merge dev into stable for new release #572
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Adding periods and underscores to the package_pattern to allow Python packages with those characters (allowable in pypi) to be added to environment YAMLs
Remaining rst files added, README.md file split Fixing label duplication warnings and other warnings Requested changes applied pyproject.toml and doc.yml file added to trigger sphinx workflow Added all READMD.md files
fix optional dependencies
Add myst parser
add sklearn, skimage, torchvision in pyproject.toml
Fix all warm import
Remove Executor as a parent to serial executor.
Consistently introduce the Plane Type to FastSurferCNN.utils Some formatting fixes across multiple files fix extract_recon_surf_time_info.py
Remove Executor from `__all__`
Revert inheritance
replace .A and .A1 with explicit array conversion
fix things for Mac and MPS
Because allow_root is always set to False, root is not compatible with computing stats for hypvinn. This changes root to True, which is suboptimal, but fine. This is only a check in segstats and it is also already checked in run_prediction before (so this is redundant).
BUG: --allow_root does not work for segstats module in hypvinn.
… FastSurfer does not detect it there. Add Code to run_fastsurfer, that detects the license from FREESURFER_HOME. Also add an environment variable to deactivate this search from inside a container.
The FreeSurfer license is often in the FREESURFER_HOME directory, but FastSurfer does not detect it there.
The doc workflow deployed to the root folder of gh_pages, not to dev or stable subdirectories. This PR fixes the subdirectory the action pushes to by fixing the github-event variable (github.ref_name instead of github.event.ref_name).
Fix the target directory of the doc workflow
Add rocm as a valid device option to build.py fix typo install_env.py for rocm remove extra } in export_pip-r.sh Fix Docker build for cuda 11.8 Add weights_only=True for torch.load to clean up torch warnings. Fix delim_whitespace warning in data_utils.py Fix AMD ROCm documentation.
The SUBJECTS_DIR/IMAGE_ID/scripts/build.log file currently only contains the information "specifically requested", which on principle only is the version number. This commit fixes the parameters to the version script, so build.log contains the expected information such as python packages, model checkpoints and git status.
Fix content of buildlog file
removing isort and black in favour of ruff
export requirements.txt and requirements.cpu.txt from respective docker images
update versions of python packages
Fix the run time calculation (rounded to integer hours in log file)
Fixes error introduced in 2f350e9
Fix the run time calculation (rounded to integer hours in log file)
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