Merge branch 'development' into 'master'

Merge new CI Test into master

See merge request !64

+PlotID/@config/config.m

@@ -22,7 +22,7 @@ classdef config < handle
             %   wizard is started by the catch block
             obj.configFileName = configFileName;
             try %Validity Check
-              tmp = what("PlotID");
+              tmp = what("+PlotID");
               tmp = strrep(tmp.path,'+PlotID','');
               defaultConfigPath = fullfile(tmp,obj.configFileName);
               if isfile(defaultConfigPath)

+PlotID/Publish.m

@@ -57,7 +57,7 @@ end
 
 % find scriptpath
 if ~isfile(scriptPath)
-    scriptPath= which(['/',scriptPath]);
+    scriptPath= which(scriptPath);
     if ~isfile(scriptPath)
         msg = ['Script path: ',scriptPath, ' not found on matlab path', newline, ...
             '- check spelling or us a path']; 

+PlotID/copyUserFCN.m

@@ -36,8 +36,8 @@ function [fListClean] = removePltIdFiles(fList)
     PltID_classlist = packageContent.classes;
     
     % Class Methods need to be listed in an additional function
-    Class_flist = cell(1,numel(packageContent.classes)); %preallocate 
-    for i=1:numel(packageContent.classes)
+    Class_flist = cell(1,numel(PltID_classlist)); %preallocate 
+    for i=1:numel(PltID_classlist)
         temp = what(['PlotID',filesep,'@',PltID_classlist{i}]);
         Class_flist{i} = temp.m; 
     end

.gitlab-ci.yml

 #Based on STFS Workshop
 stages:
-    - Run
-Test Code:
-    stage: Run
+    - Testing
+Default Test:
+    stage: Testing
     tags:
         - matlab
         - bash
@@ -18,3 +18,21 @@ Test Code:
 
         when: always
         expire_in: 1 week
+
+Example Test:
+    stage: Testing
+    tags:
+        - matlab
+        - bash
+    script:
+        - cd ./CI_files
+        - chmod +x ./run_example_test.sh
+        - ./run_example_test.sh
+        - cat ./log.txt
+    artifacts:
+        paths:
+         - ./CI_files/log.txt
+         - ./CI_files/matlab_log.txt
+
+        when: always
+        expire_in: 1 week

CI_files/default_test.m

@@ -2,8 +2,6 @@ function [result] = default_test()
 %default_test() This is a simple test if Plot ID works for the default settings
 %   Detailed explanation goes here
 
-clear; clc; close all;
-
 % set path
 % starting path of gitlab runner is in CI_files
 if contains(pwd,'CI_files')

CI_files/example_test.m

+function [result] = example_test()
+%   example This is a test if all PlotID example works run through
+
+% prevent function to be affected by clear commands in examples
+ciTest = true; 
+
+% set path
+% starting path of gitlab runner is in CI_files
+if contains(pwd,'CI_files')
+    cd .. % move one directory up
+end
+
+addpath('CI_files','Examples');
+
+% clean up, if previous run failed
+try
+    delete(['CI_files' filesep 'PlotID_export' filesep '*']);
+    delete(['CI_files' filesep '*.mat']);
+    delete(['CI_files' filesep '*.h5']);
+    rmdir(['CI_files' filesep 'PlotID_export'],'s');
+end
+
+
+exampleList = {'PlotID_example','PlotID_advanced',...
+     'PlotID_QRcode', 'PlotID_variables' };
+
+
+% initialise
+numberOfTests = numel(exampleList);
+testResults = zeros(numberOfTests,1);
+
+%start log
+fid = fopen(fullfile('CI_files','log.txt'),'w');
+txt = ['default test started ' newline];
+fprintf(fid,txt);
+
+% create Config for CI-Tests
+fid1 = fopen(fullfile('CI_files','config.json'),'w');
+configData.Author = 'CI-Test'; configData.ProjectID = 'CI-001';
+txt = jsonencode(configData,'PrettyPrint',true);
+%fprintf does not write paths correctly !!!
+fwrite(fid1,txt);
+fclose(fid1);
+
+%% Testing Loop
+for i=1:numberOfTests
+    clearvars -except i fid exampleList testResults
+    try
+        runExample(exampleList{i});
+        msg = ['example_test succeed example ', exampleList{i}];        
+    catch
+        testResults(1) = 1; %test fails
+        msg = ['example_test failed at example', exampleList{i}];
+        warning(msg);
+    end
+    
+    fprintf(fid,[msg, newline]);
+end
+
+
+%% Test result
+if any(testResults)
+    result = 1; %fail
+    warning('test failed');
+else
+    result = 0; % pass
+    disp('test succeed');
+end
+
+fclose(fid);
+
+% final clean up
+try
+    delete(['CI_files' filesep 'PlotID_export' filesep '*']);
+    delete(['CI_files' filesep '*.mat']);
+    delete(['CI_files' filesep '*.h5']);
+    rmdir(['CI_files' filesep 'PlotID_export'],'s');
+    delete(fullfile('CI_files','CI_config.json'));
+end
+
+end
+
+function runExample(scriptName)
+% runExample prevents scripts to infulence the CI script
+    run(scriptName);
+    
+end
+

CI_files/run_example_test.sh

+#!/bin/bash
+
+#matlab -r "disp(['Current folder: ' pwd])"
+matlab $@ -nodisplay -nodesktop -nosplash -logfile matlab_log.txt -r "example_test;exit(ans);"
+
+exitstatus=$?
+if [[ $exitstatus -eq '0' ]]
+then 
+    echo "matlab succeed. Exitstatus: $exitstatus"
+    exit $exitstatus
+else
+    echo "matlab failed. Exitstatus: $exitstatus"
+    exit $exitstatus
+
+fi

Examples/PlotID_QRcode.m

-clear; close all; clc;
+clearEnv;
 %%  Tag the plot with a QR code (experimental)
 % here the work flow for tagging the plot with a QR code is shown
 % the content of the qr code is the ID
 
 % plots and data
-fig(1) = figure;
+fig = figure;
 [x1, y1, datapath1] = createExampleData('matlab');
 plot(x1,y1,'-b'); box off; hold on; set(gca, 'TickDir', 'out', 'YLim', [0,4]);
 

Examples/PlotID_advanced.m

-clear; close all; clc;
+clearEnv;
 %%  Tag and export multiple plots
 % here the work flow for tagging and exporting multiple plots is shown
 

Examples/PlotID_centralized.m

-clear; close all; clc;
+clearEnv;
 %%  multiple plots from the same data-set (centralized method)
 % A central data folder is used for saving the research data files, the
 % subfolders contain linked hdf5-files (if hdf5 is used) otherwise the data

Examples/PlotID_variables.m

-clear; clc; close all;
+clearEnv;
 %% Example Script - How to pass Variables
 % This script how to pass variables instead or additional to the DataPaths
-
+addpath('Examples');
 %% Data (only necessary for this example)
 [x, y, datapath] = createExampleData('matlab');
 scriptPath = mfilename('fullpath');

Examples/clearEnv.m

+function [] = clearEnv()
+%CLEARENV clears Environment with exception for CI testing.
+
+if ~exist('ciTest', 'var') 
+    clear; close all; clc;
+end
+
+end
+

PlotID_example.m

@@ -3,7 +3,7 @@
 % please run Initilisation.m before first time use
 
 %% Clear and set environment
-clear; clc; close all;
+clearEnv; % contains clear clc, close all
 addpath('Examples');
 
 %% Data (only necessary for this example)