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* Overhaul the thalamus into steps, and add docs Load thalamus meshes from CLI input, clean CLI * Improve Blender instructions * Change thalamus region list regex This updates the regular expression used for thalamus placement-hints to be in a different format that has been tested successfully, excludes habenular and peripeduncular subregions, and to be valid for the hierarchy/annotation used at its appropriate step in the Atlas pipeline. For information on which regions were chosen and this list was created, see the internal BBP Confluence page located at "Circuits > Mouse Thalamus > Atlas-based Whole-thalamus subregion selection". This regex has been built from the region list of the desired and present thalamus regions as of the "final" version of the hierarchy and annotation built by the Atlas pipeline, which is the output of the rule `split_barrel_ccfv3_l23split`. This change is meant to go in tandem with BlueBrain/atlas-direction-vectors#27 . * Update layer names to be Atlas-Pipeline-compatible * Fix formatting errors * Attempt to update tests for new thal workflow * Replace part of test anno with region in metadata * fix test + format * format * Fix final linting issues This does a lot of small things for passing the linting. For mypy, I had to add additional ignores for the Trimesh returned types, since the ignore on the module as a whole wasn't preventing mypy from expecting `load_mesh` to return a Geometry object, which is a grandparent of Trimesh objects. I don't know if Trimesh changed their API, I couldn't figure it out from the docs, and I don't know why mypy was raising this now. In all the cases I could test or see, a proper "Trimesh" object was returned instead of the more generic Geometry. I don't think we need to worry about this. For the pylint disable W0613 (unused-argument), I needed some polymorphism for the thalamus case, but I wasn't sure how to handle that alongside the linters' type-checking. I think this is the simplest solution and is harmless. Everything else is minor. * Make Alexis changes to CLI * Apply MG code review changes --------- Co-authored-by: Austin E. Soplata <[email protected]> Co-authored-by: arnaudon <[email protected]>
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