10.5281/zenodo.1003756
https://zenodo.org/records/1003756
oai:zenodo.org:1003756
David LeBauer
David LeBauer
University of Illinois
Michael Dietze
Michael Dietze
Boston University
Rob Kooper
Rob Kooper
NCSA
Alexey Shiklomanov
Alexey Shiklomanov
Boston University
Betsy Cowdery
Betsy Cowdery
istfer
istfer
Anthony Gardella
Anthony Gardella
Boston Univeristy
Ben Bond-Lamberty
Ben Bond-Lamberty
PNNL/UMD
Shawn P. Serbin
Shawn P. Serbin
Brookhaven National Laboratory
Ann Raiho
Ann Raiho
University of Notre Dame
Anne Thomas
Anne Thomas
Chris Black
Chris Black
James Simkins
James Simkins
Ankur Desai
Ankur Desai
University of Wisconsin-Madison
jam2767
jam2767
Aman Kumar
Aman Kumar
LiamBurke24
LiamBurke24
Afshin Pourmokhtarian
Afshin Pourmokhtarian
Boston University
Christy Rollinson
Christy Rollinson
Morton Arboretum
Shubham Agarwal
Shubham Agarwal
hardimanb
hardimanb
Martin De Kauwe
Martin De Kauwe
University of New South Wales
Eugene
Eugene
Tess McCabe
Tess McCabe
kragosta
kragosta
TonyCohen
TonyCohen
zhangwenx
zhangwenx
Viskari
Viskari
Yan Zhao
Yan Zhao
jingxia
jingxia
PecanProject/pecan v1.5.1
Zenodo
2017
2017-10-06
https://github.com/PecanProject/pecan/tree/v1.5.1
10.5281/zenodo.597987
v1.5.1
Other (Open)
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.