Skip to content

Commit 3085bec

Browse files
Remi-GauRemi-Gau
authored
[MAINT] rename test data dir (#988)
* fix submodules * rename test data dir * readd ignored folders
1 parent 7912041 commit 3085bec

File tree

303 files changed

+405
-2602
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

303 files changed

+405
-2602
lines changed

‎.gitignore‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -32,6 +32,8 @@ onsets*_events.mat
3232
## from running tests in root dir
3333
*/group/*
3434
models/*
35+
derivatives/models
36+
derivatives/options
3537

3638
###############################################################################
3739
# python

‎.gitmodules‎

Lines changed: 0 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -2,10 +2,6 @@
22
path = lib/bids-matlab
33
url = https://github.com/bids-standard/bids-matlab.git
44
branch = dev
5-
[submodule "lib/spmup"]
6-
path = lib/spmup
7-
url = https://github.com/CPernet/spmup.git
8-
branch = master
95
[submodule "lib/CPP_ROI"]
106
path = lib/CPP_ROI
117
url = https://github.com/cpp-lln-lab/CPP_ROI.git

‎README.md‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
44
[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/cpp-lln-lab/bidspm/main.svg)](https://results.pre-commit.ci/latest/github/cpp-lln-lab/bidspm/main)
55
[![miss hit](https://img.shields.io/badge/code%20style-miss_hit-000000.svg)](https://misshit.org/)
66
[![Documentation Status: main](https://readthedocs.org/projects/bidspm/badge/?version=stable)](https://bidspm.readthedocs.io/en/stable/?badge=stable)
7-
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/cpp-lln-lab/bidspm/dev)
7+
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/cpp-lln-lab/bidspm/main)
88
[![tests](https://github.com/cpp-lln-lab/bidspm/actions/workflows/tests.yml/badge.svg)](https://github.com/cpp-lln-lab/bidspm/actions/workflows/tests.yml)
99
[![codecov](https://codecov.io/gh/cpp-lln-lab/bidspm/branch/main/graph/badge.svg?token=PMQYH0DIPX)](https://codecov.io/gh/cpp-lln-lab/bidspm)
1010
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3554331.svg)](https://doi.org/10.5281/zenodo.3554331)

‎docs/source/bids_stats_model.md‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -462,12 +462,12 @@ their datasets.
462462

463463
Several of the [demos](demos) have their own model and you can find several
464464
"dummy" models (without corresponding data) used for testing
465-
[in this folder](https://github.com/cpp-lln-lab/bidspm/tree/main/tests/dummyData/models).
465+
[in this folder](https://github.com/cpp-lln-lab/bidspm/tree/main/tests/data/models).
466466

467467
<!-- markdown-link-check-enable -->
468468

469469
An example of JSON file could look something like that:
470470

471-
```{literalinclude} ../../tests/dummyData/models/model-vislocalizer_smdl.json
471+
```{literalinclude} ../../tests/data/models/model-vislocalizer_smdl.json
472472
:language: json
473473
```

‎tests/.gitignore‎

Lines changed: 12 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -10,19 +10,21 @@ tmp
1010

1111
*/*.json
1212

13-
dummyData/derivatives/bidspm-*/jobs
14-
dummyData/derivatives/bidspm-preproc/sub*
13+
data/derivatives/bidspm-*/jobs
14+
data/derivatives/bidspm-preproc/sub*
1515

16-
dummyData/derivatives/bidspm-preproc/desc-skullstripped.json
16+
data/derivatives/bidspm-preproc/desc-skullstripped.json
1717

18-
dummyData/derivatives/bidspm-stats/sub*
19-
dummyData/derivatives/bidspm-stats/derivatives
20-
dummyData/derivatives/bidspm-stats/README
21-
dummyData/derivatives/bidspm-stats/CHANGES
22-
dummyData/derivatives/bidspm-stats/*.json
18+
data/derivatives/bidspm-stats/sub*
19+
data/derivatives/bidspm-stats/derivatives
20+
data/derivatives/bidspm-stats/README
21+
data/derivatives/bidspm-stats/CHANGES
22+
data/derivatives/bidspm-stats/*.json
23+
data/derivatives/bidspm-stats/LICENSE
24+
data/derivatives/bidspm-stats/.gitignore
2325

24-
dummyData/bidspm-raw/sub*
26+
data/bidspm-raw/sub*
2527

26-
dummyData/derivatives/bidspm-roi
28+
data/derivatives/bidspm-roi
2729

2830
test_reports/*.md

‎tests/Makefile‎

Lines changed: 8 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -3,20 +3,21 @@ clean: clean_local
33
mkdir bids-examples && touch bids-examples/.gitkeep
44

55
clean_local:
6-
rm -rf dummyData/derivatives/bidspm-preproc/sub-*
7-
rm -rf dummyData/derivatives/bidspm-stats/sub-*
8-
rm -rf dummyData/bidspm-raw/sub-*
9-
rm -rf dummyData/derivatives/bidspm-stats/group
10-
rm -rf dummyData/derivatives/bidspm-*/jobs
6+
rm -rf data/derivatives/bidspm-preproc/sub-*
7+
rm -rf data/derivatives/bidspm-stats/sub-*
8+
rm -rf data/bidspm-raw/sub-*
9+
rm -rf data/derivatives/bidspm-stats/group
10+
rm -rf data/derivatives/bidspm-*/jobs
1111

1212
data: clean
1313
sh createDummyDataSet.sh
1414
rm -rf bids-examples/
1515
git clone https://github.com/bids-standard/bids-examples.git --depth 1
1616
cp bids-examples/synthetic/dataset_description.json bids-examples/synthetic/derivatives/fmriprep
1717
touch bids-examples/.gitkeep
18-
wget -O moae_spm12.zip https://files.de-1.osf.io/v1/resources/3vufp/providers/osfstorage/62ab741be6f3ec09a7e48d13/?zip=
19-
unzip -d ./dummyData/MoAE/derivatives/spm12 moae_spm12.zip
18+
wget --quiet -O moae_spm12.zip https://files.de-1.osf.io/v1/resources/3vufp/providers/osfstorage/62ab741be6f3ec09a7e48d13/?zip=
19+
mkdir -p data/MoAE/derivatives/spm12
20+
unzip -d ./data/MoAE/derivatives/spm12 moae_spm12.zip
2021

2122
clean_openneuro:
2223
rm -rf openneuro/*

‎tests/createDummyDataSet.sh‎

Lines changed: 10 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -4,10 +4,10 @@
44

55
# defines where the BIDS data set will be created
66
start_dir=$(pwd) # relative to starting directory
7-
raw_dir=${start_dir}/dummyData/bidspm-raw
8-
preproc_dir=${start_dir}/dummyData/derivatives/bidspm-preproc
9-
stats_dir=${start_dir}/dummyData/derivatives/bidspm-stats
10-
roi_dir=${start_dir}/dummyData/derivatives/bidspm-roi
7+
raw_dir=${start_dir}/data/bidspm-raw
8+
preproc_dir=${start_dir}/data/derivatives/bidspm-preproc
9+
stats_dir=${start_dir}/data/derivatives/bidspm-stats
10+
roi_dir=${start_dir}/data/derivatives/bidspm-roi
1111

1212
subject_list='ctrl01 blind01 01'
1313
session_list='01 02'
@@ -231,8 +231,8 @@ for subject in ${subject_list}; do
231231
for run in $(seq 1 2); do
232232

233233
filename=${this_dir}/rp_${basename}_run-${run}${suffix}.txt
234-
cp dummyData/tsv_files/rp.txt "${filename}"
235-
cp dummyData/tsv_files/rp.tsv ${this_dir}/${basename}_run-${run}_desc-confounds_regressors.tsv
234+
cp data/tsv_files/rp.txt "${filename}"
235+
cp data/tsv_files/rp.tsv ${this_dir}/${basename}_run-${run}_desc-confounds_regressors.tsv
236236

237237
for desc in ${desc_label_list}; do
238238
touch ${this_dir}/${basename}_run-${run}_space-individual_desc-${desc}${suffix}.nii
@@ -259,8 +259,8 @@ for subject in ${subject_list}; do
259259

260260
### derivatives
261261
filename=${this_dir}/rp_sub-${subject}_ses-${ses}_task-${task_name}${suffix}.txt
262-
cp dummyData/tsv_files/rp.txt "${filename}"
263-
cp dummyData/tsv_files/rp.tsv ${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}_desc-confounds_regressors.tsv
262+
cp data/tsv_files/rp.txt "${filename}"
263+
cp data/tsv_files/rp.tsv ${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}_desc-confounds_regressors.tsv
264264

265265
desc_label_list='preproc smth6'
266266
for desc in ${desc_label_list}; do
@@ -333,7 +333,7 @@ for subject in ${subject_list}; do
333333
this_dir=${stats_dir}/sub-${subject}/task-${task}_space-IXI549Space_FWHM-6
334334
mkdir -p ${this_dir}
335335

336-
cp dummyData/mat_files/SPM.mat ${this_dir}/SPM.mat
336+
cp data/mat_files/SPM.mat ${this_dir}/SPM.mat
337337

338338
touch ${this_dir}/mask.nii
339339

@@ -354,7 +354,7 @@ for subject in ${subject_list}; do
354354
this_dir=${stats_dir}/sub-${subject}/task-${task}_space-IXI549Space_FWHM-6_node-globalSignal
355355
mkdir -p ${this_dir}
356356

357-
cp dummyData/mat_files/SPM.mat ${this_dir}/SPM.mat
357+
cp data/mat_files/SPM.mat ${this_dir}/SPM.mat
358358

359359
touch ${this_dir}/mask.nii
360360

‎tests/dummyData/MoAE/.gitignore‎ renamed to ‎tests/data/MoAE/.gitignore‎

File renamed without changes.

‎tests/dummyData/MoAE/derivatives/bidspm-preproc/dataset_description.json‎ renamed to ‎tests/data/MoAE/derivatives/bidspm-preproc/dataset_description.json‎

File renamed without changes.

‎tests/data/MoAE/derivatives/bidspm-preproc/desc-skullstripped.json‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,3 @@
1+
{
2+
"SkullStripped": true
3+
}

0 commit comments

Comments
 (0)