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Fixup and enhance invocation of run_tests.sh #434

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Apr 19, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/validate_datasets.yml
Original file line number Diff line number Diff line change
Expand Up @@ -86,5 +86,5 @@ jobs:
- name: Validate all BIDS datasets using bids-validator
run: |
cat ./run_tests.sh
bash ./run_tests.sh
./run_tests.sh
shell: bash
4 changes: 2 additions & 2 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@ script that is provided in this repository. This script makes use of the
handles some special case examples (see
[Validator Exceptions](#validator-exceptions)).

Simply run `bash run_tests.sh` in a command line from the root of the
Simply run `./run_tests.sh` in a command line from the root of the
`bids-examples` repository.

### Validator exceptions
Expand Down Expand Up @@ -304,4 +304,4 @@ DO NOT EDIT DIRECTLY.
|:------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------|:--------------------------------|:-------------------------------------------------------------------------------------------------------------|:-------------------------------------------------|:-------------------------------------------|
| [ds000117](https://github.com/bids-standard/bids-examples/tree/master/ds000117) | A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task | anat, beh, dwi, fmap, func, meg | T1w, beh, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans | [link](https://openneuro.org/datasets/ds000117/) | [@RikHenson](https://github.com/RikHenson) |
| [eeg_ds003645s_hed_demo](https://github.com/bids-standard/bids-examples/tree/master/eeg_ds003645s_hed_demo) | Shows usage of Hierarchical Event Descriptor (HED) in .tsv files | eeg, beh | channels, eeg, events, participants, scans | [link](https://openneuro.org/datasets/ds003645) | [@VisLab](https://github.com/VisLab) |
| [synthetic](https://github.com/bids-standard/bids-examples/tree/master/synthetic) | A synthetic dataset | anat, beh, func | T1w, beh, bold, events, physio, scans, sessions, stim | n/a | [@effigies](https://github.com/effigies) |
| [synthetic](https://github.com/bids-standard/bids-examples/tree/master/synthetic) | A synthetic dataset | anat, beh, func | T1w, beh, bold, events, physio, scans, sessions, stim | n/a | [@effigies](https://github.com/effigies) |
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I believe this table is generated automatically. If it will get reverted with the next regeneration, then it would be better to fix up the script.

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yes that's true

though I cannot see what actually got changed: I suspect a whitespace so I don't think it matters much

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probably "no newline" at the end of file?

def add_tables(df: pd.DataFrame, output_file: Path) -> None:

And it got auto-inserted by the editor the last person touching this file was using?

4 changes: 2 additions & 2 deletions run_tests.sh
100644 → 100755
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
#!/bin/bash
#!/usr/bin/env bash

rc = 0;
rc=0;
for i in $(ls -d */ | grep -v node_modules); do
echo "Validating dataset" $i

Expand Down