Cannot use totalspineseg in singularity anymore

[lchauvin]

Hello,

Since recently (few days / weeks ago), I cannot use totalspineseg in a singularity image.

I installed totalspineseg using pip in the singularity image like this, in a requirement file:

totalspineseg[neuropoly]

and in the image definition file:

${SCT_DIR}/bin/sct_deepseg totalspineseg -install

I believe it was still working few days ago, but now I have this error:

File "/opt/sct/sct_wrapper.py", line 1923, in segment_vertebrae
  sct_deepseg.main(['totalspineseg', '-i', in_image, '-o', os.path.join(totalspineseg_dir, 'out.nii.gz'),
File "/opt/sct/spinalcordtoolbox/scripts/sct_deepseg.py", line 489, in main
  im_lst, target_lst = inference.segment_non_ivadomed(
File "/opt/sct/spinalcordtoolbox/deepseg/inference.py", line 137, in segment_non_ivadomed
  fnames_out, targets = inference(path_img=fname_in, tmpdir=tmpdir, predictor=net, device=device, **extra_inference_kwargs)
File "/opt/sct/spinalcordtoolbox/deepseg/inference.py", line 411, in segment_totalspineseg
  tss_inference(
File "/opt/sct/python/envs/venv_sct/lib/python3.10/site-packages/totalspineseg/inference.py", line 446, in inference
  add_trainer("nnUNetTrainerDAExt")
File "/opt/sct/python/envs/venv_sct/lib/python3.10/site-packages/auglab/add_trainer.py", line 45, in add_trainer
  shutil.copy(source_trainer, output_path)
File "/opt/sct/python/envs/venv_sct/lib/python3.10/shutil.py", line 417, in copy
  copyfile(src, dst, follow_symlinks=follow_symlinks)
File "/opt/sct/python/envs/venv_sct/lib/python3.10/shutil.py", line 256, in copyfile
  with open(dst, 'wb') as fdst:
OSError: [Errno 30] Read-only file system: '/opt/sct/python/envs/venv_sct/lib/python3.10/site-packages/nnunetv2/training/nnUNetTrainer/nnUNetTrainerDAExt.py'

It seems the code try to copy some files inside the package, but after building the singularity image, this is a read-only directory.

Thanks.

[NathanMolinier]

related to spinalcordtoolbox/spinalcordtoolbox#5121

I will work on a fix as soon as possible !

[NathanMolinier]

Hello @lchauvin ! Thanks again for reporting this issue. I just updated Auglab's code to not copy if the path already exists. Could you rebuild your container following these steps:

1. Install your packages normally
2. Run the command auglab_add_nnunettrainer -t nnUNetTrainerDAExt when building your container
3. Once built retry your command.

Also, I noticed that you are using totalspineseg as the task name. Just to let you know, in a more recent version of SCT the task was renamed spine and the default execution only runs the first step of totalspineseg (see https://spinalcordtoolbox.com/stable/user_section/command-line/deepseg/spine.html)