Merge branch 'main' of https://github.com/cpp-lln-lab/CPP_SPM into main

.github/workflows/matlab_workflow_script.m

@@ -9,7 +9,12 @@
 cd(fullfile(root_dir, 'MOxUnit', 'MOxUnit'));
 run moxunit_set_path();
 
-cd(fullfile(root_dir));
+cd(root_dir);
 initCppSpm();
 addpath(fullfile(root_dir, 'tests', 'utils'));
+
+cd demos/MoAE;
+download_moae_ds(true);
+
+cd(root_dir);
 run run_tests();

.github/workflows/run_tests.yml

@@ -63,19 +63,14 @@ jobs:
         
     - name: Update octave path
       run: |
-        octave $OCTFLAGS --eval "initCppSpm; savepath();"
-        octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'tests', 'utils')); savepath();"        
+        octave $OCTFLAGS --eval "initCppSpm; savepath(); exit;"
+        octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'tests', 'utils')); savepath(); exit;"        
 
     - name: Prepare data
       run: |
-        inputs_folder='demos/MoAE/inputs/'
-        mkdir $inputs_folder
-        curl http://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip --output $inputs_folder'MoAEpilot.zip'
-        unzip $inputs_folder'MoAEpilot.zip' -d $inputs_folder
-        mv $inputs_folder/MoAEpilot $inputs_folder/raw
+        octave $OCTFLAGS --eval "initCppSpm; cd demos/MoAE; download_moae_ds(true); exit;"
         cd tests
-        sh createDummyDataSet.sh
-        cd ..
+        make data
 
     - name: Run tests
       run: |

.github/workflows/run_tests_matlab.yml

@@ -39,11 +39,6 @@ jobs:
 
       - name: Prepare data
         run: |
-          inputs_folder='demos/MoAE/inputs/'
-          mkdir $inputs_folder
-          curl http://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip --output $inputs_folder'MoAEpilot.zip'
-          unzip $inputs_folder'MoAEpilot.zip' -d $inputs_folder
-          mv $inputs_folder/MoAEpilot $inputs_folder/raw
           cd tests
           make data
 

.github/workflows/update_submodules.yml

@@ -30,8 +30,6 @@ name: update submodules
 on:
   push:
     branches:
-      - main
-      - master
       - dev
   schedule:
     - cron: "0 0 1 * *"

.gitignore

@@ -20,6 +20,9 @@ venv/*
 ## visual studio code
 .vscode
 
+cfg
+group
+
 ## MATLAB / OCTAVE gitignore template
 
 # From : https://github.com/github/gitignore/blob/master/Global/MATLAB.gitignore

demos/MoAE/download.m

@@ -0,0 +1,65 @@
+function filename = download(URL, output_dir, verbose)
+  %
+  % USAGE::
+  %
+  %   filename = download(URL, output_dir, verbose)
+  %
+  % (C) Copyright 2021 Remi Gau
+  if nargin < 2
+    output_dir = pwd;
+  end
+
+  msg = sprintf('Downloading dataset from:\n %s\n\n', URL);
+  print_to_screen(msg, verbose);
+
+  tokens = regexp(URL, '/', 'split');
+  protocol = tokens{1};
+
+  filename = tokens{end};
+
+  if exist(filename, 'file')
+    delete(filename);
+  end
+
+  if strcmp(protocol, 'http:')
+
+    if isunix()
+      if verbose
+        system(sprintf('wget %s', URL));
+      else
+        system(sprintf('wget -q %s', URL));
+      end
+    else
+      urlwrite(URL, filename);
+    end
+
+    % move file in case it was not downloaded in the root dir
+    if ~exist(fullfile(output_dir, filename), 'file')
+      print_to_screen([filename ' --> ' output_dir], verbose);
+      movefile(filename, fullfile(output_dir, filename));
+    end
+    filename = fullfile(output_dir, filename);
+
+  else
+
+    ftp_server = tokens{3};
+    ftpobj = ftp(ftp_server);
+
+    filename = strjoin(tokens(4:end), '/');
+    filename = mget(ftpobj, filename, output_dir);
+
+  end
+
+  if iscell(filename)
+    filename = filename{1};
+  end
+
+  print_to_screen(' Done\n\n', verbose);
+
+end
+
+function print_to_screen(msg, verbose)
+  if verbose
+    fprintf(1, msg);
+  end
+end

demos/MoAE/download_moae_ds.m

@@ -17,13 +17,18 @@ function download_moae_ds(downloadData)
     spm_mkdir(fullfile(working_directory, 'inputs'));
 
     %% Get data
-    fprintf('%-10s:', 'Downloading dataset...');
-    urlwrite(URL, 'MoAEpilot.zip');
-    fprintf(1, ' Done\n\n');
+    filename = download(URL, fullfile(working_directory, 'inputs'), true);
 
     fprintf('%-10s:', 'Unzipping dataset...');
-    unzip('MoAEpilot.zip');
-    movefile('MoAEpilot', fullfile(working_directory, 'inputs', 'raw'));
+    unzip(filename);
+    if isOctave()
+      movefile(fullfile(working_directory, 'inputs', 'MoAEpilot'), ...
+               fullfile(working_directory, 'inputs', 'raw'));
+      delete(filename);
+    else
+      movefile('MoAEpilot', fullfile(working_directory, 'inputs', 'raw'));
+      delete(filename);
+    end
     fprintf(1, ' Done\n\n');
 
   end

tests/.gitignore

@@ -3,4 +3,5 @@
 */*.json
 group/*
 dummyData/derivatives/cpp_spm*/sub-*/
-dummyData/copy/
+dummyData/copy/
+bids-examples

tests/Makefile

@@ -12,6 +12,7 @@ data:
 	rm -f bids-examples/.gitkeep
 	git clone https://github.com/bids-standard/bids-examples.git --depth 1
 	cp bids-examples/synthetic/dataset_description.json bids-examples/synthetic/derivatives/fmriprep
+	touch bids-examples/.gitkeep
 
 clean_openneuro:
 	rm -rf openneuro/*

tests/miss_hit.cfg

@@ -1 +1,3 @@
 regex_function_name: "(test(_unit){0,1}_[a-z]+|[a-z]+)(([A-Z]){1}[A-Za-z0-9]+)*"
+
+exclude_dir: "bids-examples"