[ENH & REF] improve and refactor UI

.gitignore

@@ -2,30 +2,31 @@
 *DS_Store
 
 # exclude content of logfiles folders
-*output*
+output
+
 *.mat
 
 # exclude temp files from tests and coverage
 *test_code_report.txt
 test_report.log
 *coverage*
+test_report.log
+check_my_code_report.txt
 
 *filteredBy*
 
 tests/*.nii*
 tests/*.json*
 tests/*.tsv*
 
-# exclude report from check_my_code
-check_my_code_report.txt
-
 # jupyter notebook checkpoints
+.ipynb_checkpoints
 notebooks/source/*
-notebooks/output/*
 notebooks/new_experiment/*
 
 # ignore node js files
 node_modules/*
+package.json
 package-lock.json
 package.json
 
@@ -34,14 +35,11 @@ package.json
 
 # virtual env
 cpp_bids/*
-env/
+env
 
 # documentation
 docs/build/*
 
-# jupyter notebooks
-.ipynb_checkpoints
-
 ## MATLAB / OCTAVE gitignore template
 
 # From : https://github.com/github/gitignore/blob/master/Global/MATLAB.gitignore

Makefile

@@ -2,13 +2,16 @@
 MATLAB = /usr/local/MATLAB/R2017a/bin/matlab
 ARG    = -nodisplay -nosplash -nodesktop
 
+<<<<<<< HEAD
+=======
 .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
 
+>>>>>>> 3a67904c66439e90c8fc528ac8729254b91d56d6
 lint:
 	mh_style --fix && mh_metric --ci && mh_lint
 

README.md

@@ -1,3 +1,5 @@
+<!-- markdown-link-check-disable -->
+
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/cpp-lln-lab/CPP_BIDS/master?filepath=notebooks%2Fbasic_usage.ipynb)
 [![Documentation Status: stable](https://readthedocs.org/projects/cpp-bids/badge/?version=stable)](https://cpp-bids.readthedocs.io/en/stable/?badge=stable)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4007674.svg)](https://doi.org/10.5281/zenodo.4007674)
@@ -6,6 +8,8 @@
 [![codecov](https://codecov.io/gh/cpp-lln-lab/CPP_BIDS/branch/master/graph/badge.svg)](https://codecov.io/gh/cpp-lln-lab/CPP_BIDS)
 [![All Contributors](https://img.shields.io/badge/all_contributors-3-orange.svg?style=flat-square)](#contributors-)
 
+<!-- markdown-link-check-enable -->
+
 # CPP_BIDS
 
 A set of function for matlab and octave to create

checkCppBidsDependencies.m

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

docs/source/index.rst

@@ -10,7 +10,7 @@ Welcome to CPP BIDS documentation!
    set_up
    function_description
    utilities
-   gui
+   ui
 
 A set of function for matlab and octave to create
 `BIDS-compatible <https://bids-specification.readthedocs.io/en/stable/>`_

docs/source/ui.rst

@@ -0,0 +1,16 @@
+User interface
+*****************
+
+List of functions in the ``ui`` folder: those are mostly to handle the "graphic interface"
+that can be used to deal with ``userInputs()``.
+
+----
+
+.. automodule:: src.ui
+
+.. autofunction:: askUserCli
+.. autofunction:: askUserGui
+
+.. autofunction:: createQuestionnaire
+.. autofunction:: askForGroupAndOrSession
+.. autofunction:: getIsQuestionToAsk

docs/source/utilities.rst

@@ -17,7 +17,3 @@ List of functions in the ``utils`` folder.
 .. autofunction:: returnNamesExtraColumns
 .. autofunction:: returnNbColumns
 .. autofunction:: setDefaultFields
-
-.. automodule:: src.gui
-
-.. autofunction:: askUserCli

runTests.m

@@ -6,31 +6,28 @@ function runTests()
 
     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
+    thisPath = fileparts(mfilename('fullpath'));
 
+    cd(thisPath);
     fprintf('\nHome is %s\n', getenv('HOME'));
 
     warning('OFF');
 
-    folderToCover = fullfile(pwd, 'src');
-    testFolder = fullfile(pwd, 'tests');
+    addpath(fullfile(thisPath, 'lib', 'JSONio'));
+    addpath(fullfile(thisPath, 'lib', 'bids-matlab'));
+
+    folderToCover = fullfile(thisPath, 'src');
+    addpath(genpath(folderToCover));
+    testFolder = fullfile(thisPath, 'tests');
+    addpath(testFolder);
 
     addpath(fullfile(testFolder, 'utils'));
 
     success = moxunit_runtests(testFolder, ...
                                '-verbose', '-recursive', '-with_coverage', ...
                                '-cover', folderToCover, ...
                                '-cover_xml_file', 'coverage.xml', ...
-                               '-cover_html_dir', fullfile(pwd, 'coverage_html'));
+                               '-cover_html_dir', fullfile(thisPath, 'coverage_html'));
 
     if success
         system('echo 0 > test_report.log');

src/checkCFG.m

@@ -202,8 +202,10 @@
                                       'output');
 
     fieldsToSet.subject.askGrpSess = [true true];
-    fieldsToSet.subject.sessionNb = 1; % in case no session was provided
-    fieldsToSet.subject.subjectGrp = ''; % in case no group was provided
+    fieldsToSet.subject.sessionNb = []; % in case no session was provided
+    fieldsToSet.subject.subjectGrp = []; % in case no group was provided
+    fieldsToSet.subject.runNb = [];
+    fieldsToSet.subject.subjectNb = [];
 
     fieldsToSet.testingDevice = 'pc';