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Adopt Nipreps-style Config object #1040

Merged
merged 128 commits into from
Mar 22, 2024
Merged

Adopt Nipreps-style Config object #1040

merged 128 commits into from
Mar 22, 2024

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tsalo
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@tsalo tsalo commented Jan 22, 2024 •
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Closes #816, closes #734.

Changes proposed in this pull request

  • Consolidate shared parameters in a Config object.
  • Consolidate skip_<integration-test-name> shortcuts into skip_integration.
  • Add several BIDS App-related parameters:
    • --write-graph
    • --boilerplate-only
    • --debug
    • --md-only-boilerplate
    • --reports-only
    • --low-mem: Not sure if this works.
    • --config-file

Documentation that should be reviewed

@tsalo tsalo mentioned this pull request Jan 22, 2024
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tsalo and others added 28 commits March 12, 2024 11:15
@tsalo
Merge branch 'main' into nipreps-config-2
b7809ca
@tsalo
Merge remote-tracking branch 'upstream/main' into nipreps-config-2
644e783
@tsalo
Fix output directory for atlases.
099be6d
@tsalo
Merge remote-tracking branch 'upstream/main' into nipreps-config-2
dad2387
@tsalo
Merge remote-tracking branch 'upstream/main' into nipreps-config-2
1fa6c4d
@tsalo
Update test_workflows_connectivity.py
597428d
@tsalo
Update test_workflows_connectivity.py
74fb2a3
@tsalo
Merge remote-tracking branch 'upstream/main' into nipreps-config-2
007c3df
@tsalo
Reproduce PennLINC#1086.
4e57106
@tsalo
Minor change.
6b79d6e
@tsalo
Merge branch 'main' into nipreps-config-2
2a181bf
@tsalo
Merge remote-tracking branch 'upstream/main' into nipreps-config-2
a416591
@tsalo
Update run.py
46d07d1
@tsalo
Reimplement PennLINC#1096.
33fb1d1
@tsalo
Run isort.
d69e3a7
@tsalo
Merge remote-tracking branch 'upstream/main' into nipreps-config-2
069ee24
@tsalo
Fix paths.
3ed828a
@tsalo
Update expected outputs.
09627fa
@tsalo
Merge remote-tracking branch 'upstream/main' into nipreps-config-2
c6f6e63
@tsalo
Update test_cli.py
09fc3bd
@tsalo
Update utils.py
caf59e1
@tsalo
Drop the trailing xcp_d.
dd035df
@tsalo
Merge remote-tracking branch 'upstream/main' into nipreps-config-2
5f38407
@tsalo
Update parser.py
6b1a446
@tsalo
Merge branch 'main' into nipreps-config-2
41f3773
@tsalo
Merge remote-tracking branch 'upstream/main' into nipreps-config-2
ff3ef07
@tsalo
Merge remote-tracking branch 'upstream/main' into nipreps-config-2
e6a0d6a
@tsalo
Move atlases and custom_confounds to execution.
abd7589
@tsalo tsalo merged commit fe8e22e into PennLINC:main Mar 22, 2024
19 of 20 checks passed
@tsalo tsalo deleted the nipreps-config-2 branch March 22, 2024 21:26
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@mattcieslak mattcieslak Awaiting requested review from mattcieslak

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Adopt configuration approach from nipreps tools Add --config-file option
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@tsalo