fix: upgrade pip and drop napari[all] to unblock CI#529
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Pin pip resolution was hitting ResolutionTooDeep (2,000,000 rounds) because napari[all] pulls unpinned plugin packages (magicgui, npe2, napari-svg, napari-console, napari-plugin-manager, napari-plugin-engine) whose newer PyPI releases conflict with what napari 0.5.4 allows. The codebase only uses napari.Viewer and napari.utils.colormaps directly, so the [all] extra is unnecessary; PyQt5 is already installed via apt. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Ubuntu 22.04's system pip (22.0.2) cannot resolve the napari dependency graph against current PyPI. CI install-and-test was hanging for hours and eventually failing with ResolutionTooDeep: 2000000 (verified by reproducing the same backtracking pattern locally with pip==22.0.2). pip 23+ handles the same dependency set in seconds. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Alpaca233
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Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
CI's
install-and-testhas been failing on every PR since April 14 withpip._vendor.resolvelib.resolvers.ResolutionTooDeep: 2000000. Last green master run was April 3 (#524). No commits to setup files in that window — the regression is purely from new releases on PyPI dragging Ubuntu's pip 22.0.2 into unbounded backtracking.Root cause: Ubuntu 22.04 ships pip 22.0.2, whose resolver cannot handle the napari dependency graph against current PyPI. Verified by reproducing the same backtracking pattern locally with
pip==22.0.2(got stuck onnapari-svg,magicgui,npe2, etc. — exact same packages CI bounces on). Modern pip (23+) resolves the same dependency set in seconds.Changes
setup_22.04.sh. This is the actual fix.[all]extra fromnapari==0.5.4. The codebase only importsnapari.Viewerandnapari.utils.colormaps; PyQt5 is already installed via apt on line 28. The[all]extra additionally pulls innapari-plugin-managerand a redundant Qt backend, neither of which Squid uses. Reduces conflict surface as a secondary cleanup.Test plan
install-and-testjob completes in roughly the same ~14 min as it did pre-regressionpython3 main_hcs.py --simulationlaunches and the live / multi-channel / mosaic napari widgets work — sanity check that no plugin we silently relied on was in[all]Notes
The previous run on this branch (24947389105, with only
[all]removed) was still hanging in setup at 60+ min when I cancelled it — that confirmed dropping[all]alone wasn't enough, sincemagicgui/npe2/napari-svg/napari-console/napari-plugin-engineare core napari deps, not extras. The pip upgrade is what actually unblocks resolution.Long-term follow-up worth considering: commit a frozen
requirements.txtso the project is immune to transitive PyPI releases breaking installs.🤖 Generated with Claude Code