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[MAINT] update listing and add validation #485

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[MAINT] update listing and add validation #485

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e1c247f
[MAINT] update listing and add validation
Remi-Gau Mar 3, 2025
1bb99ce
add rich
Remi-Gau Mar 3, 2025
0f35153
fix
Remi-Gau Mar 3, 2025
8f96be1
fix
Remi-Gau Mar 3, 2025
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15 changes: 14 additions & 1 deletion .github/workflows/validation.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,4 +17,17 @@ jobs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: codespell-project/actions-codespell@master
- uses: codespell-project/actions-codespell@master

check_listing:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: install python
uses: actions/setup-python@v5
with:
python-version: 3.13
- name: install dependencies
run: pip install -r tools/requirements.txt
- name: check that all datasets are listed in dataset_listing.tsv
run: python tools/print_dataset_listing.py
1 change: 1 addition & 0 deletions dataset_listing.tsv
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Expand Up @@ -82,3 +82,4 @@ mrs_fmrs Functional MRS data involving a pain stimulus task from 15 subjects [li
2d_mb_pcasl Siemens 2D MultiBand Multi-delay PCASL (m0 and noRF included within timeseries) [link](https://osf.io/xrkc4/) [@aptinis](https://github.com/aptinis) anat, fmap, perf T1w, asl, aslcontext, epi
xeeg_hed_score EEG and iEEG data with annotations of artifacts, seizures and modulators using HED-SCORE [@dorahermes](https://github.com/dorahermes) anat, eeg, ieeg T1w, channels, coordsystem, eeg, electrodes, events, ieeg
dwi_deriv exemplifies the storage of diffusion MRI derivates that may be generated on the Siemens XA platform. dwi dwi
pheno004 dataset containing a mismatch of subjects with MRI data and tabular phenotypic data to be considered a whole dataset of participants for the sake of the participants.tsv file [@ericearl](https://github.com/ericearl) anat T1w, ace, demographics
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@effigies
seems pybids is indexing the content of phenotype folder and parsing the files trying to get some suffixes: hence why we have ace and demographics in the suffix column here.

is that something we want in terms of behavior for pybids?

In am not convinced it is but maybe I am missing something.

2 changes: 1 addition & 1 deletion tools/print_dataset_listing.py
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Expand Up @@ -11,7 +11,7 @@
from bids import BIDSLayout
from rich import print

folders_to_skip = ["docs", ".git", ".github", "tools", "env", "site", ".vscode"]
folders_to_skip = ["docs", ".git", ".github", "tools", "env", ".venv", "site", ".vscode"]
suffixes_to_remove = ["README", "description", "participants", "CITATION"]
column_order = [
"name",
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3 changes: 2 additions & 1 deletion tools/requirements.txt
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@@ -1,3 +1,4 @@
pybids
pandas
tabulate
tabulate
rich