From bef2c05da80c617ea7ca6d5cef83796ce1d333ab Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Fri, 19 Jul 2024 15:22:12 -0400
Subject: [PATCH 1/8] add neuronexus allego

---
 .../extractors/neoextractors/__init__.py      |  2 +
 .../extractors/neoextractors/neuronexus.py    | 66 +++++++++++++++++++
 2 files changed, 68 insertions(+)
 create mode 100644 src/spikeinterface/extractors/neoextractors/neuronexus.py

diff --git a/src/spikeinterface/extractors/neoextractors/__init__.py b/src/spikeinterface/extractors/neoextractors/__init__.py
index bf52de7c1d..5ecceb4b39 100644
--- a/src/spikeinterface/extractors/neoextractors/__init__.py
+++ b/src/spikeinterface/extractors/neoextractors/__init__.py
@@ -9,6 +9,7 @@
 from .mearec import MEArecRecordingExtractor, MEArecSortingExtractor, read_mearec
 from .mcsraw import MCSRawRecordingExtractor, read_mcsraw
 from .neuralynx import NeuralynxRecordingExtractor, NeuralynxSortingExtractor, read_neuralynx, read_neuralynx_sorting
+from .neuronexus import NeuronexusRecordingExtractor, read_neuronexus
 from .neuroscope import (
     NeuroScopeRecordingExtractor,
     NeuroScopeSortingExtractor,
@@ -54,6 +55,7 @@
     MCSRawRecordingExtractor,
     NeuralynxRecordingExtractor,
     NeuroScopeRecordingExtractor,
+    NeuronexusRecordingExtractor,
     NixRecordingExtractor,
     OpenEphysBinaryRecordingExtractor,
     OpenEphysLegacyRecordingExtractor,
diff --git a/src/spikeinterface/extractors/neoextractors/neuronexus.py b/src/spikeinterface/extractors/neoextractors/neuronexus.py
new file mode 100644
index 0000000000..e8bf470e25
--- /dev/null
+++ b/src/spikeinterface/extractors/neoextractors/neuronexus.py
@@ -0,0 +1,66 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+from spikeinterface.core.core_tools import define_function_from_class
+
+from .neobaseextractor import NeoBaseRecordingExtractor, NeoBaseSortingExtractor
+
+
+class NeuronexusRecordingExtractor(NeoBaseRecordingExtractor):
+    """
+    Class for reading data from Neuronexus Allego.
+
+    Based on :py:class:`neo.rawio.NeuronexusRawIO`
+
+    Parameters
+    ----------
+    file_path : str
+        The file path to the metadata .xdat.json file of an Allego session
+    stream_id : str, default: None
+        If there are several streams, specify the stream id you want to load.
+    stream_name : str, default: None
+        If there are several streams, specify the stream name you want to load.
+    all_annotations : bool, default: False
+        Load exhaustively all annotations from neo.
+    use_names_as_ids : bool, default: False
+        Determines the format of the channel IDs used by the extractor. If set to True, the channel IDs will be the
+        names from NeoRawIO. If set to False, the channel IDs will be the ids provided by NeoRawIO.
+
+        In Neuronexus the ids provided by NeoRawIO are the hardware channel ids stored as `ntv_chan_name` within
+        the metada and the names are the `chan_names`
+
+
+    """
+
+    NeoRawIOClass = "NeuronexusRawIO"
+
+    def __init__(
+        self,
+        file_path,
+        stream_id=None,
+        stream_name=None,
+        all_annotations=False,
+        use_names_as_ids=False,
+    ):
+        neo_kwargs = self.map_to_neo_kwargs(file_path)
+        NeoBaseRecordingExtractor.__init__(
+            self,
+            stream_id=stream_id,
+            stream_name=stream_name,
+            all_annotations=all_annotations,
+            use_names_as_ids=use_names_as_ids,
+            **neo_kwargs,
+        )
+
+        self._kwargs.update(dict(file_path=str(Path(file_path).absolute())))
+
+    @classmethod
+    def map_to_neo_kwargs(cls, file_path):
+
+        neo_kwargs = {"filename": str(file_path)}
+
+        return neo_kwargs
+
+
+read_neuronexus = define_function_from_class(source_class=NeuronexusRecordingExtractor, name="read_neuronexus")

From 9040d8b50e04fd4b2c8e2bf8d070ce9726dc7406 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Wed, 24 Jul 2024 12:34:26 -0400
Subject: [PATCH 2/8] add tests

---
 src/spikeinterface/extractors/tests/test_neoextractors.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/src/spikeinterface/extractors/tests/test_neoextractors.py b/src/spikeinterface/extractors/tests/test_neoextractors.py
index acd7ebe8ad..450a06c4e9 100644
--- a/src/spikeinterface/extractors/tests/test_neoextractors.py
+++ b/src/spikeinterface/extractors/tests/test_neoextractors.py
@@ -181,6 +181,14 @@ class NeuroScopeSortingTest(SortingCommonTestSuite, unittest.TestCase):
     ]
 
 
+class NeuronexusRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
+    ExtractorClass = NeuronexusRecordingExtractor
+    downloads = ["neuronexus"]
+    entities = [
+        ("neuronexus/allego_1/allego_2__uid0701-13-04-49.xdat.json", {"stream_id": "0"}),
+    ]
+
+
 class PlexonRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
     ExtractorClass = PlexonRecordingExtractor
     downloads = ["plexon"]

From 359e52496ea4df81899aa9bf09462913ffb718f1 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Fri, 16 Aug 2024 08:20:49 -0400
Subject: [PATCH 3/8] fix neuronexus name

---
 src/spikeinterface/extractors/neoextractors/neuronexus.py | 8 ++++----
 src/spikeinterface/extractors/tests/test_neoextractors.py | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/spikeinterface/extractors/neoextractors/neuronexus.py b/src/spikeinterface/extractors/neoextractors/neuronexus.py
index e8bf470e25..1787320179 100644
--- a/src/spikeinterface/extractors/neoextractors/neuronexus.py
+++ b/src/spikeinterface/extractors/neoextractors/neuronexus.py
@@ -7,9 +7,9 @@
 from .neobaseextractor import NeoBaseRecordingExtractor, NeoBaseSortingExtractor
 
 
-class NeuronexusRecordingExtractor(NeoBaseRecordingExtractor):
+class NeuroNexusRecordingExtractor(NeoBaseRecordingExtractor):
     """
-    Class for reading data from Neuronexus Allego.
+    Class for reading data from NeuroNexus Allego.
 
     Based on :py:class:`neo.rawio.NeuronexusRawIO`
 
@@ -33,7 +33,7 @@ class NeuronexusRecordingExtractor(NeoBaseRecordingExtractor):
 
     """
 
-    NeoRawIOClass = "NeuronexusRawIO"
+    NeoRawIOClass = "NeuroNexusRawIO"
 
     def __init__(
         self,
@@ -63,4 +63,4 @@ def map_to_neo_kwargs(cls, file_path):
         return neo_kwargs
 
 
-read_neuronexus = define_function_from_class(source_class=NeuronexusRecordingExtractor, name="read_neuronexus")
+read_neuronexus = define_function_from_class(source_class=NeuroNexusRecordingExtractor, name="read_neuronexus")
diff --git a/src/spikeinterface/extractors/tests/test_neoextractors.py b/src/spikeinterface/extractors/tests/test_neoextractors.py
index 450a06c4e9..98bbb1bf3d 100644
--- a/src/spikeinterface/extractors/tests/test_neoextractors.py
+++ b/src/spikeinterface/extractors/tests/test_neoextractors.py
@@ -182,7 +182,7 @@ class NeuroScopeSortingTest(SortingCommonTestSuite, unittest.TestCase):
 
 
 class NeuronexusRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
-    ExtractorClass = NeuronexusRecordingExtractor
+    ExtractorClass = NeuroNexusRecordingExtractor
     downloads = ["neuronexus"]
     entities = [
         ("neuronexus/allego_1/allego_2__uid0701-13-04-49.xdat.json", {"stream_id": "0"}),

From ad61187a7c51868dc902770ec537b3a9ed61df58 Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Fri, 20 Sep 2024 08:24:15 -0400
Subject: [PATCH 4/8] Heberto feedback

---
 .../extractors/neoextractors/neuronexus.py       | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/spikeinterface/extractors/neoextractors/neuronexus.py b/src/spikeinterface/extractors/neoextractors/neuronexus.py
index 1787320179..bfaae7bf7f 100644
--- a/src/spikeinterface/extractors/neoextractors/neuronexus.py
+++ b/src/spikeinterface/extractors/neoextractors/neuronexus.py
@@ -17,9 +17,9 @@ class NeuroNexusRecordingExtractor(NeoBaseRecordingExtractor):
     ----------
     file_path : str
         The file path to the metadata .xdat.json file of an Allego session
-    stream_id : str, default: None
+    stream_id : str | None, default: None
         If there are several streams, specify the stream id you want to load.
-    stream_name : str, default: None
+    stream_name : str | None, default: None
         If there are several streams, specify the stream name you want to load.
     all_annotations : bool, default: False
         Load exhaustively all annotations from neo.
@@ -37,11 +37,11 @@ class NeuroNexusRecordingExtractor(NeoBaseRecordingExtractor):
 
     def __init__(
         self,
-        file_path,
-        stream_id=None,
-        stream_name=None,
-        all_annotations=False,
-        use_names_as_ids=False,
+        file_path: str | Path,
+        stream_id: str | None = None,
+        stream_name: str | None = None,
+        all_annotations: bool = False,
+        use_names_as_ids: bool = False,
     ):
         neo_kwargs = self.map_to_neo_kwargs(file_path)
         NeoBaseRecordingExtractor.__init__(
@@ -53,7 +53,7 @@ def __init__(
             **neo_kwargs,
         )
 
-        self._kwargs.update(dict(file_path=str(Path(file_path).absolute())))
+        self._kwargs.update(dict(file_path=str(Path(file_path).resolve())))
 
     @classmethod
     def map_to_neo_kwargs(cls, file_path):

From 3fc601a29359277fc4aaa11b750a30bb45ac6311 Mon Sep 17 00:00:00 2001
From: Zach McKenzie <92116279+zm711@users.noreply.github.com>
Date: Fri, 27 Sep 2024 10:58:15 -0400
Subject: [PATCH 5/8] Fix capitalization

---
 src/spikeinterface/extractors/neoextractors/__init__.py   | 4 ++--
 src/spikeinterface/extractors/tests/test_neoextractors.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/spikeinterface/extractors/neoextractors/__init__.py b/src/spikeinterface/extractors/neoextractors/__init__.py
index 5ecceb4b39..dfa947740b 100644
--- a/src/spikeinterface/extractors/neoextractors/__init__.py
+++ b/src/spikeinterface/extractors/neoextractors/__init__.py
@@ -9,7 +9,7 @@
 from .mearec import MEArecRecordingExtractor, MEArecSortingExtractor, read_mearec
 from .mcsraw import MCSRawRecordingExtractor, read_mcsraw
 from .neuralynx import NeuralynxRecordingExtractor, NeuralynxSortingExtractor, read_neuralynx, read_neuralynx_sorting
-from .neuronexus import NeuronexusRecordingExtractor, read_neuronexus
+from .neuronexus import NeuronNexusRecordingExtractor, read_neuronexus
 from .neuroscope import (
     NeuroScopeRecordingExtractor,
     NeuroScopeSortingExtractor,
@@ -55,7 +55,7 @@
     MCSRawRecordingExtractor,
     NeuralynxRecordingExtractor,
     NeuroScopeRecordingExtractor,
-    NeuronexusRecordingExtractor,
+    NeuroNexusRecordingExtractor,
     NixRecordingExtractor,
     OpenEphysBinaryRecordingExtractor,
     OpenEphysLegacyRecordingExtractor,
diff --git a/src/spikeinterface/extractors/tests/test_neoextractors.py b/src/spikeinterface/extractors/tests/test_neoextractors.py
index 98bbb1bf3d..1251774fce 100644
--- a/src/spikeinterface/extractors/tests/test_neoextractors.py
+++ b/src/spikeinterface/extractors/tests/test_neoextractors.py
@@ -181,7 +181,7 @@ class NeuroScopeSortingTest(SortingCommonTestSuite, unittest.TestCase):
     ]
 
 
-class NeuronexusRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
+class NeuroNexusRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
     ExtractorClass = NeuroNexusRecordingExtractor
     downloads = ["neuronexus"]
     entities = [

From 1d64fc7014de581415b9aeadc39ef735b9dbc390 Mon Sep 17 00:00:00 2001
From: Zach McKenzie <92116279+zm711@users.noreply.github.com>
Date: Fri, 27 Sep 2024 11:03:11 -0400
Subject: [PATCH 6/8] oops

---
 src/spikeinterface/extractors/neoextractors/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/spikeinterface/extractors/neoextractors/__init__.py b/src/spikeinterface/extractors/neoextractors/__init__.py
index dfa947740b..03d517b46e 100644
--- a/src/spikeinterface/extractors/neoextractors/__init__.py
+++ b/src/spikeinterface/extractors/neoextractors/__init__.py
@@ -9,7 +9,7 @@
 from .mearec import MEArecRecordingExtractor, MEArecSortingExtractor, read_mearec
 from .mcsraw import MCSRawRecordingExtractor, read_mcsraw
 from .neuralynx import NeuralynxRecordingExtractor, NeuralynxSortingExtractor, read_neuralynx, read_neuralynx_sorting
-from .neuronexus import NeuronNexusRecordingExtractor, read_neuronexus
+from .neuronexus import NeuroNexusRecordingExtractor, read_neuronexus
 from .neuroscope import (
     NeuroScopeRecordingExtractor,
     NeuroScopeSortingExtractor,

From 1dea1cf512609e8ed8ebc0c1438caa8d3e5858be Mon Sep 17 00:00:00 2001
From: zm711 <92116279+zm711@users.noreply.github.com>
Date: Mon, 30 Sep 2024 08:29:19 -0400
Subject: [PATCH 7/8] add assert messaging

---
 src/spikeinterface/extractors/tests/common_tests.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/spikeinterface/extractors/tests/common_tests.py b/src/spikeinterface/extractors/tests/common_tests.py
index 5432efa9f3..61cfc2a153 100644
--- a/src/spikeinterface/extractors/tests/common_tests.py
+++ b/src/spikeinterface/extractors/tests/common_tests.py
@@ -52,8 +52,11 @@ def test_open(self):
                 num_samples = rec.get_num_samples(segment_index=segment_index)
 
                 full_traces = rec.get_traces(segment_index=segment_index)
-                assert full_traces.shape == (num_samples, num_chans)
-                assert full_traces.dtype == dtype
+                assert full_traces.shape == (
+                    num_samples,
+                    num_chans,
+                ), f"{full_traces.shape} != {(num_samples, num_chans)}"
+                assert full_traces.dtype == dtype, f"{full_traces.dtype} != {dtype=}"
 
                 traces_sample_first = rec.get_traces(segment_index=segment_index, start_frame=0, end_frame=1)
                 assert traces_sample_first.shape == (1, num_chans)

From 8c99c87a3529cc75b40acd88e0cee0ecd4891456 Mon Sep 17 00:00:00 2001
From: Heberto Mayorquin <h.mayorquin@gmail.com>
Date: Wed, 9 Oct 2024 14:53:48 -0600
Subject: [PATCH 8/8] Update
 src/spikeinterface/extractors/neoextractors/neuronexus.py

Co-authored-by: Zach McKenzie <92116279+zm711@users.noreply.github.com>
---
 src/spikeinterface/extractors/neoextractors/neuronexus.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/spikeinterface/extractors/neoextractors/neuronexus.py b/src/spikeinterface/extractors/neoextractors/neuronexus.py
index bfaae7bf7f..dca482b28a 100644
--- a/src/spikeinterface/extractors/neoextractors/neuronexus.py
+++ b/src/spikeinterface/extractors/neoextractors/neuronexus.py
@@ -15,7 +15,7 @@ class NeuroNexusRecordingExtractor(NeoBaseRecordingExtractor):
 
     Parameters
     ----------
-    file_path : str
+    file_path : str | Path
         The file path to the metadata .xdat.json file of an Allego session
     stream_id : str | None, default: None
         If there are several streams, specify the stream id you want to load.