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Migrate cellfinder
into this package
#29
Conversation
This reconciles the two divergent histories of the old `brainglobe-scripts` and `cellfinder` (CLI tool).
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Looks good - think I need some minor clarifications to help me understand things better!
pyproject.toml
Outdated
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napari = ["napari[pyside2]", "brainglobe-napari-io", "cellfinder-napari<1.0.0"] |
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Probably also slightly out-of-scope for this PR but why do we ship a Qt backend for napari
here, and the non-default one at that?
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I'm not entirely sure - this seems to have been an artefact of cellfinder since before we moved to pyproject.toml
too: https://github.com/brainglobe/cellfinder/pull/247/files#
Looking at brainreg, we're shipping napari
with a backend (albeit Qt5) there too. As an experiment I'll change this to ship with Qt5 for consistency, but my answer to "why ship a backend" is an unsatisfactory appeal to tradition 😅
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Cool - Opened brainglobe/BrainGlobe#53 for this!
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I think we went with pyside2
due to some licensing issues, but TBH I think we're just ignoring that for now.
Don't we need to ship some back-end, otherwise there's an extra installation step for users?
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Don't we need to ship some back-end, otherwise there's an extra installation step for users?
Yeah if we don't ship a backend it'll be an extra step.
Although this might mean that we're inadvertently overwriting their backend choice, if they have one installed already. EG If they have pyside installed and we then force-install napari[pyqt5], I'm not sure what that'll do to their env/machine
@alessandrofelder Have addressed the things you raised - thanks for catching them! For the napari backend, I've set to using
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Tiny suggestion, otherwise 👍
Co-authored-by: Alessandro Felder <[email protected]>
See brainglobe/BrainGlobe#45
Moves the existing
cellfinder
workflow into this package. Also then restructures the repository so that we can package the workflows without packaging the benchmarks and test data, to avoid users obtaining a bloated install.To the reviewer:
Key info to check is in the README and pyproject. The remaining 6000-lines or so are just the new inclusion of what is currently in the
cellfinder
package.On Merge:
brainglobe-workflows
version 1TODO List:
cellfinder
CLI tool and give it a temporarycellfinder
aliascellfinder
problem)Move Docker API secrets into this repo to allow for deployment (if we still want this?)Purge Docker images