PEcAn v1.9.0

[1.9.0] - 2025-05-25

Added

• Documentation of make options including addition of make help
• Removed reference to PEcAn VM from documentation #3478
• Add make option to document a single package with make documentation pathto/package
• settings$host$qsub and settings$host$modellauncher$qsub.extra will now expand @NJOBS@ to the number of models in the run, allowing e.g. --array=1-@NJOBS@. Note that qsub still by default submits every model as a separate job, so for now this is mostly useful for custom modellauncher scripts
• Added automated pkgdown documentation for all PEcAn packages (@divine7022, #3482):
  • Compiled pages are live at https://pecanproject.github.io/package-documentation and inside Docker at pecan.localhost/pkgdocs/, and these are automatically updated each time a PR to the source packages is merged.
  • You can compile all pkgdown pages locally at any time with make pkgdocs.

Fixed

• api to correctly use x_var from request in plotResults #3528
• rstudio username is now set using DEFAULT_USER
• ed2 did not compile with newer rocker images
• api did not compile with newer rocker images
• maespa did not compile with new fortran compiler
• updated github action to build docker images
• PEcAn.SIPNET now accepts relative paths in its input XML (#3418). Previously all files referenced in the autogenerated job.sh needed to be specified as absolute paths.
• R version 4.4 installs Python 3.12 which wants to leverage os managed packages instead, install python3-pika using apt.

Changed

• Docker images now use R 4.4 by default, with other supported versions available by appending the R version to the tag, e.g. pecan/base:develop-R4.2.
• Is is now easier to run PEcAn workflows with no active database connection by setting settings$database$bety$write to FALSE or missing (#3398, #3419). In this mode you are reponsible for providing the correct paths/ids for all needed files, and run metadata are not written back to the database.
• The following components have changed their licensing. With approval of all their contributors, we now provide them under a BSD 3-clause license rather than the previously used NCSA Open Source license. As a reminder, we intend to relicense the entire system and this list will expand as we gather permission from the relevant copyright owners.
  • apps/api
  • Shiny apps dbsync, BenchmarkReport, Data-Ingest, Elicitation, ForecastingDashboard, global-sensitivity, Pecan.depend, SDAdashboard, and ViewMet
  • Base packages PEcAn.all, PEcAn.DB, PEcAn.QAQC, PEcAn.remote, PEcAn.settings, PEcAn.visualization, and PEcAn.workflow
  • Model packages PEcAn.BASGRA, PEcAn.CLM45, PEcAn.DALEC, PEcAn.dvmdostem, PEcAn.FATES, PEcAn.GDAY, PEcAn.JULES, PEcAn.LDNDC, PEcAn.LINKAGES, PEcAn.LPJGUESS, PEcAn.MAAT, PEcAn.MAESPA, PEcAn.PRELES, PEcAn.SIBCASA, PEcAn.SIPNET, PEcAn.STICS, and the new model package template.
  • Modules PEcAn.allometry, PEcAn.assim.batch, PEcAn.data.mining, PEcAn.emulator, PEcAn.MA, PEcAn.photosynthesis, PEcAn.priors, and PEcAn.RTM.
• Renamed master branch to main
• PEcAn.all::pecan_version() now reports commit hashes as well as version numbers for each installed package.

Removed

• Remove Browndog support for conversions (#3348, @Sweetdevil144).
• Package PEcAn.PRELES is no longer built or tested by default, because of ongoing build failures in the RPreles package it depends on.
  Install it manually as needed, and be aware it is not being routinely checked by CI (so if you're checking it, please file bugs and submit fixes!).