[WIP] Set up Copilot instructions for repository

.github/copilot-instructions.md

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+# Copilot Instructions for teal
+
+## Project Overview
+
+`teal` is a Shiny-based interactive exploration framework for analyzing clinical trial data. It provides a modular architecture for building data analysis applications with dynamic filtering, data visualization, and reporting capabilities.
+
+## Language and Framework
+
+- **Primary Language**: R (>= 4.1)
+- **Framework**: Shiny (>= 1.8.1)
+- **Package Type**: R package following CRAN standards
+- **Architecture**: Modular Shiny applications using `teal_module` and `teal_modules` objects
+
+## Key Dependencies
+
+- `teal.data` - for creating and loading data
+- `teal.slice` - for filtering panel functionality
+- `teal.reporter` - for generating reports
+- `teal.widgets` - for Shiny components
+- `teal.code` - for code tracking and reproducibility
+- `bslib` - for modern UI components
+- `shinyjs` - for JavaScript interactions
+
+## Code Style and Standards
+
+### R Code Style
+
+- Follow the [tidyverse style guide](https://style.tidyverse.org/)
+- Maximum line length: 120 characters (configured in `.lintr`)
+- Use `lintr` for code quality checks
+- Use roxygen2 comments for documentation
+- Use lifecycle badges (`lifecycle::badge()`) for deprecation notices
+
+### Documentation Requirements
+
+- All exported functions must have roxygen2 documentation with `@param`, `@return`, and `@export` tags
+- Include `@examples` or `@examplesShinylive` for public functions
+- Use `@keywords internal` for internal functions
+- Document S3 methods and classes appropriately
+
+### Testing
+
+- Use `testthat` (>= 3.2.0) for unit tests
+- Use `shinytest2` for interactive Shiny module testing
+- Test files are in `tests/testthat/` directory
+- Follow naming convention: `test-*.R` for unit tests, `test-shinytest2-*.R` for Shiny tests
+- Aim for comprehensive test coverage
+
+## Development Workflow
+
+### Building and Checking
+
+- Run `R CMD check --as-cran` for CRAN-compliant checks
+- Use `roxygen2` to generate documentation
+- Environment variable `NOT_CRAN=true` enables additional tests
+- The package uses `staged.dependencies` for managing cross-repository dependencies
+
+### Linting
+
+- Configuration in `.lintr` file
+- Run linter checks before committing
+- SuperLinter runs on pull requests
+
+### Pre-commit Hooks
+
+- Pre-commit hooks are configured in `.pre-commit-config.yaml`
+- Recommended to use `pre-commit` tool with R hooks
+
+## Architecture Patterns
+
+### Teal Modules
+
+- Modules are created using `module()` function with `label`, `server`, `ui`, and `datanames` parameters
+- Server functions use `moduleServer(id, function(input, output, session) {...})`
+- UI functions use `NS(id)` for proper namespacing
+- The `datanames` parameter controls which datasets are shown in the module
+
+### Data Handling
+
+- Use `teal_data` objects for data management
+- Use `teal_data_module()` for dynamic data loading
+- Hidden datasets (prefixed with `.`) are not displayed in the application
+- Support for CDISC data, independent datasets, and MultiAssayExperiment objects
+
+### Filtering
+
+- Filtering is managed via `teal_slices()` objects
+- Module-specific filters can be configured
+- Snapshot functionality for capturing/restoring filter states
+
+### Reporting
+
+- Reporting functionality via `teal.reporter::Reporter` objects
+- Modules can implement report card generation
+- Reporter can be disabled globally by setting `reporter = NULL`
+
+## Common Patterns
+
+### Creating a Teal Module
+
+```r
+my_module <- module(
+  label = "Module Label",
+  server = function(id, data) {
+    moduleServer(id, function(input, output, session) {
+      # Module server logic
+    })
+  },
+  ui = function(id) {
+    ns <- NS(id)
+    # Module UI
+  },
+  datanames = c("dataset1", "dataset2")
+)
+```
+
+### Teal Application Initialization
+
+```r
+app <- init(
+  data = teal_data(...),
+  modules = modules(
+    module(...),
+    module(...)
+  ),
+  filter = teal_slices(...)
+)
+```
+
+### Transform Modules (Decorators)
+
+- Use `teal_transform_module()` for output transformations
+- Can modify plot or table outputs from modules
+- Use `make_teal_transform_server()` to reduce boilerplate
+
+## File Organization
+
+- **R/**: Source code files
+  - Module files: `module_*.R`
+  - Main entry point: `init.R`
+  - Data structures: `teal_slices.R`, `teal_data_module.R`, etc.
+  - Utilities: `utils.R`, `validate_inputs.R`, `validations.R`
+- **tests/testthat/**: Test files
+- **man/**: Generated documentation (auto-generated, do not edit manually)
+- **vignettes/**: Package vignettes and tutorials
+- **inst/**: Installation files including CSS/JS assets
+
+## Important Notes
+
+### Reserved Labels
+
+- `"global_filters"` - reserved for the mapping argument in `teal_slices()`
+- `"Report previewer"` - reserved for the report previewer module
+
+### Deprecation
+
+- Use `lifecycle::badge("deprecated")` in documentation
+- Deprecated functions should include guidance on alternatives
+- Follow semantic versioning for breaking changes
+
+### Dependencies
+
+- Minimize dependencies following [tinyverse](https://www.tinyverse.org/) recommendations
+- Specify minimum versions in DESCRIPTION when compatibility requires it
+- Format: `package (>= version)` or `package (>= version.9000)` for development versions
+
+## Security
+
+- Do not commit sensitive information (PII, PHI, PCI)
+- Report security vulnerabilities to vulnerability.management[@]roche.com
+- Do not use public GitHub issues for security concerns
+
+## Contributing
+
+- Branch naming: `<issue_id>_<short_description>` (use underscores)
+- For multi-repo changes: `<issue_id>_<issue_repo>_<short_description>`
+- Use `staged.dependencies` for cross-repository dependencies
+- Minimum 5% code contribution or top 5 contributor status for author attribution
+
+## Useful Resources
+
+- [Project Documentation](https://insightsengineering.github.io/teal/)
+- [CONTRIBUTING.md](.github/CONTRIBUTING.md) - Detailed contribution guidelines
+- [CODE_OF_CONDUCT.md](.github/CODE_OF_CONDUCT.md) - Community standards
+- [pharmaverse Slack](https://pharmaverse.slack.com) - `teal` channel for questions