#22 Migrate neuroimaging BIDS data to the main BIDS directory

[willstrawson]

BIDS fmri data is now in the main BIDS directory thanks to code inside subject_dir_assimilate/ . I've experimented with importing my own functions, hence why everything's inside one directory. Next step is to integrate my functions script with yours.

Edit: checklist for this PR to be merged

• [x] check files in the new organisation still run on the cluster
• [x] Update the docstrings of all functions
• [x] Detail steps to do for the fMRI data migration in bin/README.md
• [x] Move content in bin/src to bin/adie
• [ ] Optional: write test

[willstrawson]

@htwangtw Hellooo

[willstrawson]

Hey @htwangtw, I've ran the three scripts (1. run_heudiconv.py, 2. cisc_to_adie_conservsion.py, 3. migrate_existing_subject.py) with a test case and they all work 💯

See what you think but I'm happy to close this PR

[sourcery-ai[bot]]

Sourcery Code Quality Report

Merging this PR leaves code quality unchanged.

Quality metrics	Before	After	Change
Complexity	1.85 ⭐	1.85 ⭐	0.00
Method Length	54.12 ⭐	54.12 ⭐	0.00
Working memory	8.98 🙂	8.98 🙂	0.00
Quality	72.51% 🙂	72.51% 🙂	0.00%

Other metrics	Before	After	Change
Lines	772	926	154

Changed files	Quality Before	Quality After	Quality Change
adie/init.py	%	%	%
adie/bids.py	78.31% ⭐	78.31% ⭐	0.00%
adie/dataset.py	71.46% 🙂	71.46% 🙂	0.00%
adie/nback.py	80.58% ⭐	80.58% ⭐	0.00%
adie/spike.py	65.16% 🙂	65.16% 🙂	0.00%
adie/scripts/beh2bids.py	65.83% 🙂	65.83% 🙂	0.00%
adie/tests/init.py	100.00% ⭐	100.00% ⭐	0.00%
adie/tests/test_beh2bids.py	71.40% 🙂	71.40% 🙂	0.00%
adie/tests/test_bids.py	100.00% ⭐	100.00% ⭐	0.00%
adie/tests/test_dataset.py	79.87% ⭐	79.87% ⭐	0.00%
adie/tests/test_nback.py	80.59% ⭐	80.59% ⭐	0.00%
adie/tests/test_spike.py	84.89% ⭐	84.89% ⭐	0.00%
adie/tests/utils.py	91.65% ⭐	91.65% ⭐	0.00%
bin/generate_participant.py	81.42% ⭐	81.42% ⭐	0.00%
bin/nback_derivative.py	42.03% 😞	42.03% 😞	0.00%

Here are some functions in these files that still need a tune-up:

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
adie/scripts/beh2bids.py	main	4 ⭐	169 😞	25 ⛔	42.56% 😞	Try splitting into smaller methods. Extract out complex expressions
adie/tests/test_beh2bids.py	test_beh2bids	0 ⭐	95 🙂	13 😞	64.49% 🙂	Extract out complex expressions
adie/spike.py	smr2array	1 ⭐	107 🙂	11 😞	65.16% 🙂	Extract out complex expressions
adie/tests/test_beh2bids.py	test_find_file	1 ⭐	131 😞	9 🙂	66.11% 🙂	Try splitting into smaller methods
adie/scripts/beh2bids.py	process_smr	3 ⭐	70 🙂	12 😞	66.73% 🙂	Extract out complex expressions

Legend and Explanation

The emojis denote the absolute quality of the code:

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• 🙂 good
• 😞 poor
• ⛔ very poor

The 👍 and 👎 indicate whether the quality has improved or gotten worse with this pull request.

---

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Let us know what you think of it by mentioning @sourcery-ai in a comment.

[htwangtw]

If there's any changes to these files you want to make in the future, open new PR to update!