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Napari deprecation updates #44

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Merged
merged 3 commits into from
Aug 18, 2025
Merged

Napari deprecation updates #44

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574a3f2
border_color to edge color since napari deprecated it
HaleySchuhl Aug 15, 2025
3baedeb
replace make_napari_viewer with napari_open
HaleySchuhl Aug 15, 2025
59939f5
remove libegl1-mesa from CI setup?
HaleySchuhl Aug 15, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/continuous-integration.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ jobs:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: |
sudo apt-get install --no-install-recommends libyaml-dev libegl1-mesa libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-shape0 libxcb-cursor0 xserver-xephyr
sudo apt-get install --no-install-recommends libyaml-dev libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-shape0 libxcb-cursor0 xserver-xephyr
python -m pip install --upgrade pip
pip install flake8 pytest pytest-cov pytest-qt pytest-xvfb ipython anyio
- name: Lint with flake8
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4 changes: 2 additions & 2 deletions plantcv/annotate/napari_label_classes.py
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Expand Up @@ -82,7 +82,7 @@ def napari_label_classes(img, classes=False, size=10,
for x in classes:
if x not in keys:
viewer.add_points(np.array([]), name=x, symbol='square',
edge_color=random.choice(color),
border_color=random.choice(color),
face_color=random.choice(color), size=size)
keys = napari_classes(viewer)

Expand All @@ -95,7 +95,7 @@ def napari_label_classes(img, classes=False, size=10,
else:
viewer.add_points(importdata[key], name=key,
symbol='square',
edge_color=random.choice(color),
border_color=random.choice(color),
face_color=random.choice(color),
size=size)

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7 changes: 3 additions & 4 deletions tests/test_napari_classes.py
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Original file line number Diff line number Diff line change
@@ -1,14 +1,13 @@
import numpy as np
from plantcv.annotate import napari_classes
from plantcv.annotate import napari_classes, napari_open


def test_napari_classes(make_napari_viewer):
def test_napari_classes():
"""Test for PlantCV.Annotate"""
# Read in test data
viewer = make_napari_viewer(show=False)
img = np.zeros((100, 100))
coor = [(25, 25), (50, 50)]
viewer.add_image(img)
viewer = napari_open(img, show=False)
viewer.add_points(np.array(coor), symbol="square", name="total",
face_color="red", size=30)
viewer.add_points(np.array(coor), symbol="square", name="test",
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