shnizzedy / cpac

A Python package that wraps C-PAC, enabling users to install `cpac` with `pip install cpac` and run from the command line.

How to work with Jon^※

My work hours

I strive to maintain a healthy work-life balance. We also recently (2023 April) had a baby. In service of that effort, for my primary employment I try to be available 20 hours per week, around the babe's schedule.

What’s the best way to communicate with me?

I'm a bit hard of hearing and a bit of a stutterer, so I prefer written to spoken communication. I check the following in order of frequency:

1. CMI-CNL Slack
2. text messages
3. work (@childmind.org) email
4. GitHub issues
5. other Slack workspaces
6. Brainhack Mattermost
7. personal (@vasegurt.com) email

If I don’t respond, try:

1. ^※
2. reaching out to someone else relevant to the question / project
3. sending me a reminder

What makes me grumpy?

Demands for action combined with unwillingness to explain the target of said action.

^※

How do I like to give feedback?

Timely, constructively, and specifically.

How do I like to receive feedback?

Specifically, action-oriented, and visually.

One of my goals for the coming year

I hope to carve out enough time to help my friend Dr. Bu realize his design for the *Comics History Index*.

Topics I’m always happy to talk about

Art, particularly music, literature, and film.

Other things you might want to know

• My favorite baked good — pie
• Spouses/partners/kiddos/pets — one spouse
• Fruit on pizza — yes, especially jalapeño + pineapple ^※
• My coffee order — decaf café au lait

Some badges 📛

This work^※ is licensed under a Creative Commons Attribution-ShareAlike 2.5 Generic License.

cpac's Issues

✨ Add `crash` command

View Crash Files

✨ Add util to read crashfiles

Ref Re: Nuisance regression error on singularity:

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

nipypecli crash [CRASHFILE]

🥒 Automatically touch paths that Nipype crashfiles expect

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.

📚 Clarify / emphasize automatic binding

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.

✨ Add `enter` command

to enter container

🔬 Add unit tests for Singularity

🐛 `--pipeline_override`s are not parsing correctly

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'

📚 Flesh out documentation

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

🐳 For some crashfiles, Singularity will load them but Docker will not

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):

[…]

✨ Add `pull` command

To pull Docker / Singularity image without running

🕵️ Investigate whether `output_dir` is used anywhere other than `run`

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

🔨 Bind directory for `--pipeline_file`

🏭 Automate necessary bindings

📛 Name this package (for clarity on GitHub and PyPI)

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)

🏁 Windows: `pwd` not available

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.

✨Ⓢ Add support for Singularity

This initial version only works with Docker images.

Related: FCP-INDI/theodore#4

Ⓢ Add support for Singularity ≥ v3.0

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.

📛🚜 Update source repo links

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

⚙️ Set up default and customizable config files

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

✨ Add support for utils

Ref ae9c419

🖥️ `-B` as the last flag before the C-PAC command throws off the parsing

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

✨ Add `group` command

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

🛠️ Build configuration errors

1. Python ModuleNotFoundError: No module named 'yaml'

2. BASH $ cpac --version cpac unknown