[ENH] Misc

.github/workflows/bids_validator.yml

@@ -37,7 +37,7 @@ jobs:
 
     - name: Install BIDS validator
       run: |
-        sudo npm install -g bids-validator@1.6.2
+        sudo npm install -g bids-validator@1.9.0
 
     - name: Create dummy dataset and validate it
       run: |

.gitignore

@@ -1,16 +1,13 @@
 # exclude mac file
 *DS_Store
 
-# exclude matlab autosaves and octave workspace info
-*.m~
-*octave-workspace
-
 # exclude content of logfiles folders
 *output*
 *.mat
 
 # exclude temp files from tests and coverage
 *test_code_report.txt
+test_report.log
 *coverage*
 
 *filteredBy*
@@ -23,20 +20,60 @@ tests/*.tsv*
 check_my_code_report.txt
 
 # jupyter notebook checkpoints
-notebooks/.ipynb_checkpoints/*
 notebooks/source/*
 notebooks/output/*
 notebooks/new_experiment/*
 
 # ignore node js files
 node_modules/*
 package-lock.json
+package.json
 
 # visual studio code stuff
 .vscode
 
 # virtual env
 cpp_bids/*
+env/
 
 # documentation
 docs/build/*
+
+# jupyter notebooks
+.ipynb_checkpoints
+
+## MATLAB / OCTAVE gitignore template
+
+# From : https://github.com/github/gitignore/blob/master/Global/MATLAB.gitignore
+
+# Windows default autosave extension
+*.asv
+
+# OSX / *nix default autosave extension
+*.m~
+
+# Compiled MEX binaries (all platforms)
+*.mex*
+
+# Packaged app and toolbox files
+*.mlappinstall
+*.mltbx
+
+# Generated helpsearch folders
+helpsearch*/
+
+# Simulink code generation folders
+slprj/
+sccprj/
+
+# Matlab code generation folders
+codegen/
+
+# Simulink autosave extension
+*.autosave
+
+# Simulink cache files
+*.slxc
+
+# Octave session info
+octave-workspace

CITATION.cff

@@ -2,7 +2,7 @@ cff-version: 1.2.0
 
 title: "CPP BIDS"
 
-version: 2.1.1dev
+version: 2.1.2dev
 
 abstract: A lightweight Octave/MATLAB toolbox to help create BIDS data sets from source.
 

Makefile

@@ -0,0 +1,25 @@
+# TODO make more general to use the local matlab version
+MATLAB = /usr/local/MATLAB/R2017a/bin/matlab
+ARG    = -nodisplay -nosplash -nodesktop
+
+.PHONY: clean manual clean_demos fix_submodule
+clean: clean_demos
+	rm -rf version.txt
+
+fix_submodule:
+	git submodule update --init --recursive && git submodule update --recursive
+
+lint:
+	mh_style --fix && mh_metric --ci && mh_lint
+
+test:
+	$(MATLAB) $(ARG) -r "runTests; exit()"
+
+version.txt: CITATION.cff
+	grep -w "^version" CITATION.cff | sed "s/version: /v/g" > version.txt
+
+validate_cff: CITATION.cff
+	cffconvert --validate
+
+manual:
+	cd docs && sh create_manual.sh

checkCppBidsDependencies.m

@@ -46,7 +46,9 @@ function checkCppBidsDependencies(cfg)
         CPP_BIDS_INITIALIZED = true();
 
     else
-        fprintf(1, '\n\nCPP_BIDS already initialized\n\n');
+        if cfg.verbose
+            fprintf(1, '\n\nCPP_BIDS already initialized\n\n');
+        end
 
     end
 

docs/create_manual.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+sphinx-build -M latexpdf source build
+
+cp build/latex/cppbids.pdf cpp_spm-manual.pdf

docs/source/conf.py

@@ -22,7 +22,7 @@
 author = 'the CPP BIDS dev team'
 
 # The full version, including alpha/beta/rc tags
-release = 'v1.0.0'
+release = 'v2.1.2dev'
 
 
 # -- General configuration ---------------------------------------------------

docs/source/utilities.rst

@@ -13,8 +13,6 @@ List of functions in the ``utils`` folder.
 .. autofunction:: isPositiveInteger
 .. autofunction:: nanPadding
 .. autofunction:: printCreditsCppBids
-.. autofunction:: removeAllDateSuffix
-.. autofunction:: removeDateSuffix
 .. autofunction:: returnHeaderName
 .. autofunction:: returnNamesExtraColumns
 .. autofunction:: returnNbColumns

runTests.m

@@ -0,0 +1,42 @@
+function runTests()
+    %
+    % (C) Copyright 2022 CPP_BIDS developers
+
+    % Elapsed time is ??? seconds.
+
+    tic;
+
+    cd(fileparts(mfilename('fullpath')));
+
+    cfg.verbose = 0;
+    checkCppBidsDependencies(cfg);
+
+    if bids.internal.is_github_ci
+        fprintf(1, '\nThis is github CI\n');
+    else
+        fprintf(1, '\nThis is not github CI\n');
+    end
+
+    fprintf('\nHome is %s\n', getenv('HOME'));
+
+    warning('OFF');
+
+    folderToCover = fullfile(pwd, 'src');
+    testFolder = fullfile(pwd, 'tests');
+
+    success = moxunit_runtests( ...
+                               testFolder, ...
+                               '-verbose', '-recursive', '-with_coverage', ...
+                               '-cover', folderToCover, ...
+                               '-cover_xml_file', 'coverage.xml', ...
+                               '-cover_html_dir', fullfile(pwd, 'coverage_html'));
+
+    if success
+        system('echo 0 > test_report.log');
+    else
+        system('echo 1 > test_report.log');
+    end
+
+    toc;
+
+end

src/convertSourceToRaw.m

@@ -34,26 +34,31 @@ function convertSourceToRaw(cfg)
 
     copyfile(sourceDir, rawDir);
 
-    % list subjects
-    subjects = cellstr(bids.internal.file_utils('List', rawDir, 'dir', '^sub-.*$'));
+    BIDS = bids.layout(rawDir,  'use_schema', false);
 
-    if isequal(subjects, {''})
-        error('No subjects found in BIDS directory.');
-    end
+    data = bids.query(BIDS, 'data');
+    metadata = bids.query(BIDS, 'metadata');
 
-    % go through the subject files and parses them to remove the date suffix
-    for su = 1:numel(subjects)
+    for i = 1:size(data, 1)
+        bf = bids.File(data{i});
+        if isfield(bf.entities, 'date')
+            % TODO probably JSON renaming should be passed to bids-matlab
+            sourceJson = fullfile(fileparts(bf.path), bf.json_filename);
+            bf.entities.date = '';
+            bf.rename('dry_run', false, 'force', true);
+            bids.util.jsonencode(fullfile(fileparts(bf.path), bf.json_filename), metadata{i});
+            delete(sourceJson);
+        end
+    end
 
-        sess = cellstr(bids.internal.file_utils('List', ...
-                                                fullfile(rawDir, ...
-                                                         subjects{su}), ...
-                                                'dir', ...
-                                                '^ses-.*$'));
+    BIDS = bids.layout(rawDir,  'use_schema', false);
+    data = bids.query(BIDS, 'data', 'suffix', {'stim', 'physio' }, 'ext', '.tsv');
 
-        for se = 1:numel(sess)
-            removeAllDateSuffix(rawDir, subjects{su}, sess{se});
+    for i = 1:size(data, 1)
+        gzip(data{i});
+        if exist(data{i}, 'file')
+            delete(data{i});
         end
-
     end
 
 end

src/saveEventsFile.m

@@ -10,8 +10,10 @@
     %                ``'init'``, ``'init_stim'``, ``'open'``, ``'save'`` or ``'close'``.
     %                For more information on each case see below.
     % :type action: string
+    %
     % :param cfg: Configuration variable. See ``checkCFG()``.
     % :type cfg: structure
+    %
     % :param logFile: (n x 1) The ``logFile`` variable that contains the n events
     %                 you want to save must be a nx1 structure.
     % :type logFile: structure

src/utils/isPositiveInteger.m

@@ -13,11 +13,25 @@
     %
     % (C) Copyright 2020 CPP_BIDS developers
 
-    trueOrFalse = ~any([ ...
-                        ~isnumeric(input2check), ...
-                        isnan(input2check), ...
-                        fix(input2check) ~= input2check, ...
-                        input2check < 0 ...
-                       ]);
+    if ~isnumeric(input2check)
+        trueOrFalse = false;
+        return
+    end
+
+    if numel(size(input2check)) > 2 || all(size(input2check) > 1)
+        bids.internal.error_handling(mfilename(), ...
+                                     'sizeIssue', ...
+                                     'Input must be scalar or vector.', ...
+                                     false);
+    end
+
+    if size(input2check, 1) > 1
+        input2check = input2check';
+    end
+
+    trueOrFalse = any(~any([isnan(input2check); ...
+                            fix(input2check) ~= input2check; ...
+                            input2check < 0 ...
+                           ]));
 
 end