climatehealth development notes

Unreleased

1.0.1

• CRAN resubmission focused on Fedora Linux check reliability and test stability.
• Fixed INLA model execution under check-core constraints:
  • limits INLA thread usage when _R_CHECK_LIMIT_CORES_ is set
  • keeps compatibility across INLA versions by conditionally passing thread-related arguments only when supported
• Hardened CRAN behavior for fragile INLA end-to-end disease tests:
  • retained CRAN-safe skips for diarrhea and malaria integration paths
  • avoids Fedora-specific parallel worker failures seen in prior checks
• Improved integration-test governance in CI:
  • heavy integration tests are opt-in via RUN_INTEGRATION=true
  • standard PR/push CI remains fast and high-signal by default
• Build hygiene improvement:
  • excludes .covrignore from package build input via .Rbuildignore

1.0.0

• Added new descriptive statistics public APIs:
  • run_descriptive_stats()
  • run_descriptive_stats_api()
• Added run-scoped output folders for descriptive stats:
  • <output_path>/descriptive_stats/<run_id>/All/
  • <output_path>/descriptive_stats/<run_id>/<Region>/
• Kept backward-compatible aliases with runtime deprecation warnings:
  • common_descriptive_stats_core()
  • common_descriptive_stats()
  • common_descriptive_stats_api()
• Improved descriptive stats robustness:
  • correlation now validates and filters numeric columns explicitly
  • centralized preflight column and parameter validation for enabled features
  • typed summary behavior for non-numeric columns
  • safer plot device cleanup with managed PDF helper
• Expanded tests for wrapper behavior, run-folder outputs, API payload validation, endpoint-style contract responses, and deprecated alias compatibility.
• Moved API runtime assets previously held in climatehealth_pipelines into the package:
  • plumber routes and startup scripts under inst/plumber/
  • throttling modules and tests
  • package-scoped API and developer config templates under inst/extdata/config_templates/
  • operational helper scripts under inst/scripts/
• Improved package/API compatibility for runtime usage:
  • enabled API mode in plumber runtime
  • added direct endpoint bindings for descriptive statistics, malaria, and diarrhea
  • enforced API-safe return payloads for malaria and diarrhea in API mode
  • extended internals to accept API-style record payloads and map records
  • updated throttle estimation to size JSON-record payloads instead of file paths
• Cleaned up the air pollution module:
  • standardized argument and variable naming
  • refreshed documentation
  • resolved R CMD check notes for global variable bindings
  • added backward-compatible support for legacy air_pollution_do_analysis() argument names
  • expanded air pollution regression and integration tests