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

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e64309c
:bug: Fix import (probably merge error)
shnizzedy Jul 3, 2024
74c0950
:bug: Import local variables in `get_scan_params`
shnizzedy Jul 5, 2024
17257e3
:recycle: Dedupe function node imports
shnizzedy Jul 5, 2024
ddf2103
:construction: WIP :bug: Fix `get_scan_params`
shnizzedy Jul 6, 2024
52aa366
:recycle: DRY `fetch_and_convert`|`fetch`|`check`|`check2`
shnizzedy Jul 8, 2024
c5c39b0
:bug: Tell Nipype to import typehint type
shnizzedy Jul 8, 2024
6a5b723
:recycle: DRY params, sub, scan
shnizzedy Jul 8, 2024
3ebb9f4
:white_check_mark: Add tests for `fetch` refactor
shnizzedy Jul 8, 2024
7d6f0ee
:pencil2: Fix TR capitalization
shnizzedy Jul 8, 2024
b19907a
:bug: Use C-PAC Function node
shnizzedy Jul 8, 2024
b013ccc
:package: Init `Function`
shnizzedy Jul 8, 2024
c7819d1
:art: Remove unnecessary initializations
shnizzedy Jul 8, 2024
f194377
:recycle: Exclusively use custom `Function` Nodes + :rotating_light: …
shnizzedy Jul 8, 2024
af65a2e
:bug: Fix circular import
shnizzedy Jul 8, 2024
b414d17
:truck: Move engine resources to own submodule
shnizzedy Jul 8, 2024
821bcaa
:construction: Split ResourcePool into three classes with docstrings
shnizzedy Jul 8, 2024
979b0a9
:pencil2: Fix f-string missing `f`
shnizzedy Jul 9, 2024
06612ff
:white_check_mark: Move BIDS examples to a fixture
shnizzedy Jul 9, 2024
7a76603
:construction: WIP :recycle: Move `ResourcePool` init from functions …
shnizzedy Jul 10, 2024
646f49d
:white_check_mark: Restore engine unit tests
shnizzedy Jul 10, 2024
3334a2a
:construction_worker: Replace non-`\w`-non-dot characters with hyphens
shnizzedy Jul 10, 2024
bbf3e97
:recycle: Fold `initiate_rpool` into `ResourcePool.__init__`
shnizzedy Jul 10, 2024
f1f7705
:recycle: Finish moving `create_func_datasource` from func to method
shnizzedy Jul 10, 2024
515b791
:recycle: EmptyConfiguration → Preconfiguration('blank')
shnizzedy Jul 11, 2024
3c2220d
:pencil2: Import Path for signature
shnizzedy Jul 11, 2024
8a24441
:recycle: Pass `part_id` through to `DataPaths`
shnizzedy Jul 11, 2024
87fb1c0
:white_check_mark: Skip NHP configs if no torch installed
shnizzedy Jul 11, 2024
3af1407
:white_check_mark: Use abspath for BIDS-examples
shnizzedy Jul 11, 2024
98c8bb8
:construction: :recycle: Continue updating calls to `ResourcePool` me…
shnizzedy Jul 11, 2024
4d9934d
:construction: WIP :recycle: Fix `StratPool.__init__`
shnizzedy Jul 11, 2024
6b6f7f4
🐛 Fix `get_scan_params` (#2129)
shnizzedy Jul 12, 2024
1cc3914
:art: :technologist: Clarify typing
shnizzedy Jul 12, 2024
199bd60
:white_check_mark: `pytest.Cache.makedir` → `pytest.Cache.mkdir`
shnizzedy Jul 12, 2024
ec32f34
:pencil2: Pipe inside quotation marks
shnizzedy Jul 13, 2024
b1f16ed
:art: Type `ResourcePool.get_strats`
shnizzedy Jul 13, 2024
02d1a14
:white_check_mark: Remove dir instead of file
shnizzedy Jul 13, 2024
1b11462
:technologist: Add `__repr__` method to `Resource`
shnizzedy Jul 13, 2024
9ba084e
:arrow_up: Bump zipp from 3.16.0 to 3.19.1
dependabot[bot] Jul 9, 2024
bb6cbae
:bug: Fix circular import
shnizzedy Jul 15, 2024
1058c94
:art: Define `_Pool.__contains__` and `Resource.__contains__`
shnizzedy Jul 15, 2024
aaa37a9
:recycle: Move `StratDict().rpool[json]` to `StratDict().json`
shnizzedy Jul 15, 2024
a40c449
⬆️ Bump zipp from 3.16.0 to 3.19.1 (#2132)
shnizzedy Jul 15, 2024
4280fc6
:recycle: Dedupe loop through `self.node_blocks.items()`
shnizzedy Jul 15, 2024
c22db11
:bug: Remove extra curly braces
shnizzedy Jul 15, 2024
90d96b1
:white_check_mark: Update test for new `Resource` class
shnizzedy Jul 15, 2024
e25479f
:bug: Fix auto-`quick_single`
shnizzedy Jul 15, 2024
faf8ab9
:white_check_mark: Check if `bids-examples` is empty before moving on
shnizzedy Jul 15, 2024
5ea19ef
:twisted_rightwards_arrow: Merge `develop` into `engine/(th)r(e)esour…
shnizzedy Jul 15, 2024
abb4809
:art: Type `connect_pipeline`
shnizzedy Jul 15, 2024
6207348
:zap: Replace some `deepcopy` calls
shnizzedy Jul 15, 2024
588df00
:recycle: Typehint `StratPool.append_name`
shnizzedy Jul 16, 2024
fc2714a
:recycle: Clarify `ResourcePool.gather_pipes`
shnizzedy Jul 16, 2024
d30496c
:recycle: Move `connect_pipeline` from standalone function to `Resour…
shnizzedy Jul 17, 2024
a9a3c48
:coffin: Remove `_Pool.node_data` method
shnizzedy Jul 17, 2024
3613f8c
:construction_worker: Livelog pytest
shnizzedy Jul 17, 2024
4bf5f00
:recycle: Move `post_process` method back into `ResourcePool`
shnizzedy Jul 17, 2024
b0b94c9
:recycle: Move `filter_name` method into `StratPool`
shnizzedy Jul 17, 2024
29b481d
:recycle: Move `filtered_movement` property into `StratPool`
shnizzedy Jul 17, 2024
48e8b90
:recycle: Move `derivative_xfm` back into `ResourcePool`
shnizzedy Jul 17, 2024
74629ac
:coffin: Remove unused `flatten_prov` method
shnizzedy Jul 17, 2024
748b98e
:recycle: Move `get_resource_strats_from_prov` back into `ResourcePool`
shnizzedy Jul 17, 2024
52c38bf
:coffin: Remove unused `generate_prov_list` method
shnizzedy Jul 17, 2024
f2423a2
:recycle: Move `get_cpac_provenance` and `regressor_dct` into `StratP…
shnizzedy Jul 17, 2024
0f9099c
:recycle: Split `get_json` across `ResourcePool` and `StratPool`
shnizzedy Jul 17, 2024
6fb1dc1
:coffin: Remove unused `get_pipe_idxs` method
shnizzedy Jul 17, 2024
a004ab6
:coffin: Remove unused `update_resource` method
shnizzedy Jul 17, 2024
69cb603
:recycle: Move `copy_resource` method into `StratPool`
shnizzedy Jul 17, 2024
0a0b5a0
:recycle: Move `get_json_info` back into `ResourcePool`
shnizzedy Jul 17, 2024
839c7cd
:coffin: Remove unused `set_json_info` method
shnizzedy Jul 17, 2024
b8ca36c
:coffin: Remove unused `get_strat_info` method
shnizzedy Jul 17, 2024
2fc7244
:recycle: Move `get_raw_label` back into `ResourcePool`
shnizzedy Jul 17, 2024
14c3e32
:coffin: Remove unused `get_entire_rpool` method
shnizzedy Jul 17, 2024
77ffc16
:coffin: Remove unused `wrap_block` function
shnizzedy Jul 17, 2024
ef402e5
:recycle: Move `_get_pipe_number` back into `ResourcePool`
shnizzedy Jul 17, 2024
c944940
:recycle: Move `create_func_datasource` method into `ResourcePool`
shnizzedy Jul 17, 2024
cf85273
:coffin: Remove unused `get_name` method
shnizzedy Jul 17, 2024
84274b9
:recycle: Move `_config_lookup` method into `ResourcePool`
shnizzedy Jul 17, 2024
8389d5b
:recycle: Move `json_outdir_ingress` method into `ResourcePool`
shnizzedy Jul 17, 2024
2e97e51
:recycle: Move `initialize_nipype_wf` method into `ResourcePool`
shnizzedy Jul 17, 2024
a855222
:coffin: Remove unused function `run_node_blocks`
shnizzedy Jul 17, 2024
0d848b9
:recycle: Replace calls to `grab_tiered_dct` with direct config lookup
shnizzedy Jul 17, 2024
7571455
:recycle: Move `_check_null` from method to private function
shnizzedy Jul 17, 2024
4a05442
:construction_worker: Pre-clone `bids-examples`
shnizzedy Jul 17, 2024
dd0985f
:pencil2: Fix typo (~~"tpyes"~~ → "types")
shnizzedy Jul 18, 2024
7b04cc8
:white_check_mark: Unlink symlink instead of rmtree
shnizzedy Jul 18, 2024
3b00764
:twisted_rightwards_arrows: Merge 'origin/develop' into 'engine/(th)r…
shnizzedy Jul 18, 2024
75e38e0
:memo: Update CHANGELOG re: #2131
shnizzedy Jul 18, 2024
f5dd824
:art: Standardize docstring format across changes.
shnizzedy Jul 18, 2024
6c96667
:bug: Fix conflicting class name
shnizzedy Jul 18, 2024
763af4e
:art: More docstring updates for ResourcePool refactor
shnizzedy Jul 18, 2024
61eeef4
:bug: Fix memoization
shnizzedy Jul 19, 2024
2402a2c
:pencil2: A little more docstring cleanup
shnizzedy Jul 19, 2024
8d80941
:art: Qualify refs to documented functions.
shnizzedy Jul 19, 2024
836d100
:art: Remove duplicate imports
shnizzedy Jul 19, 2024
0a53108
:goal_net: Catch and release no-regressors
shnizzedy Jul 19, 2024
5a6fa79
:arrow_up: Bump setuptools from 68.0.0 to 70.0.0
dependabot[bot] Jul 15, 2024
384f1e7
⬆️ Bump setuptools from 68.0.0 to 70.0.0 (#2134)
shnizzedy Jul 26, 2024
532322d
Merge pull request #2 from FCP-INDI/engine/(th)re(e)sources
sgiavasis Aug 9, 2024
494f0c7
:twisted_rightwards_arrows: Merge develop into bids_ingress
shnizzedy Aug 15, 2024
64a775b
:goal_net: Raise exception instead of warn + exit(1)
shnizzedy Aug 15, 2024
ce729d5
:bulb: Remove resolved #TODO comment
shnizzedy Aug 15, 2024
27318d7
:package: Require pandas for build
shnizzedy Aug 15, 2024
39f41bb
:memo: Update type in docstring
shnizzedy Aug 19, 2024
43a9b27
:white_check_mark: Fix test inputs
shnizzedy Aug 22, 2024
5bbc1e6
:white_check_mark: Use tmp_path for pipeline tests
shnizzedy Aug 23, 2024
d5722da
:white_check_mark: Update doctest for sub_group instead of sub_dict
shnizzedy Aug 23, 2024
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🚚 Move engine resources to own submodule
shnizzedy committed Jul 8, 2024
commit b414d172ac6fa208d48a4010d484d5440c2da721
50 changes: 50 additions & 0 deletions CPAC/pipeline/engine/__init__.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,50 @@
# Copyright (C) 2021-2024 C-PAC Developers

# This file is part of C-PAC.

# C-PAC is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or (at your
# option) any later version.

# C-PAC is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
# License for more details.

# You should have received a copy of the GNU Lesser General Public
# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
"""C-PAC engine."""

from .engine import (
func_outdir_ingress,
ingress_freesurfer,
ingress_output_dir,
ingress_pipeconfig_paths,
ingress_raw_anat_data,
json_outdir_ingress,
NodeBlock,
run_node_blocks,
set_iterables,
strip_template,
wrap_block,
)
from .resource import initiate_rpool, NodeData, ResourcePool

__all__ = [
"func_outdir_ingress",
"ingress_freesurfer",
"ingress_raw_anat_data",
"ingress_output_dir",
"ingress_pipeconfig_paths",
"ingress_raw_func_data",
"initiate_rpool",
"json_outdir_ingress",
"NodeBlock",
"NodeData",
"ResourcePool",
"run_node_blocks",
"set_iterables",
"strip_template",
"wrap_block",
]
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