From 9c2d3ee1c5b906900ec2f3b59bad2dfc53e09a93 Mon Sep 17 00:00:00 2001 From: Jan Gleixner Date: Tue, 10 Nov 2026 10:12:40 +0100 Subject: [PATCH] install_env.sh: get Qt via napari-spatialdata[test,all] (SIT-412) napari-spatialdata#406 made its all extra install napari[pyqt6], so the explicit napari[pyqt6] stopgap from #26 is no longer needed. --- src/spatialdata_data_converter/commands/install_env.sh | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/spatialdata_data_converter/commands/install_env.sh b/src/spatialdata_data_converter/commands/install_env.sh index 2fee682..f942736 100755 --- a/src/spatialdata_data_converter/commands/install_env.sh +++ b/src/spatialdata_data_converter/commands/install_env.sh @@ -72,7 +72,7 @@ conda activate $ENV # TODO: ideally we won't need all these packages. They should either be dependencies of spatialdata-data-converter or add as extras when installing the (napari-)spatialdata(-io|-plot) packages # fontconfig is a requirement of vispy when running pytest # no conda-forge `pyqt` here: it is PyQt5 (Qt 5.15), but napari>=0.10 needs Qt>=6.7, and qtpy would pick PyQt5 -# over a Qt6 binding; napari[pyqt6] (pip, below) provides the Qt binding instead +# over a Qt6 binding; napari-spatialdata's `all` extra (pip, below) provides PyQt6 instead mamba install pytorch torchvision torchaudio cpuonly rclone joblib -c pytorch -c conda-forge -y mamba install -c conda-forge nbconvert pytest pytest-xdist jupyter ipywidgets jupyterlab chardet unzip papermill watermark python-igraph leidenalg rclone pytorch-lightning monai fontconfig -y pip install jupyter-black watermark @@ -101,8 +101,7 @@ PACKAGES=( -e "$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