fix: GH workflow test

.github/workflows/check-metabolictasks.yml

@@ -10,10 +10,9 @@ jobs:
       matrix:
         task-type: [essential, verification]
     steps:
+      - name: Checkout
+        uses: actions/checkout@v3
 
-    - name: Checkout
-      uses: actions/checkout@v3
-
-    - name: Check ${{ matrix.task-type }} metabolic tasks
-      run: |
-        /usr/local/bin/matlab -nodisplay -nosplash -nodesktop -r "addpath(genpath('.')); testMetabolicTasks('${{ matrix.task-type }}'); exit;"
+      - name: Check ${{ matrix.task-type }} metabolic tasks
+        run: |
+          /usr/local/bin/matlab -nodisplay -nosplash -nodesktop -r "addpath(genpath('.')); testMetabolicTasks('${{ matrix.task-type }}');"

.github/workflows/yaml-conversion.yml

@@ -8,10 +8,9 @@ jobs:
     timeout-minutes: 60
 
     steps:
+      - name: Checkout
+        uses: actions/checkout@v3
 
-    - name: Checkout
-      uses: actions/checkout@v3
-
-    - name: Run conversion script
-      run: |
-        /usr/local/bin/matlab -nodisplay -nosplash -nodesktop -r "addpath(genpath('.')); run('code/test/testYamlConversion.m'); exit;" 
+      - name: Run conversion script
+        run: |
+          /usr/local/bin/matlab -nodisplay -nosplash -nodesktop -r "addpath(genpath('.')); testYamlConversion"

.github/workflows/yaml-validation.yml

@@ -25,5 +25,8 @@ jobs:
           ## Return non-zero exit code on warnings as well as errors
           # strict: # optional, default is false
 
+      - name: Basic MEMOTE tests
+        run: python code/test/memoteTest.py
+
       - name: Test import with cobrapy and consistency with annotation files
-        run: python code/test/sanityCheck.py
+        run: python code/test/sanityCheck.py

code/io/importYaml.m

@@ -226,7 +226,7 @@
 
             otherwise
                 if readSubsystems
-                    subSystems = {regexprep(tline_value, '^ *- (.+)$','$1')};
+                    subSystems(end+1,1) = {regexprep(tline_value, '^ *- (.+)$','$1')};
 
                 % resolve the equation
                 elseif readEquation

code/test/memoteTest.py

@@ -0,0 +1,18 @@
+import cobra
+import memote.support.basic
+
+if __name__ == "__main__":
+    try:
+        model = cobra.io.load_yaml_model("model/Human-GEM.yml")
+
+        # Use the MEMOTE way of testing
+        # https://github.com/opencobra/memote/blob/c8bd3fe75e2d955deaec824d1e93ebe60e754710/tests/test_for_support/test_for_basic.py#L908-L909
+        rxns, num = memote.support.basic.find_duplicate_reactions(model)
+        assert num == 0, "Duplicate reactions found: {}".format(rxns)
+
+        # Make sure all reactions have at least one metabolite
+        for r in model.reactions:
+            assert len(r.metabolites) > 0, "Reaction with no metabolite found: {}".format(r.id)
+    except AssertionError as e:
+        print(e)
+        exit(1)

code/test/testMetabolicTasks.m

@@ -10,7 +10,8 @@
 %
 
 if nargin < 1
-    error('Task type is missing!');
+    disp('::error::Task type is missing!');
+    exit(1)
 end
 
 % Get model path
@@ -28,7 +29,8 @@
 elseif taskType == "verification"
     taskFile=fullfile(modelPath,'data','metabolicTasks','metabolicTasks_VerifyModel.txt');
 else
-    error('Unknown task type is provided.');
+    warning('::error::Unknown task type is provided.');
+    exit(1)
 end
 verificationTasks = parseTaskList(taskFile);
 
@@ -38,6 +40,6 @@
     fprintf('Suceeded with %s tasks.\n', taskType)
     status = 1;
 else
-    error('Failed in %s tasks.', taskType);
+    warning('::error::Failed in %s tasks.', taskType);
+    exit(1)
 end
-

code/test/testYamlConversion.m

@@ -2,42 +2,40 @@
 % test the functions for yaml import/export see if the conversion process
 % changes the model content
 %
-% Usage: status = testYamlConversion
-%
-
 
 % Get model path
 [ST, I]=dbstack('-completenames');
 modelPath=fileparts(fileparts(fileparts(ST(I).file)));
 
-% Import yaml model
-ymlFile=fullfile(modelPath,'model','Human-GEM.yml');
-model = importYaml(ymlFile, true);
+% export to yml and then import back
+try
 
-% make sure there is no intermediate Yaml file under the current folder
-warning('off', 'MATLAB:DELETE:FileNotFound')
-if exist('testYamlConversion.yml','file')
-    delete testYamlConversion.yml;
-end
+    % Import yaml model
+    ymlFile=fullfile(modelPath,'model','Human-GEM.yml');
+    model = importYaml(ymlFile, true);
 
+    % make sure there is no intermediate Yaml file under the current folder
+    warning('off', 'MATLAB:DELETE:FileNotFound')
+    if exist('testYamlConversion.yml','file')
+        delete testYamlConversion.yml;
+    end
 
-% export to yml and then import back
-try
     exportYaml(model,'testYamlConversion.yml');
     importedHumanGEM = importYaml('testYamlConversion.yml', true);
-catch
-    error('There are problems during the conversion import and export');
-end
 
-% remove intermediate Yaml file
-delete testYamlConversion.yml;
+    % remove intermediate Yaml file
+    delete testYamlConversion.yml;
 
-% compare the imported model from yaml with the original one
-if isequal(model, importedHumanGEM)
-    % model conversion between Matlab and Yaml files is successful
-    disp('The conversion was successful.')
-    status = 1;
-else
-    error('There are problems during the conversion between Matlab and Yaml files');
+    % compare the imported model from yaml with the original one
+    if ~isequal(model, importedHumanGEM)
+        warning('::error::Re-imported model is diffrent from export');
+        exit(1);
+    end
+catch
+    warning('::error::There are problems during the conversion import and export');
+    exit(1)
 end
 
+% model conversion between Matlab and Yaml files is successful
+disp('The conversion was successful.')
+exit(0)

model/Human-GEM.yml

@@ -307292,8 +307292,8 @@
     - !!omap
       - id: "MAR20111"
       - name: "MAR20111"
-      - metabolties: !!omap
-          - MAM1261m: -1
+      - metabolites: !!omap
+          - MAM01261m: -1
           - MAM01597m: 1
           - MAM02007m: -1
           - MAM02040m: -1