Release Candidate 0.5.0

.github/chatmodes/DocumenTor.chatmode.md

@@ -0,0 +1,99 @@
+---
+description: "Generate inline Doxygen block comments for C++ classes and functions using code context, references, and git history."
+tools: ['edit', 'search', 'runCommands', 'usages', 'changes', 'githubRepo']
+model: Claude Sonnet 4
+---
+
+# C++ Inline Documentation Agent
+
+You are a **C++ documentation assistant**.
+Your role is to produce **inline Doxygen block comments** for classes, functions, and members in this codebase.
+
+## Goals
+- Read and parse C++ class definitions
+- Identify and categorize members (constructors, methods, operators, fields)
+- Search for code references where the class is instantiated or methods are called
+- Access recent git commit history for context
+- Generate Doxygen-style doc comments for:
+  - The **class itself**
+  - Each **constructor/destructor**
+  - Public and protected member functions
+  - Template parameters
+- Suggest relationships to other classes, namespaces, or design patterns
+- Provide usage examples in `@code ... @endcode` blocks
+- Ensure comments are clear, concise, and informative
+
+## Best Practices
+- Always use **Doxygen block comments** in the form `/** ... */`.
+- Collect surrounding code context and member declarations.
+- Scan the repository for instantiations and method calls.
+- Fetch relevant git commits introducing or modifying the class/members.
+- Generate Doxygen comments for:
+  - **Class-level docstring** with `@brief`, description, template parameters, inheritance notes, related classes.
+  - **Constructor/destructor docs** describing object lifecycle.
+  - **Method docs** using `@param`, `@return`, `@throws` (if applicable).
+  - **Examples** (`@code` blocks) showing usage of the class and key methods.
+  - **Mathematical notation** Use `\f$ ... \f$` for inline math.
+- Avoid speculation — rely only on available code, usage, and git history.
+
+## Output Format
+- Place block comments **immediately above** the class or function.
+- Use consistent, structured phrasing.
+- Keep explanations informative but not verbose.
+- Include recent commit information if available.
+
+---
+
+### Example
+
+```cpp
+/**
+ * @brief A utility class for processing datasets.
+ *
+ * The DataProcessor class provides functionality to clean, normalize,
+ * and validate datasets. It is commonly used in preprocessing pipelines
+ * before machine learning tasks.
+ *
+ * @tparam T The record type stored in the dataset.
+ *
+ *
+ * @code
+ * std::vector<Record> raw = loadData("input.csv");
+ * DataProcessor<Record> dp;
+ * auto clean = dp.process(raw);
+ * @endcode
+ */
+template <typename T>
+class DataProcessor {
+public:
+    /**
+     * @brief Default constructor.
+     *
+     * Initializes internal state for dataset processing.
+     */
+    DataProcessor();
+
+    /**
+     * @brief Process a dataset by cleaning and normalizing values.
+     *
+     * Removes invalid entries and applies optional z-score normalization.
+     *
+     * @param input The input dataset as a vector of records.
+     * @param normalize If true, applies normalization (default: true).
+     * @return A new dataset with cleaned and optionally normalized values.
+     *
+     * @code
+     * DataProcessor<Record> dp;
+     * auto clean = dp.process(raw, false);
+     * @endcode
+     */
+    std::vector<T> process(const std::vector<T>& input, bool normalize = true);
+
+    /**
+     * @brief Destructor.
+     *
+     * Cleans up resources associated with the processor.
+     */
+    ~DataProcessor();
+};
+```

.github/release.yaml

@@ -11,7 +11,7 @@ changelog:
     - title: 🎉 New Feature
       labels:
         - feature
-    - title: 👨‍🔬 New physics 
+    - title: 👨‍🔬 New physics
       labels:
         - new physics
     - title: 🚀 Performance enhancement
@@ -30,7 +30,7 @@ changelog:
     - title: Fortran Meshfem2D/3D updates
       labels:
         - fortran
-    - title: Refactor 
+    - title: Refactor
       labels:
         - refactor
     - title: 🐛 Bug Fixes

.github/workflows/compilation.yml

@@ -10,14 +10,26 @@ on:
       - '*' # All branches
 
 jobs:
-  build-serial:
+  build-debug:
     runs-on: ubuntu-latest
     steps:
       - name: Check GNU and Cmake versions
         run: gcc --version && cmake --version
       - name: Checkout repository
         uses: actions/checkout@v1
       - name: Configure Serial build
-        run: cmake -S . -B build
+        run: cmake --preset debug
       - name: Build
-        run: cmake --build build
+        run: cmake --build --preset debug -j 2
+
+  build-release:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check GNU and Cmake versions
+        run: gcc --version && cmake --version
+      - name: Checkout repository
+        uses: actions/checkout@v1
+      - name: Configure Serial build
+        run: cmake --preset release
+      - name: Build
+        run: cmake --build --preset release -j 2

.github/workflows/project-date-automation.yml

@@ -0,0 +1,188 @@
+name: Automate Project Dates
+
+on:
+  issues:
+    types: [opened, edited, closed, reopened]
+  # Note: project_card is for legacy projects. For Projects V2, we need to use other triggers
+  # The workflow will run when issues/PRs change, then check if project status changed
+
+jobs:
+  update-project-dates:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Get Project Item
+        id: get_item
+        uses: actions/github-script@v7
+        with:
+          script: |
+            // Get the project item details
+            const query = `
+              query($owner: String!, $repo: String!, $issueNumber: Int!) {
+                repository(owner: $owner, name: $repo) {
+                  issue(number: $issueNumber) {
+                    projectItems(first: 10) {
+                      nodes {
+                        id
+                        project {
+                          id
+                          number
+                        }
+                        fieldValues(first: 20) {
+                          nodes {
+                            ... on ProjectV2ItemFieldSingleSelectValue {
+                              name
+                              field {
+                                ... on ProjectV2SingleSelectField {
+                                  name
+                                }
+                              }
+                            }
+                            ... on ProjectV2ItemFieldDateValue {
+                              date
+                              field {
+                                ... on ProjectV2Field {
+                                  name
+                                }
+                              }
+                            }
+                          }
+                        }
+                      }
+                    }
+                  }
+                }
+              }
+            `;
+
+            const variables = {
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issueNumber: context.issue?.number || context.payload.pull_request?.number
+            };
+
+            if (!variables.issueNumber) {
+              console.log('No issue or PR number found');
+              return;
+            }
+
+            const result = await github.graphql(query, variables);
+            const projectItems = result.repository.issue.projectItems.nodes;
+
+            for (const item of projectItems) {
+              console.log(`Processing project item: ${item.id}`);
+
+              // Find status field value
+              let currentStatus = null;
+              let startDate = null;
+              let endDate = null;
+              let statusFieldId = null;
+              let startDateFieldId = null;
+              let endDateFieldId = null;
+
+              // First, get field IDs from the project
+              const projectQuery = `
+                query($projectId: ID!) {
+                  node(id: $projectId) {
+                    ... on ProjectV2 {
+                      fields(first: 20) {
+                        nodes {
+                          ... on ProjectV2Field {
+                            id
+                            name
+                          }
+                          ... on ProjectV2SingleSelectField {
+                            id
+                            name
+                          }
+                        }
+                      }
+                    }
+                  }
+                }
+              `;
+
+              const projectResult = await github.graphql(projectQuery, {
+                projectId: item.project.id
+              });
+
+              const fields = projectResult.node.fields.nodes;
+
+              // Map field names to IDs (using exact field names)
+              for (const field of fields) {
+                if (field.name.toLowerCase() === 'status') {
+                  statusFieldId = field.id;
+                } else if (field.name === 'Start Date') {
+                  startDateFieldId = field.id;
+                } else if (field.name === 'End Date') {
+                  endDateFieldId = field.id;
+                }
+              }
+
+              // Get current field values
+              for (const fieldValue of item.fieldValues.nodes) {
+                if (fieldValue.field?.name?.toLowerCase() === 'status') {
+                  currentStatus = fieldValue.name;
+                } else if (fieldValue.field?.name === 'Start Date') {
+                  startDate = fieldValue.date;
+                } else if (fieldValue.field?.name === 'End Date') {
+                  endDate = fieldValue.date;
+                }
+              }
+
+              console.log(`Current status: ${currentStatus}`);
+              console.log(`Start date: ${startDate}`);
+              console.log(`End date: ${endDate}`);
+
+              const today = new Date().toISOString().split('T')[0];
+
+              // Only update dates if they don't already exist (this prevents overwriting existing dates)
+              // Update start date if status is "In progress 🧑‍💻" and no start date exists
+              if (currentStatus === 'In progress 🧑‍💻' && !startDate && startDateFieldId) {
+                console.log('Setting start date to today');
+                await github.graphql(`
+                  mutation($projectId: ID!, $itemId: ID!, $fieldId: ID!, $value: Date!) {
+                    updateProjectV2ItemFieldValue(input: {
+                      projectId: $projectId
+                      itemId: $itemId
+                      fieldId: $fieldId
+                      value: { date: $value }
+                    }) {
+                      projectV2Item {
+                        id
+                      }
+                    }
+                  }
+                `, {
+                  projectId: item.project.id,
+                  itemId: item.id,
+                  fieldId: startDateFieldId,
+                  value: today
+                });
+              }
+
+              // Update end date if status is "Done ✅" and no end date exists
+              if (currentStatus === 'Done ✅' && !endDate && endDateFieldId) {
+                console.log('Setting end date to today');
+                await github.graphql(`
+                  mutation($projectId: ID!, $itemId: ID!, $fieldId: ID!, $value: Date!) {
+                    updateProjectV2ItemFieldValue(input: {
+                      projectId: $projectId
+                      itemId: $itemId
+                      fieldId: $fieldId
+                      value: { date: $value }
+                    }) {
+                      projectV2Item {
+                        id
+                      }
+                    }
+                  }
+                `, {
+                  projectId: item.project.id,
+                  itemId: item.id,
+                  fieldId: endDateFieldId,
+                  value: today
+                });
+              }
+            }
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/unittests.yml

@@ -19,9 +19,24 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v1
       - name: Configure
-        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=Release -D BUILD_TESTS=ON
+        run: cmake --preset release
       - name: Build
-        run: cmake --build build
+        run: cmake --build --preset release -j 2
       - name: Run all tests
-        run: cd build/tests/unit-tests
+        run: cd build/release/tests/unit-tests
+          && ctest --verbose
+  # This job is for building and testing with IO dependencies like HDF5 and ADIOS2
+  build-and-test-with-io-dependencies:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check GNU and Cmake versions
+        run: gcc --version && cmake --version
+      - name: Checkout repository
+        uses: actions/checkout@v1
+      - name: Configure
+        run: cmake --preset release-io
+      - name: Build
+        run: cmake --build --preset release-io -j 2
+      - name: Run all tests
+        run: cd build/release-io/tests/unit-tests
           && ctest --verbose

.gitignore

@@ -2,6 +2,7 @@ CMakeUserPresets.json
 .vscode/
 .DS_Store
 build*/*
+build
 _build/
 _templates/
 public/
@@ -35,3 +36,7 @@ test*.hpp
 include/specfem_setup.hpp
 install
 bin
+
+
+**/__pycache__
+.github/prompts/ConciseDocument.prompt.md