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PEcAn 1.7.0

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@robkooper robkooper released this 10 Dec 17:45
· 8017 commits to develop since this release
v1.7.0
e697a0a

Many updates to docker. Docker is now becoming more stable and can be used for new installations. Please check on the PEcAn slack channel if you want to start to use the docker installation.

This version replaces google maps in the web interface with leaflet. During this conversion we also sped up the rendering of the markers on the map. They are now grouped together, clicking a group marker will zoom into that area. You can always search in the box on the left to filter the markers if you know the sitename.

Below is a full list of all changes in this release.

Fixes

  • Removed google maps and replaced with leaflet #2105
  • Added ability to add a new site from web interface
  • Small updated to models/ed/R/model2netcdf.ED2.R to fix issue realted to writing the time_bounds time attribute. Needed to add a check for which file types exitst (e.g. -E-, -T-, etc) and only write the appropriate attribute(s).
  • Fixed error in read_web_config which would filter out all variables.
  • Docker:
    • Make sure web interface posts RabbitMQ messages even after editing files (fixes #2151)
    • Can specify name of docker cluster using PECAN_FQDN and PECAN_NAME (fixes #2128)
    • Fixed issue where setting username/password for rabbitmq would break web submit (fixes #2185)
    • data image only registers sipnet and ed, has all data pre-downloaded
  • ED2:
    • Fix processing of ed2in_tags from XML. Now numbers (e.g. <TRAIT_PLASTICITY_SCHEME>0</TRAIT_PLASTICITY_SCHEME>) and numeric vectors (e.g. <INCLUDE_THESE_PFT>9,10,11,12</INCLUDE_THESE_PFT>) are correctly written to ED2IN without quotes.

Added

  • NEW FEATURE: PEcAn R API (PR #2192). Features include:
    • Modified docker/receiver.py to accept a pecan_json object containing a JSON version of the PEcAn settings. Can now Use RabbitMQ HTTP API (called from R with httr) to send a settings list (function submit_workflow)
    • Helper functions to make it easier to build the settings object, and to register a new workflow.
    • Helper functions for tracking workflow status
    • Helper functions for accessing workflow output files through THREDDS. All files are accessible through fileServer (basically, direct download), and NetCDF files are also readable through OpenDAP.
      • THREDDS catalog filter has been removed, so that all workflow outputs are available to THREDDS.
      • Added another datasetScan to the THREDDS catalog to search for dbfiles. Now, model inputs (e.g. meteorology files) are accessible via THREDDS as well.
  • Lots of new documentation for running PEcAn using Docker
  • Added Docker container with documentation #2160
  • Download method (method) argument for data.atmosphere::download.CRUNCEP, which defaults to opendap (as it was), but can be switched to the slower but more robust NetCDF subset (ncss).
  • In download.CRUNCEP, check target coordinate against the land-sea mask. If sea, pick the nearest land pixel within 1 degree of target. This facilitates doing runs at coastal sites that may get masked out.
  • Added a prototype of the THREDDS data server (TDS) to the PEcAn Docker stack.
  • Added portainer to the PEcAn Docker stack to easily look at running containers.
  • Added ability to specify short name for a host (hostlist->displayname)
  • ED2:
    • Add ability to pass arbitrary arguments to the ED binary through the pecan.xml (#2183; fixes #2146).
    • Add new model tag <all_pfts>. If "false" (default), set ED2IN's INCLUDE_THESE_PFT to only PFTs explicitly configured through PEcAn. If "true", use all 17 of ED2's PFTs.
    • Add new model tag <barebones_ed2in>. If "true", only write ED2IN tags, and do not include comment annotations. If "false" (default), try to transfer comments from ED2IN template to target ED2IN. Because of comments are written by matching line numbers, leaving this as "false" can lead to unexpected results whenever <ed2in_tags> contains tags missing from the ED2IN template.
    • Add some additional documentation for ED2 pecan.xml tags.

Removed

Changed

  • PEcAn.utils::do_conversions has been moved to PEcAn.workflow::do_conversions.
    PEcAn.utils::do_conversions still works for now with a warning, but is deprecated and will be removed in the future.
  • Docker:
    • Change base image for R code from r-base to rocker/tidyverse:3.5.1. This (1) saves build time (because many R packages and system dependencies are pre-installed), and (2) enhances reproducibility (because of the strict versioning rules of the rocker packages)
    • Re-factor web interface RabbitMQ create connections and post messages into their own PHP functions.
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