Merge pull request #79 from cpp-lln-lab/remi-highres_pip_refactor

major refactoring reporting for duty

Author: Remi-Gau

.gitignore

@@ -2,12 +2,13 @@
 .DS_Store
 *.asv
 *.m~
+*.mat
 *.nii
 *.xml
 *.log
 *.html
+*.zip
 
-*.mat
 
 # files in the demo folder related to running the demo analysis
 demo/*.zip

.travis.yml

@@ -37,10 +37,12 @@ before_install:
   - make -C spm12/src PLATFORM=octave distclean
   - make -C spm12/src PLATFORM=octave
   - make -C spm12/src PLATFORM=octave install
-  - cd tests
 
 script:
   - octave $OCTFLAGS --eval "runTests"
   - cat test_report.log | grep 0
 
+after_success:
+  - bash <(curl -s https://codecov.io/bash)
+
 

README.md

@@ -1,13 +1,20 @@
+**Code quality and style**
+
 [![](https://img.shields.io/badge/Octave-CI-blue?logo=Octave&logoColor=white)](https://github.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline/actions)
 ![](https://github.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline/workflows/CI/badge.svg) 
 
-[![Build Status](https://travis-ci.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline.svg?branch=master)](https://travis-ci.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline)
+**Unit tests and coverage**
 
+[![Build Status](https://travis-ci.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline.svg?branch=master)](https://travis-ci.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline)
 [![codecov](https://codecov.io/gh/cpp-lln-lab/CPP_BIDS_SPM_pipeline/branch/master/graph/badge.svg)](https://codecov.io/gh/cpp-lln-lab/CPP_BIDS_SPM_pipeline)
 
+**How to cite**
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3556173.svg)](https://doi.org/10.5281/zenodo.3556173)
+
+**Contributors**
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
 [![All Contributors](https://img.shields.io/badge/all_contributors-5-orange.svg?style=flat-square)](#contributors)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3556173.svg)](https://doi.org/10.5281/zenodo.3556173)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 # Instructions for SPM12 Preprocessing Pipeline

demo/batch_download_run.m

@@ -18,7 +18,8 @@
 WD = fileparts(mfilename('fullpath'));
 
 % we add all the subfunctions that are in the sub directories
-addpath(genpath(fullfile(WD, '..')));
+addpath(genpath(fullfile(WD, '..', 'src')));
+addpath(genpath(fullfile(WD, '..', 'lib')));
 
 %% Set options
 opt = getOption();
@@ -37,7 +38,7 @@
 opt.STC_referenceSlice = [];
 opt.sliceOrder = [];
 opt.funcVoxelDims = [];
-opt.JOBS_dir = fullfile(opt.dataDir, '..', 'derivatives', 'SPM12_CPPL', 'JOBS', opt.taskName);
+opt.jobsDir = fullfile(opt.dataDir, '..', 'derivatives', 'SPM12_CPPL', 'JOBS', opt.taskName);
 
 % specify the model file that contains the contrasts to compute
 opt = rmfield(opt, 'model');
@@ -63,9 +64,9 @@
                     'NIDM', true);
 
 %% Get data
-fprintf('%-40s:', 'Downloading dataset...');
-urlwrite(URL, 'MoAEpilot.zip');
-unzip('MoAEpilot.zip', fullfile(WD, 'output'));
+% fprintf('%-40s:', 'Downloading dataset...');
+% urlwrite(URL, 'MoAEpilot.zip');
+% unzip('MoAEpilot.zip', fullfile(WD, 'output'));
 
 %% Check dependencies
 % If toolboxes are not in the MATLAB Directory and needed to be added to
@@ -80,10 +81,10 @@
 checkDependencies();
 
 %% Run batches
-BIDS_copyRawFolder(opt, 1);
-BIDS_STC(opt);
-BIDS_SpatialPrepro(opt);
-BIDS_Smoothing(FWHM, opt);
-BIDS_FFX(1, FWHM, opt, 0);
-BIDS_FFX(2, FWHM, opt, 0);
-BIDS_Results(FWHM, opt, 0);
+bidsCopyRawFolder(opt, 1);
+bidsSTC(opt);
+bidsSpatialPrepro(opt);
+bidsSmoothing(FWHM, opt);
+bidsFFX(1, FWHM, opt, 0);
+bidsFFX(2, FWHM, opt, 0);
+bidsResults(FWHM, [], opt, 0);

getOption.m

@@ -68,7 +68,7 @@
     opt.funcVoxelDims = [];
 
     % Suffix output directory for the saved jobs
-    opt.JOBS_dir = fullfile( ...
+    opt.jobsDir = fullfile( ...
         opt.dataDir, '..', 'derivatives', ...
         'SPM12_CPPL', 'JOBS', opt.taskName);
 

miss_hit.cfg

@@ -1,6 +1,6 @@
 # styly guide (https://florianschanda.github.io/miss_hit/style_checker.html)
 line_length: 100
-regex_function_name: "[a-z]+(([A-Z]){1}[A-Za-z]+)*"
+regex_function_name: "[a-z]+(_*([a-zA-Z0-9]){1}[A-Za-z]+)*" # almost anything goes in the root folder
 suppress_rule: "copyright_notice"
 exclude_dir: "lib"
 

runTests.m

@@ -0,0 +1,23 @@
+warning('OFF');
+
+addpath(fullfile(pwd, 'spm12'));
+addpath(genpath(fullfile(pwd, 'src')));
+addpath(genpath(fullfile(pwd, 'lib')));
+
+spm('defaults', 'fMRI');
+
+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

subfun/checkDependencies.m src/checkDependencies.msubfun/checkDependencies.m renamed to src/checkDependencies.m

@@ -1,4 +1,6 @@
-function [fileName, subFuncDataDir] = getBoldFilename(BIDS, subNumber, sessions, runs, opt)
+function [fileName, subFuncDataDir] = getBoldFilename(varargin)
+
+    [BIDS, subNumber, sessions, runs, opt] = deal(varargin{:});
 
     % get the filename for this bold run for this task
     fileName =  getInfo(BIDS, subNumber, opt, 'Filename', sessions, runs, 'bold');