Draft pre-init ingression

tsalo commented 3 months ago

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

Changes proposed in this pull request

Documentation that should be reviewed

tsalo commented 3 months ago

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 commented 3 months ago

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 commented 3 months ago

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 :warning:
qsirecon/workflows/base.py	0.00%	13 Missing :warning:
qsirecon/workflows/recon/anatomical.py	0.00%	1 Missing :warning:

Additional details and impacted files

```diff @@ 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](https://app.codecov.io/gh/PennLINC/qsirecon/pull/102/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=PennLINC) | Coverage Δ | | |---|---|---| | [](https://app.codecov.io/gh/PennLINC/qsirecon/pull/102/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=PennLINC) | `33.74% <20.00%> (?)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=PennLINC#carryforward-flags-in-the-pull-request-comment) to find out more.

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tsalo commented 3 months ago

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

PennLINC / qsirecon