Unit testing BpodSystem and protocol running locally and on GitHub Actions

.github/workflows/runAllTests.yml

@@ -25,14 +25,14 @@ jobs:
       - name: Setup environment
         uses: matlab-actions/run-command@v2
         with:
-          command: addpath('Tests'); setupGithubEnvironment;
+          command: addpath('Tests/'); setupGithubEnvironment;
 
       # Runs a set of commands using the runners shell
       - name: Run all tests
         uses: matlab-actions/run-tests@v2
         with:
-          source-folder: Functions/
-          select-by-folder: Tests/BpodLib/
+          source-folder: Functions/; Tests/
+          select-by-folder: Tests/BpodLib/; Tests/Integrations/
 
   test-windows:
     runs-on: windows-latest
@@ -48,11 +48,11 @@ jobs:
       - name: Setup environment
         uses: matlab-actions/run-command@v2
         with:
-          command: addpath('Tests'); setupGithubEnvironment;
+          command: addpath('Tests/'); setupGithubEnvironment;
 
       # Runs a set of commands using the runners shell
       - name: Run all tests
         uses: matlab-actions/run-tests@v2
         with:
-          source-folder: Functions/
-          select-by-folder: Tests/BpodLib/
+          source-folder: Functions/; Tests/
+          select-by-folder: Tests/BpodLib/; Tests/Integrations/

.gitignore

@@ -0,0 +1,2 @@
+*.asv
+.vscode

Bpod.m

@@ -101,8 +101,7 @@ function Bpod(varargin)
         end
     end
 end
-BpodLib.calibration.liquid.io.report(BpodSystem.CalibrationTables.LiquidCal)
-BpodLib.path.verifyPathing(BpodSystem);
+
 
 function emulator_setup(varargin)
 % Runs setup with emulator mode flag set to 'true'.
@@ -119,10 +118,12 @@ function emulator_setup(varargin)
 BpodSystem.SetupHardware();
 BpodSystem.InitializeGUI();
 BpodSystem.Status.Initialized = true;
+BpodLib.calibration.liquid.io.report(BpodSystem.CalibrationTables.LiquidCal)
+BpodLib.path.verifyPathing(BpodSystem);
 evalin('base', 'global BpodSystem')
 
 function emulator_dialog
-% Launches a GUI indicating that hardware connection has failed.
+% Launches a  non-modal GUI indicating that hardware connection has failed.
 % Prompts the user to start emulator mode or close the program.
 global BpodSystem
 BpodErrorSound;

Functions/+BpodLib/+BpodObject/+setup/updatePathAndSettings.m

@@ -120,10 +120,10 @@ function updatePathAndSettings(BpodSystem, varargin)
     if strcmp(BpodLib.calibration.liquid.utils.checkCOM(BpodSystem), 'no')
         if p.Results.verbose
             warning('BpodLib:Calibration:Liquid:CheckCOM', 'Calibration file does not match the detected state machine''s USB serial port.');
-            msg = msgbox(sprintf("Detected state machine USB serial port (%s) does not match the port used to create the current liquid calibration: (%s).\nPlease either initialize a multi-machine setup or re-run calibration.", ...
-                BpodLib.utils.getCurrentCOM(BpodSystem), BpodSystem.CalibrationTables.LiquidCal.metadata.COM), ...
-                'Calibration USB Port mismatch', 'warn', 'modal');
-            uiwait(msg)
+            BpodSystem.GUIHandles.LiquidCalWarningMessageBox = ...
+                msgbox(sprintf("Detected state machine USB serial port (%s) does not match the port used to create the current liquid calibration: (%s).\nPlease either initialize a multi-machine setup or re-run calibration.", ...
+                    BpodLib.utils.getCurrentCOM(BpodSystem), BpodSystem.CalibrationTables.LiquidCal.metadata.COM), ...
+                    'Calibration USB Port mismatch', 'warn', 'non-modal');
         end
     end
 catch err

Functions/+BpodLib/+launcher/+ui/loadProtocols.m

@@ -0,0 +1,6 @@
+function loadProtocols(BpodSystem)
+% Update the list of available protocols in the GUI
+
+ProtocolNames = BpodLib.launcher.findProtocols(BpodSystem);
+set(BpodSystem.GUIHandles.ProtocolSelector, 'String', ProtocolNames);
+end

Functions/+BpodLib/+launcher/+ui/loadSettings.m

@@ -0,0 +1,9 @@
+function loadSettings(BpodSystem, protocolName, subjectName)
+% Populate UI with settings files for the selected subject and protocol
+
+settingsFileNames = BpodLib.launcher.findSettings(BpodSystem.Path.DataFolder, protocolName, subjectName);
+
+set(BpodSystem.GUIHandles.SettingsSelector, 'String', settingsFileNames);
+set(BpodSystem.GUIHandles.SettingsSelector,'Value',1);
+
+end

Functions/+BpodLib/+launcher/+ui/loadSubjects.m

@@ -0,0 +1,9 @@
+function loadSubjects(BpodSystem, protocolName)
+% Load all subjects in the data folder that have a folder for the given protocol
+
+subjectNames = BpodLib.launcher.findSubjects(BpodSystem.Path.DataFolder, protocolName, BpodSystem.GUIData.DummySubjectString);
+
+set(BpodSystem.GUIHandles.SubjectSelector,'String',subjectNames);
+set(BpodSystem.GUIHandles.SubjectSelector,'Value',1);
+
+end

Functions/+BpodLib/+launcher/+ui/setDataFilePath.m

@@ -0,0 +1,14 @@
+function setDataFilePath(BpodSystem, protocolName, subjectName)
+
+dataFolder = BpodSystem.Path.DataFolder;
+dataFilePath = BpodLib.launcher.createDataFilePath(dataFolder, protocolName, subjectName);
+localDir = dataFolder(max(find(dataFolder(1:end-1) == filesep)+1):end);
+[~, fileName, ext] = fileparts(dataFilePath);
+fileName = [fileName ext];
+
+BpodSystem.Path.CurrentDataFile = dataFilePath;
+
+set(BpodSystem.GUIHandles.DataFilePathDisplay, 'String',... 
+    [filesep fullfile(localDir, subjectName, protocolName, 'Session Data') filesep],'interpreter','none');
+set(BpodSystem.GUIHandles.DataFileDisplay, 'String', fileName);
+end

Functions/+BpodLib/+launcher/createDataFilePath.m

@@ -0,0 +1,20 @@
+function dataFilePath = createDataFilePath(dataFolder, protocolName, subjectName)
+% Create a file path for the data file to be saved
+%
+% Inputs
+% ------
+% dataFolder : char
+%     The path to the data folder (e.g. Local Data/Data/)
+% protocolName : char
+%     The name of the protocol
+% subjectName : char
+%     The name of the subject
+
+dateInfo = datestr(now, 30);
+dateInfo(dateInfo == 'T') = '_';
+fileName = [subjectName '_' protocolName '_' dateInfo '.mat'];
+
+
+dataFilePath = fullfile(dataFolder, subjectName, protocolName, 'Session Data', fileName);
+
+end

Functions/+BpodLib/+launcher/createDefaultSettingsFile.m

@@ -0,0 +1,11 @@
+function createDefaultSettingsFile(dataFolder, subjectName, protocolName)
+% Create a default (empty) settings file for the given subject and protocol
+% Only creates the file if it does not already exist
+
+defaultSettingsFilePath = fullfile(dataFolder, subjectName, protocolName, 'Session Settings', 'DefaultSettings.mat');
+if ~exist(defaultSettingsFilePath)
+    ProtocolSettings = struct;
+    save(defaultSettingsFilePath, 'ProtocolSettings')
+end
+
+end

Functions/+BpodLib/+launcher/findProtocols.m

@@ -0,0 +1,50 @@
+function ProtocolNames = findProtocols(BpodSystem)
+% ProtocolNames = findProtocols(BpodSystem)
+% Returns a cell array of protocol names found in the ProtocolFolder
+
+
+if strcmp(BpodSystem.Path.ProtocolFolder, BpodSystem.SystemSettings.ProtocolFolder)  % todo: make this less janky?
+    startPos = 3;
+else
+    startPos = 2;
+end
+Candidates = dir(BpodSystem.Path.ProtocolFolder);
+ProtocolNames = cell(0);
+nProtocols = 0;
+for x = startPos:length(Candidates)
+    if Candidates(x).isdir
+        ProtocolFolder = fullfile(BpodSystem.Path.ProtocolFolder, Candidates(x).name);
+        Contents = dir(ProtocolFolder);
+        nItems = length(Contents);
+        Found = 0;
+        for y = 3:nItems
+            if strcmp(Contents(y).name, [Candidates(x).name '.m'])
+                Found = 1;
+            end
+        end
+        if Found
+            ProtocolName = Candidates(x).name;
+        else
+            ProtocolName = ['<' Candidates(x).name '>'];
+        end
+        nProtocols = nProtocols + 1;
+        ProtocolNames{nProtocols} = ProtocolName;
+    end
+end
+
+if isempty(ProtocolNames)
+    ProtocolNames = {'No Protocols Found'};
+else
+    % Sort to put organizing directories first
+    Types = ones(1,nProtocols);
+    for i = 1:nProtocols
+        ProtocolName = ProtocolNames{i};
+        if ProtocolName(1) == '<'
+            Types(i) = 0;
+        end
+    end
+    [a, Order] = sort(Types);
+    ProtocolNames = ProtocolNames(Order);
+end
+
+end

Functions/+BpodLib/+launcher/findSettings.m

@@ -0,0 +1,18 @@
+function settingsFileNames = findSettings(dataFolder, protocolName, subjectName)
+% Find all settings files in the Settings folder for a given protocol and subject
+
+settingsPath = fullfile(dataFolder, subjectName, protocolName, 'Session Settings');
+candidates = dir(settingsPath);
+nSettingsFiles = 0;
+settingsFileNames = cell(1);
+for x = 3:length(candidates)
+    extension = candidates(x).name;
+    extension = extension(end-2:end);
+    if strcmp(extension, 'mat')
+        nSettingsFiles = nSettingsFiles + 1;
+        name = candidates(x).name;
+        settingsFileNames{nSettingsFiles} = name(1:end-4);
+    end
+end
+
+end

Functions/+BpodLib/+launcher/findSubjects.m

@@ -0,0 +1,21 @@
+function subjectNames = findSubjects(dataFolder, protocolName, dummySubjectString)
+% Find all subjects in the data folder that have a folder for the given protocol
+
+candidateSubjects = dir(dataFolder);
+subjectNames = cell(1);
+nSubjects = 1;
+subjectNames{1} = dummySubjectString;
+for x = 1:length(candidateSubjects)
+    if x > 2
+        if candidateSubjects(x).isdir
+            if ~strcmp(candidateSubjects(x).name, dummySubjectString)
+                testpath = fullfile(dataFolder,candidateSubjects(x).name,protocolName);
+                if exist(testpath) == 7
+                    nSubjects = nSubjects + 1;
+                    subjectNames{nSubjects} = candidateSubjects(x).name;
+                end
+            end
+        end
+    end
+end
+end