From 070ca34588a1647f8b4128b7af6bc29e402519d0 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Mon, 3 Jun 2024 14:05:40 -0400
Subject: [PATCH 01/21] debug customization for run conversion

---
 src/neuroconv/nwbconverter.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/neuroconv/nwbconverter.py b/src/neuroconv/nwbconverter.py
index 2a354b6e6..a69ae57f9 100644
--- a/src/neuroconv/nwbconverter.py
+++ b/src/neuroconv/nwbconverter.py
@@ -220,10 +220,9 @@ def run_conversion(
             backend=backend,
             verbose=getattr(self, "verbose", False),
         ) as nwbfile_out:
-            if backend_configuration is None:
-                # Otherwise assume the data has already been added to the NWBFile
-                self.add_to_nwbfile(nwbfile_out, metadata=metadata, conversion_options=conversion_options)
+            self.add_to_nwbfile(nwbfile_out, metadata=metadata, conversion_options=conversion_options)
 
+            if backend_configuration is None:
                 backend_configuration = self.get_default_backend_configuration(nwbfile=nwbfile_out, backend=backend)
 
             configure_backend(nwbfile=nwbfile_out, backend_configuration=backend_configuration)

From 27897dbb2b1e93e614b0527e6282272fa459a8bf Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Mon, 3 Jun 2024 14:32:08 -0400
Subject: [PATCH 02/21] protect non-None passed file

---
 src/neuroconv/nwbconverter.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/neuroconv/nwbconverter.py b/src/neuroconv/nwbconverter.py
index a69ae57f9..c524c74ba 100644
--- a/src/neuroconv/nwbconverter.py
+++ b/src/neuroconv/nwbconverter.py
@@ -220,7 +220,8 @@ def run_conversion(
             backend=backend,
             verbose=getattr(self, "verbose", False),
         ) as nwbfile_out:
-            self.add_to_nwbfile(nwbfile_out, metadata=metadata, conversion_options=conversion_options)
+            if nwbfile is not None:
+                self.add_to_nwbfile(nwbfile=nwbfile_out, metadata=metadata, conversion_options=conversion_options)
 
             if backend_configuration is None:
                 backend_configuration = self.get_default_backend_configuration(nwbfile=nwbfile_out, backend=backend)

From 723a1746bbde5bbecaa1a97af91d137e2f8dfe01 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 4 Jun 2024 09:31:45 -0400
Subject: [PATCH 03/21] correct for mutation logic

---
 src/neuroconv/nwbconverter.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/neuroconv/nwbconverter.py b/src/neuroconv/nwbconverter.py
index c524c74ba..a460fe906 100644
--- a/src/neuroconv/nwbconverter.py
+++ b/src/neuroconv/nwbconverter.py
@@ -203,6 +203,7 @@ def run_conversion(
             conversion specification is requested.
         """
         backend = _resolve_backend(backend, backend_configuration)
+        no_nwbfile_provided = nwbfile is None  # Otherwise, variable reference may mutate later on inside the context
 
         if metadata is None:
             metadata = self.get_metadata()
@@ -220,7 +221,7 @@ def run_conversion(
             backend=backend,
             verbose=getattr(self, "verbose", False),
         ) as nwbfile_out:
-            if nwbfile is not None:
+            if no_nwbfile_provided:
                 self.add_to_nwbfile(nwbfile=nwbfile_out, metadata=metadata, conversion_options=conversion_options)
 
             if backend_configuration is None:

From a6fe35d939ab04b1af689500899c3c8ddcbdb760 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 4 Jun 2024 10:07:01 -0400
Subject: [PATCH 04/21] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 628dd18fc..ec6778e63 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -35,6 +35,7 @@
 * Fixed a bug when adding ragged arrays to the electrode and units table. [PR #870](https://github.com/catalystneuro/neuroconv/pull/870)
 * Fixed a bug where `write_recording` will call an empty nwbfile when passing a path. [PR #877](https://github.com/catalystneuro/neuroconv/pull/877)
 * Fixed a bug that failed to properly include time alignment information in the output NWB file for objects added from any `RecordingInterface` in combination with `stub_test=True`. [PR #884](https://github.com/catalystneuro/neuroconv/pull/884)
+* Fixed a bug that prevented passing `nwbfile=None` and a `backend_configuration` to `NWBConverter.run_conversion`. [PR #885](https://github.com/catalystneuro/neuroconv/pull/885)
 
 ### Improvements
 * Fixed docstrings related to backend configurations for various methods. [PR #822](https://github.com/catalystneuro/neuroconv/pull/822)

From 17fbb02baac58d814cada99da59c05039d6661fc Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 4 Jun 2024 10:08:12 -0400
Subject: [PATCH 05/21] mirror in base interface as well

---
 src/neuroconv/basedatainterface.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/neuroconv/basedatainterface.py b/src/neuroconv/basedatainterface.py
index adb0528ce..192d30ed8 100644
--- a/src/neuroconv/basedatainterface.py
+++ b/src/neuroconv/basedatainterface.py
@@ -153,6 +153,7 @@ def run_conversion(
                 " use DataInterface.add_to_nwbfile."
             )
         backend = _resolve_backend(backend, backend_configuration)
+        no_nwbfile_provided = nwbfile is None  # Otherwise, variable reference may mutate later on inside the context
 
         if metadata is None:
             metadata = self.get_metadata()
@@ -165,10 +166,10 @@ def run_conversion(
             backend=backend,
             verbose=getattr(self, "verbose", False),
         ) as nwbfile_out:
+            if no_nwbfile_provided:
+                self.add_to_nwbfile(nwbfile=nwbfile_out, metadata=metadata, conversion_options=conversion_options)
+            
             if backend_configuration is None:
-                # In this case, assume the relevant data has not been added to the NWBFile
-                self.add_to_nwbfile(nwbfile=nwbfile_out, metadata=metadata, **conversion_options)
-
                 backend_configuration = self.get_default_backend_configuration(nwbfile=nwbfile_out, backend=backend)
 
             configure_backend(nwbfile=nwbfile_out, backend_configuration=backend_configuration)

From 26b174641fe98942b068adbc8647d25d2f2e96ba Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 4 Jun 2024 14:08:25 +0000
Subject: [PATCH 06/21] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/neuroconv/basedatainterface.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/neuroconv/basedatainterface.py b/src/neuroconv/basedatainterface.py
index 192d30ed8..1658ba302 100644
--- a/src/neuroconv/basedatainterface.py
+++ b/src/neuroconv/basedatainterface.py
@@ -168,7 +168,7 @@ def run_conversion(
         ) as nwbfile_out:
             if no_nwbfile_provided:
                 self.add_to_nwbfile(nwbfile=nwbfile_out, metadata=metadata, conversion_options=conversion_options)
-            
+
             if backend_configuration is None:
                 backend_configuration = self.get_default_backend_configuration(nwbfile=nwbfile_out, backend=backend)
 

From 194a77de7d3147c1d8fd43f37e20661f31f32490 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 4 Jun 2024 10:21:31 -0400
Subject: [PATCH 07/21] adjust passing of conversion options in interface

---
 src/neuroconv/basedatainterface.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/neuroconv/basedatainterface.py b/src/neuroconv/basedatainterface.py
index 1658ba302..961e234ae 100644
--- a/src/neuroconv/basedatainterface.py
+++ b/src/neuroconv/basedatainterface.py
@@ -167,7 +167,7 @@ def run_conversion(
             verbose=getattr(self, "verbose", False),
         ) as nwbfile_out:
             if no_nwbfile_provided:
-                self.add_to_nwbfile(nwbfile=nwbfile_out, metadata=metadata, conversion_options=conversion_options)
+                self.add_to_nwbfile(nwbfile=nwbfile_out, metadata=metadata, **conversion_options)
 
             if backend_configuration is None:
                 backend_configuration = self.get_default_backend_configuration(nwbfile=nwbfile_out, backend=backend)

From 2d3e44d22ccb1a90727284d30b04e2ab4671666d Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 4 Jun 2024 12:00:33 -0400
Subject: [PATCH 08/21] fix interface behavior

---
 src/neuroconv/basedatainterface.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/neuroconv/basedatainterface.py b/src/neuroconv/basedatainterface.py
index 961e234ae..3ebb5f1fa 100644
--- a/src/neuroconv/basedatainterface.py
+++ b/src/neuroconv/basedatainterface.py
@@ -153,7 +153,6 @@ def run_conversion(
                 " use DataInterface.add_to_nwbfile."
             )
         backend = _resolve_backend(backend, backend_configuration)
-        no_nwbfile_provided = nwbfile is None  # Otherwise, variable reference may mutate later on inside the context
 
         if metadata is None:
             metadata = self.get_metadata()
@@ -166,8 +165,8 @@ def run_conversion(
             backend=backend,
             verbose=getattr(self, "verbose", False),
         ) as nwbfile_out:
-            if no_nwbfile_provided:
-                self.add_to_nwbfile(nwbfile=nwbfile_out, metadata=metadata, **conversion_options)
+            # Unlike an NWBConverter, the interface usage always assumes you want to add the objects to the NWB file
+            self.add_to_nwbfile(nwbfile=nwbfile_out, metadata=metadata, **conversion_options)
 
             if backend_configuration is None:
                 backend_configuration = self.get_default_backend_configuration(nwbfile=nwbfile_out, backend=backend)

From 0bbdbddd41a2a283c2f7ad495a213001b93858ec Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 4 Jun 2024 12:02:19 -0400
Subject: [PATCH 09/21] revert for consistency

---
 src/neuroconv/basedatainterface.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/neuroconv/basedatainterface.py b/src/neuroconv/basedatainterface.py
index 3ebb5f1fa..961e234ae 100644
--- a/src/neuroconv/basedatainterface.py
+++ b/src/neuroconv/basedatainterface.py
@@ -153,6 +153,7 @@ def run_conversion(
                 " use DataInterface.add_to_nwbfile."
             )
         backend = _resolve_backend(backend, backend_configuration)
+        no_nwbfile_provided = nwbfile is None  # Otherwise, variable reference may mutate later on inside the context
 
         if metadata is None:
             metadata = self.get_metadata()
@@ -165,8 +166,8 @@ def run_conversion(
             backend=backend,
             verbose=getattr(self, "verbose", False),
         ) as nwbfile_out:
-            # Unlike an NWBConverter, the interface usage always assumes you want to add the objects to the NWB file
-            self.add_to_nwbfile(nwbfile=nwbfile_out, metadata=metadata, **conversion_options)
+            if no_nwbfile_provided:
+                self.add_to_nwbfile(nwbfile=nwbfile_out, metadata=metadata, **conversion_options)
 
             if backend_configuration is None:
                 backend_configuration = self.get_default_backend_configuration(nwbfile=nwbfile_out, backend=backend)

From c947c74b04b40533ce24098fcded0ca311616749 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 4 Jun 2024 12:04:36 -0400
Subject: [PATCH 10/21] adjust test

---
 tests/test_ecephys/test_mock_nidq_interface.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/tests/test_ecephys/test_mock_nidq_interface.py b/tests/test_ecephys/test_mock_nidq_interface.py
index bfe5ae0e6..51eddd366 100644
--- a/tests/test_ecephys/test_mock_nidq_interface.py
+++ b/tests/test_ecephys/test_mock_nidq_interface.py
@@ -1,3 +1,4 @@
+import pathlib
 from datetime import datetime
 
 from hdmf.testing import TestCase
@@ -74,13 +75,13 @@ def test_mock_metadata(self):
         expected_start_time = datetime(2020, 11, 3, 10, 35, 10)
         assert metadata["NWBFile"]["session_start_time"] == expected_start_time
 
-    def test_mock_run_conversion(self):
+    def test_mock_run_conversion(self, tmpdir: pathlib.Path):
         interface = MockSpikeGLXNIDQInterface()
 
         metadata = interface.get_metadata()
 
-        nwbfile = mock_NWBFile()
-        interface.run_conversion(nwbfile=nwbfile, metadata=metadata)
+        nwbfile_path = tmpdir / "TestMockSpikeGLXNIDQInterface" / "test_mock_run_conversion.nwb"
+        interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)
 
         assert "Neuropixel-Imec" in nwbfile.devices
         assert "NIDQChannelGroup" in nwbfile.electrode_groups

From b8db570e617aa2736897030efcd5f5487fa0d589 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 4 Jun 2024 12:51:23 -0400
Subject: [PATCH 11/21] undo unittest.TestCase

---
 .../test_ecephys/test_mock_nidq_interface.py  | 142 +++++++++---------
 1 file changed, 70 insertions(+), 72 deletions(-)

diff --git a/tests/test_ecephys/test_mock_nidq_interface.py b/tests/test_ecephys/test_mock_nidq_interface.py
index 51eddd366..07482f466 100644
--- a/tests/test_ecephys/test_mock_nidq_interface.py
+++ b/tests/test_ecephys/test_mock_nidq_interface.py
@@ -8,82 +8,80 @@
 from neuroconv.tools.testing import MockSpikeGLXNIDQInterface
 
 
-class TestMockSpikeGLXNIDQInterface(TestCase):
-    maxDiff = None
-
-    def test_current_default_inferred_ttl_times(self):
-        interface = MockSpikeGLXNIDQInterface()
-
-        channel_names = ["nidq#XA0", "nidq#XA1", "nidq#XA2", "nidq#XA3", "nidq#XA4", "nidq#XA5", "nidq#XA6", "nidq#XA7"]
-        inferred_starting_times = list()
-        for channel_index, channel_name in enumerate(channel_names):
-            inferred_starting_times.append(interface.get_event_times_from_ttl(channel_name=channel_name))
-
-        expected_ttl_times = [[1.0 * (1 + 2 * period) + 0.1 * channel for period in range(3)] for channel in range(8)]
-        for channel_index, channel_name in enumerate(channel_names):
-            inferred_ttl_times = interface.get_event_times_from_ttl(channel_name=channel_name)
-            assert_array_almost_equal(x=inferred_ttl_times, y=expected_ttl_times[channel_index], decimal=4)
-
-    def test_explicit_original_default_inferred_ttl_times(self):
-        interface = MockSpikeGLXNIDQInterface(signal_duration=7.0, ttl_times=None, ttl_duration=1.0)
-
-        channel_names = ["nidq#XA0", "nidq#XA1", "nidq#XA2", "nidq#XA3", "nidq#XA4", "nidq#XA5", "nidq#XA6", "nidq#XA7"]
-        expected_ttl_times = [[1.0 * (1 + 2 * period) + 0.1 * channel for period in range(3)] for channel in range(8)]
-        for channel_index, channel_name in enumerate(channel_names):
-            inferred_ttl_times = interface.get_event_times_from_ttl(channel_name=channel_name)
-            assert_array_almost_equal(x=inferred_ttl_times, y=expected_ttl_times[channel_index], decimal=4)
-
-    def test_custom_inferred_ttl_times(self):
-        custom_ttl_times = [[1.2], [3.6], [0.7, 4.5], [5.1]]
-        interface = MockSpikeGLXNIDQInterface(ttl_times=custom_ttl_times)
-
-        channel_names = ["nidq#XA0", "nidq#XA1", "nidq#XA2", "nidq#XA3"]
-        for channel_index, channel_name in enumerate(channel_names):
-            inferred_ttl_times = interface.get_event_times_from_ttl(channel_name=channel_name)
-            assert_array_almost_equal(x=inferred_ttl_times, y=custom_ttl_times[channel_index], decimal=4)
-
-    def test_mock_metadata(self):
-        interface = MockSpikeGLXNIDQInterface()
-
-        metadata = interface.get_metadata()
-
-        expected_ecephys_metadata = {
-            "Ecephys": {
-                "Device": [
-                    {"description": "no description", "manufacturer": "Imec", "name": "Neuropixel-Imec"},
-                ],
-                "ElectrodeGroup": [
-                    {
-                        "name": "NIDQChannelGroup",
-                        "description": "A group representing the NIDQ channels.",
-                        "device": "Neuropixel-Imec",
-                        "location": "unknown",
-                    },
-                ],
-                "Electrodes": [
-                    {"name": "group_name", "description": "Name of the ElectrodeGroup this electrode is a part of."}
-                ],
-                "ElectricalSeriesNIDQ": {
-                    "name": "ElectricalSeriesNIDQ",
-                    "description": "Raw acquisition traces from the NIDQ (.nidq.bin) channels.",
+
+def test_current_default_inferred_ttl_times(self):
+    interface = MockSpikeGLXNIDQInterface()
+
+    channel_names = ["nidq#XA0", "nidq#XA1", "nidq#XA2", "nidq#XA3", "nidq#XA4", "nidq#XA5", "nidq#XA6", "nidq#XA7"]
+    inferred_starting_times = list()
+    for channel_index, channel_name in enumerate(channel_names):
+        inferred_starting_times.append(interface.get_event_times_from_ttl(channel_name=channel_name))
+
+    expected_ttl_times = [[1.0 * (1 + 2 * period) + 0.1 * channel for period in range(3)] for channel in range(8)]
+    for channel_index, channel_name in enumerate(channel_names):
+        inferred_ttl_times = interface.get_event_times_from_ttl(channel_name=channel_name)
+        assert_array_almost_equal(x=inferred_ttl_times, y=expected_ttl_times[channel_index], decimal=4)
+
+def test_explicit_original_default_inferred_ttl_times(self):
+    interface = MockSpikeGLXNIDQInterface(signal_duration=7.0, ttl_times=None, ttl_duration=1.0)
+
+    channel_names = ["nidq#XA0", "nidq#XA1", "nidq#XA2", "nidq#XA3", "nidq#XA4", "nidq#XA5", "nidq#XA6", "nidq#XA7"]
+    expected_ttl_times = [[1.0 * (1 + 2 * period) + 0.1 * channel for period in range(3)] for channel in range(8)]
+    for channel_index, channel_name in enumerate(channel_names):
+        inferred_ttl_times = interface.get_event_times_from_ttl(channel_name=channel_name)
+        assert_array_almost_equal(x=inferred_ttl_times, y=expected_ttl_times[channel_index], decimal=4)
+
+def test_custom_inferred_ttl_times(self):
+    custom_ttl_times = [[1.2], [3.6], [0.7, 4.5], [5.1]]
+    interface = MockSpikeGLXNIDQInterface(ttl_times=custom_ttl_times)
+
+    channel_names = ["nidq#XA0", "nidq#XA1", "nidq#XA2", "nidq#XA3"]
+    for channel_index, channel_name in enumerate(channel_names):
+        inferred_ttl_times = interface.get_event_times_from_ttl(channel_name=channel_name)
+        assert_array_almost_equal(x=inferred_ttl_times, y=custom_ttl_times[channel_index], decimal=4)
+
+def test_mock_metadata(self):
+    interface = MockSpikeGLXNIDQInterface()
+
+    metadata = interface.get_metadata()
+
+    expected_ecephys_metadata = {
+        "Ecephys": {
+            "Device": [
+                {"description": "no description", "manufacturer": "Imec", "name": "Neuropixel-Imec"},
+            ],
+            "ElectrodeGroup": [
+                {
+                    "name": "NIDQChannelGroup",
+                    "description": "A group representing the NIDQ channels.",
+                    "device": "Neuropixel-Imec",
+                    "location": "unknown",
                 },
-            }
+            ],
+            "Electrodes": [
+                {"name": "group_name", "description": "Name of the ElectrodeGroup this electrode is a part of."}
+            ],
+            "ElectricalSeriesNIDQ": {
+                "name": "ElectricalSeriesNIDQ",
+                "description": "Raw acquisition traces from the NIDQ (.nidq.bin) channels.",
+            },
         }
-        print(metadata["Ecephys"])
-        self.assertDictEqual(d1=metadata["Ecephys"], d2=expected_ecephys_metadata["Ecephys"])
+    }
+    print(metadata["Ecephys"])
+    self.assertDictEqual(d1=metadata["Ecephys"], d2=expected_ecephys_metadata["Ecephys"])
 
-        expected_start_time = datetime(2020, 11, 3, 10, 35, 10)
-        assert metadata["NWBFile"]["session_start_time"] == expected_start_time
+    expected_start_time = datetime(2020, 11, 3, 10, 35, 10)
+    assert metadata["NWBFile"]["session_start_time"] == expected_start_time
 
-    def test_mock_run_conversion(self, tmpdir: pathlib.Path):
-        interface = MockSpikeGLXNIDQInterface()
+def test_mock_run_conversion(self, tmpdir: pathlib.Path):
+    interface = MockSpikeGLXNIDQInterface()
 
-        metadata = interface.get_metadata()
+    metadata = interface.get_metadata()
 
-        nwbfile_path = tmpdir / "TestMockSpikeGLXNIDQInterface" / "test_mock_run_conversion.nwb"
-        interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)
+    nwbfile_path = tmpdir / "TestMockSpikeGLXNIDQInterface" / "test_mock_run_conversion.nwb"
+    interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)
 
-        assert "Neuropixel-Imec" in nwbfile.devices
-        assert "NIDQChannelGroup" in nwbfile.electrode_groups
-        assert nwbfile.electrodes.id[:] == [0, 1, 2, 3, 4, 5, 6, 7]
-        assert "ElectricalSeriesNIDQ" in nwbfile.acquisition
+    assert "Neuropixel-Imec" in nwbfile.devices
+    assert "NIDQChannelGroup" in nwbfile.electrode_groups
+    assert nwbfile.electrodes.id[:] == [0, 1, 2, 3, 4, 5, 6, 7]
+    assert "ElectricalSeriesNIDQ" in nwbfile.acquisition

From 4aeb979b40140f7a069617ae60f3e637fddafbe9 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 4 Jun 2024 16:51:34 +0000
Subject: [PATCH 12/21] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 tests/test_ecephys/test_mock_nidq_interface.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tests/test_ecephys/test_mock_nidq_interface.py b/tests/test_ecephys/test_mock_nidq_interface.py
index 07482f466..a64dc3f61 100644
--- a/tests/test_ecephys/test_mock_nidq_interface.py
+++ b/tests/test_ecephys/test_mock_nidq_interface.py
@@ -8,7 +8,6 @@
 from neuroconv.tools.testing import MockSpikeGLXNIDQInterface
 
 
-
 def test_current_default_inferred_ttl_times(self):
     interface = MockSpikeGLXNIDQInterface()
 
@@ -22,6 +21,7 @@ def test_current_default_inferred_ttl_times(self):
         inferred_ttl_times = interface.get_event_times_from_ttl(channel_name=channel_name)
         assert_array_almost_equal(x=inferred_ttl_times, y=expected_ttl_times[channel_index], decimal=4)
 
+
 def test_explicit_original_default_inferred_ttl_times(self):
     interface = MockSpikeGLXNIDQInterface(signal_duration=7.0, ttl_times=None, ttl_duration=1.0)
 
@@ -31,6 +31,7 @@ def test_explicit_original_default_inferred_ttl_times(self):
         inferred_ttl_times = interface.get_event_times_from_ttl(channel_name=channel_name)
         assert_array_almost_equal(x=inferred_ttl_times, y=expected_ttl_times[channel_index], decimal=4)
 
+
 def test_custom_inferred_ttl_times(self):
     custom_ttl_times = [[1.2], [3.6], [0.7, 4.5], [5.1]]
     interface = MockSpikeGLXNIDQInterface(ttl_times=custom_ttl_times)
@@ -40,6 +41,7 @@ def test_custom_inferred_ttl_times(self):
         inferred_ttl_times = interface.get_event_times_from_ttl(channel_name=channel_name)
         assert_array_almost_equal(x=inferred_ttl_times, y=custom_ttl_times[channel_index], decimal=4)
 
+
 def test_mock_metadata(self):
     interface = MockSpikeGLXNIDQInterface()
 
@@ -73,6 +75,7 @@ def test_mock_metadata(self):
     expected_start_time = datetime(2020, 11, 3, 10, 35, 10)
     assert metadata["NWBFile"]["session_start_time"] == expected_start_time
 
+
 def test_mock_run_conversion(self, tmpdir: pathlib.Path):
     interface = MockSpikeGLXNIDQInterface()
 

From 22dba430ea03661b96e9a615578ccf504a3e2568 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 4 Jun 2024 13:34:58 -0400
Subject: [PATCH 13/21] remove self

---
 tests/test_ecephys/test_mock_nidq_interface.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/test_ecephys/test_mock_nidq_interface.py b/tests/test_ecephys/test_mock_nidq_interface.py
index a64dc3f61..e8c2ec821 100644
--- a/tests/test_ecephys/test_mock_nidq_interface.py
+++ b/tests/test_ecephys/test_mock_nidq_interface.py
@@ -8,7 +8,7 @@
 from neuroconv.tools.testing import MockSpikeGLXNIDQInterface
 
 
-def test_current_default_inferred_ttl_times(self):
+def test_current_default_inferred_ttl_times():
     interface = MockSpikeGLXNIDQInterface()
 
     channel_names = ["nidq#XA0", "nidq#XA1", "nidq#XA2", "nidq#XA3", "nidq#XA4", "nidq#XA5", "nidq#XA6", "nidq#XA7"]
@@ -22,7 +22,7 @@ def test_current_default_inferred_ttl_times(self):
         assert_array_almost_equal(x=inferred_ttl_times, y=expected_ttl_times[channel_index], decimal=4)
 
 
-def test_explicit_original_default_inferred_ttl_times(self):
+def test_explicit_original_default_inferred_ttl_times():
     interface = MockSpikeGLXNIDQInterface(signal_duration=7.0, ttl_times=None, ttl_duration=1.0)
 
     channel_names = ["nidq#XA0", "nidq#XA1", "nidq#XA2", "nidq#XA3", "nidq#XA4", "nidq#XA5", "nidq#XA6", "nidq#XA7"]
@@ -32,7 +32,7 @@ def test_explicit_original_default_inferred_ttl_times(self):
         assert_array_almost_equal(x=inferred_ttl_times, y=expected_ttl_times[channel_index], decimal=4)
 
 
-def test_custom_inferred_ttl_times(self):
+def test_custom_inferred_ttl_times():
     custom_ttl_times = [[1.2], [3.6], [0.7, 4.5], [5.1]]
     interface = MockSpikeGLXNIDQInterface(ttl_times=custom_ttl_times)
 
@@ -42,7 +42,7 @@ def test_custom_inferred_ttl_times(self):
         assert_array_almost_equal(x=inferred_ttl_times, y=custom_ttl_times[channel_index], decimal=4)
 
 
-def test_mock_metadata(self):
+def test_mock_metadata():
     interface = MockSpikeGLXNIDQInterface()
 
     metadata = interface.get_metadata()
@@ -76,7 +76,7 @@ def test_mock_metadata(self):
     assert metadata["NWBFile"]["session_start_time"] == expected_start_time
 
 
-def test_mock_run_conversion(self, tmpdir: pathlib.Path):
+def test_mock_run_conversion(tmpdir: pathlib.Path):
     interface = MockSpikeGLXNIDQInterface()
 
     metadata = interface.get_metadata()

From b76d36f90cac7195eeacd584649567b1edbee63a Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 4 Jun 2024 14:51:56 -0400
Subject: [PATCH 14/21] make parent folder first and overwrite if necessary

---
 .../test_ecephys/test_mock_nidq_interface.py  | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/tests/test_ecephys/test_mock_nidq_interface.py b/tests/test_ecephys/test_mock_nidq_interface.py
index e8c2ec821..ea92c75d6 100644
--- a/tests/test_ecephys/test_mock_nidq_interface.py
+++ b/tests/test_ecephys/test_mock_nidq_interface.py
@@ -3,6 +3,7 @@
 
 from hdmf.testing import TestCase
 from numpy.testing import assert_array_almost_equal
+from pynwb import NWBHDF5IO
 from pynwb.testing.mock.file import mock_NWBFile
 
 from neuroconv.tools.testing import MockSpikeGLXNIDQInterface
@@ -81,10 +82,16 @@ def test_mock_run_conversion(tmpdir: pathlib.Path):
 
     metadata = interface.get_metadata()
 
-    nwbfile_path = tmpdir / "TestMockSpikeGLXNIDQInterface" / "test_mock_run_conversion.nwb"
-    interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)
+    test_directory = tmpdir / "TestMockSpikeGLXNIDQInterface"
+    test_directory.mkdir(exist_ok=True)
+    nwbfile_path = test_directory / "test_mock_run_conversion.nwb"
+    interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata, overwrite=True)
 
-    assert "Neuropixel-Imec" in nwbfile.devices
-    assert "NIDQChannelGroup" in nwbfile.electrode_groups
-    assert nwbfile.electrodes.id[:] == [0, 1, 2, 3, 4, 5, 6, 7]
-    assert "ElectricalSeriesNIDQ" in nwbfile.acquisition
+    
+    with NWBHDF5IO(path=nwbfile_path, mode="r") as io:
+        nwbfile = io.read()
+
+        assert "Neuropixel-Imec" in nwbfile.devices
+        assert "NIDQChannelGroup" in nwbfile.electrode_groups
+        assert nwbfile.electrodes.id[:] == [0, 1, 2, 3, 4, 5, 6, 7]
+        assert "ElectricalSeriesNIDQ" in nwbfile.acquisition

From 1c1fb8f2e4288d4197c2eb142377a865db73818a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 4 Jun 2024 18:52:35 +0000
Subject: [PATCH 15/21] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 tests/test_ecephys/test_mock_nidq_interface.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/test_ecephys/test_mock_nidq_interface.py b/tests/test_ecephys/test_mock_nidq_interface.py
index ea92c75d6..5c7937ffc 100644
--- a/tests/test_ecephys/test_mock_nidq_interface.py
+++ b/tests/test_ecephys/test_mock_nidq_interface.py
@@ -87,7 +87,6 @@ def test_mock_run_conversion(tmpdir: pathlib.Path):
     nwbfile_path = test_directory / "test_mock_run_conversion.nwb"
     interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata, overwrite=True)
 
-    
     with NWBHDF5IO(path=nwbfile_path, mode="r") as io:
         nwbfile = io.read()
 

From 35f2606c6f2d5aacda6d67fbeb09a489a37dab1c Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 4 Jun 2024 15:56:47 -0400
Subject: [PATCH 16/21] Update tests/test_ecephys/test_mock_nidq_interface.py

---
 tests/test_ecephys/test_mock_nidq_interface.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_ecephys/test_mock_nidq_interface.py b/tests/test_ecephys/test_mock_nidq_interface.py
index 5c7937ffc..7af2de6ba 100644
--- a/tests/test_ecephys/test_mock_nidq_interface.py
+++ b/tests/test_ecephys/test_mock_nidq_interface.py
@@ -71,7 +71,7 @@ def test_mock_metadata():
         }
     }
     print(metadata["Ecephys"])
-    self.assertDictEqual(d1=metadata["Ecephys"], d2=expected_ecephys_metadata["Ecephys"])
+    assert metadata["Ecephys"] == expected_ecephys_metadata["Ecephys"]
 
     expected_start_time = datetime(2020, 11, 3, 10, 35, 10)
     assert metadata["NWBFile"]["session_start_time"] == expected_start_time

From bfb3ab3dff16c1ae9040fcf5c13e999163154952 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 4 Jun 2024 16:04:01 -0400
Subject: [PATCH 17/21] Update tests/test_ecephys/test_mock_nidq_interface.py

---
 tests/test_ecephys/test_mock_nidq_interface.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_ecephys/test_mock_nidq_interface.py b/tests/test_ecephys/test_mock_nidq_interface.py
index 7af2de6ba..b3fba81f1 100644
--- a/tests/test_ecephys/test_mock_nidq_interface.py
+++ b/tests/test_ecephys/test_mock_nidq_interface.py
@@ -83,7 +83,7 @@ def test_mock_run_conversion(tmpdir: pathlib.Path):
     metadata = interface.get_metadata()
 
     test_directory = tmpdir / "TestMockSpikeGLXNIDQInterface"
-    test_directory.mkdir(exist_ok=True)
+    test_directory.mkdir(exists_ok=True)
     nwbfile_path = test_directory / "test_mock_run_conversion.nwb"
     interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata, overwrite=True)
 

From f92c82207bde6133d5e312ecf40d23bbab1dce28 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 4 Jun 2024 16:12:10 -0400
Subject: [PATCH 18/21] Update tests/test_ecephys/test_mock_nidq_interface.py

---
 tests/test_ecephys/test_mock_nidq_interface.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_ecephys/test_mock_nidq_interface.py b/tests/test_ecephys/test_mock_nidq_interface.py
index b3fba81f1..7af2de6ba 100644
--- a/tests/test_ecephys/test_mock_nidq_interface.py
+++ b/tests/test_ecephys/test_mock_nidq_interface.py
@@ -83,7 +83,7 @@ def test_mock_run_conversion(tmpdir: pathlib.Path):
     metadata = interface.get_metadata()
 
     test_directory = tmpdir / "TestMockSpikeGLXNIDQInterface"
-    test_directory.mkdir(exists_ok=True)
+    test_directory.mkdir(exist_ok=True)
     nwbfile_path = test_directory / "test_mock_run_conversion.nwb"
     interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata, overwrite=True)
 

From bffd106e92ea69933ce7fc366ffb847d2b16c0d0 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 4 Jun 2024 16:14:08 -0400
Subject: [PATCH 19/21] Update tests/test_ecephys/test_mock_nidq_interface.py

---
 tests/test_ecephys/test_mock_nidq_interface.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_ecephys/test_mock_nidq_interface.py b/tests/test_ecephys/test_mock_nidq_interface.py
index 7af2de6ba..617e684c0 100644
--- a/tests/test_ecephys/test_mock_nidq_interface.py
+++ b/tests/test_ecephys/test_mock_nidq_interface.py
@@ -82,7 +82,7 @@ def test_mock_run_conversion(tmpdir: pathlib.Path):
 
     metadata = interface.get_metadata()
 
-    test_directory = tmpdir / "TestMockSpikeGLXNIDQInterface"
+    test_directory = pathllib.Path(tmpdir) / "TestMockSpikeGLXNIDQInterface"
     test_directory.mkdir(exist_ok=True)
     nwbfile_path = test_directory / "test_mock_run_conversion.nwb"
     interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata, overwrite=True)

From e6930dcdfcb701395b7c1b8ce01fdc73ccf09eda Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 4 Jun 2024 17:08:43 -0400
Subject: [PATCH 20/21] Update tests/test_ecephys/test_mock_nidq_interface.py

---
 tests/test_ecephys/test_mock_nidq_interface.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_ecephys/test_mock_nidq_interface.py b/tests/test_ecephys/test_mock_nidq_interface.py
index 617e684c0..134551546 100644
--- a/tests/test_ecephys/test_mock_nidq_interface.py
+++ b/tests/test_ecephys/test_mock_nidq_interface.py
@@ -82,7 +82,7 @@ def test_mock_run_conversion(tmpdir: pathlib.Path):
 
     metadata = interface.get_metadata()
 
-    test_directory = pathllib.Path(tmpdir) / "TestMockSpikeGLXNIDQInterface"
+    test_directory = pathlib.Path(tmpdir) / "TestMockSpikeGLXNIDQInterface"
     test_directory.mkdir(exist_ok=True)
     nwbfile_path = test_directory / "test_mock_run_conversion.nwb"
     interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata, overwrite=True)

From c221b5239350d0a861e7e1620778ea97debd6e4c Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 4 Jun 2024 17:19:12 -0400
Subject: [PATCH 21/21] Update test_mock_nidq_interface.py

---
 tests/test_ecephys/test_mock_nidq_interface.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_ecephys/test_mock_nidq_interface.py b/tests/test_ecephys/test_mock_nidq_interface.py
index 134551546..cd4287fc0 100644
--- a/tests/test_ecephys/test_mock_nidq_interface.py
+++ b/tests/test_ecephys/test_mock_nidq_interface.py
@@ -92,5 +92,5 @@ def test_mock_run_conversion(tmpdir: pathlib.Path):
 
         assert "Neuropixel-Imec" in nwbfile.devices
         assert "NIDQChannelGroup" in nwbfile.electrode_groups
-        assert nwbfile.electrodes.id[:] == [0, 1, 2, 3, 4, 5, 6, 7]
+        assert list(nwbfile.electrodes.id[:]) == [0, 1, 2, 3, 4, 5, 6, 7]
         assert "ElectricalSeriesNIDQ" in nwbfile.acquisition