🐛 Bugfixes for many pipelines project #2194

shnizzedy · 2025-03-06T20:52:35Z

Fixes

Fixes all the issues documented in many_pipelines dashboard by @tamsinrogers

Description

These fixes were merged to a separate "many_pipes" development branch; this PR brings them back into the develop branch.

We probably want to wait until that last issue is resolved before we merge?

Checklist

My pull request has a descriptive title (not a vague title like Update index.md).
My pull request targets the develop branch of the repository.
My commit messages follow best practices.
My code follows the established code style of the repository.
I added tests for the changes I made (if applicable).
I updated the changelog.
I added or updated documentation (if applicable).
I tried running the project locally and verified that there are no visible errors.

Developer Certificate of Origin

Developer Certificate of Origin
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Suite D4700
San Francisco, CA, 94129

Everyone is permitted to copy and distribute verbatim copies of this
license document, but changing it is not allowed.


Developer's Certificate of Origin 1.1

By making a contribution to this project, I certify that:

(a) The contribution was created in whole or in part by me and I
    have the right to submit it under the open source license
    indicated in the file; or

(b) The contribution is based upon previous work that, to the best
    of my knowledge, is covered under an appropriate open source
    license and I have the right under that license to submit that
    work with modifications, whether created in whole or in part
    by me, under the same open source license (unless I am
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    in the file; or

(c) The contribution was provided directly to me by some other
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✨Allow FS ingress from command line

…res-bold_desc-brain_T1w if needed

This reverts commit fa8d481.

…emplate_res-bold_desc-brain_T1w if needed" This reverts commit 68e3c41.

…rm_timeseries_to_T1template_abcd if resource space-template_res-bold_desc-brain_T1w is missing

…m bold_mask_anatomical_resampled as two separate sub worflows that can be reused

Fix missing resource `space-template_res-bold_desc-brain_T1w`

…n nodeblock

…istration nodeblock" This reverts commit a2f8d23.

…of T1w mask

… bold/mask mismatch issue

…ackmerge Squashed commit of the following: commit 9ea9b068c316de0fd2f945b18faa766f95adfa19 Author: Jon Clucas <[email protected]> Date: Mon Nov 4 21:57:33 2024 -0500 🚚 Move entrypoint scripts into CPAC/_entrypoints Ref 38a0d10

…to 'many_pipelines'

…ipelines'

🐛 Patch `NetCorr._list_outputs`

Co-authored-by: Jon Cluce <[email protected]>

for more information, see https://pre-commit.ci

shnizzedy · 2025-03-10T19:20:31Z

Idk if we care to include #2171 and #2172 in this release, but if we do, it's probably easier to merge in one of these sequences:

or

Co-authored-by: Jon Cluce <[email protected]>

✨ Inventory Resources

… container

Overwrite transform

🚸 Add where-to-find information to missing resource nodeblock connection errors

sgiavasis

Basically everything we already approved.
Will need to look for merge errors to be safe.

e-kenneally and others added 30 commits March 26, 2024 17:15

Make command line option for fs ingress

924ecef

Make filename parsing more generalizable

d433513

Change reg workflow to produce consistent outputs

20572de

Merge pull request #2095 from FCP-INDI/feature/fs-ingress-cmdline

4d26732

✨Allow FS ingress from command line

Remove restore-brain option from pipeline config

9f81479

Modified warp_timeseries_to_T1template_abcd to create space-template_…

68e3c41

…res-bold_desc-brain_T1w if needed

Remove coregistration -> reference option

03a503c

added bold_mask to the list of nodeblock outputs

fa8d481

Revert "added bold_mask to the list of nodeblock outputs"

d68a733

This reverts commit fa8d481.

Revert "Modified warp_timeseries_to_T1template_abcd to create space-t…

4239a5f

…emplate_res-bold_desc-brain_T1w if needed" This reverts commit 68e3c41.

🐛 Fix bug in fs ingress commandline

72f24bc

appending the nodeblock bold_mask_anatomical_resampled inside transfo…

4818a20

…rm_timeseries_to_T1template_abcd if resource space-template_res-bold_desc-brain_T1w is missing

Abstracted anat_brain_to_bold_res and anat_brain_mask_to_bold_res fro…

c493e80

…m bold_mask_anatomical_resampled as two separate sub worflows that can be reused

Merge pull request #2096 from FCP-INDI/fix_flo_issues

436d8fa

Fix missing resource `space-template_res-bold_desc-brain_T1w`

added template space warped mask as an output in the ANTs Registratio…

a2f8d23

…n nodeblock

Edited ANTs registration to output the template mask file as well

5ca3a1b

Revert "added template space warped mask as an output in the ANTs Reg…

cc285fd

…istration nodeblock" This reverts commit a2f8d23.

changed bold_mask_anatomical_resampled to take in brain_mask instead …

66894a4

…of T1w mask

input bold data to node swapped with reorient-bold to resolve RAI/RPI…

dc41bf4

… bold/mask mismatch issue

🚨 Lint in preparation for merge from

5d6a9ca

🔀 Merge unrelated changes from branch 'feature/check_orientations' in…

d28aa5f

…to 'many_pipelines'

🔀 Merge changes from branch 'feature/check_orientations' into 'many_p…

dc5663c

…ipelines'

adding f to f-string fixing typo

590b437

changing bold to desc-reorient_bold

043a004

🐛 👽 Patch NetCorr._list_outputs

c725a9d

✏️ Fix "perged" typo in comment

f1dac0c

Merge pull request #2163 from FCP-INDI/ts_Z_corr

12bc033

🐛 Patch `NetCorr._list_outputs`

➕ Reorient resources to set orientation in config (#2161)

5f20500

✨ Add inventory utility

be61d7f

birajstha and others added 9 commits March 6, 2025 17:46

Update CPAC/pipeline/schema.py

a8adeb4

Co-authored-by: Jon Cluce <[email protected]>

Update CPAC/pipeline/test/test_schema_validation.py

8cf804f

Co-authored-by: Jon Cluce <[email protected]>

Update CPAC/registration/registration.py

8c4a7af

Co-authored-by: Jon Cluce <[email protected]>

Update CPAC/registration/registration.py

76bd2ae

Co-authored-by: Jon Cluce <[email protected]>

[pre-commit.ci] auto fixes from pre-commit.com hooks

ba2cff4

for more information, see https://pre-commit.ci

revert back adding error handler dir

82e5b93

adding to changelog

22f3a86

fixing test for overwrite trasnsform

a91c854

fixing test for overwrite trasnsform

01cc822

birajstha and others added 13 commits March 10, 2025 22:14

Update CPAC/pipeline/schema.py

2388a1b

Co-authored-by: Jon Cluce <[email protected]>

Update CPAC/pipeline/test/test_schema_validation.py

9396a0c

Co-authored-by: Jon Cluce <[email protected]>

Merge branch 'many_pipes' into inventory_error_message

74da7d9

Merge pull request #2171 from FCP-INDI/resource_inventory

0877614

✨ Inventory Resources

Merge branch 'many_pipes' into inventory_error_message

75e3d5c

Merge branch 'many_pipes' into overwrite_transform

996a7be

👷 🔊 Log git config --global url

77f4769

👷 🐳 🔧 🔒 Don't force SSH when git cloneing test data in test image…

740ad1d

… container

🔀 Merge branch 'CVE-2023-51664' into inventory_error_message

df2a841

🚚 Move global fixtures to own file

30dfc6f

✅ Adjust paths for updated test

766bfd4

Merge pull request #2190 from FCP-INDI/overwrite_transform

0e954fd

Overwrite transform

Merge branch 'develop' into many_pipes

36678a7

birajstha approved these changes Mar 17, 2025

View reviewed changes

Merge pull request #2172 from FCP-INDI/inventory_error_message

7438a7c

🚸 Add where-to-find information to missing resource nodeblock connection errors

sgiavasis approved these changes Mar 18, 2025

View reviewed changes

Merge branch 'develop' into many_pipes

c203faf

sgiavasis merged commit dc500a6 into develop Mar 20, 2025
24 checks passed

github-project-automation bot moved this to ✅ Done in C-PAC Development Mar 20, 2025

shnizzedy mentioned this pull request May 9, 2025

👔🔧 Add "organism" to pipeline config #2230

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🐛 Bugfixes for many pipelines project #2194

🐛 Bugfixes for many pipelines project #2194

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shnizzedy commented Mar 6, 2025

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🐛 Bugfixes for many pipelines project #2194

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shnizzedy commented Mar 6, 2025

Fixes

Description

Checklist

Developer Certificate of Origin

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shnizzedy commented Mar 10, 2025

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