4 create docker imageinterface

[bendhouseart]

Adding docker support to this pipeline

[bendhouseart]

I would convert this to a draft, but that's a paid feature. Please don't merge this as it's not there just yet.

[bendhouseart]

Alright, seems to be running "mostly" fine. Running into an error with templateflow, see below.

Given the following command:

python run.py --bids_dir ~/Data/sharing/test2 --output_dir ~/Data/sharing/test2/derivatives/petprep_extract_tacs --wm --n_procs 6 --petprep_hmc --docker

Returns this:

240313-17:21:12,24 nipype.workflow INFO:
         [Node] Finished "convert_brainmask", elapsed time 0.44942s.
240313-17:21:12,34 nipype.workflow INFO:
         [Node] Finished "convert_brainmask", elapsed time 0.466654s.
240313-17:21:12,437 nipype.workflow INFO:
         [Node] Finished "convert_wm_seg_file", elapsed time 0.868988s.
240313-17:21:12,450 nipype.workflow INFO:
         [Node] Finished "convert_wm_seg_file", elapsed time 0.884125s.
240313-17:21:13,508 nipype.workflow ERROR:
         Node create_weighted_average_pet.a0 failed to run on host adb5e6912ae8.
240313-17:21:13,508 nipype.workflow ERROR:
         Saving crash info to /workdir/crash-20240313-172113-UID331122-create_weighted_average_pet.a0-5acdf884-9649-454c-86d7-02bfc1e9d09a.pklz
Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/usr/local/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/usr/local/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/usr/local/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node create_weighted_average_pet.

Traceback:
        Traceback (most recent call last):
          File "/usr/local/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 397, in run
            runtime = self._run_interface(runtime)
          File "/usr/local/lib/python3.9/site-packages/nipype/interfaces/utility/wrappers.py", line 142, in _run_interface
            out = function_handle(**args)
          File "<string>", line 4, in create_weighted_average_pet
          File "/usr/local/lib/python3.9/site-packages/niworkflows/interfaces/bids.py", line 52, in <module>
            import templateflow as tf
          File "/usr/local/lib/python3.9/site-packages/templateflow/__init__.py", line 18, in <module>
            from . import api
          File "/usr/local/lib/python3.9/site-packages/templateflow/api.py", line 8, in <module>
            from .conf import TF_LAYOUT, TF_S3_ROOT, TF_USE_DATALAD, requires_layout
          File "/usr/local/lib/python3.9/site-packages/templateflow/conf/__init__.py", line 53, in <module>
            _init_cache()
          File "/usr/local/lib/python3.9/site-packages/templateflow/conf/__init__.py", line 50, in _init_cache
            _update_s3(TF_HOME, local=True, overwrite=True)
          File "/usr/local/lib/python3.9/site-packages/templateflow/conf/_s3.py", line 19, in update
            retval = _update_skeleton(skel_file, dest, overwrite=overwrite, silent=silent)
          File "/usr/local/lib/python3.9/site-packages/templateflow/conf/_s3.py", line 54, in _update_skeleton
            zipref.extractall(str(dest))
          File "/usr/local/lib/python3.9/zipfile.py", line 1642, in extractall
            self._extract_member(zipinfo, path, pwd)
          File "/usr/local/lib/python3.9/zipfile.py", line 1692, in _extract_member
            os.mkdir(targetpath)
        FileExistsError: [Errno 17] File exists: '/.cache/templateflow/tpl-VALiDATe29'

Comment references commit a436604

[bendhouseart]

Fixed running in docker by switching over to a patched version of templateflow see fix -> templateflow/python-client#131

Trivial on the face of it, but took quite a while to track down and have the fix applied upstream at templateflow.