Draft pre-init ingression

[tsalo]

Just a template for integrating @smeisler's ingression package.

Changes proposed in this pull request

Documentation that should be reviewed

[tsalo]

The conflict is caused by:
    qsirecon 0.1.dev50+gfb6bacf depends on nibabel<=5.2.0
    ingress2qsirecon 0.1.0 depends on nibabel<6.0.0 and >=5.2.1

The conflict is caused by:
    qsirecon 0.1.dev679+g60e4cea.d20240830 depends on nilearn==0.10.1
    ingress2qsirecon 0.1.0 depends on nilearn<0.11.0 and >=0.10.4

[smeisler]

None of my versions pinned for ingress2qsirecon are strictly necessary, so if it would be easier for you if I change it to match qsiprep/recon, let me know.

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 20.00000% with 32 lines in your changes missing coverage. Please review.

Project coverage is 33.74%. Comparing base (361e27f) to head (69f3fd7).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
qsirecon/cli/parser.py	25.00%	15 Missing and 3 partials ⚠️
qsirecon/workflows/base.py	0.00%	13 Missing ⚠️
qsirecon/workflows/recon/anatomical.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #102      +/-   ##
==========================================
+ Coverage   33.68%   33.74%   +0.05%     
==========================================
  Files          56       56              
  Lines        6937     6855      -82     
  Branches      910      901       -9     
==========================================
- Hits         2337     2313      -24     
+ Misses       4496     4437      -59     
- Partials      104      105       +1     

Flag	Coverage Δ
	33.74% <20.00%> (?)

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[tsalo]

Now that tests are passing, @smeisler do you want to take over this PR and add any tests you might want?

[mattcieslak]

A few minor questions, but I think this looks great

[mattcieslak]

great idea to add this to the docs

[mattcieslak]

Is there a need to unpin this one?

[smeisler]

ah this was a holdout from some dependency differences between qsirecon and i2q, we should be able to pin it

[smeisler]

done in last commit

[mattcieslak]

could you switch this to use pathlib instead of op? I think we're going to try to consistently use it to be in line with nipreps

[smeisler]

Think I changed this, untested so far:

if config.workflow.input_type in ("hcpya", "ukb"):
        import shutil

        from ingress2qsirecon.data import load_resource
        from ingress2qsirecon.utils.functions import create_layout
        from ingress2qsirecon.utils.workflows import create_ingress2qsirecon_wf

        # Fake BIDS directory to be created
        config.execution.bids_dir = work_dir / "bids"

        # Make fake BIDS files
        bids_scaffold = load_resource("bids_scaffold")
        if not (config.execution.bids_dir / "dataset_description.json").exists():
            shutil.copytree(
                bids_scaffold,
                config.execution.bids_dir,
                dirs_exist_ok=True,
            )

[mattcieslak]

Excellent!