[INFRA] run tests on mac OS and windows for matlab

+bids/+internal/format_path.m

@@ -22,11 +22,11 @@
   end
 
   if ischar(pth)
-    pth = strrep(pth, '\', '/');
+    pth = strrep(pth, '\', '\\');
 
   elseif iscell(pth)
     for i = 1:numel(pth)
-      pth{i} = pathToPrint(pth{i});
+      pth{i} = strrep(pth{i}, '\', '\\');
     end
   end
 

+bids/+internal/is_github_ci.m

@@ -4,8 +4,9 @@
   is_github = false;
 
   GITHUB_WORKSPACE = getenv('HOME');
+  IS_CI = getenv('CI');
 
-  if strcmp(GITHUB_WORKSPACE, '/home/runner')
+  if IS_CI
 
     is_github = true;
     pth = GITHUB_WORKSPACE;

+bids/+internal/nansum.m

@@ -0,0 +1,22 @@
+function y = nansum(varargin)
+  %
+  % nansum wrapper to deal with missing toolbox or octave
+
+  % (C) Copyright 2023 Remi Gau
+
+  if ~isempty(which('nansum'))
+    y = nansum(varargin{:});
+    return
+  end
+
+  if bids.internal.is_octave()
+    tolerant = false;
+    bids.internal.error_handling(mfilename(), ...
+                                 'notImplemented', ...
+                                 'nansum not implemented', tolerant);
+    return
+  end
+
+  y = sum(varargin{:}, 'omitnan');
+
+end

+bids/+util/create_participants_tsv.m

@@ -55,7 +55,7 @@
   if ~isempty(layout.participants)
     msg = sprintf(['"participant.tsv" already exist for the following dataset. ', ...
                    'Will not overwrite.\n', ...
-                   '\t%s'], layout.pth);
+                   '\t%s'], bids.internal.format_path(layout.pth));
     bids.internal.error_handling(mfilename(), 'participantFileExist', msg, tolerant, verbose);
     return
   end

+bids/+util/create_scans_tsv.m

@@ -104,7 +104,9 @@
       if exist(fullfile(layout.pth, scans_file), 'file')
         msg = sprintf(['"scans.tsv" %s already exist for the following dataset.', ...
                        'Will not overwrite.\n', ...
-                       '\t%s'], scans_file, layout.pth);
+                       '\t%s'], ...
+                      bids.internal.format_path(scans_file), ...
+                      bids.internal.format_path(layout.pth));
         bids.internal.error_handling(mfilename(), 'scansFileExist', msg, true, verbose);
         continue
       end

+bids/+util/tsvread.m

@@ -6,7 +6,7 @@
   %
   %   file_content = tsvread(filename, field_to_return, hdr)
   %
-  % :param filename: filename (can be gzipped) {txt,mat,csv,tsv,json}ename
+  % :param filename: filename (can be gzipped) {txt,mat,csv,tsv,json}
   % :type filename: string
   %
   % :param field_to_return: name of field to return if data stored in a structure
@@ -200,6 +200,15 @@
   if S(end) ~= eol
     S = [S eol];
   end
+  % Byte order mark (BOM),U+FEFF,0xEF,0xBB,0xBF
+  % matlab case
+  if S(1) == 65279
+    S(1) = [];
+  end
+  % octave case
+  if numel(S) > 2 && isequal(S(1:3), [239 187 191])
+    S(1:3) = [];
+  end
   S = regexprep(S, {'\r\n', '\r', '(\n)\1+'}, {'\n', '\n', '$1'});
 
   % -Get column names from header line (non-numeric first line)

+bids/copy_to_derivative.m

@@ -316,9 +316,9 @@ function copy_with_symlink(src, target, unzip_files, verbose)
   if  isunix
 
     if unzip_files && is_gunzipped(src)
-      command = sprintf('gunzip --keep --force --stdout %s > %s', src, target(1:end - 3));
+      command = sprintf('gunzip -kfc %s > %s', src, target(1:end - 3));
     else
-      command = sprintf('cp --recursive --dereference --force %s %s', src, target);
+      command = sprintf('cp -rLf %s %s', src, target);
     end
 
     status = system(command);

+bids/layout.m

@@ -749,7 +749,9 @@
       % to avoid excessive warning as sym link are not files
       if ~exist(dest, 'file')
         if ~BIDS.is_datalad_ds
-          msg = ['IntendedFor file ' dest ' from ' file.filename ' not found'];
+          msg = sprintf('IntendedFor file %s from %s not found', ...
+                        bids.internal.format_path(dest), ...
+                        bids.internal.format_path(file.filename));
           bids.internal.error_handling(mfilename, 'IntendedForMissing', msg, tolerant, verbose);
         end
         continue

.github/workflows/run_tests_matlab.yml

@@ -0,0 +1,62 @@
+---
+name: 'matlab: tests'
+
+on:
+  push:
+    branches:
+    - master
+    - dev
+  pull_request:
+    branches: ['*']
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  test:
+
+
+    strategy:
+      fail-fast: false
+      matrix:
+        version: [R2021a, R2021b, R2022a, R2022b]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    runs-on: ${{matrix.os}}
+
+    steps:
+    - name: Install MATLAB
+      uses: matlab-actions/[email protected]
+      with:
+        release: ${{matrix.version}}
+
+    - name: Clone bids-matlab
+      uses: actions/checkout@v3
+      with:
+        submodules: true
+        fetch-depth: 1
+
+    - name: Install dependencies
+      if: matrix.os == 'ubuntu-latest'
+      run: |
+        sudo apt-get -y -qq update
+        sudo apt-get -y install unzip wget
+
+    - name: Install bids validator
+      run: npm install -g bids-validator
+
+    - name: Install bids example
+      run: |
+        cd tests
+        make data
+
+    - name: Install Moxunit and MOcov
+      run: |
+        git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
+        git clone https://github.com/MOcov/MOcov.git --depth 1
+
+    - name: Run commands
+      uses: matlab-actions/[email protected]
+      with:
+        command: run MOxUnit/MOxUnit/moxunit_set_path(); addpath(fullfile(pwd, 'MOcov', 'MOcov')); addpath(getenv('GITHUB_WORKSPACE')); success = run_tests();
+          assert(success);

.github/workflows/tests.yml → .github/workflows/run_tests_octave.yml

@@ -1,5 +1,5 @@
 ---
-name: tests
+name: 'octave: tests'
 
 on:
   push:
@@ -19,16 +19,8 @@ jobs:
 
     runs-on: ubuntu-22.04
 
-    strategy:
-      matrix:
-        platform: [matlab, octave]
-      fail-fast: false
-
     steps:
 
-    - name: ${{ matrix.platform }} - test
-      run: echo ${{ matrix.platform }} test
-
     - name: Clone bids-matlab
       uses: actions/checkout@v3
       with:
@@ -54,7 +46,6 @@ jobs:
         git clone https://github.com/MOcov/MOcov.git --depth 1
 
     - name: Install octave
-      if: matrix.platform == 'octave'
       run: |
         sudo apt-get -y -qq update
         sudo apt-get -y install \
@@ -69,27 +60,12 @@ jobs:
         make -C MOcov install
 
     - name: Install JSONio
-      if: matrix.platform == 'octave'
       run: |
         git clone https://github.com/gllmflndn/JSONio.git --depth 1
         cd JSONio
         mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS
         octave $OCTFLAGS --eval "addpath(fullfile(pwd)); savepath();"
 
     - name: Run unit tests Octave
-      if: matrix.platform == 'octave'
       run: |
         octave $OCTFLAGS --eval "success = run_tests(); assert(success);"
-
-    - name: Install MATLAB
-      if: matrix.platform == 'matlab'
-      uses: matlab-actions/[email protected]
-      with:
-        release: R2020a
-
-    - name: Run MATLAB tests
-      if: matrix.platform == 'matlab'
-      uses: matlab-actions/[email protected]
-      with:
-        command: run MOxUnit/MOxUnit/moxunit_set_path(); addpath(fullfile(pwd, 'MOcov', 'MOcov')); addpath(getenv('GITHUB_WORKSPACE')); success = run_tests();
-          assert(success);

run_tests.m

@@ -9,6 +9,10 @@
     with_coverage = true;
   end
 
+  if ispc
+    with_coverage = false;
+  end
+
   addpath(fullfile(pwd, 'tests', 'utils'));
 
   folderToCover = fullfile(pwd, '+bids');

tests/data/bom_bug_552.tsv

@@ -0,0 +1,91 @@
+onset	duration	trial_type	value	sample
+61.824	5.0	Control	1	483
+87.296	5.0	Control	1	682
+117.632	5.0	Tapping/Right	3	919
+146.816	5.0	Tapping/Right	3	1147
+181.504	5.0	Control	1	1418
+212.864	5.0	Tapping/Left	2	1663
+240.64	5.0	Tapping/Left	2	1880
+275.712	5.0	Control	1	2154
+311.424	5.0	Tapping/Right	3	2433
+344.832	5.0	Tapping/Right	3	2694
+373.376	5.0	Tapping/Left	2	2917
+404.736	5.0	Tapping/Left	2	3162
+435.712	5.0	Tapping/Left	2	3404
+474.496	5.0	Tapping/Right	3	3707
+512.256	5.0	Tapping/Left	2	4002
+544.64	5.0	Control	1	4255
+570.368	5.0	Tapping/Left	2	4456
+609.28	5.0	Tapping/Right	3	4760
+635.904	5.0	Control	1	4968
+661.504	5.0	Tapping/Left	2	5168
+690.56	5.0	Tapping/Right	3	5395
+720.256	5.0	Tapping/Left	2	5627
+758.144	5.0	Control	1	5923
+784.384	5.0	Control	1	6128
+819.456	5.0	Tapping/Left	2	6402
+847.872	5.0	Control	1	6624
+874.368	5.0	Tapping/Left	2	6831
+900.48	5.0	Control	1	7035
+930.944	5.0	Tapping/Right	3	7273
+965.76	5.0	Tapping/Left	2	7545
+993.792	5.0	Tapping/Right	3	7764
+1021.44	5.0	Control	1	7980
+1046.784	5.0	Tapping/Right	3	8178
+1080.192	5.0	Tapping/Left	2	8439
+1106.56	5.0	Tapping/Right	3	8645
+1144.448	5.0	Tapping/Right	3	8941
+1182.72	5.0	Tapping/Left	2	9240
+1220.48	5.0	Control	1	9535
+1254.784	5.0	Tapping/Right	3	9803
+1281.408	5.0	Tapping/Left	2	10011
+1317.504	5.0	Tapping/Left	2	10293
+1354.624	5.0	Tapping/Right	3	10583
+1383.936	5.0	Control	1	10812
+1416.064	5.0	Tapping/Right	3	11063
+1456.0	5.0	Tapping/Right	3	11375
+1485.824	5.0	Tapping/Left	2	11608
+1513.344	5.0	Tapping/Right	3	11823
+1539.2	5.0	Tapping/Left	2	12025
+1565.44	5.0	Tapping/Right	3	12230
+1604.736	5.0	Tapping/Left	2	12537
+1638.016	5.0	Control	1	12797
+1673.6	5.0	Tapping/Right	3	13075
+1704.96	5.0	Control	1	13320
+1734.784	5.0	Control	1	13553
+1760.896	5.0	Tapping/Left	2	13757
+1791.104	5.0	Tapping/Right	3	13993
+1819.008	5.0	Tapping/Left	2	14211
+1857.536	5.0	Control	1	14512
+1896.832	5.0	Tapping/Left	2	14819
+1936.256	5.0	Control	1	15127
+1967.232	5.0	Tapping/Right	3	15369
+2003.328	5.0	Tapping/Right	3	15651
+2043.264	5.0	Tapping/Right	3	15963
+2070.144	5.0	Tapping/Left	2	16173
+2106.24	5.0	Tapping/Right	3	16455
+2132.992	5.0	Control	1	16664
+2166.784	5.0	Control	1	16928
+2198.4	5.0	Tapping/Right	3	17175
+2234.112	5.0	Tapping/Right	3	17454
+2270.976	5.0	Control	1	17742
+2305.536	5.0	Control	1	18012
+2334.848	5.0	Tapping/Right	3	18241
+2362.24	5.0	Tapping/Right	3	18455
+2393.216	5.0	Control	1	18697
+2432.64	5.0	Control	1	19005
+2466.304	5.0	Control	1	19268
+2505.216	5.0	Tapping/Left	2	19572
+2542.72	5.0	Tapping/Left	2	19865
+2578.432	5.0	Control	1	20144
+2606.336	5.0	Tapping/Left	2	20362
+2639.36	5.0	Tapping/Left	2	20620
+2677.504	5.0	Tapping/Right	3	20918
+2707.328	5.0	Control	1	21151
+2735.616	5.0	Control	1	21372
+2770.944	5.0	Tapping/Left	2	21648
+2806.912	5.0	Control	1	21929
+2833.408	5.0	Tapping/Left	2	22136
+2869.376	5.0	Control	1	22417
+2908.032	5.0	Tapping/Right	3	22719
+2938.496	5.0	Tapping/Left	2	22957

tests/test_transformers/test_transformers_munge_multi.m

@@ -104,8 +104,9 @@ function test_multi_complex_filter_with_and()
   % THEN
   assert(all(ismember({'Famous'; 'FirstRep'}, fieldnames(new_content))));
   assertEqual(sum(strcmp(new_content.Famous, 'famous')), 52);
-  if ~bids.internal.is_octave
-    assertEqual(nansum(new_content.FirstRep), 52);
+
+  if ~isempty(which('nansum'))
+    assertEqual(bids.internal.nansum(new_content.FirstRep), 52);
   end
 
   %% GIVEN

tests/tests_utils/test_tsvread.m

@@ -37,6 +37,14 @@ function test_tsvread_basic()
 
 end
 
+function test_tsvread_bug_552()
+
+  tsv_file = fullfile(get_test_data_dir(), '..', 'data', 'bom_bug_552.tsv');
+  content = bids.util.tsvread(tsv_file);
+  assert(ismember('onset', fieldnames(content)));
+
+end
+
 function [pth, expected] = fixture()
 
   pth = fullfile(get_test_data_dir(), '..', 'data');

tests/utils/get_test_data_dir.m

@@ -7,7 +7,7 @@
 
   if strcmp(PLATFORM, 'GITHUB_ACTIONS')
 
-    data_dir = '/github/workspace/tests/';
+    data_dir = fullfile('/', 'github', 'workspace', 'tests');
 
   end
 

tests/utils/validate_dataset.m

@@ -1,5 +1,9 @@
 function validate_dataset(bids_path)
 
+  if ispc
+    return
+  end
+
   [sts, msg] = bids.validate(bids_path,  '--config.ignore=99 --ignoreNiftiHeaders');
   assertEqual(sts, 0);