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install_env.sh: get Qt via napari-spatialdata[test,all] (SIT-412) #29

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Merged
jan-glx merged 1 commit into from
Nov 10, 2026
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install_env.sh: get Qt via napari-spatialdata[test,all] (SIT-412) #29

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5 changes: 2 additions & 3 deletions src/spatialdata_data_converter/commands/install_env.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@ conda activate $ENV
# TODO: ideally we won't need all these packages. They should either be dependencies of spatialdata-data-converter or add as extras when installing the (napari-)spatialdata(-io|-plot) packages
# fontconfig is a requirement of vispy when running pytest
# no conda-forge `pyqt` here: it is PyQt5 (Qt 5.15), but napari>=0.10 needs Qt>=6.7, and qtpy would pick PyQt5
# over a Qt6 binding; napari[pyqt6] (pip, below) provides the Qt binding instead
# over a Qt6 binding; napari-spatialdata's `all` extra (pip, below) provides PyQt6 instead
mamba install pytorch torchvision torchaudio cpuonly rclone joblib -c pytorch -c conda-forge -y
mamba install -c conda-forge nbconvert pytest pytest-xdist jupyter ipywidgets jupyterlab chardet unzip papermill watermark python-igraph leidenalg rclone pytorch-lightning monai fontconfig -y
pip install jupyter-black watermark
Expand Down Expand Up @@ -101,8 +101,7 @@ PACKAGES=(
-e "$WORKSPACE/spatialdata-io" --group "$WORKSPACE/spatialdata-io/pyproject.toml:test"
-e "$WORKSPACE/spatialdata-plot" --group "$WORKSPACE/spatialdata-plot/pyproject.toml:test"
-e "$WORKSPACE/squidpy" --group "$WORKSPACE/squidpy/pyproject.toml:test"
-e "$WORKSPACE/napari-spatialdata[test]" # still a setup.cfg extra, not a dependency group
"napari[pyqt6]" # Qt binding for napari(-spatialdata) tests; napari pins compatible PyQt6/Qt versions
-e "$WORKSPACE/napari-spatialdata[test,all]" # setup.cfg extras; `all` brings the Qt binding
)
# one call: a conflict with the local spatialdata fails instead of silently pulling it from PyPI
set -o pipefail
Expand Down