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Added test for to_hierarchical_dataframe for the icephys tables #1404

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Added test for to_hierarchical_dataframe for the icephys tables #1404

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5c68e2c
Added test for to_hierarchical_dataframe for the icephys tables with …
oruebel Aug 23, 2021
870a84f
Update minimimum requirment for HDMF to bug-fix version
oruebel Aug 23, 2021
22eedc3
Update changelog
oruebel Aug 23, 2021
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1 change: 1 addition & 0 deletions CHANGELOG.md
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### Bug fixes:
- Add `environment-ros3.yml` to `MANIFEST.in` for inclusion in source distributions. @rly (#1398)
- Update HDMF minimum version to `3.1.2` to fix bug when converting the icephys metadata tables via `to_hierarchical_dataframe` when the tables contain indexed columns and add corresponding unit tests. @oruebel (#1404)

## PyNWB 2.0.0 (August 13, 2021)

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2 changes: 1 addition & 1 deletion requirements-min.txt
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# minimum versions of package dependencies for installing PyNWB
h5py==2.10 # support for selection of datasets with list of indices added in 2.10
hdmf==3.1.1
hdmf==3.1.2
numpy==1.16
pandas==1.0.5
python-dateutil==2.7
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57 changes: 57 additions & 0 deletions tests/unit/test_icephys_metadata_tables.py
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from pynwb.base import TimeSeriesReferenceVectorData
from pynwb import NWBHDF5IO
from hdmf.utils import docval, popargs
from pynwb.testing import create_icephys_testfile
from hdmf.common.hierarchicaltable import to_hierarchical_dataframe


class ICEphysMetaTestBase(TestCase):
Expand Down Expand Up @@ -889,6 +891,61 @@ def test_enforce_unique_id(self):
with self.assertRaises(ValueError):
cond.add_experimental_condition(repetitions=[0, ], id=np.int64(10))

def test_to_hierarchical_dataframe(self):
# test that to_hierarchical_dataframe works for the icephys tables when only containing regular VectorData
nwbfile = create_icephys_testfile()
temp = to_hierarchical_dataframe(nwbfile.icephys_experimental_conditions)
expected_index = [
(100000, 32.0, 10000, 'R1', 1000, 'StimType_1', 'T1', 100, 0),
(100000, 32.0, 10000, 'R1', 1000, 'StimType_1', 'T1', 100, 0),
(100000, 32.0, 10000, 'R1', 1000, 'StimType_1', 'T1', 101, 1),
(100000, 32.0, 10000, 'R1', 1000, 'StimType_1', 'T1', 101, 1),
(100000, 32.0, 10001, 'R2', 1001, 'StimType_2', 'T2', 102, 2),
(100000, 32.0, 10001, 'R2', 1001, 'StimType_2', 'T2', 102, 2),
(100000, 32.0, 10001, 'R2', 1001, 'StimType_2', 'T2', 102, 2),
(100000, 32.0, 10001, 'R2', 1002, 'StimType_3', 'T3', 103, 3),
(100000, 32.0, 10001, 'R2', 1002, 'StimType_3', 'T3', 103, 3),
(100000, 32.0, 10001, 'R2', 1002, 'StimType_3', 'T3', 103, 3),
(100001, 24.0, 10002, 'R1', 1003, 'StimType_1', 'T1', 104, 4),
(100001, 24.0, 10002, 'R1', 1003, 'StimType_1', 'T1', 104, 4),
(100001, 24.0, 10002, 'R1', 1003, 'StimType_1', 'T1', 105, 5),
(100001, 24.0, 10002, 'R1', 1003, 'StimType_1', 'T1', 105, 5),
(100001, 24.0, 10003, 'R2', 1004, 'StimType_2', 'T2', 106, 6),
(100001, 24.0, 10003, 'R2', 1004, 'StimType_2', 'T2', 106, 6),
(100001, 24.0, 10003, 'R2', 1004, 'StimType_2', 'T2', 106, 6),
(100001, 24.0, 10003, 'R2', 1005, 'StimType_3', 'T3', 107, 7),
(100001, 24.0, 10003, 'R2', 1005, 'StimType_3', 'T3', 107, 7),
(100001, 24.0, 10003, 'R2', 1005, 'StimType_3', 'T3', 107, 7)]
self.assertListEqual(temp.index.tolist(), expected_index)

def test_to_hierarchical_dataframe_with_indexed_custom_column(self):
# test that to_hierarchical_dataframe works for the icephys tables when containing also VectorIndex columns
nwbfile = create_icephys_testfile()
nwbfile.icephys_experimental_conditions.add_column('newcol', 'abc', data=[1, 2, 3], index=[2, 3])
temp = to_hierarchical_dataframe(nwbfile.icephys_experimental_conditions)
expected_index = [
(100000, 32.0, (1, 2), 10000, 'R1', 1000, 'StimType_1', 'T1', 100, 0),
(100000, 32.0, (1, 2), 10000, 'R1', 1000, 'StimType_1', 'T1', 100, 0),
(100000, 32.0, (1, 2), 10000, 'R1', 1000, 'StimType_1', 'T1', 101, 1),
(100000, 32.0, (1, 2), 10000, 'R1', 1000, 'StimType_1', 'T1', 101, 1),
(100000, 32.0, (1, 2), 10001, 'R2', 1001, 'StimType_2', 'T2', 102, 2),
(100000, 32.0, (1, 2), 10001, 'R2', 1001, 'StimType_2', 'T2', 102, 2),
(100000, 32.0, (1, 2), 10001, 'R2', 1001, 'StimType_2', 'T2', 102, 2),
(100000, 32.0, (1, 2), 10001, 'R2', 1002, 'StimType_3', 'T3', 103, 3),
(100000, 32.0, (1, 2), 10001, 'R2', 1002, 'StimType_3', 'T3', 103, 3),
(100000, 32.0, (1, 2), 10001, 'R2', 1002, 'StimType_3', 'T3', 103, 3),
(100001, 24.0, (3,), 10002, 'R1', 1003, 'StimType_1', 'T1', 104, 4),
(100001, 24.0, (3,), 10002, 'R1', 1003, 'StimType_1', 'T1', 104, 4),
(100001, 24.0, (3,), 10002, 'R1', 1003, 'StimType_1', 'T1', 105, 5),
(100001, 24.0, (3,), 10002, 'R1', 1003, 'StimType_1', 'T1', 105, 5),
(100001, 24.0, (3,), 10003, 'R2', 1004, 'StimType_2', 'T2', 106, 6),
(100001, 24.0, (3,), 10003, 'R2', 1004, 'StimType_2', 'T2', 106, 6),
(100001, 24.0, (3,), 10003, 'R2', 1004, 'StimType_2', 'T2', 106, 6),
(100001, 24.0, (3,), 10003, 'R2', 1005, 'StimType_3', 'T3', 107, 7),
(100001, 24.0, (3,), 10003, 'R2', 1005, 'StimType_3', 'T3', 107, 7),
(100001, 24.0, (3,), 10003, 'R2', 1005, 'StimType_3', 'T3', 107, 7)]
self.assertListEqual(temp.index.tolist(), expected_index)


class NWBFileTests(TestCase):
"""
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