Merge `bids2table` integration for BIDS ingress and RPool creation from main C-PAC repo#1

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sgiavasis wants to merge 321 commits intosgiavasis:developfrom

FCP-INDI:bids_ingress

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Commits on Sep 17, 2024

Commits on Sep 18, 2024

:alien: Import `Traversable` from `importlib.abc` for older Python compatibility
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:memo: Add bandpass header fix to CHANGELOG
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Commits on Sep 20, 2024

Merge branch 'develop' into 2144/type_error
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Commits on Sep 23, 2024

Commits on Oct 2, 2024

🐛 Dynamically capture 1D header (#2153)
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Commits on Oct 3, 2024

:heavy_plus_sign: orientation checks for resources added to PipeConfigs

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Update CPAC/pipeline/utils.py

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Update CPAC/pipeline/engine.py

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Update CPAC/pipeline/engine.py

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Update CPAC/pipeline/engine.py

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Update CPAC/pipeline/engine.py

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Update CPAC/pipeline/engine.py

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Update CPAC/pipeline/utils.py

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Update CPAC/pipeline/utils.py

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Update CPAC/pipeline/utils.py

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Update CPAC/pipeline/utils.py

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Update CPAC/pipeline/utils.py

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adding desired-orientation as a config key

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

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reorienting all files before rpool initialization
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[pre-commit.ci] auto fixes from pre-commit.com hooks

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moved orientation check and reorient if necessary to the wf
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[pre-commit.ci] auto fixes from pre-commit.com hooks

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renaming output name correctly
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handle for read-only template files
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adding reorient nodes in anat, func, freesurfer and template ingress nodes
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fix a typo in orientation flag for resample
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[pre-commit.ci] auto fixes from pre-commit.com hooks

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updating the orientation flag at other places where resolve_resolution is being used
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reverting adding reorient node at the very begining and passing orientation set in config in the existing nodes for reorientations
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[pre-commit.ci] auto fixes from pre-commit.com hooks

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empty
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updated tests
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updated the changelog
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replaced RPI to take in config value in few more places
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adding cfg as parameter in lesion_preproc
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sending only orientation not all cfg
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fixed positions of args in lesion_preproc and added default RPI
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Optimized cosine filter and added Doc strings
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reshaping removed in input array
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resolving conflict and resbase with develop

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nb changed to nib

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Optimized cosine filter and added Doc strings
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rebasing to develop
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fix duplicate commit
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added link to the algorithm
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Update CPAC/nuisance/utils/compcor.py

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corrected docs and implemented for different axis values

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moving remove_mean check out of the loop to avoid accidental overwriting of X
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correcting assignment of X as per selection of remove_mean

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Merge pull request #2091 from birajstha/optimize-cosine-filter
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Commits on Oct 11, 2024

Merge pull request #2155 from FCP-INDI/fix/S_parameter
sgiavasis
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Commits on Oct 14, 2024

Commits on Oct 21, 2024

:alembic: Test correlations with new SHA
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Commits on Nov 7, 2024

changing bold to desc-reorient_bold
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Commits on Nov 11, 2024

:bug: :alien: Patch `NetCorr._list_outputs`
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Commits on Nov 18, 2024

:pencil2: Fix "perged" typo in comment
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Commits on Nov 21, 2024

Merge pull request #2163 from FCP-INDI/ts_Z_corr
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Commits on Dec 5, 2024

Commits on Dec 11, 2024

➕ Reorient resources to set orientation in config (#2161)
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Commits on Jan 7, 2025

:children_crossing: Specify default in helpstring
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Commits on Jan 9, 2025

Commits on Jan 10, 2025

:twisted_rightwards_arrows: Merge remote-tracking branch 'origin/develop' into slurm/run-correlations
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Commits on Jan 15, 2025

:sparkles: Pick up more hard-coded resources
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:children_crossing: Increase indent before missing resource sources
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:bug: Restore outputs removed from "freesurfer_abcd_preproc" to "freesurfer_reconall"
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Commits on Feb 27, 2025

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:twisted_rightwards_arrows: Merge \`develop\` into \`slurm/run-correlations\`
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👽️ Update Dockerfile `LABEL`s re: deprecated `LegacyKeyValueFormat` (#2195)
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Commits on Mar 14, 2025

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Commits on Mar 20, 2025

Merge pull request #2194 from FCP-INDI/many_pipes
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Commits on Mar 21, 2025

Commits on Mar 26, 2025

:pencil2: Put `tj-actions/changed-files` in correct place in CHANGELOG
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Commits on Mar 28, 2025

removing TODO from config (#2201)
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Commits on Apr 2, 2025

🔧 Turn on XCP-QC by default in preconfigs (#2204)
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Commits on Apr 9, 2025

Merge pull request #2199 from FCP-INDI/fs_ingress_reorient
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Commits on Apr 10, 2025

Commits on Apr 12, 2025

:memo: Type-annotate `Outputs.reference`

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Commits on Apr 14, 2025

♻️ DRY up output key collection for group config (#2210)
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Commits on Apr 25, 2025

Commits on Apr 29, 2025

:bug: Fix `TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType'`
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Commits on Apr 30, 2025

🐛 Fix `TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType'` (#2229)
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