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Make tensorstore optional #44

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merged 10 commits into from
Oct 13, 2023
Merged

Make tensorstore optional #44

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a7c1112
Make tensorstore optional, rename to open_zarr
jni Oct 11, 2023
96c9bee
Make tensorstore an optional dependency
jni Oct 11, 2023
0358eb1
Remove unused imports
jni Oct 11, 2023
8ce40fe
Add docstring and simplify code
jni Oct 11, 2023
1f63256
Add docstring and simplify code
jni Oct 11, 2023
2012a03
Formatting
jni Oct 11, 2023
cfe8d95
Remove outdated unused class
jni Oct 11, 2023
41dac65
Update test workflow
jni Oct 12, 2023
b1b95b4
Fix tox.ini
jni Oct 13, 2023
3204a38
Use mode='a' when opening zarr array
jni Oct 13, 2023
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4 changes: 2 additions & 2 deletions .github/workflows/test_and_deploy.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ jobs:
strategy:
matrix:
platform: [ubuntu-latest, windows-latest, macos-latest]
python-version: [3.8, 3.9, '3.10']
python-version: ['3.9', '3.10', '3.11']

steps:
- uses: actions/checkout@v2
Expand Down Expand Up @@ -51,7 +51,7 @@ jobs:

# this runs the platform-specific tests declared in tox.ini
- name: Test with tox
uses: GabrielBB/xvfb-action@v1
uses: aganders3/headless-gui@v1
with:
run: python -m tox
env:
Expand Down
4 changes: 3 additions & 1 deletion setup.cfg
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Expand Up @@ -34,7 +34,6 @@ install_requires =
qtpy
scipy
scikit-image
tensorstore
toolz
zarr

Expand All @@ -56,5 +55,8 @@ testing =
pytest-qt
napari[pyqt5]

all =
tensorstore

[options.package_data]
zarpaint = napari.yaml
4 changes: 2 additions & 2 deletions src/zarpaint/__init__.py
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Expand Up @@ -3,7 +3,7 @@
except ImportError:
__version__ = "unknown"

from ._zarpaint import create_labels, open_tensorstore
from ._zarpaint import create_labels, open_zarr
from ._dims_chooser import DimsSorter, set_axis_labels
from ._watershed import watershed_split
from ._add_3d_points import add_points_3d_with_alt_click
Expand All @@ -12,7 +12,7 @@

__all__ = [
'create_labels',
'open_tensorstore',
'open_zarr',
'DimsSorter',
'set_axis_labels',
'watershed_split',
Expand Down
6 changes: 2 additions & 4 deletions src/zarpaint/_tests/test_copy_data.py
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Original file line number Diff line number Diff line change
@@ -1,8 +1,6 @@
from napari.layers import Labels
from zarpaint import copy_data
import numpy as np
import tensorstore as ts
from zarpaint import open_tensorstore
from zarpaint import open_zarr
import zarr

def test_copy_data(make_napari_viewer):
Expand All @@ -19,7 +17,7 @@ def test_copy_data(make_napari_viewer):
def test_copy_data_tensorstore(make_napari_viewer, tmp_path):
viewer = make_napari_viewer()
labels_layer1 = viewer.add_labels(np.random.randint(0, 2**23, size=(10, 20, 30)))
array2 = open_tensorstore(tmp_path/"example.zarr", shape=(2, 10, 20, 30), chunks=(1, 1, 20, 30))
array2 = open_zarr(tmp_path / "example.zarr", shape=(2, 10, 20, 30), chunks=(1, 1, 20, 30))
labels_layer2 = viewer.add_labels(array2)
viewer.dims.set_point(axis=0, value=1)
widget = copy_data()
Expand Down
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