Merge branch 'develop' into develop

Author: mdietze

.github/workflows/docker-stack-sipnet.yml

@@ -51,6 +51,7 @@ jobs:
         docker compose up --wait -d postgres
         docker run --rm --network pecan_pecan pecan/db:ci
         docker run --rm --network pecan_pecan --volume pecan_pecan:/data --env FQDN=docker pecan/data:develop
+        docker run --rm --network pecan_pecan --volume pecan_pecan:/data pecan/data:develop chown -R "$(id -u):$(id -g)" /data
         docker image rm pecan/db:ci pecan/data:develop
     
     - name: Run required containers

CHANGELOG.md

@@ -5,19 +5,24 @@ section for the next release.
 
 For more information about this file see also [Keep a Changelog](http://keepachangelog.com/) .
 
-## [Unreleased]
+## [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.
@@ -38,7 +43,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 ### Removed
 
 - Remove Browndog support for conversions (#3348, @Sweetdevil144).
-- Packages PEcAn.PRELES is no longer built or tested by default, because of ongoing build failures in the `RPreles` package it depends on.
+- 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!).
 
 ## [1.8.0] - 2024-07-12

DEV-INTRO.md

@@ -169,7 +169,7 @@ Linux & Mac
 
 ```bash
 # Change ownership of /data directory in pecan volume to the current user
-docker run -ti --rm --network pecan_pecan --volume pecan_pecan:/data pecan/data:develop chown -R "$(id -u).$(id -g)" /data
+docker run -ti --rm --network pecan_pecan --volume pecan_pecan:/data pecan/data:develop chown -R "$(id -u):$(id -g)" /data
 
 docker run -ti --user="$(id -u)" --rm --network pecan_pecan --volume pecan_pecan:/data --env FQDN=docker pecan/data:develop
 ```

apps/api/Dockerfile

@@ -17,7 +17,7 @@ EXPOSE 8000
 RUN apt-get update \
   &&  apt-get install libsodium-dev -y \
   &&  rm -rf /var/lib/apt/lists/* \
-  &&  Rscript -e "devtools::install_version('promises', '1.1.0')" \
+  &&  Rscript -e "devtools::install_version('promises')" \
   &&  Rscript -e "devtools::install_version('webutils', '1.1')" \
   &&  Rscript -e "install.packages('pool')" \
   &&  Rscript -e "devtools::install_github('rstudio/swagger')" \

apps/api/R/runs.R

@@ -237,8 +237,9 @@ getRunOutputFile <- function(req, run_id, filename, res){
 #' @author Tezan Sahu
 #* @get /<run_id>/graph/<year>/<y_var>
 #* @serializer contentType list(type='image/png')
+plotResults <- function(req, run_id, year, y_var, width = 800, height = 600, res) {
+  x_var <- ifelse(!is.null(req$args$xvar), req$args$xvar, "time")
 
-plotResults <- function(req, run_id, year, y_var, x_var="time", width=800, height=600, res) {
   # Get workflow_id for the run
   Run <- tbl(global_db_pool, "runs") %>%
     filter(id == !!run_id)
@@ -273,7 +274,7 @@ plotResults <- function(req, run_id, year, y_var, x_var="time", width=800, heigh
 
   # Plot & return
   filename <- paste0(Sys.getenv("DATA_DIR", "/data/"), "workflows/temp", stringi::stri_rand_strings(1, 10), ".png")
-  PEcAn.visualization::plot_netcdf(datafile, y_var, x_var, as.integer(width), as.integer(height), year=year, filename=filename)
+  PEcAn.visualization::plot_netcdf(datafile, y_var, x_var, as.integer(width), as.integer(height), filename=filename, year=year)
   img_bin <- readBin(filename,'raw',n = file.info(filename)$size)
   file.remove(filename)
   return(img_bin)

base/all/DESCRIPTION

@@ -1,7 +1,7 @@
 Package: PEcAn.all
 Type: Package
 Title: PEcAn Functions Used for Ecological Forecasts and Reanalysis
-Version: 1.8.0.9000
+Version: 1.9.0
 Authors@R: c(person("Mike", "Dietze", role = c("aut"),
                      email = "dietze@bu.edu"),
              person("David", "LeBauer", role = c("aut", "cre"),

base/all/NEWS.md

@@ -1,4 +1,4 @@
-# PEcAn.all 1.8.0.9000
+# PEcAn.all 1.9.0
 
 ## License change
 * PEcAn.all is now distributed under the BSD three-clause license instead of the NCSA Open Source license.

base/all/data/pecan_releases.csv

@@ -32,3 +32,4 @@
 "v1.7.1",2019-09-20,1.7.1
 "v1.7.2",2021-10-08,1.7.2
 "v1.8.0",2024-07-12,1.8.0
+"v1.9.0",2025-05-25,1.9.0