apptainer / singularity version requirement

[celstark]

Running your container in apptainer 1.3.4 is just fine. Running it in 1.2.5 (or older versions of singularity) gives the following:

apptainer --version
apptainer version 1.2.5-1.el9

apptainer exec code/dcm2bids_3.2.0.sif dcm2bids --help
Traceback (most recent call last):
  File "/venv/bin/dcm2bids", line 5, in <module>
    from dcm2bids.cli.dcm2bids import main
  File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1322, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1262, in _find_spec
  File "/venv/lib/python3.12/site-packages/__editable___dcm2bids_3_2_0_finder.py", line 20, in find_spec
    return cls._find_spec(fullname, Path(pkg_path))
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/venv/lib/python3.12/site-packages/__editable___dcm2bids_3_2_0_finder.py", line 38, in _find_spec
    if candidate.exists():
       ^^^^^^^^^^^^^^^^^^
  File "/venv/lib/python3.12/pathlib.py", line 860, in exists
    self.stat(follow_symlinks=follow_symlinks)
  File "/venv/lib/python3.12/pathlib.py", line 840, in stat
    return os.stat(self, follow_symlinks=follow_symlinks)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
PermissionError: [Errno 13] Permission denied: '/dcm2bids/dcm2bids/__init__.py'

The prior 3.1.0 though was fine:

apptainer exec code/dcm2bids_3.1.0.sif dcm2bids --help
usage: dcm2bids [-h] -d DICOM_DIR [DICOM_DIR ...] -p PARTICIPANT [-s SESSION] -c CONFIG [-o OUTPUT_DIR] [--auto_extract_entities] [--bids_validate]
                [--force_dcm2bids] [--skip_dcm2niix] [--clobber] [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-v]

Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure

options:
  -h, --help            show this help message and exit
...

Note, it does run in the newer apptainer:

apptainer --version
apptainer version 1.3.4-1.el9

apptainer exec code/dcm2bids_3.1.0.sif dcm2bids --help
usage: dcm2bids [-h] -d DICOM_DIR [DICOM_DIR ...] -p PARTICIPANT [-s SESSION] -c CONFIG [-o OUTPUT_DIR] [--auto_extract_entities] [--bids_validate]
                [--force_dcm2bids] [--skip_dcm2niix] [--clobber] [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-v]

Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure

options:
  -h, --help            show this help message and exit
...

[arnaudbore]

Thank you for the issue. I will check if I can make it work otherwise I will need to tell people to update apptainer.

[ColleenHughes]

Hi, I am seeing a similar error using apptainer 1.3.6 FYI. Python install works fine, which is fine for my purpose.

[collhugh@i65 cont_imgs]$ apptainer run dcm2bids_3.2.0.sif --help INFO: gocryptfs not found, will not be able to use gocryptfs Traceback (most recent call last): File "/venv/bin/dcm2bids", line 5, in <module> from dcm2bids.cli.dcm2bids import main File "<frozen importlib._bootstrap>", line 1360, in _find_and_load File "<frozen importlib._bootstrap>", line 1322, in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 1262, in _find_spec File "/venv/lib/python3.12/site-packages/__editable___dcm2bids_3_2_0_finder.py", line 20, in find_spec return cls._find_spec(fullname, Path(pkg_path)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/venv/lib/python3.12/site-packages/__editable___dcm2bids_3_2_0_finder.py", line 38, in _find_spec if candidate.exists(): ^^^^^^^^^^^^^^^^^^ File "/venv/lib/python3.12/pathlib.py", line 860, in exists self.stat(follow_symlinks=follow_symlinks) File "/venv/lib/python3.12/pathlib.py", line 840, in stat return os.stat(self, follow_symlinks=follow_symlinks) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ PermissionError: [Errno 13] Permission denied: '/dcm2bids/dcm2bids/__init__.py'

[SamGuay]

I have a simple hunch for this issue — can you try to run it with these flags?

apptainer run -e --containall --no-home dcm2bids_3.2.0.sif --help

The -e (--cleanenv) flag prevents host environment variables from leaking into the container, and --containall (and optionally --no-home, which avoids mounting your home directory) might be masking or conflicting with internal paths in the container vs your host.

I had this error once running another container and solved it this way so hopefully it will clear up the permission error!

https://unfmontreal.github.io/Dcm2Bids/3.2.0/how-to/container/ has the -e and --containall options specified so that might be a reason why we never encountered this issue in the past 🤔