fix set up

cpp-lln-lab · Jul 31, 2024 · 9933b6c · 9933b6c
1 parent 3d6544a
commit 9933b6c
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Showing 3 changed files with 39 additions and 33 deletions.
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -118,6 +118,7 @@ jobs:
                 mv moae_fmriprep fmriprep
 
         -   name: Get data for testing QA
+            if: matrix.os == 'ubuntu-latest'
             run: |
                 cd demos/openneuro/
                 make data_ds000114_mriqc

diff --git a/.github/workflows/tests_octave.yml b/.github/workflows/tests_octave.yml
@@ -61,7 +61,7 @@ jobs:
         -   name: Install dependencies
             run: |
                 sudo apt-get -y -qq update
-                sudo apt-get -y install unzip wget
+                sudo apt-get -y install unzip wget git-annex
 
         -   name: Install Node
             uses: actions/setup-node@v4
@@ -79,6 +79,11 @@ jobs:
                 submodules: recursive
                 fetch-depth: 0
 
+        -   name: Install datalad
+            run: |
+                python -m pip install --upgrade pip setuptools
+                pip install datalad
+
         -   name: Install validators
             run: make install
 

diff --git a/tests/tests_slow/tests_workflows/QA/test_bidsQA.m b/tests/tests_slow/tests_workflows/QA/test_bidsQA.m
@@ -11,50 +11,46 @@
 
 function test_bidsQA_raw()
 
-  %   markTestAs('slow');
-  %
-  %     opt = setOptions('vislocalizer');
-  %
-  %      expectedOutput = fullfile(opt.dir.output, ...
-  %         'reports', ...
-  %         'bidspm-raw_split_by-task.png');
-  %
-  %     if exist(expectedOutput, 'file')
-  %         delete(expectedOutput)
-  %     end
-  %
-  %     bidsQA(opt)
-  %
-  %     assertEqual(exist(expectedOutput, 'file'), 2)
+  markTestAs('slow');
 
-end
+  opt = setOptions('vislocalizer');
 
-function test_bidsQA_mriqc()
+  expectedOutput = fullfile(opt.dir.output, ...
+                            'reports', ...
+                            'bidspm-raw_split_by-task.png');
+
+  if exist(expectedOutput, 'file')
+    delete(expectedOutput);
+  end
 
-  %   markTestAs('slow');
-  %
-  % if ispc()
-  % moxunit_throw_test_skipped_exception('requires datalad setup');
-  % end
-  %
-  %   ds000114mriqc = spm_file(fullfile(getTestDir(), ...
-  %                                     '..', 'demos', 'openneuro', ...
-  %                                     'inputs', 'ds000114-mriqc'), 'cpath');
-  %
-  %   opt.dir.input = ds000114mriqc;
-  %
-  %   bidsQA(opt);
+  bidsQA(opt);
+
+  assertEqual(exist(expectedOutput, 'file'), 2);
 
 end
 
-function test_bidsQA_bidspm()
+function test_bidsQA_mriqc()
 
   markTestAs('slow');
 
-  if ispc()
+  if ispc() || ismac()
     moxunit_throw_test_skipped_exception('requires datalad setup');
   end
 
+  ds000114mriqc = spm_file(fullfile(getTestDir(), ...
+                                    '..', 'demos', 'openneuro', ...
+                                    'inputs', 'ds000114-mriqc'), 'cpath');
+
+  opt.dir.input = ds000114mriqc;
+
+  bidsQA(opt);
+
+end
+
+function test_bidsQA_bidspm()
+
+  markTestAs('slow');
+
   opt = setOptions('vislocalizer');
 
   opt.dir.input = opt.dir.preproc;
@@ -77,6 +73,10 @@ function test_bidsQA_fmriprep()
 
   markTestAs('slow');
 
+  if ispc() || ismac()
+    moxunit_throw_test_skipped_exception('requires datalad setup');
+  end
+
   ds000114fmriprep = spm_file(fullfile(getTestDir(), ...
                                        '..', 'demos', 'openneuro', ...
                                        'inputs', 'ds000114-fmriprep'), 'cpath');