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[MAINT] update bids matlab #254

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Merged
merged 4 commits into from
Dec 6, 2023
Merged

[MAINT] update bids matlab #254

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7fa0bb5
update bids matlab
Remi-Gau Dec 6, 2023
94aa529
remove levels from trial type column
Remi-Gau Dec 6, 2023
b2246fc
add dummy term URL
Remi-Gau Dec 6, 2023
12ff9c5
try proper URI
Remi-Gau Dec 6, 2023
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2 changes: 1 addition & 1 deletion lib/bids-matlab
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Submodule bids-matlab updated 28 files
+1 −1 +bids/+transformers_list/Merge_identical_rows.m
+12 −12 +bids/transformers.m
+0 −1 .github/ISSUE_TEMPLATE/bug_report.yml
+1 −1 .github/dependabot.yml
+4 −5 .github/workflows/run_examples.yml
+6 −6 .github/workflows/run_tests_matlab.yml
+2 −3 .github/workflows/run_tests_octave.yml
+3 −10 .github/workflows/update_schema.yml
+6 −6 .github/workflows/validate.yml
+3 −4 .pre-commit-config.yaml
+5 −1 .readthedocs.yml
+2 −2 CITATION.cff
+0 −5 CONTRIBUTING.md
+3 −34 DECISION-MAKING.md
+20 −674 LICENSE
+1 −1 Makefile
+31 −17 README.md
+2 −2 demos/README.md
+1 −1 demos/spm/facerep/code/convert_facerep_ds.m
+1 −1 docs/requirements.txt
+11 −61 docs/source/general_information.md
+1 −1 docs/source/layout_query.rst
+1 −1 schema.json
+7 −4 tests/test_bids_file.m
+46 −6 tests/test_bids_schema.m
+1 −1 tests/test_transformers/test_transformers_side_functions.m
+6 −3 tests/tests_private/test_append_to_layout.m
+1 −1 version.txt
3 changes: 1 addition & 2 deletions src/createDataDictionary.m
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Original file line number Diff line number Diff line change
Expand Up @@ -48,8 +48,7 @@ function createDataDictionary(cfg, logFile)
startTime = logFile(1).StartTime;
end

jsonContent = struct( ...
'SamplingFrequency', samplingFrequency, ...
jsonContent = struct('SamplingFrequency', samplingFrequency, ...
'StartTime', startTime, ...
'Columns', []);
end
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9 changes: 3 additions & 6 deletions src/saveEventsFile.m
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Original file line number Diff line number Diff line change
Expand Up @@ -182,15 +182,12 @@
% before calling openFile.

% initialize holy trinity (onset, trial_type, duration) columns
logFile(1).columns = struct('onset', struct( ...
'Description', ...
logFile(1).columns = struct('onset', struct('Description', ...
'time elapsed since experiment start', ...
'Units', 's'), ...
'trial_type', struct( ...
'Description', 'types of trial', ...
'trial_type', struct('Description', 'types of trial', ...
'Levels', struct()), ...
'duration', struct( ...
'Description', ...
'duration', struct('Description', ...
'duration of the event or the block', ...
'Units', 's') ...
);
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5 changes: 2 additions & 3 deletions src/utils/initializeExtraColumns.m
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@
fieldsToSet.bids.LongName = '';
fieldsToSet.bids.Description = '';
fieldsToSet.bids.Levels = struct();
fieldsToSet.bids.TermURL = '';
fieldsToSet.bids.TermURL = 'https://www.TODO.later';
fieldsToSet.bids.Units = '';

% convert the cell of column name into a structure
Expand All @@ -35,8 +35,7 @@

for iExtraColumn = 1:nbExtraColumns
extraColumnName = logFile(1).extraColumns{iExtraColumn};
tmp.(extraColumnName) = struct( ...
'length', 1);
tmp.(extraColumnName) = struct('length', 1);
tmp.(extraColumnName) = setDefaultFields(tmp.(extraColumnName), fieldsToSet);
end

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8 changes: 4 additions & 4 deletions tests/testData/eventsDataDictionary.json
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Original file line number Diff line number Diff line change
Expand Up @@ -15,28 +15,28 @@
"LongName": "",
"Description": "",
"Levels": {},
"TermURL": "",
"TermURL": "https://www.TODO.later",
"Units": ""
},
"LHL24_01": {
"LongName": "",
"Description": "",
"Levels": {},
"TermURL": "",
"TermURL": "https://www.TODO.later",
"Units": ""
},
"LHL24_02": {
"LongName": "",
"Description": "",
"Levels": {},
"TermURL": "",
"TermURL": "https://www.TODO.later",
"Units": ""
},
"LHL24_03": {
"LongName": "",
"Description": "",
"Levels": {},
"TermURL": "",
"TermURL": "https://www.TODO.later",
"Units": ""
}
}
10 changes: 5 additions & 5 deletions tests/testData/stimDataDictionary.json
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Original file line number Diff line number Diff line change
Expand Up @@ -12,35 +12,35 @@
"Description": "",
"Levels": {},
"LongName": "",
"TermURL": "",
"TermURL": "https://www.TODO.later",
"Units": ""
},
"LHL24_01": {
"Description": "",
"Levels": {},
"LongName": "",
"TermURL": "",
"TermURL": "https://www.TODO.later",
"Units": ""
},
"LHL24_02": {
"Description": "",
"Levels": {},
"LongName": "",
"TermURL": "",
"TermURL": "https://www.TODO.later",
"Units": ""
},
"LHL24_03": {
"Description": "",
"Levels": {},
"LongName": "",
"TermURL": "",
"TermURL": "https://www.TODO.later",
"Units": ""
},
"is_Fixation": {
"Description": "",
"Levels": {},
"LongName": "",
"TermURL": "",
"TermURL": "https://www.TODO.later",
"Units": ""
}
}
6 changes: 3 additions & 3 deletions tests/test_saveEventsFileInit.m
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ function test_saveEventsFileInitExtraColumns()
expectedStrcut(1).extraColumns.Speed.bids.LongName = '';
expectedStrcut(1).extraColumns.Speed.bids.Description = '';
expectedStrcut(1).extraColumns.Speed.bids.Levels = struct();
expectedStrcut(1).extraColumns.Speed.bids.TermURL = '';
expectedStrcut(1).extraColumns.Speed.bids.TermURL = 'https://www.TODO.later';
expectedStrcut(1).extraColumns.Speed.bids.Units = '';

%% test
Expand All @@ -83,13 +83,13 @@ function test_saveEventsFileInitExtraColumnsArray()
expectedStrcut(1).extraColumns.Speed.bids.LongName = '';
expectedStrcut(1).extraColumns.Speed.bids.Description = '';
expectedStrcut(1).extraColumns.Speed.bids.Levels = struct();
expectedStrcut(1).extraColumns.Speed.bids.TermURL = '';
expectedStrcut(1).extraColumns.Speed.bids.TermURL = 'https://www.TODO.later';
expectedStrcut(1).extraColumns.Speed.bids.Units = '';
expectedStrcut(1).extraColumns.LHL24.length = 3;
expectedStrcut(1).extraColumns.LHL24.bids.LongName = '';
expectedStrcut(1).extraColumns.LHL24.bids.Description = '';
expectedStrcut(1).extraColumns.LHL24.bids.Levels = struct();
expectedStrcut(1).extraColumns.LHL24.bids.TermURL = '';
expectedStrcut(1).extraColumns.LHL24.bids.TermURL = 'https://www.TODO.later';
expectedStrcut(1).extraColumns.LHL24.bids.Units = '';

%% test
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