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build: stop installing basicpy/aicsimageio, which break the NumPy 2 stack #641

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Alpaca233 merged 1 commit into from
Sep 6, 2026
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build: stop installing basicpy/aicsimageio, which break the NumPy 2 stack #641

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16 changes: 11 additions & 5 deletions software/setup_22.04.sh
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Expand Up @@ -72,17 +72,23 @@ sudo apt remove -y python3-pyqt5 python3-pyqt5.qtsvg 2>/dev/null || true
pip3 uninstall -y PyQt5 PyQt5-Qt5 PyQt5-sip 2>/dev/null || true
pip3 install "PyQt6==6.11.0" "PyQt6-Qt6==6.11.2" "PyQt6-sip==13.12.0"

# install libraries. No "numpy<2" pin: napari 0.7 only needs numpy>=1.24, but the rest of
# the current stack (opencv-python 5.x, pyqtgraph 0.14, ...) targets NumPy 2 and the
# pinned-back packages aicsimageio drags in (tifffile 2023.2, zarr 2.15, lxml 4.9) were
# verified to work with it.
# install libraries. No "numpy<2" pin: napari 0.7 only needs numpy>=1.24, and the rest of
# the current stack (opencv-python 5.x, pyqtgraph 0.14, ...) targets NumPy 2.
#
# aicsimageio and basicpy are deliberately NOT installed. basicpy pins scipy<1.13
# (peng-lab/BaSiCPy#173) and scipy 1.12 ships no NumPy-2 wheel, so pip resolves the whole
# environment back to numpy 1.26 -- which then violates napari's scipy>=1.14 and
# opencv 5.x's numpy>=2, leaving `pip check` failing and napari unimportable. Their only
# consumer is control/stitcher.py, which nothing in the application imports; stitching
# lives in the separate Cephla-Lab/image-stitcher repo. If you need that module, install
# these two into a dedicated venv rather than this one.
pip3 install pyqtgraph qtpy pyserial pandas imageio crc==1.3.0 lxml numpy tifffile scipy pyreadline3
pip3 install opencv-python-headless opencv-contrib-python-headless
# napari pinned to a tested release (patch releases change its vispy/Qt constraints). The
# [pyqt6] extra is what makes pip enforce napari's Qt blocklist against the PyQt6 above.
# tensorstore is required by control/ndviewer_light and by tests/control/core/test_zarr_writer.py,
# which begins with pytest.importorskip("tensorstore") -- without it ~79 zarr tests silently skip.
pip3 install "napari[pyqt6]==0.7.1" scikit-image dask_image ome_zarr tensorstore aicsimageio basicpy pytest pytest-qt pytest-xvfb gitpython matplotlib pydantic_xml pyvisa hidapi filelock lxml_html_clean psutil mcp ndv
pip3 install "napari[pyqt6]==0.7.1" scikit-image dask_image ome_zarr tensorstore pytest pytest-qt pytest-xvfb gitpython matplotlib pydantic_xml pyvisa hidapi filelock lxml_html_clean psutil mcp ndv

# Optional: PI V-308 / C-414 focus stage (USE_PI_FOCUS_STAGE). Safe to skip if unused;
# squid.stage.pi imports it lazily and only needs it to connect to real hardware, so
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