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Changelog

FLAREr 3.9 (public release)

A major release introducing GLM-native restart files and serverless (FaaSr) execution. FLARE 3.9 requires a build of GLM-AED with the NetCDF restart capacity (GLM-AED version 4); see Restart files below for how to obtain it.

Data assimilation

  • New optional da_setup fields: use_inflation_factor and use_one_step_lag (decouples state and parameter updates).
  • New required add_random_noise field controlling how process noise is added.
  • Optional log-space handling of water-quality observations via log_transform_wq_obs and log_transform_wq_zero_collapse to avoid zero-clamping bias.
  • Reflective bounds and a minimum parameter standard deviation to stabilise parameter estimation; fixes to parameter inflation.
  • Option to initialize parameters from a normal distribution.

Observations

  • New optional assimilate column in observations_config.csv (integer 0/1; defaults to 1 when absent). Setting assimilate = 0 keeps a variable simulated, tracked, and written to forecast output but excludes it from the EnKF update. Existing configurations without the column are unaffected.

Restart files

  • GLM-native restart support. Restart files are now zip archives containing the FLARE DA state (NetCDF) plus per-ensemble GLM restart files, rather than a plain NetCDF file. Old .nc restart files are not compatible with 4.0.
  • Requires GLM-AED version 4, which adds the NetCDF restart capacity this feature depends on. GLM-AED 4 is currently available on the v4alpha branch of GLM-AED and can be installed via the GLMAEDr package: remotes::install_github("flare-forecast/GLMAEDr").
  • New restart_save_timesteps option in output_settings controls which timesteps (relative to forecast_start_datetime) are saved as restart files.

Storage backends and FaaSr

  • All object I/O is routed through a single layer (flare_io.R) that targets one of three backends — local, s3, or faasr — selected by the use_s3 and use_faasr flags in configure_run.yml. The default (both FALSE) is local, so existing configurations are unaffected.
  • Integration with FaaSr for serverless execution on platforms such as GitHub Actions, AWS Lambda, and OpenWhisk. Setting use_faasr: TRUE routes I/O through the FaaSr runtime’s DataStore helpers.
  • New exported, backend-agnostic I/O wrappers: flare_get_file(), flare_put_file(), flare_delete_file(), flare_get_folder_list(), and flare_arrow_s3_bucket().
  • New initialize_faasr() function validates FaaSr/S3 configuration at startup. Anonymous (public, read-only) S3 DataStores are supported.

Inputs and models

  • GLM-AED phytoplankton parameter calibration: parameters stored in aed_phyto_pars.csv can now be calibrated by referencing that file in the par_file column of parameter_calibration_config.csv.
  • Added support for the GLMAEDr package for installing and managing the GLM binary.
  • Note: Windows is not currently supported, as GLM-AED version 4 binaries are not yet built for Windows. Use macOS or Linux (e.g. via WSL2) until Windows v4 binaries are available.
  • Support for plunging inflows and dynamic benthic variables (the latter not assimilated).

Documentation and performance

  • New and expanded vignettes: concepts, configuration, drivers, and DA hyperparameters.
  • Performance improvements to run_da_forecast() and the forecast write step.

Bug fixes

  • Restored the weather uncertainty option.
  • Fixed system2() error handling in run_glm.R.
  • Fixed an issue where targets were not pre-ordered.
  • Fixed an inflow sub_elev issue.
  • Fixed a FaaSr bucket bug.

FLAREr 3.0.3

  • Added sim_name option to run_flare() to support scenario based forecasting workflows.

FLAREr 3.0.2

  • Fixed bug associated with the daily diagnostics where the depths defaulted to a logical if all depth values were NA
  • Fixed bug associated with plotting daily diagnostics

FLAREr 3.0.1

  • Fix bug in check_noaa_ready() that assumed a specific value for future_met_model
  • Fixes to testing suite

FLAREr 3.0.0

  • Able to one parameter from a set of parameters that share the same name (e.g., the temperature in one of three sediment zones)
  • Separate inflow and outflow models
  • Openmeteo API as an option for meteorological inputs
  • Updates to restart capacity that now requires GLM-AED version 3.4 or higher
  • Access to daily summaries (e.g., lake.csv) from GLM-AED in FLAREr output
  • Flexible paths for directory and partitioning of driver files. Uses glue::glue to create path from internal variables.