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Conda dependencies #332

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Dhananjhay
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This PR removes the equivolume logic from the laminar coordinate method, effectively eliminating hippunfold's dependency on the nighres package. This change serves as a stepping stone toward synchronizing and integrating hippunfold with the conda environment.

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@akhanf I've only removed equivolume as a choice from the config/snakebids.yml but I was wondering If I should clean the code-base more extensively. For example, I believe we no longer need scripts/equivolume_coords.py and scripts/pre_equivolume_coords.pyand the relevant logic in wraps.smk, common.smk and autotop.smk. Moreover, I can edit algorithms.md and pipeline.md to reflect that equivolume is no longer offered as a choice in laminar_coords_method.

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akhanf commented Dec 16, 2024

We haven't decided yet what route we will take so no need to clean up yet. But this should at least allow you to progress on the pure conda hippunfold

@jordandekraker jordandekraker changed the title Remove equivolume choice from laminar coordinate method Conda dependencies Dec 17, 2024
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