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@robkooper robkooper released this 08 Oct 20:48
· 4036 commits to master since this release
v1.7.2
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Due to dependencies, PEcAn is now using R 4.0.3 for Docker images.

This is a major change:

  • Newer version of R
  • Ubuntu 20.04 instead of Debian.

Fixed

  • Removed sender.py and now allow the submission of workflows from inside the rstudio container.
  • Use TRAEFIK_FRONTEND_RULE in compose file and TRAEFIK_HOST in env.example, using TRAEFIK_HOST everywhere now. Make sure TRAEFIK_HOST is used in .env
  • Use initial biomass pools for Sorghum and Setaria #2495, #2496
  • PEcAn.DB::betyConnect() is now smarter, and will try to use either config.php or environment variables to create a connection. It has switched to use db.open helper function (#2632).
  • PEcAn.utils::tranformstats() assumed the statistic names column of its input was a factor. It now accepts character too, and returns the same class given as input (#2545).
  • fixed and added tests for get.rh function in PEcAn.data.atmosphere
  • Invalid .zenodo.json that broke automatic archiving on Zenodo (b56ef53)
  • Fixed a filehandle leak in multi-year runs of PEcAn.BIOCRO::met2model.BIOCRO: It was only closing the last input file it processed (#2485).
  • Fix issue with cruncep download: use netcdf subset (ncss) method instead of opendap (#2424).
  • The parse option to PEcAn.utils::read_web_config had no effect when expand was TRUE (#2421).
  • Fixed a typo that made PEcAn.DB::symmetric_setdiff falsely report no differences (#2428).
  • sipnet2netcdf will now only extract the data for the year requested (#2187)
  • Fixed Priors vignette (#2439).
  • When building sipnet model would not set correct model version
  • Update pecan/depends docker image to have latest Roxygen and devtools.
  • Update ED docker build, will now build version 2.2.0 and git
  • Do not override meta-analysis settings random-effects = FALSE #2625
  • model2netcdf.ED2 no longer detecting which varibles names -T- files have based on ED2 version (#2623)
  • Changed docker-compose.yml to use user & group IDs of the operating system user (#2572)
  • gSSURGO file download now added as inputs into BETY through extract_soil_gssurgo (#2666)
  • ensure Tleaf converted to K for temperature corrections in PEcAn.photosynthesis::fitA (#2726)
  • fix bug in summarize.result to output stat, which is needed to turn on RE in the meta-analysis (#2753)
  • ensure that control treatments always receives the random effect index of 1; rename madata.Rdata to jagged.data.Rdata and include database ids and names useful for calculating parameter estimates by treatment (#2756)
  • ensure that existing meta-analysis results can be used for pfts with cultivars (#2761)
  • Major code cleanup by GSoC student @moki1202, fixing many check warnings across 10 packages
    (#2771, #2773, #2774, #2775, #2805, #2815, #2826, #2830, #2857)

Changed

  • Removed deprecated mstmip_vars and mstmip_local; now all functions use the combined standard_vars.csv
  • RabbitMQ is set to be 3.8 since the 3.9 version can no longer be configured with environment variables.
  • Removed old api, now split into rpecanapi and apps/api.
  • Replaced tmvtnorm package with TruncatedNormal package for speed up per #2621.
  • Continuous integration changes: Added experimental GitHub Actions CI builds (#2544), streamlined Travis CI builds, added a fourth R version (second-newest old release; currently R 3.5) to Travis test matrix (#2592).
  • Functions that update database entries no longer pass created_at or updated_at timestamps. The database now updates these itself and ensures they are consistently in UTC (#1083).
  • PEcAn.DB::insert_table now uses DBI::dbAppendTable internally instead of manually constructed SQL (#2552).
  • Rebuilt documentation using Roxygen 7. Readers get nicer formatting of usage sections, writers get more flexible behavior when inheriting parameters and less hassle when maintaining namespaces (#2524).
  • Renamed functions that looked like S3 methods but were not:
    • PEcAn.priors: plot.posterior.density->plot_posterior.density, plot.prior.density->plot_prior.density, plot.trait->plot_trait (#2439).
    • PEcAn.visualization: plot.netcdf->plot_netcdf (#2526).
    • PEcAn.assim.sequential: Remote.Sync.launcher -> Remote_Sync_launcher (#2652)
  • Stricter package checking: make check and CI builds will now fail if R CMD check returns any ERRORs or any "newly-added" WARNINGs or NOTEs. "Newly-added" is determined by strict string comparison against a check result saved 2019-09-03; messages that exist in the reference result do not break the build but will be fixed as time allows in future refactorings (#2404).
  • No longer writing an arbitrary num for each PFT, this was breaking ED runs potentially.
  • The pecan/data container has no longer hardcoded path for postgres
  • PEcAn.JULES: Removed dependency on ncdf4.helpers package, which has been removed from CRAN (#2511).
  • data.remote: Arguments to the function call_MODIS() have been changed (issue #2519).
  • Changed precipitaion downscale in PEcAn.data.atmosphere::download.NOAA_GEFS_downscale. Precipitation was being downscaled via a spline which was causing fake rain events. Instead the 6 hr precipitation flux values from GEFS are preserved with 0's filling in the hours between.
  • Changed dbfile.input.insert to work with inputs (i.e soils) that don't have start and end dates associated with them
  • Default behavior for stop_on_error is now TRUE for non-ensemble runs; i.e., workflows that run only one model simulation (or omit the ensemble XML group altogether) will fail if the model run fails. For ensemble runs, the old behavior is preserved; i.e., workflows will continue even if one of the model runs failed. This behavior can also be manually controlled by setting the new run -> stop_on_error XML tag to TRUE or FALSE.
  • Several functions have been moved out of PEcAn.utils into other packages (#2830, #2857):
    • ensemble.filename, get.results, runModule.get.results, read.sa.output, sensitivity.filename,
      and write.sa.configs have been moved to PEcAn.uncertainty.
    • create.base.plot, dhist, plot_data and theme_border have been moved to PEcAn.visualizaton.

Added

  • BioCro can export Aboveground Biomass (#2790)
  • Functionality for generating the same ensemble parameter sets with randtoolbox functions.
  • Functionality for joint sampling from the posteriors using randtoolbox functions.
  • BASGRA-SDA couplers.
  • Now creates docker images during a PR, when merged it will push them to docker hub and github packages
  • New functionality to the PEcAn API to GET information about PFTs, formats & sites, submit workflows in XML or JSON formats & download relevant inputs/outputs/files related to runs & workflows (#2674 #2665 #2662 #2655)
  • Functions to send/receive messages to/from rabbitmq.
  • Documentation in DEV-INTRO.md on development in a docker environment (#2553)
  • PEcAn API that can be used to talk to PEcAn servers. Endpoints to GET the details about the server that user is talking to, PEcAn models, workflows & runs. Authetication enabled. (#2631)
  • New versioned ED2IN template: ED2IN.2.2.0 (#2143) (replaces ED2IN.git)
  • model_info.json and Dockerfile to template (#2567)
  • Dockerize BASGRA_N model.
  • Basic coupling for models BASGRA_N and STICS.
  • PEcAn.priors now exports functions priorfig and plot_densities (#2439).
  • Models monitoring container for Docker now shows a webpage with models it has seen
  • Added small container to check if certain services are up, used as initi container for kubernetes
  • Documentation how to run ED using singularity
  • PEcAn.DB gains new function get_postgres_envvars, which tries to look up connection parameters from Postgres environment variables (if they are set) and return them as a list ready to be passed to db.open. It should be especially useful when writing tests that need to run on systems with many different database configurations (#2541).
  • New shiny application to show database synchronization status (shiny/dbsync)
  • Ability to run with MERRA-2 meteorology (reanalysis product based on GEOS-5 model)
  • Ability to run with ICOS Ecosystem products

Removed

  • Removed travis integration
  • Removed the sugarcane and db folders from web, this removes the simple DB editor in the web folder. (#2532)
  • Removed ED2IN.git (#2599) 'definitely going to break things for people' - but they can still use PEcAn <=1.7.1
  • Database maintenance scripts vacuum.bety.sh and reindex.bety.sh have been moved to the BeTY database repository (#2563).
  • Scripts dump.pgsql.sh and dump.mysql.sh have been deleted. See the "BeTY database administration" chapter of the PEcAn documentation for current recommendations (#2563).
  • Old dependency management scripts check.dependencies.sh, update.dependencies.sh, and install_deps.R have been deleted. Use generate_dependencies.R and the automatic dependency handling built into make install instead (#2563).
  • Deprecated copies of functions previously moved to other packages have been removed from PEcAn.utils (#2830):
    • do_conversions and runModule.run.write.configs, run.write.configs. These are now in PEcAn.workflow
    • get.ensemble.samples, read.ensemble.output, write.ensemble.configs. These are now in PEcAn.uncertainty
    • logger.debug, logger.error, logger.getLevel, logger.info, logger.setLevel,
      logger.setOutputFile, logger.setQuitOnSevere, logger.setWidth, logger.severe, logger.warn.
      These are now in PEcAn.logger

Contributors

moki1202
Assets 2
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