Remove freesurfer dependencies and add tests#29

Merged

m-reuter merged 46 commits intomainfrom remove-freesurfer

Sep 4, 2024

+585-157

Commits on Sep 4, 2024

Added dependencies

kdiers
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m-reuter
committed
Removed FreeSurfer checks, shell commands

kdiers
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m-reuter
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Removed mri_binarize, mri_mc, mris_convert

kdiers
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Removed mri_pretess, currently without replacement

kdiers
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BrainPrint Pytests

engrosamaali91
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resolving errors

engrosamaali91
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fixing errors

engrosamaali91
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fixing errors again

engrosamaali91
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fixing errors

engrosamaali91
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resolving errors

engrosamaali91
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fixing line lenght error

engrosamaali91
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Isort and formatted

engrosamaali91
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Black run

engrosamaali91
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spell correction

engrosamaali91
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Modified relative paths and test files copied to utils/tests directory

engrosamaali91
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black run

engrosamaali91
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Removed duplicate test files

kdiers
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Convert Path to str

kdiers
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Formatting

kdiers
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Revised tests

kdiers
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Fixed typo

kdiers
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Added transform to surface RAS

kdiers
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Added keeping largest component, removing free vertices

kdiers
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Updated dummy test for create_aseg_surfaces

kdiers
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Formatting

kdiers
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Black formatting

kdiers
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Isort formatting

kdiers
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Ruff formatting

kdiers
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Changed marching cube algorithm to Lorensen

kdiers
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Removed ventricles, striatum; merged cerebellum cortex and cerebellum white matter

kdiers
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adding local runner functionality to pytest workflow

taha-abdullah
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adding a new test to check for file existence in brainprint output

taha-abdullah
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isort and black changes

taha-abdullah
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Removed uuid in filenames; formatting

kdiers
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Updated README

kdiers
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Removed local tests

kdiers
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Formatting

kdiers
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Removed deprecated structures

kdiers
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Updated pytest workflow

kdiers
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m-reuter
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Updated pytest workflow

kdiers
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m-reuter
committed
Updated pytest workflow

kdiers
authored and
m-reuter
committed
Updated pytest workflow

kdiers
authored and
m-reuter
committed
Updated pytest workflow

kdiers
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m-reuter
committed
Black / ruff formatting

kdiers
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m-reuter
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fix line too long and unused var in loop
m-reuter
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run test on all PR and pushes to main, also use latest lapy release
m-reuter
committed