Merge pull request #774 from Remi-Gau/fix

[FIX] fix and tidy failing workflows

Author: Remi-Gau

.github/workflows/run_system_tests_matlab.yml

@@ -1,4 +1,4 @@
-name: system tests with matlab
+name: "matlab: system tests"
 
 # Uses the cron schedule for github actions
 #

.github/workflows/run_system_tests_octave.yml

@@ -1,4 +1,4 @@
-name: "system tests with octave"
+name: "octave: system tests"
 
 # Uses the cron schedule for github actions
 #

.github/workflows/run_tests_matlab.yml

@@ -1,4 +1,4 @@
-name: tests and coverage with matlab
+name: "matlab: tests"
 
 on:
 

.github/workflows/run_tests_octave.yml

@@ -1,4 +1,4 @@
-name: "tests with octave"
+name: "octave: tests"
 
 on:
 

README.md

@@ -1,20 +1,17 @@
-<!-- markdown-link-check-disable -->
-
 <!-- .. only:: html -->
 
+[![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)
+[![miss hit](https://img.shields.io/badge/code%20style-miss_hit-000000.svg)](https://misshit.org/)
 [![Documentation Status: main](https://readthedocs.org/projects/bidspm/badge/?version=stable)](https://bidspm.readthedocs.io/en/stable/?badge=stable)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/cpp-lln-lab/bidspm/dev)
-[![miss_hit](https://github.com/cpp-lln-lab/bidspm/actions/workflows/miss_hit.yml/badge.svg)](https://github.com/cpp-lln-lab/bidspm/actions/workflows/miss_hit.yml)
-[![tests with octave](https://github.com/cpp-lln-lab/bidspm/actions/workflows/run_tests_octave.yml/badge.svg)](https://github.com/cpp-lln-lab/bidspm/actions/workflows/run_tests_octave.yml)
 [![tests with matlab](https://github.com/cpp-lln-lab/bidspm/actions/workflows/run_tests_matlab.yml/badge.svg)](https://github.com/cpp-lln-lab/bidspm/actions/workflows/run_tests_matlab.yml)
+[![tests with octave](https://github.com/cpp-lln-lab/bidspm/actions/workflows/run_tests_octave.yml/badge.svg)](https://github.com/cpp-lln-lab/bidspm/actions/workflows/run_tests_octave.yml)
 [![system tests with matlab](https://github.com/cpp-lln-lab/bidspm/actions/workflows/run_system_tests_matlab.yml/badge.svg)](https://github.com/cpp-lln-lab/bidspm/actions/workflows/run_system_tests_matlab.yml)
-[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
-[![codecov](https://codecov.io/gh/cpp-lln-lab/bidspm/branch/master/graph/badge.svg?token=PMQYH0DIPX)](https://codecov.io/gh/cpp-lln-lab/bidspm)
+[![system tests with octave](https://github.com/cpp-lln-lab/bidspm/actions/workflows/run_system_tests_octave.yml/badge.svg)](https://github.com/cpp-lln-lab/bidspm/actions/workflows/run_system_tests_octave.yml)
+[![codecov](https://codecov.io/gh/cpp-lln-lab/bidspm/branch/main/graph/badge.svg?token=PMQYH0DIPX)](https://codecov.io/gh/cpp-lln-lab/bidspm)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3554331.svg)](https://doi.org/10.5281/zenodo.3554331)
 [![All Contributors](https://img.shields.io/badge/all_contributors-14-orange.svg?style=flat-square)](https://github.com/cpp-lln-lab/bidspm#contributors)
 
-<!-- markdown-link-check-enable -->
-
 # bidspm
 
 This is a Matlab / Octave toolbox to perform MRI data analysis on a
@@ -45,15 +42,15 @@ bidspm()
 ```
 
 Please see our
-[documentation](https://bidspm.readthedocs.io/en/stable/general_information.html)
+[documentation](https://bidspm.readthedocs.io/en/latest/general_information.html)
 for more info.
 
 ## Usage
 
 For some of its functionality bidspm has a BIDS app like API.
 
 See
-[this page for more information](https://bidspm.readthedocs.io/en/stable/bids_app_api.html).
+[this page for more information](https://bidspm.readthedocs.io/en/latest/usage_notes.html).
 
 ### Preprocessing
 
@@ -87,7 +84,7 @@ bidspm(bids_dir, output_dir, 'subject', ...
 ```
 
 Please see our
-[documentation](https://bidspm.readthedocs.io/en/stable/bids_app_api.html) for
+[documentation](https://bidspm.readthedocs.io/en/latest/usage_notes.html) for
 more info.
 
 ## Features
@@ -138,7 +135,7 @@ used to perform:
 -   GLM auto-correlation check
 
 Please see our
-[documentation](https://bidspm.readthedocs.io/en/stable/index.html) for more
+[documentation](https://bidspm.readthedocs.io/en/latest/index.html) for more
 info.
 
 ## Citation

demos/MoAE/test_moae.m

@@ -34,19 +34,18 @@
 
 optionsFile = fullfile(WD, 'options', 'options_task-auditory.json');
 
-space = {'IXI549Space'
+space = {'individual'
+         'IXI549Space'
          'IXI549Space'
-         'individual'
          'individual'};
-ignore = {{''}
+ignore = {{'unwarp'}
           {'unwarp', 'qa'}
-          {'unwarp'}
           {''}
-         };
+          {''}};
 
-models = {fullfile(WD, 'models', 'model-MoAE_smdl.json')
+models = {fullfile(WD, 'models', 'model-MoAEindividual_smdl.json')
+          fullfile(WD, 'models', 'model-MoAE_smdl.json')
           fullfile(WD, 'models', 'model-MoAE_smdl.json')
-          fullfile(WD, 'models', 'model-MoAEindividual_smdl.json')
           fullfile(WD, 'models', 'model-MoAEindividual_smdl.json')};
 
 for iOption = 1:numel(space)

demos/face_repetition/test_face_rep.m

@@ -30,6 +30,13 @@
 
 model_file = fullfile(WD, 'models', 'model-faceRepetition_smdl.json');
 
+% skip unwarping with octave to avoid failure in CI
+% see https://github.com/cpp-lln-lab/bidspm/issues/769
+ignore = {''};
+if isOctave
+  ignore = {'unwarp'};
+end
+
 for iResolution = 2:3
 
   opt.pipeline.name = ['bidspm-res' num2str(iResolution)];
@@ -46,6 +53,7 @@
          'action', 'preprocess', ...
          'task', {'facerepetition'}, ...
          'space', {'IXI549Space'}, ...
+         'ignore', ignore, ...
          'options', opt);
 
   %% stats