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Merge pull request #1585 from PrincetonUniversity/devel
Release Candidate 0.5.0
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‎.github/chatmodes/DocumenTor.chatmode.md‎

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

‎.github/release.yaml‎

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- title: 🎉 New Feature
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labels:
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- feature
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- title: 👨‍🔬 New physics
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- title: 👨‍🔬 New physics
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labels:
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- new physics
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- title: 🚀 Performance enhancement
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- title: Fortran Meshfem2D/3D updates
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labels:
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- fortran
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- title: Refactor
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- title: Refactor
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labels:
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- refactor
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- title: 🐛 Bug Fixes

‎.github/workflows/compilation.yml‎

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

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

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

‎.github/workflows/unittests.yml‎

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

‎.gitignore‎

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.vscode/
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.DS_Store
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build*/*
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build
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_build/
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_templates/
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public/
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include/specfem_setup.hpp
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install
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bin
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**/__pycache__
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.github/prompts/ConciseDocument.prompt.md

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