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Support zarr v3 #387

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9c2a264
Support zarr v3
alejoe91 Dec 11, 2025
66a0489
oups
alejoe91 Dec 11, 2025
9e0e92d
Upgrade to zarr v3
alejoe91 Mar 20, 2026
bb77631
Merge branch 'main' into zarrv3
alejoe91 Mar 23, 2026
71482bb
Merge branch 'main' of github.com:SpikeInterface/probeinterface into …
alejoe91 Jul 2, 2026
94f1352
Merge branch 'main' of github.com:SpikeInterface/probeinterface into …
alejoe91 Jul 15, 2026
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Merge branch 'main' of github.com:SpikeInterface/probeinterface into …
alejoe91 Jul 31, 2026
5e6f9bd
Merge branch 'zarrv3' of github.com:alejoe91/probeinterface into zarrv3
alejoe91 Jul 31, 2026
77c4238
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alejoe91 Jul 31, 2026
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2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ test = [
"scipy",
"pandas",
"h5py",
"zarr>=2.16.0,<3.0.0",
"zarr>=3,<4"
]

docs = [
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8 changes: 4 additions & 4 deletions src/probeinterface/probe.py
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Expand Up @@ -1232,7 +1232,7 @@ def add_probe_to_zarr_group(self, group: "zarr.Group") -> None:
# add fields and contact annotations
for field_name, (dtype, offset) in probe_arr.dtype.fields.items():
data = probe_arr[field_name]
group.create_dataset(name=field_name, data=data, dtype=dtype, chunks=False)
group.create_array(name=field_name, data=data, chunks=data.shape)

# Annotations as a group (special attributes are stored as annotations)
annotations_group = group.create_group("annotations")
Expand All @@ -1241,8 +1241,8 @@ def add_probe_to_zarr_group(self, group: "zarr.Group") -> None:

# Add planar contour
if self.probe_planar_contour is not None:
group.create_dataset(
name="probe_planar_contour", data=self.probe_planar_contour, dtype="float64", chunks=False
group.create_array(
name="probe_planar_contour", data=self.probe_planar_contour, chunks=self.probe_planar_contour.shape
)

def to_zarr(self, folder_path: str | Path) -> None:
Expand Down Expand Up @@ -1299,7 +1299,7 @@ def from_zarr_group(group: "zarr.Group") -> "Probe":
probe_arr_keys.append(key)
dtype.append((key, dset.dtype))
if num_contacts is None:
num_contacts = len(dset)
num_contacts = dset.shape[0]

# Create a structured array from the datasets
probe_arr = np.zeros(num_contacts, dtype=dtype)
Expand Down
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