🔀 Backmerge sgiavasis/C-PAC-1#2 to `bids_ingress` branch for sgiavasis/C-PAC-1#1 - #2142

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shnizzedy wants to merge 106 commits into

bids_ingressfrom

backmerge/resourcepool-split

Commits on Jun 5, 2024

implementing bids2table for anat data configuration
Biraj Shrestha
committed
34e7bed

Commits on Jun 6, 2024

building rpool
Biraj Shrestha
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c8295e0

Commits on Jun 12, 2024

refactoring the rpool object to have subfields for easy browsing of resource

Biraj Shrestha
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Biraj Shrestha
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5ca4fb7

Commits on Jun 14, 2024

removing unused keys from the rpool

Biraj Shrestha
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Biraj Shrestha
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d8300d5

Commits on Jun 27, 2024

Introduced resource object in the rpool.

Biraj Shrestha
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Biraj Shrestha
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f3a6d4f
Added method write_to_disk(path) to the ResourcePool and Resource class.

Biraj Shrestha
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Biraj Shrestha
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a853fc9
Merge pull request #2125 from birajstha/bids_ingress
birajstha
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ee092d6
added sub- and ses- in the relative paths

Biraj Shrestha
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Biraj Shrestha
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b1bbc36
Merge pull request #2126 from birajstha/bids_ingress
birajstha
authored
4aab3f7
only write .json files to .nii.gz image files

Biraj Shrestha
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Biraj Shrestha
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e85550d
Merge pull request #2127 from birajstha/bids_ingress
birajstha
authored
2ca9598

Commits on Jul 8, 2024

Commits on Jul 9, 2024

:white_check_mark: Move BIDS examples to a fixture
shnizzedy
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06612ff

Commits on Jul 10, 2024

Commits on Jul 11, 2024

Merge 'origin/develop' into bids_ingress
e-kenneally
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f55b930
:recycle: EmptyConfiguration → Preconfiguration('blank')
shnizzedy
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515b791
:pencil2: Import Path for signature
shnizzedy
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3c2220d
:recycle: Pass `part_id` through to `DataPaths`
shnizzedy
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8a24441
:white_check_mark: Skip NHP configs if no torch installed
shnizzedy
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87fb1c0
:white_check_mark: Use abspath for BIDS-examples
shnizzedy
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3af1407
fix merge error
e-kenneally
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29cab04
:construction: :recycle: Continue updating calls to `ResourcePool` methods
shnizzedy
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98c8bb8
:construction: WIP :recycle: Fix `StratPool.__init__`
shnizzedy
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4d9934d

Commits on Jul 12, 2024

:art: :technologist: Clarify typing
shnizzedy
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1cc3914
:white_check_mark: `pytest.Cache.makedir` → `pytest.Cache.mkdir`
shnizzedy
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199bd60

Commits on Jul 13, 2024

Commits on Jul 15, 2024

:bug: Fix circular import
shnizzedy
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bb6cbae
:art: Define `_Pool.__contains__` and `Resource.__contains__`
shnizzedy
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1058c94
:recycle: Move `StratDict().rpool[json]` to `StratDict().json`
shnizzedy
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aaa37a9
:recycle: Dedupe loop through `self.node_blocks.items()`
shnizzedy
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4280fc6
:bug: Remove extra curly braces
shnizzedy
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c22db11
:white_check_mark: Update test for new `Resource` class
shnizzedy
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90d96b1
:bug: Fix auto-`quick_single`
shnizzedy
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e25479f
:white_check_mark: Check if `bids-examples` is empty before moving on
shnizzedy
committed
faf8ab9
:twisted_rightwards_arrow: Merge `develop` into `engine/(th)r(e)esources`
shnizzedy
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5ea19ef
:art: Type `connect_pipeline`
shnizzedy
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abb4809

Commits on Jul 16, 2024

new ResourcePool structure

Biraj Shrestha
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Biraj Shrestha
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4093b3b
ResourcePool modified as per nee specs

Biraj Shrestha
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Biraj Shrestha
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a46218d
Merge branch 'bids_ingress' of https://github.com/FCP-INDI/C-PAC into bids_ingress

Biraj Shrestha
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Biraj Shrestha
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b5e4131
fixing sub_dict/sub_group variable names after branch update

Biraj Shrestha
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Biraj Shrestha
committed
5c1eece
:zap: Replace some `deepcopy` calls
shnizzedy
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6207348
:recycle: Typehint `StratPool.append_name`
shnizzedy
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588df00
:recycle: Clarify `ResourcePool.gather_pipes`
shnizzedy
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fc2714a

Commits on Jul 17, 2024

:recycle: Move `connect_pipeline` from standalone function to `ResourcePool` method
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d30496c
:coffin: Remove `_Pool.node_data` method
shnizzedy
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a9a3c48
:construction_worker: Livelog pytest
shnizzedy
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3613f8c
:recycle: Move `post_process` method back into `ResourcePool`
shnizzedy
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4bf5f00
:recycle: Move `filter_name` method into `StratPool`
shnizzedy
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b0b94c9
:recycle: Move `filtered_movement` property into `StratPool`
shnizzedy
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29b481d
:recycle: Move `derivative_xfm` back into `ResourcePool`
shnizzedy
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48e8b90
:coffin: Remove unused `flatten_prov` method
shnizzedy
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74629ac
:recycle: Move `get_resource_strats_from_prov` back into `ResourcePool`
shnizzedy
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748b98e
:coffin: Remove unused `generate_prov_list` method
shnizzedy
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52c38bf
:recycle: Move `get_cpac_provenance` and `regressor_dct` into `StratPool`
shnizzedy
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f2423a2
:recycle: Split `get_json` across `ResourcePool` and `StratPool`
shnizzedy
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0f9099c
:coffin: Remove unused `get_pipe_idxs` method
shnizzedy
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6fb1dc1
:coffin: Remove unused `update_resource` method
shnizzedy
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a004ab6
:recycle: Move `copy_resource` method into `StratPool`
shnizzedy
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69cb603
:recycle: Move `get_json_info` back into `ResourcePool`
shnizzedy
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0a0b5a0
:coffin: Remove unused `set_json_info` method
shnizzedy
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839c7cd
:coffin: Remove unused `get_strat_info` method
shnizzedy
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b8ca36c
:recycle: Move `get_raw_label` back into `ResourcePool`
shnizzedy
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2fc7244
:coffin: Remove unused `get_entire_rpool` method
shnizzedy
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14c3e32
:coffin: Remove unused `wrap_block` function
shnizzedy
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77ffc16
:recycle: Move `_get_pipe_number` back into `ResourcePool`
shnizzedy
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ef402e5
:recycle: Move `create_func_datasource` method into `ResourcePool`
shnizzedy
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c944940
:coffin: Remove unused `get_name` method
shnizzedy
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cf85273
:recycle: Move `_config_lookup` method into `ResourcePool`
shnizzedy
committed
84274b9
:recycle: Move `json_outdir_ingress` method into `ResourcePool`
shnizzedy
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8389d5b
:recycle: Move `initialize_nipype_wf` method into `ResourcePool`
shnizzedy
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2e97e51
:coffin: Remove unused function `run_node_blocks`
shnizzedy
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a855222
:recycle: Replace calls to `grab_tiered_dct` with direct config lookup
shnizzedy
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0d848b9
:recycle: Move `_check_null` from method to private function
shnizzedy
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7571455
:construction_worker: Pre-clone `bids-examples`
shnizzedy
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4a05442

Commits on Jul 18, 2024

:pencil2: Fix typo (~~"tpyes"~~ → "types")
shnizzedy
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dd0985f
:white_check_mark: Unlink symlink instead of rmtree
shnizzedy
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7b04cc8
:twisted_rightwards_arrows: Merge 'origin/develop' into 'engine/(th)re(e)sources'
shnizzedy
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3b00764
:memo: Update CHANGELOG re: #2131
shnizzedy
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75e38e0
:art: Standardize docstring format across changes.
shnizzedy
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f5dd824
:bug: Fix conflicting class name
shnizzedy
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6c96667
:art: More docstring updates for ResourcePool refactor
shnizzedy
committed
763af4e

Commits on Jul 19, 2024

reconfigured Resource class and added get_resource() to the ResourcePool class

Biraj Shrestha
authored and
Biraj Shrestha
committed
250de03
:bug: Fix memoization
shnizzedy
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61eeef4
:pencil2: A little more docstring cleanup
shnizzedy
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2402a2c
:art: Qualify refs to documented functions.
shnizzedy
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8d80941
:art: Remove duplicate imports
shnizzedy
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836d100
:goal_net: Catch and release no-regressors
shnizzedy
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0a53108
added upper/lower case insensitive check for the entity values

Biraj Shrestha
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Biraj Shrestha
committed
61d8b6d

Commits on Aug 9, 2024

Merge pull request #2 from FCP-INDI/engine/(th)re(e)sources
sgiavasis
authored
532322d

Commits on Aug 15, 2024

Commits on Aug 19, 2024

:memo: Update type in docstring
shnizzedy
committed
39f41bb

Commits on Aug 22, 2024

:white_check_mark: Fix test inputs
shnizzedy
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43a9b27

Commits on Aug 23, 2024