shnizzedy / cpac Goto Github PK

Describe the bug
Running cpac --platform docker crash $CRASHFILE vs cpac --platform singularity crash $CRASHFILE:

Docker:

TypeError: sequence item 1: expected str instance, NoneType found

Singularity:

Nipype version 1.1.2
Traceback (most recent call last):

[…]

1. Python ModuleNotFoundError: No module named 'yaml'

2. BASH $ cpac --version cpac unknown

to enter container

To reduce the amount of per-run typing / configuring required

The documentation and comments are pretty bare-bones as of 1ed5370.

To pull Docker / Singularity image without running

Once this repository moves to /FCP-INDI, we'll need to update the internal links to the source repository:

https://github.com/shnizzedy/cpac-python-package/blob/1ed5370015faff7134706d39e1074830e200c076/setup.cfg#L11

https://github.com/shnizzedy/cpac-python-package/blob/93443379aef9e941a14b0f0f183c4325261310a6/README.rst#L21-L28

https://github.com/FCP-INDI/C-PAC/blob/66c5695b2e8dae46361d2ffb532fb52144f393a5/CPAC/__main__.py#L130-L165

v0.2.2 enables Singularity ≥ 2.5.0, but Singularity 3.0 is sufficiently different from Singularity 2 that this package does not yet work with Singularity 3.

Example:

cpac run s3://fcp-indi/data/Projects/ADHD200/RawDataBIDS ~/outputs_p test_config --pipeline_file ~/pipelinecarbs2.yml --pipeline_override="maxCoresPerParticipant : 6"

error: argument --pipeline_override: Invalid configuration: 'maxCoresPerParticipant'

You can pass more than one custom binding, so instead of running, for example, it'll try to bind ./run:./run

The main pain point I was trying to resolve with this package is having to repeat yourself with binding directories and using the directories in the command; the wrapper should bind any directories you need from the command + your data config file without you having to tell it to.

The documentation should make this feature clearer / more prominent.

Ref ae9c419

If it's not, we could drop the optional argument since it'll get overwritten by the positional argument anyway.

This initial version only works with Docker images.

Related: FCP-INDI/theodore#4

pwd is not available on Windows, so

https://github.com/shnizzedy/cpac-python-package/blob/9c3dcd6a2102b49fc7014a50a8043d7e4c97485b/src/cpac/backends/platform.py#L59

won't work on Windows.

I changed the name in https://github.com/shnizzedy/cpac-python-package/blob/1ed5370015faff7134706d39e1074830e200c076/setup.cfg#L6

from cpac to cpac_py when I was testing the packaging for PyPI since CPAC was already taken on test PyPI (@sgiavasis, I since noticed you own CPAC on test PyPI, and the project cpac doesn't exist yet on real PyPI, so if we want to call it cpac, we certainly can)

Errors like

• …instance must be a pathlike object…

traits.trait_errors.TraitError: The 'in_file' trait of a SkullStripInputSpec instance must be a pathlike object or string representing an existing file, but a value of '/outputs/working/resting_preproc_sub-0010002_ses-1/anat_preproc_afni_0/anat_skullstrip/sub-0010002_ses-1_run-1_T1w_resample.nii.gz' <class 'str'> was specified.

• …instance must be a list of items which are an existing file name…

traits.trait_errors.TraitError: The 'transforms' trait of an ApplyTransformsInputSpec instance must be a list of items which are an existing file name or 'identity', but a value of ['/out/working/resting_preproc_sub-PA265_sub-PA265/anat_mni_ants_register_0/calc_ants_warp/transform3Warp.nii.gz', '/out/working/resting_preproc_sub-PA265_sub-PA265/anat_mni_ants_register_0/calc_ants_warp/transform2Affine.mat', '/out/working/resting_preproc_sub-PA265_sub-PA265/anat_mni_ants_register_0/calc_ants_warp/transform1Rigid.mat', '/out/working/resting_preproc_sub-PA265_sub-PA265/anat_mni_ants_register_0/calc_ants_warp/transform0DerivedInitialMovingTranslation.mat', '/out/working/resting_preproc_sub-PA265_sub-PA265/_scan_rest/change_transform_type_0/updated_affine.txt'] <class 'list'> was specified.

occur when the environment loading a crashfile in an environment that differs from the environment in which the file was pickled. Just touching those is enough for those types of error to resolve and produce an output more useful for debugging.

View Crash Files

Ref Re: Nuisance regression error on singularity:

We needed nipype 1.1.2 loaded, and to view the file:

nipypecli crash [CRASHFILE]