UserWarning,
exc_msg='Specifying starting_time and timestamps is not supported.'):
obj.__init__(
name="test_ts",
data=[11, 12, 13, 14, 15],
unit="volts",
starting_time=1.0,
timestamps=[1, 2, 3, 4, 5]
)


class TestImage(TestCase):
def test_init(self):
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