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PecanProject/pecan v1.5.1

David LeBauer; Michael Dietze; Rob Kooper; Alexey Shiklomanov; Betsy Cowdery; istfer; Anthony Gardella; Ben Bond-Lamberty; Shawn P. Serbin; Ann Raiho; Anne Thomas; Chris Black; James Simkins; Ankur Desai; jam2767; Aman Kumar; LiamBurke24; Afshin Pourmokhtarian; Christy Rollinson; Shubham Agarwal; hardimanb; Martin De Kauwe; Eugene; Tess McCabe; kragosta; TonyCohen; zhangwenx; Viskari; Yan Zhao; jingxia

Fixes
  • Fixed hyperparameter draws in PDA
  • Show workflowid in the URL when run is finshed and user clicks results (#1659)
  • PEcAn.BIOCRO now uses PEcAn-standard variable names. As a result, two output variables have been renamed but keep their existing units and definitions:
  • StemBiom renamed to AbvGrndWood
  • RootBiom renamed to root_carbon_content
  • Improved make install logic (#1558)
  • Fixed remote code execution #1545
  • Added check for NA end/start year in read.output
  • Fixed jagify bug for raw field data
  • Fixed bug (order of dims in nc_create) introduced in model2netcdf.DALEC by standard_vars changes
  • Cleaned up NAMESPACE and source code of PEcAn.DB (#1520)
  • Debugged python script in call_MODIS in data.remote to allow MODIS downloads
  • Fixed FATES build script to work on ubuntu SIPNET output netcdf now includes LAI; some variable names changed to match standard
  • Cleanup of leap year logic, using new PEcAn.utils::days_in_year(year) function (#801).
  • Replace many hard-coded unit conversions with udunits2::ud.convert for consistency, readability, and clarity
  • Refactored extract_soil_nc to create soil2netcdf, which will write soil data out in PEcAn standard.
  • Added a new retry.func() to base/utils to provide ability to re-try a function X times before stopping. Currently using this function in the download.CRUNCEP() function to handle slow responses from THREDDS.
  • Reformatted call_MODIS netcdf output to reflect the orientation of the MODIS grid
  • Remote execution is more robust to errors in the submission process, not just the actual model execution
  • PRELES model run script bug fix
Added
  • Functionality to pass hyperparameters via settings
  • Created new (and very rudimentary) web interface for downloading data from the dataone federation into the PEcAn database. More updates to come.
  • Expanded initial conditions workflow for pool-based models, including PEcAn.data.land::prepare_pools to calculate pools from IC file (to be coupled with write.configs)
  • New PEcAn.utils::days_in_year(year) function that should make it easier to work with leap years.
  • New PEcAn.data.atmosphere::solar_angle function that replaces math that occurs in some models.
  • New PEcAn.benchmarking::align_pft fucntion that aligns data assosiated with two different plant functional types
  • #1594 shiny/workflowPlot Adding interactiveness using ggploltly
  • #1594 shiny/workflowPlot Load outputs from multiple runs of the model
  • #1594 shiny/workflowPlot Ways to toggle geometries (e.g. geom_point vs. geom_line).
  • #1594 shiny/workflowPlot Smoothing using geom_smooth (Slider for specifying moving window width)
  • #1594 shiny/workflowPlot Comparing model output vs loaded data according to tutorial
  • Allow SIPNET and DALEC met files and model2netcdf to start or end mid year
  • A Pre-release database clean up script that deletes unused/unassosiated entries from the database
Changed
  • Clean up directory structure:
    • Move base packages (utils, settings, db, visualizaton) to a base directory, for consistency with modules and models
    • Move logger.* functions out of the PEcAn.utils package and into the PEcAn.logger package
    • Move remote functions out of the PEcAn.utils package and into their own PEcAn.remote package.
  • #1594 shiny/workflowPlot Refactoring of code. get_workflow_ids in db/R/query.dplyr.R changed with ensemble = FALSE. Also allowing to load all workflow IDs. load_data_single_run and var_names_all also moved from shiny/workflowPlot/server.R to query.dplyr.R
  • PEcAn.remote::start.model.runs has been significantly refactored to be less redundant and more robust betyConnect function in query.dplyr.R is now refactored into read_web_config so that the the Data-Ingest app can leverage read_web_config and provide it with a machine specific filepath for .../dbfiles
  • Rpreles and Maeswrap package moved to suggest checked for within package function.
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