Fix and silence warnings

ipfx/bin/make_stimulus_ontology.py

@@ -23,7 +23,7 @@ def make_stimulus_ontology(stims):
         scode = stim['stimulus_code']
 
         # code tags
-        m = re.search("(.*)\d{6}$", scode)
+        m = re.search(r"(.*)\d{6}$", scode)
         if m:
             code_name, = m.groups()
             tags.add((CODE, code_name, scode))

ipfx/dataset/ephys_nwb_data.py

@@ -308,7 +308,7 @@ def get_clamp_mode(self,sweep_number):
 
     def get_spike_times(self, sweep_number):
         spikes = self.nwb.get_processing_module('spikes')
-        sweep_spikes = spikes.get_data_interface(f"Sweep_{sweep_number}")
+        sweep_spikes = spikes.get(f"Sweep_{sweep_number}")
         return sweep_spikes.timestamps
 
     @staticmethod

ipfx/nwb_append.py

@@ -59,7 +59,7 @@ def append_spike_times(input_nwb_path: PathLike,
                             unit='seconds',
                             data=wrapped_spike_times,
                             name=f"Sweep_{sweep_num}")
-            spike_module.add_data_interface(ts)
+            spike_module.add(ts)
 
         nwbfile.add_processing_module(spike_module)
 

ipfx/time_series_utils.py

@@ -50,11 +50,14 @@ def calculate_dvdt(v, t, filter=None):
         dv = np.diff(v)
 
     dt = np.diff(t)
-    dvdt = 1e-3 * dv / dt  # in V/s = mV/ms
 
-    # some data sources, such as neuron, occasionally report 
+    # some data sources, such as neuron, occasionally report
     # duplicate timestamps, so we require that dt is not 0
-    return dvdt[np.fabs(dt) > sys.float_info.epsilon]
+    mask = np.fabs(dt) > sys.float_info.epsilon
+
+    dvdt = 1e-3 * dv[mask] / dt[mask]  # in V/s = mV/ms
+
+    return dvdt
 
 
 def has_fixed_dt(t):

pytest.ini

@@ -6,4 +6,9 @@ markers =
     requires_inhouse_data: require inhouse data
 
 filterwarnings =
+    error
     ignore:add_child is deprecated. Set the parent attribute instead.:DeprecationWarning
+    ignore::marshmallow.warnings.RemovedInMarshmallow4Warning
+    ignore::marshmallow.warnings.ChangedInMarshmallow4Warning
+    ignore:scipy.misc is deprecated and will be removed in 2.0.0
+    ignore:.*behaviour will change in pandas 3.0!.*:FutureWarning

requirements.txt

@@ -11,6 +11,7 @@ pillow
 pyabf
 pynwb==3.1.2
 pyYAML
+python-dateutil
 ruamel.yaml<0.18.0
 scipy
 simplejson

tests/attach_metadata/test_cli.py

@@ -14,6 +14,8 @@
 import pytest
 from ipfx.utilities import inject_sweep_table
 
+from dateutil.tz import tzlocal
+
 class CliRunner:
 
     def __init__(
@@ -54,7 +56,7 @@ def simple_nwb(base_path):
     nwbfile = pynwb.NWBFile(
         session_description="test session",
         identifier='test session',
-        session_start_time=datetime.now()
+        session_start_time=datetime.now(tzlocal())
     )
 
     inject_sweep_table(nwbfile)
@@ -149,6 +151,7 @@ def test_cli_nwb2(cli_runner):
             [1, 2, 3]
         )
 
+@pytest.mark.filterwarnings("ignore:.*Use of icephys_filtering is deprecated and will be removed in PyNWB 4.0. Use the IntracellularElectrode.filtering field instead")
 def test_cli_mies(cli_runner):
     in_nwb_path = os.path.join(cli_runner.tmpdir, "input.nwb")
     out_nwb_path = os.path.join(cli_runner.tmpdir, "meta.nwb")

tests/attach_metadata/test_nwb2_sink.py

@@ -15,6 +15,7 @@
 import pynwb
 import h5py
 
+from dateutil.tz import tzlocal
 from ipfx.attach_metadata.sink import nwb2_sink
 from ipfx.utilities import inject_sweep_table
 
@@ -24,7 +25,7 @@ def nwbfile():
     _nwbfile = pynwb.NWBFile(
         session_description="test session",
         identifier='test session',
-        session_start_time=datetime.now()
+        session_start_time=datetime.now(tzlocal())
     )
     dev = pynwb.device.Device(name="my_device")
     _nwbfile.add_device(dev)
@@ -78,6 +79,8 @@ def test_get_subject(nwbfile, set_none):
     assert nwbfile.subject.subject_id == "foo"
 
 
+@pytest.mark.filterwarnings("ignore:.*Value with data type int64 is being converted to data type uint64.*")
+@pytest.mark.filterwarnings("ignore:.*It is recommended that NWB files using the HDF5 backend use the '.nwb' extension.")
 def test_serialize(tmpdir_factory, nwbfile):
     out_path = os.path.join(
         str(tmpdir_factory.mktemp("test_serialize")),
@@ -88,7 +91,6 @@ def test_serialize(tmpdir_factory, nwbfile):
     sink._data = io.BytesIO()
     sink._h5_file = h5py.File(sink._data, "w")
     sink._nwb_io = pynwb.NWBHDF5IO(
-        path=sink._h5_file.filename,
         mode="w",
         file=sink._h5_file
     )
@@ -101,6 +103,7 @@ def test_serialize(tmpdir_factory, nwbfile):
         assert obt.identifier == "test session"
 
 
+@pytest.mark.filterwarnings("ignore:.*Value with data type int64 is being converted to data type uint64.*")
 def test_roundtrip(tmpdir_factory, nwbfile):
     tmpdir = str(tmpdir_factory.mktemp("test_serialize"))
     first_path = os.path.join(tmpdir, "first.nwb")
@@ -135,6 +138,7 @@ def test_roundtrip(tmpdir_factory, nwbfile):
         "Mus musculus"
     ],
 ])
+@pytest.mark.filterwarnings("ignore:.*Value with data type int64 is being converted to data type uint64.*")
 def test_register(
         tmpdir_factory, nwbfile, name, value, sweep_id, getter, expected
 ):

tests/dataset/test_ephys_nwb_data.py

@@ -7,6 +7,7 @@
 from pynwb.icephys import CurrentClampStimulusSeries, CurrentClampSeries
 import numpy as np
 from ipfx.utilities import inject_sweep_table
+from dateutil.tz import tzlocal
 
 from dictdiffer import diff
 
@@ -28,8 +29,8 @@ def nwbfile_to_test():
     nwbfile = pynwb.NWBFile(
         session_description="test nwb data",
         identifier='test session',
-        session_start_time=datetime.datetime.now(),
-        file_create_date=datetime.datetime.now()
+        session_start_time=datetime.datetime.now(tzlocal()),
+        file_create_date=datetime.datetime.now(tzlocal())
     )
 
     device = nwbfile.create_device(name='electrode_0')
@@ -102,14 +103,17 @@ def nwb_data(tmp_nwb_path):
     return EphysNWBData(nwb_file=tmp_nwb_path, ontology=ontology)
 
 
+@pytest.mark.filterwarnings("ignore:.*Value with data type int64 is being converted to data type uint64.*")
 def test_get_stimulus_unit(nwb_data):
     assert nwb_data.get_stimulus_unit(sweep_number=4) == "Amps"
 
 
+@pytest.mark.filterwarnings("ignore:.*Value with data type int64 is being converted to data type uint64.*")
 def test_get_stimulus_code(nwb_data):
     assert nwb_data.get_stimulus_code(sweep_number=4) == "STIMULUS_CODE"
 
 
+@pytest.mark.filterwarnings("ignore:.*Value with data type int64 is being converted to data type uint64.*")
 def test_get_sweep_data(nwb_data):
 
     expected = {
@@ -124,6 +128,7 @@ def test_get_sweep_data(nwb_data):
     assert list(diff(expected, obtained, tolerance=0.001)) == []
 
 
+@pytest.mark.filterwarnings("ignore:.*Value with data type int64 is being converted to data type uint64.*")
 def test_get_sweep_attrs(nwb_data):
 
     expected = {
@@ -140,12 +145,14 @@ def test_get_sweep_attrs(nwb_data):
     print(expected)
     assert expected == obtained
 
+@pytest.mark.filterwarnings("ignore:.*Value with data type int64 is being converted to data type uint64.*")
 def test_get_clamp_mode(nwb_data):
 
     attrs = nwb_data.get_sweep_attrs(4);
 
     assert attrs['clamp_mode'] == "CurrentClamp"
 
+@pytest.mark.filterwarnings("ignore:.*Value with data type int64 is being converted to data type uint64.*")
 def test_get_full_recording_date(nwb_data):
     assert nwb_data.get_full_recording_date() == nwb_data.nwb.session_start_time
 

tests/dataset/test_hbg_nwb_data.py

@@ -27,10 +27,12 @@ def hbg_nwb_data(tmp_nwb_path):
     return HBGNWBData(nwb_file=tmp_nwb_path, ontology=ontology)
 
 
+@pytest.mark.filterwarnings("ignore:.*Value with data type int64 is being converted to data type uint64.*")
 def test_create_hbg(hbg_nwb_data):
     assert isinstance(hbg_nwb_data,HBGNWBData)
 
 
+@pytest.mark.filterwarnings("ignore:.*Value with data type int64 is being converted to data type uint64.*")
 def test_get_sweep_metadata(hbg_nwb_data):
 
     expected = {
@@ -48,6 +50,8 @@ def test_get_sweep_metadata(hbg_nwb_data):
     obtained = hbg_nwb_data.get_sweep_metadata(sweep_number=4)
     assert expected == obtained
 
+
+@pytest.mark.filterwarnings("ignore:.*Value with data type int64 is being converted to data type uint64.*")
 def  test_get_stimulus_code_ext(hbg_nwb_data):
 
     expected = 'STIMULUS_CODE'

tests/dataset/test_mies_nwb_data.py

@@ -42,10 +42,12 @@ def get_value(self, key, sweep_num, default):
                        ontology=ontology)
 
 
+@pytest.mark.filterwarnings("ignore:.*Value with data type int64 is being converted to data type uint64.*")
 def test_create_mies(mies_nwb_data):
     assert isinstance(mies_nwb_data, MIESNWBData)
 
 
+@pytest.mark.filterwarnings("ignore:.*Value with data type int64 is being converted to data type uint64.*")
 def test_get_sweep_metadata(mies_nwb_data):
 
     expected = {

tests/test_append_nwb.py

@@ -3,6 +3,8 @@
 import pynwb
 import numpy as np
 
+from dateutil.tz import tzlocal
+
 from ipfx.nwb_append import append_spike_times
 
 
@@ -11,8 +13,8 @@ def make_skeleton_nwb2_file(nwb2_file_name):
     nwbfile = pynwb.NWBFile(
         session_description='test icephys',
         identifier='session_uuid',
-        session_start_time=datetime.datetime.now(),
-        file_create_date=datetime.datetime.now()
+        session_start_time=datetime.datetime.now(tzlocal()),
+        file_create_date=datetime.datetime.now(tzlocal())
     )
 
     device = nwbfile.create_device(name='electrode_0')
@@ -49,5 +51,5 @@ def test_embed_spike_times_into_nwb(tmpdir_factory):
 
         spikes = nwbfile.get_processing_module('spikes')
         for sweep_num, spike_times in sweep_spike_times.items():
-            sweep_spikes = spikes.get_data_interface(f"Sweep_{sweep_num}").timestamps
+            sweep_spikes = spikes.get(f"Sweep_{sweep_num}").timestamps
             assert np.allclose(sweep_spikes, spike_times)

tests/test_ephys_extractor.py

@@ -43,7 +43,7 @@ def test_extractors_no_values():
     SpikeFeatureExtractor()
     SpikeTrainFeatureExtractor(start=0, end=0)
 
-
+@pytest.mark.filterwarnings("ignore:.*encountered in divide:RuntimeWarning")
 def test_extractor_wrong_inputs(spike_test_pair):
     data = spike_test_pair
 

tests/test_mies_nwb_pipeline_output.py

@@ -43,6 +43,7 @@ def rebase(new_base: str, path: str, mkdir: bool = False) ->  str:
 
 @pytest.mark.slow
 @pytest.mark.parametrize('input_json,output_json', test_specimens_params)
+@pytest.mark.filterwarnings("ignore:.*Use of icephys_filtering is deprecated and will be removed in PyNWB 4.0. Use the IntracellularElectrode.filtering field instead")
 def test_mies_nwb_pipeline_output(input_json, output_json, tmpdir_factory):
     """
     Runs pipeline, saves to a json file and compares to the existing pipeline output.