Update testing workflow (#57)

* Rename "update" workflow to "run_tests"

* Remove steps pushing badges to gh-badges branch

Not necessary

* Only test on pushed to main and PRs to main

* Run tests for earliest and latest matlab releases that are available

* Fix indent error

* Update run_tests.yml

* Update run_tests.yml

* Update Collection.m

Use containers.Map if dictionarry is unavailable for compatibility

* Update Collection.m

* Fix bugs in Collection after introducing use of fallback to containers.Map if dictionary is unavailable

* Add metatype registry.

Singleton class for storing cached metatype objects for the openminds type classes

* Create badge for latest release only

* Update run_tests.yml

Fix yaml error

* Update run_tests.yml

Author: ehennestad

.github/workflows/update.yml .github/workflows/run_tests.yml.github/workflows/update.yml renamed to .github/workflows/run_tests.yml

@@ -5,7 +5,7 @@ on:
   # This way tests will run on any push to a feature branch and when feature 
   # branches are merged to main, but not repeated when PRs are actually merged. 
   push:
-    branches-ignore: ["pipeline", "gh-badges"]
+    branches: [ "main" ]
     paths-ignore:
       - '*README.md'
       - '*md'
@@ -18,9 +18,14 @@ on:
 jobs:
   # This workflow contains a single job called "test"
   test:
-    name: Test openMINDS_MATLAB
-    # The type of runner that the job will run on
+    name: Test openMINDS_MATLAB (${{ matrix.MATLABVersion }})
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        MATLABVersion: [R2021b, R2024b]
+    env:
+      LatestMATLABVersion: R2024b
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
@@ -30,31 +35,36 @@ jobs:
 
       - name: Set up MATLAB
         uses: matlab-actions/setup-matlab@v2
+        with:
+          release: ${{ matrix.MATLABVersion }}
 
       # Check for MATLAB code issues in the project.
       - name: Check for MATLAB code issues
+        if: matrix.MATLABVersion == env.LatestMATLABVersion
         uses: matlab-actions/run-command@v2
-        if: always()
         with:
           command: addpath(genpath("tools")),codecheckToolbox()
 
       # Upload code issues report
       - name: Upload SARIF file
+        if: matrix.MATLABVersion == env.LatestMATLABVersion
         uses: github/codeql-action/upload-sarif@v3
         with:
           # Path to SARIF file relative to the root of the repository
           sarif_file: docs/reports/code_issues.sarif
 
       # Run all tests in the project.
       - name: Run tests
-        uses: matlab-actions/run-command@v2
         if: always()
+        uses: matlab-actions/run-command@v2
         with:
-          command: addpath(genpath("tools")), testToolbox()
+          command: |
+            doCreateBadge = "${{ matrix.MATLABVersion }}" == "${{ env.LatestMATLABVersion }}";
+            addpath(genpath("tools")), testToolbox("CreateBadge", doCreateBadge)
 
       # Commit updated SVG badges for the issues and tests (if changed)
       - name: Commit svg badges if updated
-        if: always()
+        if: matrix.MATLABVersion == env.LatestMATLABVersion
         continue-on-error: true
         run: |
           git config user.name "${{ github.workflow }} by ${{ github.actor }}"
@@ -70,8 +80,8 @@ jobs:
           fi
 
       - name: Upload code coverage report to Codecov (https://app.codecov.io/gh/openMetadataInitiative/openMINDS_MATLAB)
+        if: matrix.MATLABVersion == env.LatestMATLABVersion
         uses: codecov/codecov-action@v4
-        if: always()
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: docs/reports/codecoverage.xml
@@ -82,36 +92,12 @@ jobs:
         if: always()
         with:
           files: "docs/reports/test-results.xml"
+          check_name: "Test Results (${{ matrix.MATLABVersion }})"
 
       # Save the contents of the reports directory as an artifact
       - name: Save reports directory
         uses: actions/upload-artifact@v4
         if: always()
         with:
-          name: reports
+          name: reports-${{ matrix.MATLABVersion }}
           path: docs/reports
-
-      - name: Checkout gh-badges branch
-        uses: actions/checkout@v4
-        with:
-          ref: gh-badges
-          path: gh-badges
-          token: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Push to gh-badges
-        run: |
-          cp .github/badges/code_issues.svg gh-badges/.github/badges/code_issues.svg
-          cp .github/badges/tests.svg gh-badges/.github/badges/tests.svg
-          cd gh-badges
-
-          git config user.name "${{ github.workflow }} by ${{ github.actor }}"
-          git config user.email "<>"
-
-          # Only proceed with commit and push if changes are detected
-          if [[ $(git add .github/badges/* --dry-run | wc -l) -gt 0 ]]; then
-            git add .github/badges/*
-            git commit -m "Update code issues and tests badges"
-            git push -f
-          else
-            echo "Nothing to commit"
-          fi

code/+openminds/@Collection/Collection.m

@@ -47,17 +47,22 @@
         % Description of the metadata collection
         Description (1,1) string
     end
+
+    properties (Dependent, Access = private)
+        NumNodes
+        NumTypes
+    end
 
     properties (SetAccess = protected)
         % Nodes - Dictionary storing instances as values with identifiers
         % as keys
-        Nodes (1,1) dictionary
+        Nodes {mustBeA(Nodes, ["dictionary", "containers.Map"])} = containers.Map %#ok<MCHDP>
     end
 
     properties (SetAccess = protected, Hidden)
         % TypeMap - Keeps a map/dictionary of types and instance ids to
         % efficiently extract instances of a specific type.
-        TypeMap (1,1) dictionary
+        TypeMap {mustBeA(TypeMap, ["dictionary", "containers.Map"])} = containers.Map %#ok<MCHDP>
     end
 
     properties
@@ -105,8 +110,14 @@
             end
 
             % Initialize protected maps
-            obj.Nodes = dictionary;
-            obj.TypeMap = dictionary;
+            if exist("isMATLABReleaseOlderThan", "file") ...
+                    && not(isMATLABReleaseOlderThan("R2022b"))
+                obj.Nodes = dictionary;
+                obj.TypeMap = dictionary;
+            else % Backwards compatibility
+                obj.Nodes = containers.Map;
+                obj.TypeMap = containers.Map;
+            end
 
             obj.initializeFromInstances(instance)
 
@@ -115,15 +126,33 @@
         end
     end
 
+    methods
+        function numNodes = get.NumNodes(obj)
+            if isa(obj.Nodes, 'dictionary')
+                numNodes = numEntries(obj.Nodes);
+            elseif isa(obj.Nodes, 'containers.Map')
+                numNodes = length(obj.Nodes);
+            end
+        end
+                
+        function numTypes = get.NumTypes(obj)
+            if isa(obj.TypeMap, 'dictionary')
+                numTypes = numEntries(obj.TypeMap);
+            elseif isa(obj.TypeMap, 'containers.Map')
+                numTypes = length(obj.TypeMap);
+            end
+        end
+    end
+
     methods
         function len = length(obj)
-            len = numEntries(obj.Nodes);
+            len = obj.NumNodes;
         end
 
         function tf = isKey(obj, identifier)
         % isKey - Check if collection has a node with the given key / identifier
             tf = false;
-            if isConfigured(obj.Nodes)
+            if obj.NumNodes > 0
                 if isKey(obj.Nodes, identifier)
                     tf = true;
                 end
@@ -161,7 +190,7 @@ function add(obj, instance, options)
             % Todo:work for arrays
             tf = false;
 
-            if isConfigured(obj.Nodes)
+            if obj.NumNodes > 0
                 if isKey(obj.Nodes, instance.id)
                     tf = true;
                 end
@@ -179,14 +208,18 @@ function remove(obj, instance)
                 error('Unexpected type "%s" for instance argument', class(instance))
             end
 
-            if isConfigured(obj.Nodes) && isKey(obj.Nodes, instanceId)
+            if obj.NumNodes > 0 && isKey(obj.Nodes, instanceId)
                 try 
                     instanceType = class( obj.Nodes{instanceId} );
                 catch % < R2023a
                     instance = obj.Nodes(instanceId);
                     instanceType = class( instance{1} );
                 end
-                obj.Nodes(instanceId) = [];
+                if isa(obj.Nodes, "dictionary")
+                    obj.Nodes(instanceId) = [];
+                else
+                    obj.Nodes.remove(instanceId);
+                end
 
                 allIds = obj.TypeMap(instanceType);
                 obj.TypeMap(instanceType) = { setdiff( allIds{1}, instanceId ) };
@@ -196,11 +229,11 @@ function remove(obj, instance)
         end
 
         function instance = get(obj, nodeKey)
-            if isMATLABReleaseOlderThan("R2023b")
+            if exist("isMATLABReleaseOlderThan", "file") && not( isMATLABReleaseOlderThan("R2023b") )
+                instance = obj.Nodes{nodeKey};
+            else
                 instance = obj.Nodes(nodeKey);
                 instance = instance{1};
-            else
-                instance = obj.Nodes{nodeKey};
             end
         end
 
@@ -212,7 +245,7 @@ function remove(obj, instance)
 
             tf = false;
 
-            if ~isConfigured(obj.Nodes)
+            if obj.NumNodes == 0
                 return
             end
 
@@ -232,14 +265,23 @@ function remove(obj, instance)
 
             instances = [];
 
-            if ~isConfigured(obj.Nodes)
+            if obj.NumNodes == 0
                 return
             end
 
             instanceKeys = obj.getInstanceKeysForType(type);
             if isempty(instanceKeys); return; end
 
-            instances = obj.Nodes(instanceKeys);
+            if isa(obj.Nodes, 'dictionary')
+                instances = obj.Nodes(instanceKeys);
+            else
+                instances = cell(1, numel(instanceKeys));
+                for i = 1:numel(instanceKeys)
+                    instances{i} = obj.Nodes(instanceKeys{i});
+                end
+                instances = [instances{:}];
+            end
+
             instances = [instances{:}]; % Create non-cell array
 
             % Filter by property values:
@@ -255,7 +297,12 @@ function remove(obj, instance)
         end
 
         function updateLinks(obj)
-            for instance = obj.Nodes.values
+            allInstances = obj.Nodes.values;
+            if isa(obj.Nodes, 'containers.Map')
+                allInstances = [allInstances{:}];
+            end
+
+            for instance = allInstances
                 obj.addNode(instance{1}, ...
                     'AddSubNodesOnly', true, ...
                     'AbortIfNodeExists', false);
@@ -380,7 +427,7 @@ function load(obj, filePath)%, options)
                 return
             end
 
-            if isConfigured(obj.Nodes)
+            if obj.NumNodes > 0
                 if isKey(obj.Nodes, instance.id)
                     % warning('Node with id %s already exists in collection', instance.id)
                     if options.AbortIfNodeExists
@@ -395,7 +442,7 @@ function load(obj, filePath)%, options)
 
                 % Add to TypeMap: Todo: Separate method
                 instanceType = class(instance);
-                if isConfigured(obj.TypeMap) && isKey(obj.TypeMap, instanceType)
+                if obj.NumTypes > 0 && isKey(obj.TypeMap, instanceType)
                     if isMATLABReleaseOlderThan("R2023b")
                         existingInstances = obj.TypeMap(instanceType);
                         obj.TypeMap(instanceType) = {[existingInstances{:}, string(instance.id)]};
@@ -472,15 +519,20 @@ function initializeFromInstances(obj, instance)
         function instanceKeys = getInstanceKeysForType(obj, instanceType)
         % getInstanceKeysForType Get all ids for instances of a given type
 
-            if isConfigured(obj.TypeMap)
+            if obj.NumTypes > 0
                 typeKeys = obj.TypeMap.keys;
 
                 isMatch = strcmp(typeKeys, instanceType.ClassName);
                 if any(isMatch)
-                    if isMATLABReleaseOlderThan("R2023b")
-                        instanceKeys = string( obj.TypeMap(typeKeys(isMatch)) );
-                    else
-                        instanceKeys = obj.TypeMap{typeKeys(isMatch)};
+                    if isa(obj.TypeMap, 'dictionary')
+                        if isMATLABReleaseOlderThan("R2023b")
+                            instanceKeys = string( obj.TypeMap(typeKeys(isMatch)) );
+                        else
+                            instanceKeys = obj.TypeMap{typeKeys(isMatch)};
+                        end
+                    elseif isa(obj.TypeMap, 'containers.Map')
+                        instanceKeys = obj.TypeMap(typeKeys{isMatch});
+                        instanceKeys = instanceKeys{1};
                     end
                 else
                     instanceKeys = {};

code/+openminds/@Collection/loadInstances.m

@@ -83,21 +83,11 @@ function resolveLinks(instance, instanceIds, instanceCollection)
         return
     end
 
-    persistent schemaInspectorMap
-    if isempty(schemaInspectorMap)
-        schemaInspectorMap = dictionary;
-    end
-
-    instanceType = class(instance);
-    if ~isConfigured(schemaInspectorMap) || ~isKey(schemaInspectorMap, instanceType)
-        schemaInspectorMap(instanceType) = openminds.internal.SchemaInspector(instance);
-    end
-
-    schemaInspector = schemaInspectorMap(instanceType);
+    metaType = openminds.internal.meta.fromInstance(instance);
 
-    for i = 1:schemaInspector.NumProperties
-        thisPropertyName = schemaInspector.PropertyNames{i};
-        if schemaInspector.isPropertyWithLinkedType(thisPropertyName)
+    for i = 1:metaType.NumProperties
+        thisPropertyName = metaType.PropertyNames{i};
+        if metaType.isPropertyWithLinkedType(thisPropertyName)
             linkedInstances = instance.(thisPropertyName);
 
             resolvedInstances = cell(size(linkedInstances));
@@ -137,7 +127,7 @@ function resolveLinks(instance, instanceIds, instanceCollection)
                 instance.(thisPropertyName) = resolvedInstances;
             end
 
-        elseif schemaInspector.isPropertyWithEmbeddedType(thisPropertyName)
+        elseif metaType.isPropertyWithEmbeddedType(thisPropertyName)
             embeddedInstances = instance.(thisPropertyName);
 
             for j = 1:numel(embeddedInstances)

code/internal/+openminds/+abstract/Schema.m

@@ -27,7 +27,7 @@
     end
 
     properties (Abstract, Constant, Hidden)
-        LINKED_PROPERTIES struct %todo: name and classname, not openminds uri
+        LINKED_PROPERTIES struct
         EMBEDDED_PROPERTIES struct
     end