From 3f2f3c3a5e2269c194bbbdb89356acff95999f86 Mon Sep 17 00:00:00 2001
From: Thomas Braun <thomas.braun@byte-physics.de>
Date: Tue, 19 Aug 2025 12:43:00 +0200
Subject: [PATCH 01/13] pytest.ini: Ignore marshmallow warnings

Created #575 to fix them.
---
 pytest.ini | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pytest.ini b/pytest.ini
index 626d70ba..4fa723ff 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -7,3 +7,5 @@ markers =
 
 filterwarnings =
     ignore:add_child is deprecated. Set the parent attribute instead.:DeprecationWarning
+    ignore::marshmallow.warnings.RemovedInMarshmallow4Warning
+    ignore::marshmallow.warnings.ChangedInMarshmallow4Warning

From eaa1509767339aa305d166df2ec69cd479a5c035 Mon Sep 17 00:00:00 2001
From: Thomas Braun <thomas.braun@byte-physics.de>
Date: Tue, 19 Aug 2025 13:30:24 +0200
Subject: [PATCH 02/13] ipfx/bin/make_stimulus_ontology.py: Avoid unknown
 escape sequence

This fixes the warning:

  /home/thomas/devel/ipfx/ipfx/bin/make_stimulus_ontology.py:26: DeprecationWarning: invalid escape sequence \d
    m = re.search("(.*)\d{6}$", scode)
---
 ipfx/bin/make_stimulus_ontology.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ipfx/bin/make_stimulus_ontology.py b/ipfx/bin/make_stimulus_ontology.py
index 8f3c734b..6ba43ebf 100755
--- a/ipfx/bin/make_stimulus_ontology.py
+++ b/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))

From a55716f72f6254f20b486f5e41ae7b352f22e384 Mon Sep 17 00:00:00 2001
From: Thomas Braun <thomas.braun@byte-physics.de>
Date: Tue, 19 Aug 2025 13:48:17 +0200
Subject: [PATCH 03/13] tests/test_ephys_extractor.py: Ignore divide by zero
 warnings

The whole purpose of the tests is to trigger that case.
---
 tests/test_ephys_extractor.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/test_ephys_extractor.py b/tests/test_ephys_extractor.py
index 080f3529..2c15c76d 100644
--- a/tests/test_ephys_extractor.py
+++ b/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
 
@@ -103,6 +103,7 @@ def test_extractor_on_zero_voltage():
     ext.process(t, v, i)
 
 
+@pytest.mark.filterwarnings("ignore:.*encountered in divide:RuntimeWarning")
 def test_extractor_on_variable_time_step(spike_test_var_dt):
     data = spike_test_var_dt
 

From f9f4836993b93e2bd6a8f9ccdab5ae28b2c61af2 Mon Sep 17 00:00:00 2001
From: Thomas Braun <thomas.braun@byte-physics.de>
Date: Tue, 19 Aug 2025 14:33:46 +0200
Subject: [PATCH 04/13] tests: Add missing timezone for NWB datetime entries

This avoids warnings. The additional dependency is already required by
pynwb.
---
 requirements.txt                        | 1 +
 tests/attach_metadata/test_cli.py       | 4 +++-
 tests/attach_metadata/test_nwb2_sink.py | 3 ++-
 tests/dataset/test_ephys_nwb_data.py    | 5 +++--
 tests/test_append_nwb.py                | 6 ++++--
 5 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index a6e90e15..73620e56 100755
--- a/requirements.txt
+++ b/requirements.txt
@@ -11,6 +11,7 @@ pillow
 pyabf
 pynwb==3.1.2
 pyYAML
+python-dateutil
 ruamel.yaml<0.18.0
 scipy
 simplejson
diff --git a/tests/attach_metadata/test_cli.py b/tests/attach_metadata/test_cli.py
index 2c025def..bd1acaba 100644
--- a/tests/attach_metadata/test_cli.py
+++ b/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)
diff --git a/tests/attach_metadata/test_nwb2_sink.py b/tests/attach_metadata/test_nwb2_sink.py
index 1df7a1e6..49d65c91 100644
--- a/tests/attach_metadata/test_nwb2_sink.py
+++ b/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)
diff --git a/tests/dataset/test_ephys_nwb_data.py b/tests/dataset/test_ephys_nwb_data.py
index 0b0d046d..6bafc54c 100644
--- a/tests/dataset/test_ephys_nwb_data.py
+++ b/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')
diff --git a/tests/test_append_nwb.py b/tests/test_append_nwb.py
index 73ae5ba6..ba1f8283 100644
--- a/tests/test_append_nwb.py
+++ b/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')

From 5fe2c4fe0871cec9fbf81d0b9f277cd143993b64 Mon Sep 17 00:00:00 2001
From: Thomas Braun <thomas.braun@byte-physics.de>
Date: Tue, 19 Aug 2025 14:51:58 +0200
Subject: [PATCH 05/13] test_XXX_nwb_data.py/test_nwb2_sink.py: Ignore
 DtypeConversionwarning

This ignores the following and similiar warnings:

tests/dataset/test_mies_nwb_data.py: 2 warnings
  /home/thomas/.venvs/ipfx-3.9/lib/python3.9/site-packages/hdmf/build/objectmapper.py:267: DtypeConversionWarning: Spec 'CurrentClampSeries/sweep_number': Value with data type int64 is being converted to data type uint64 (min specification: uint32).
    warnings.warn(full_warning_msg, DtypeConversionWarning)

tests/attach_metadata/test_nwb2_sink.py: 10 warnings
tests/dataset/test_ephys_nwb_data.py: 6 warnings
tests/dataset/test_hbg_nwb_data.py: 3 warnings
tests/dataset/test_mies_nwb_data.py: 2 warnings
  /home/thomas/.venvs/ipfx-3.9/lib/python3.9/site-packages/hdmf/build/objectmapper.py:267: DtypeConversionWarning: Spec 'SweepTable/sweep_number': Value with data type int64 is being converted to data type uint64 (min specification: uint32).
    warnings.warn(full_warning_msg, DtypeConversionWarning)

tests/dataset/test_ephys_nwb_data.py: 6 warnings
tests/dataset/test_hbg_nwb_data.py: 3 warnings
tests/dataset/test_mies_nwb_data.py: 2 warnings
  /home/thomas/.venvs/ipfx-3.9/lib/python3.9/site-packages/hdmf/build/objectmapper.py:267: DtypeConversionWarning: Spec 'CurrentClampStimulusSeries/sweep_number': Value with data type int64 is being converted to data type uint64 (min specification: uint32).
    warnings.warn(full_warning_msg, DtypeConversionWarning)

Both int64 and uint64 are big enough for our number of sweeps. In addition
this test is using existing files so even fixing/upgrading IPNWB would not
solve the issue.
---
 tests/attach_metadata/test_nwb2_sink.py | 3 +++
 tests/dataset/test_ephys_nwb_data.py    | 6 ++++++
 tests/dataset/test_hbg_nwb_data.py      | 4 ++++
 tests/dataset/test_mies_nwb_data.py     | 2 ++
 4 files changed, 15 insertions(+)

diff --git a/tests/attach_metadata/test_nwb2_sink.py b/tests/attach_metadata/test_nwb2_sink.py
index 49d65c91..3732553c 100644
--- a/tests/attach_metadata/test_nwb2_sink.py
+++ b/tests/attach_metadata/test_nwb2_sink.py
@@ -79,6 +79,7 @@ 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.*")
 def test_serialize(tmpdir_factory, nwbfile):
     out_path = os.path.join(
         str(tmpdir_factory.mktemp("test_serialize")),
@@ -102,6 +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")
@@ -136,6 +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
 ):
diff --git a/tests/dataset/test_ephys_nwb_data.py b/tests/dataset/test_ephys_nwb_data.py
index 6bafc54c..195f6b4f 100644
--- a/tests/dataset/test_ephys_nwb_data.py
+++ b/tests/dataset/test_ephys_nwb_data.py
@@ -103,14 +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 = {
@@ -125,6 +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 = {
@@ -141,12 +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
 
diff --git a/tests/dataset/test_hbg_nwb_data.py b/tests/dataset/test_hbg_nwb_data.py
index 97473629..0eaff806 100644
--- a/tests/dataset/test_hbg_nwb_data.py
+++ b/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'
diff --git a/tests/dataset/test_mies_nwb_data.py b/tests/dataset/test_mies_nwb_data.py
index c76fc949..c46151a0 100644
--- a/tests/dataset/test_mies_nwb_data.py
+++ b/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 = {

From d05077a35d9788dcc95cef09fbcaaf6f1ed9c5c1 Mon Sep 17 00:00:00 2001
From: Thomas Braun <thomas.braun@byte-physics.de>
Date: Tue, 19 Aug 2025 15:00:56 +0200
Subject: [PATCH 06/13] ipfx: Avoid using deprecated pynwb interfaces

This fixes the following warnings:

  /home/thomas/.venvs/ipfx-3.9/lib/python3.9/site-packages/pynwb/base.py:87: DeprecationWarning: get_data_interface is deprecated and will be removed in PyNWB 4.0. Use get instead.
    warn('get_data_interface is deprecated and will be removed in PyNWB 4.0. Use get instead.', DeprecationWarning)

tests/test_mies_nwb_pipeline_output.py: 127 warnings
  /home/thomas/.venvs/ipfx-3.9/lib/python3.9/site-packages/pynwb/base.py:82: DeprecationWarning: add_data_interface is deprecated and will be removed in PyNWB 4.0. Use add instead.
    warn('add_data_interface is deprecated and will be removed in PyNWB 4.0. Use add instead.', DeprecationWarning)
---
 ipfx/dataset/ephys_nwb_data.py | 2 +-
 ipfx/nwb_append.py             | 2 +-
 tests/test_append_nwb.py       | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/ipfx/dataset/ephys_nwb_data.py b/ipfx/dataset/ephys_nwb_data.py
index aa373f58..388ccc9b 100644
--- a/ipfx/dataset/ephys_nwb_data.py
+++ b/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
diff --git a/ipfx/nwb_append.py b/ipfx/nwb_append.py
index 32a52af9..f8bada40 100644
--- a/ipfx/nwb_append.py
+++ b/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)
 
diff --git a/tests/test_append_nwb.py b/tests/test_append_nwb.py
index ba1f8283..3a889db4 100644
--- a/tests/test_append_nwb.py
+++ b/tests/test_append_nwb.py
@@ -51,5 +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)

From 6c313a9596c9e187a954f9cdccc5736032e2f672 Mon Sep 17 00:00:00 2001
From: Thomas Braun <thomas.braun@byte-physics.de>
Date: Tue, 19 Aug 2025 15:29:30 +0200
Subject: [PATCH 07/13] test_serialize: Silence pynwb warning

pynwb 3.1.2 does currently always output a warning about a missing .nwb
ending in path even if path was not passed at all and is None.

This will be fixed in [1], ignore the warning until we require that
version.

We also drop the path argument to NWBHDF5IO as that is not needed.

[1]: https://github.com/NeurodataWithoutBorders/pynwb/pull/2130
---
 tests/attach_metadata/test_nwb2_sink.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/attach_metadata/test_nwb2_sink.py b/tests/attach_metadata/test_nwb2_sink.py
index 3732553c..592ef200 100644
--- a/tests/attach_metadata/test_nwb2_sink.py
+++ b/tests/attach_metadata/test_nwb2_sink.py
@@ -80,6 +80,7 @@ def test_get_subject(nwbfile, set_none):
 
 
 @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")),
@@ -90,7 +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
     )

From 45c30501c5728c9d61d7143f6787b96d0897312e Mon Sep 17 00:00:00 2001
From: Thomas Braun <thomas.braun@byte-physics.de>
Date: Wed, 27 Aug 2025 14:21:37 +0200
Subject: [PATCH 08/13] tests/test_mies_nwb_pipeline_output.py: Silence warning
 about icephys_filtering

This test uses existing files so even fixing/upgrading IPNWB would not
solve the issue.
---
 tests/test_mies_nwb_pipeline_output.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/test_mies_nwb_pipeline_output.py b/tests/test_mies_nwb_pipeline_output.py
index d2122ceb..952736f3 100755
--- a/tests/test_mies_nwb_pipeline_output.py
+++ b/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.

From 59468f52c3675148e1ee04049659ce4ae352b128 Mon Sep 17 00:00:00 2001
From: Thomas Braun <thomas.braun@byte-physics.de>
Date: Wed, 27 Aug 2025 14:49:36 +0200
Subject: [PATCH 09/13] tests/attach_metadata/test_cli.py: Silence warning
 about icephys_filtering

This test uses existing files so even fixing/upgrading IPNWB would not
solve the issue.
---
 tests/attach_metadata/test_cli.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/attach_metadata/test_cli.py b/tests/attach_metadata/test_cli.py
index bd1acaba..e1116abd 100644
--- a/tests/attach_metadata/test_cli.py
+++ b/tests/attach_metadata/test_cli.py
@@ -151,6 +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")

From 5b63dd2289ff73c97a1fde83d7e01d3634d8cf55 Mon Sep 17 00:00:00 2001
From: Thomas Braun <thomas.braun@byte-physics.de>
Date: Wed, 27 Aug 2025 14:25:14 +0200
Subject: [PATCH 10/13] pytest.ini: Ignore scipy.misc warning for now

This is tracked in [1].

[1]: https://github.com/AllenInstitute/ipfx/issues/576
---
 pytest.ini | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pytest.ini b/pytest.ini
index 4fa723ff..9729234f 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -9,3 +9,4 @@ filterwarnings =
     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

From b0b1dbaace3983d23e65d787ffc1e7cefa7e98a9 Mon Sep 17 00:00:00 2001
From: Thomas Braun <thomas.braun@byte-physics.de>
Date: Wed, 27 Aug 2025 15:16:48 +0200
Subject: [PATCH 11/13] pytest.ini: Ignore pandas warning about
 ChainedAssignmentError

This is tracked in [1].

[1]: https://github.com/AllenInstitute/ipfx/issues/577
---
 pytest.ini | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pytest.ini b/pytest.ini
index 9729234f..341f7f7d 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -10,3 +10,4 @@ filterwarnings =
     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

From 05c14d1656df1723183420bf9cf9fa1756f83c47 Mon Sep 17 00:00:00 2001
From: Thomas Braun <thomas.braun@byte-physics.de>
Date: Wed, 27 Aug 2025 14:24:31 +0200
Subject: [PATCH 12/13] pytest.ini: Treat warnings as errors

---
 pytest.ini | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pytest.ini b/pytest.ini
index 341f7f7d..a68d124f 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -6,6 +6,7 @@ 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

From a16a55a556ad676dfc54d2ca6682ee14582045cd Mon Sep 17 00:00:00 2001
From: Nathan Gouwens <nathang@alleninstitute.org>
Date: Tue, 9 Sep 2025 15:39:50 -0700
Subject: [PATCH 13/13] Fix underlying cause of divide-by-zero warning in test

---
 ipfx/time_series_utils.py     | 9 ++++++---
 tests/test_ephys_extractor.py | 1 -
 2 files changed, 6 insertions(+), 4 deletions(-)
 mode change 100644 => 100755 ipfx/time_series_utils.py
 mode change 100644 => 100755 tests/test_ephys_extractor.py

diff --git a/ipfx/time_series_utils.py b/ipfx/time_series_utils.py
old mode 100644
new mode 100755
index 6c3ae8be..bb290ae1
--- a/ipfx/time_series_utils.py
+++ b/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):
diff --git a/tests/test_ephys_extractor.py b/tests/test_ephys_extractor.py
old mode 100644
new mode 100755
index 2c15c76d..97ef5f39
--- a/tests/test_ephys_extractor.py
+++ b/tests/test_ephys_extractor.py
@@ -103,7 +103,6 @@ def test_extractor_on_zero_voltage():
     ext.process(t, v, i)
 
 
-@pytest.mark.filterwarnings("ignore:.*encountered in divide:RuntimeWarning")
 def test_extractor_on_variable_time_step(spike_test_var_dt):
     data = spike_test_var_dt