Update release workflow and fix code issues

.github/workflows/release.yml

@@ -3,21 +3,71 @@
 
 name: Create new release
 
-# Run workflow when a tag is created
+# Run workflow when a tag is created or it is triggered manually
 on:
   push:
     tags: 
       - 'v*'
+  workflow_dispatch:
+    inputs:
+      version:
+        description: 'Version number in major.minor.patch format, i.e 0.9.x'
+        required: true
+        type: string
 
 jobs:
   # This workflow contains:
-  # 1. a matrixed test job run across a bunch of releases of MATLAB
-  # 2. a reporting job that summarizes the tests, and updates release badge
+  # 1. a validation of the provided version number
+  # 2. a matrixed test job run across MATLAB releases from R2021b to R2024b
+  # 3. a reporting job that summarizes the tests, and updates release badge
+
+  setup_version:
+    runs-on: ubuntu-latest
+    outputs:
+      version: ${{ steps.set_version.outputs.version }}
+      version_tag: ${{ steps.set_version.outputs.version_tag }}
+    steps:
+      - name: Check for retag
+        if: ${{ contains(github.event.head_commit.message, '[skip-ci]') }}
+        run: |
+          echo "Error: Commit message contains [skip-ci], skipping."
+          exit 1
+
+      - name: Set version based on trigger type
+        id: set_version
+        run: |
+          if [[ "${{ github.event_name }}" == "workflow_dispatch" ]]; then
+            # For manual trigger, use the input version
+            VERSION="${{ github.event.inputs.version }}"
+            # Validate format
+            if [[ ! "$VERSION" =~ ^[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
+              echo "Error: Input for 'version' ('$VERSION') is not in the expected major.minor.patch format."
+              exit 1
+            fi
+            VERSION_TAG="v$VERSION"
+          else
+            # For tag trigger, use the tag name
+            VERSION_TAG="${{ github.ref_name }}"
+            # Remove 'v' prefix if present for the version number
+            VERSION="${VERSION_TAG#v}"
+
+            # Validate format
+            if [[ ! "$VERSION_TAG" =~ ^v[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
+              echo "Error: Tag name ('$VERSION_TAG') is not in the expected v*.*.* format."
+              exit 1
+            fi
+          fi
+
+          echo "Using version: $VERSION (tag: $VERSION_TAG)"
+          echo "version=$VERSION" >> $GITHUB_OUTPUT
+          echo "version_tag=$VERSION_TAG" >> $GITHUB_OUTPUT
+
   test:
+    needs: [setup_version]
     strategy:
       fail-fast: false
       matrix:
-        MATLABVersion: [R2022b, R2023a, R2023b, R2024a, R2024b]
+        MATLABVersion: [R2021b, R2022a, R2022b, R2023a, R2023b, R2024a, R2024b]
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
 
@@ -39,15 +89,6 @@ jobs:
             addpath(genpath("tools"));
             testToolbox('ReportSubdirectory',"${{ matrix.MATLABVersion }}", 'CreateBadge', false)     
 
-      # Upload code coverage information to Codecov
-      - name: Upload code coverage report to Codecov (https://app.codecov.io/gh/openMetadataInitiative/openMINDS_MATLAB)
-        uses: codecov/codecov-action@v4
-        if: always()
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          files: docs/reports/codecoverage.xml
-          env_vars: ${{ matrix.MATLABVersion }}
-
       # Save the contents of the report directory from each release into an artifact.
       - name: Save report directory
         uses: actions/upload-artifact@v4
@@ -58,11 +99,13 @@ jobs:
 
   # Report on what releases tested successfully.
   # Generate a draft release based on the tag
-  # Recreate the tag with the final version of JSON files
+  # Recreate the tag with the final version of updated files
   release:
-    needs: test
-    if: always()
+    needs: [test, setup_version]
     runs-on: ubuntu-latest
+    env:
+      VERSION: ${{ needs.setup_version.outputs.version }}
+      VERSION_TAG: ${{ needs.setup_version.outputs.version_tag }}
 
     steps:
       # Use deploy key to push back to protected branch
@@ -86,7 +129,7 @@ jobs:
       - name: Generate tested with badge
         uses: matlab-actions/run-command@v2
         with:
-          command: addpath(genpath("tools")), createTestedWithBadgeforToolbox("${{  github.ref_name }}")     
+          command: addpath(genpath("tools")), createTestedWithBadgeforToolbox("${{ env.VERSION_TAG }}")     
 
       # Publish test results from all the releases
       - name: Publish test results
@@ -99,13 +142,13 @@ jobs:
       - name: Package toolbox
         uses: matlab-actions/run-command@v2
         with:
-          command: addpath(genpath("tools")), packageToolbox("specific","${{  github.ref_name }}")     
+          command: addpath(genpath("tools")), packageToolbox("specific","${{ env.VERSION_TAG }}")     
 
       # Define the versionNumber using underscores, as this is used in the MLTBX
       - name: Set version number
         id: set_version
         run: |
-          versionNumber=$(echo "${{ github.ref_name }}" | sed 's/\./_/g')
+          versionNumber=$(echo "${{ env.VERSION_TAG }}" | sed 's/\./_/g')
           echo "versionNumber=$versionNumber" >> $GITHUB_ENV
 
       # Save the MLTBX.
@@ -120,7 +163,7 @@ jobs:
         with:
           command: | 
             addpath(genpath("tools"));
-            updateCodeMetaFile("${{  github.ref_name }}")
+            updateCodeMetaFile("${{ env.VERSION_TAG }}")
 
       # Commit the updated Contents.m
       - name: Commit updated Contents.m file
@@ -131,7 +174,7 @@ jobs:
           git status
           git add code/Contents.m
           git add codemeta.json
-          git commit -m "Final checkins for release ${{  github.ref_name }}"
+          git commit -m "Final checkins for release ${{ env.VERSION_TAG }}"
           git fetch
           git push
 
@@ -145,8 +188,8 @@ jobs:
 
       - name: Push to gh-badges
         run: |
-          mkdir -p gh-badges/.github/badges/${{  github.ref_name }}
-          cp .github/badges/${{  github.ref_name }}/tested_with.json gh-badges/.github/badges/${{  github.ref_name }}/tested_with.json
+          mkdir -p gh-badges/.github/badges/${{ env.VERSION_TAG }}
+          cp .github/badges/${{ env.VERSION_TAG }}/tested_with.json gh-badges/.github/badges/${{ env.VERSION_TAG }}/tested_with.json
           cd gh-badges
 
           git config user.name "${{ github.workflow }} by ${{ github.actor }}"
@@ -161,29 +204,35 @@ jobs:
             echo "Nothing to commit"
           fi
 
-      # Retag the repo so that the updated files are included in the release tag
+      # (Re)tag the repo so that the updated files are included in the release tag
       - name: Update tag
         if: always()
         continue-on-error: true
         run: |
           git config user.name "${{ github.workflow }} by ${{ github.actor }}"
           git config user.email "<>"
 
-          # Delete the existing tag locally and remotely
-          git tag -d "${{ github.ref_name }}" 
-          git push origin --delete "${{ github.ref_name }}"
+          # Delete the existing tag locally and remotely if it already exists
+          if git rev-parse --verify "refs/tags/${{ env.VERSION_TAG }}" > /dev/null 2>&1; then
+            # Delete the existing tag locally and remotely only if it exists
+            git tag -d "${{ env.VERSION_TAG }}"
+            git push origin --delete "${{ env.VERSION_TAG }}"
+          else
+            echo "Tag '${{ env.VERSION_TAG }}' does not exist, skipping deletion."
+          fi
 
-          # Recreate the tag with a message, including [skip ci] to prevent CI workflows
-          git tag -a "${{ github.ref_name }}" -m "Release ${{ github.ref_name }} [skip ci]" 
+          # Recreate the tag with a message, including [skip-ci] to prevent triggering CI workflows
+          git tag -a "${{ env.VERSION_TAG }}" -m "Release ${{ env.VERSION_TAG }} [skip-ci]" 
 
           # Push the new tag to the remote repository
-          git push origin "${{ github.ref_name }}"
+          git push origin "${{ env.VERSION_TAG }}"
 
       # Create the release
       - name: Create GitHub release
         uses: ncipollo/release-action@v1
         with:
           draft: true        
           artifacts: "releases/openMINDS_MATLAB_${{ env.versionNumber }}.mltbx"
+          tag: ${{ env.VERSION_TAG }}
           generateReleaseNotes: true
-          body: "![MATLAB Versions Tested](https://img.shields.io/endpoint?url=https%3A%2F%2Fraw.githubusercontent.com%2FopenMetadataInitiative%2FopenMINDS_MATLAB%2Fgh-badges%2F.github%2Fbadges%2F${{  github.ref_name }}%2Ftested_with.json)"
+          body: "![MATLAB Versions Tested](https://img.shields.io/endpoint?url=https%3A%2F%2Fraw.githubusercontent.com%2FopenMetadataInitiative%2FopenMINDS_MATLAB%2Fgh-badges%2F.github%2Fbadges%2F${{ env.VERSION_TAG }}%2Ftested_with.json)"

.github/workflows/run_tests.yml

@@ -7,8 +7,7 @@ on:
   push:
     branches: [ "main" ]
     paths-ignore:
-      - '*README.md'
-      - '*md'
+      - '*.md'
       - '.github/**'
   pull_request:
     branches: [ "main" ]

README.md

@@ -24,10 +24,9 @@
 
 ---
 
-
-MATLAB package for the openMINDS metadata framework for linked data in neuroscience. The package contains all the latest openMINDS schemas as MATLAB classes in addition to schema base classes and utility methods.
+MATLAB toolbox for creating openMINDS compliant linked metadata, supporting import and export of metadata instances in JSON-LD format.
 
-To generally learn more about the openMINDS metadata framework please go to :arrow_right: [**ReadTheDocs**](https://openminds-documentation.readthedocs.io).  
+To learn more about the openMINDS metadata framework please go to :arrow_right: [**ReadTheDocs**](https://openminds-documentation.readthedocs.io).  
 You can test and learn how to use openMINDS in MATLAB by going through a small :arrow_right: [**DEMO**](https://matlab.mathworks.com/open/github/v1?repo=openMetadataInitiative/openMINDS_MATLAB&file=code/gettingStarted.mlx) on MATLAB Online.  
 
 MathWorks provides a free basic version of [MATLAB Online](https://uk.mathworks.com/products/matlab-online.html), but you need to register for a [MathWorks Account](https://www.mathworks.com/mwaccount/register?uri=https%3A%2F%2Fwww.mathworks.com%2Fproducts%2Fmatlab.html).

code/+openminds/@Collection/Collection.m

@@ -56,13 +56,13 @@
     properties (SetAccess = protected)
         % Nodes - Dictionary storing instances as values with identifiers
         % as keys
-        Nodes {mustBeA(Nodes, ["dictionary", "containers.Map"])} = containers.Map %#ok<MCHDP>
+        Nodes {mustBeA(Nodes, ["dictionary", "containers.Map"])} = containers.Map %#ok<MCHDP> Constructor will overwrite
     end
 
     properties (SetAccess = protected, Hidden)
         % TypeMap - Keeps a map/dictionary of types and instance ids to
         % efficiently extract instances of a specific type.
-        TypeMap {mustBeA(TypeMap, ["dictionary", "containers.Map"])} = containers.Map %#ok<MCHDP>
+        TypeMap {mustBeA(TypeMap, ["dictionary", "containers.Map"])} = containers.Map %#ok<MCHDP> Constructor will overwrite
     end
 
     properties
@@ -526,7 +526,8 @@
                 if any(isMatch)
                     if isa(obj.TypeMap, 'dictionary')
                         if isMATLABReleaseOlderThan("R2023b")
-                            instanceKeys = string( obj.TypeMap(typeKeys(isMatch)) );
+                            instanceKeys = obj.TypeMap(typeKeys(isMatch));
+                            instanceKeys = instanceKeys{1};
                         else
                             instanceKeys = obj.TypeMap{typeKeys(isMatch)};
                         end

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

@@ -384,7 +384,7 @@
                     varargout = cell(1, numOutputs);
                     [varargout{:}] = builtin('subsref', obj, subs);
                 else
-                    obj = builtin('subsref', obj, subs);
+                    obj = builtin('subsref', obj, subs); %#ok<NASGU>
                 end
             end
         end

code/internal/+openminds/+internal/+generator/+abstract/ClassWriter.m

@@ -56,7 +56,8 @@
             if strcmp(firstLetter, lower(firstLetter))
                 newNameLowercase = newName;
                 newName{1}(1) = upper(firstLetter);
-                warning('Classname should start with a capital letter. Changed name from "%s" to "%s"', newNameLowercase, newName) %#ok<PFCEL>
+                warning(['Classname should start with a capital letter. ', ...
+                    'Changed name from "%s" to "%s"'], newNameLowercase, string(newName))
             end
             obj.ClassName = newName;
         end

code/internal/+openminds/+internal/+helper/listSchemasWithNonGenericLabel.m

@@ -19,10 +19,10 @@
     for i = 1:numSchemas
 
         iSchemaName = schemaTable{i, "SchemaName"};
-        iModelName = schemaTable{i, "ModuleName"};
+        iModuleName = schemaTable{i, "ModuleName"};
         iSubmoduleName = schemaTable{i, "SubModuleName"};
 
-        schemaClassFunctionName = openminds.internal.utility.string.buildClassName(iSchemaName, iSubmoduleName, iModelName);
+        schemaClassFunctionName = openminds.internal.utility.string.buildClassName(iSchemaName, iSubmoduleName, iModuleName);
         schemaFcn = str2func(schemaClassFunctionName);
 
         mc = meta.class.fromName(schemaClassFunctionName);

code/internal/+openminds/+internal/+meta/@MetaTypeRegistry/MetaTypeRegistry.m

@@ -27,7 +27,7 @@
     properties (Access = private)
         % Registry - Storage for cached Type objects
         % Uses dictionary in newer MATLAB versions, containers.Map in older ones
-        Registry {mustBeA(Registry, ["dictionary", "containers.Map"])} = containers.Map %#ok<MCHDP>
+        Registry {mustBeA(Registry, ["dictionary", "containers.Map"])} = containers.Map %#ok<MCHDP> Constructor will overwrite
     end
 
     properties (SetAccess = private)
@@ -59,13 +59,7 @@
                 options.ModelVersion (1,1) string
             end
 
-            % Initialize registry using dictionary if available (R2022b+)
-            % otherwise fall back to containers.Map
-            if exist('dictionary', 'file')
-                obj.Registry = configureDictionary('string', 'cell');
-            else
-                obj.Registry = containers.Map();
-            end
+            obj.initializeCache()
 
             % Apply options
             obj.ModelVersion = options.ModelVersion;
@@ -86,15 +80,25 @@
         % clearCache - Clear the registry cache
         %
         % This method can be used to force reloading of Type objects
+            obj.initializeCache()
+        end
+    end
+
+    methods (Access = private)
+        function initializeCache(obj)
+            % Initialize registry using dictionary if available (R2022b+)
+            % otherwise fall back to containers.Map
             if exist('dictionary', 'file')
-                obj.Registry = configureDictionary('string', 'cell');
+                if exist('configureDictionary', 'file') % From R2023b
+                    obj.Registry = configureDictionary('string', 'cell');
+                else % Fallback for R2022b and R2023a
+                    obj.Registry = dictionary(string.empty, {});
+                end
             else
                 obj.Registry = containers.Map();
             end
         end
-    end
 
-    methods (Access = private)
         function isValid = isValidKey(obj, keyName)
         % isValidKey - Check if a key is valid for the registry
         %

code/internal/+openminds/+internal/+mixin/CustomInstanceDisplay.m

@@ -58,7 +58,8 @@
 
     methods (Hidden, Access = protected) % CustomDisplay - Method implementation
 
-        function requiredProperties = getRequiredProperties(obj)
+        function requiredProperties = getRequiredProperties(~)
+            % Subclasses should override.
             requiredProperties = [];
         end
 
@@ -173,7 +174,7 @@
                 rep = matlab.display.PlainTextRepresentation(obj, repmat({str}, numRows, 1), displayConfiguration);
             elseif numObjects >= 1
                 % str = obj.DisplayString;
-                rep = fullDataRepresentation(obj, displayConfiguration, 'StringArray', arrayfun(@(i) obj(i).DisplayString, [1:numRows]', 'uni', 0) );
+                rep = fullDataRepresentation(obj, displayConfiguration, 'StringArray', arrayfun(@(i) obj(i).DisplayString, (1:numRows)', 'uni', 0) );
 
             elseif numObjects > 1
                 % rep = fullDataRepresentation(obj, displayConfiguration, 'StringArray', obj.DisplayString );

code/internal/+openminds/+internal/+serializer/JsonLdSerializer.m

@@ -36,7 +36,8 @@
             end
         end
 
-        function instances = deserialize(obj)
+        function instances = deserialize(obj) %#ok<MANU,STOUT>
+            error('Not implemented')
             % Todo:
             % json to struct
             % struct to openminds instances

code/internal/+openminds/+internal/+utility/+dir/listSourceSchemas.m

@@ -1,11 +1,10 @@
-function schemaInfo = listSourceSchemas(schemaModule, options)
+function schemaInfo = listSourceSchemas(options)
 %listSourceSchemas List information about all available schemas.
 %
 %   schemaInfo = listSourceSchemas() returns a table with information
 %   about all the available schemas.
 
     arguments
-        schemaModule = {}
         options.SchemaType (1,1) string = "schema.omi.json";
         options.SchemaFileExtension = '*.omi.json';
         options.VersionNumber (1,1) openminds.internal.utility.VersionNumber ...

code/internal/+openminds/+internal/+utility/+string/buildClassName.m

@@ -6,13 +6,9 @@
         schemaModule char
     end
 
-    schemaCategory = '';
-
     schemaName = openminds.internal.utility.string.pascalCase(schemaName);
     schemaModule = lower(schemaModule);
     schemaCategory = lower(schemaCategory);
-
-    schemaCategory = strrep( schemaCategory, 'schemas', '');
 
     if isempty(schemaCategory) % This might be empty, i.e for controlled terms
         name = strjoin({'openminds', schemaModule, schemaName}, '.');