Merge branch 'develop' into integ-testing

.github/workflows/ci-weekly.yml

@@ -13,6 +13,7 @@ jobs:
       fail-fast: false
       matrix:
         R:
+          - "4.3"
           - "devel"
     uses: ./.github/workflows/test.yml
     with:
@@ -24,6 +25,7 @@ jobs:
       fail-fast: false
       matrix:
         R:
+          - "4.3"
           - "devel"
     uses: ./.github/workflows/check.yml
     with:
@@ -36,6 +38,7 @@ jobs:
       fail-fast: false
       matrix:
         R:
+          - "4.3"
           - "devel"
     uses: ./.github/workflows/sipnet.yml
     with:

.github/workflows/depends.yml

@@ -31,6 +31,7 @@ jobs:
           - "4.1"
           - "4.2"
           - "4.3"
+          - "4.4"
           - "devel"
 
     steps:
@@ -49,11 +50,14 @@ jobs:
 
       # calculate some variables that are used later
       - name: github branch
-        # build Rdevel only on Mondays, others every day (but not twice on Mondays)
+        # build weekly-tested versions only on Mondays, others every day
+        # (but not twice on Mondays)
         if: |
           github.event_name == 'workflow_dispatch' ||
-          (matrix.R != 'devel' && github.event.schedule == '0 0 * * *') ||
-          (matrix.R == 'devel' && github.event.schedule == '30 1 * * 1')
+          (contains(fromJSON('["4.1", "4.2", "4.4"]'), matrix.R)
+            && github.event.schedule == '0 0 * * *') ||
+          (contains(fromJSON('["4.3", "devel"]'), matrix.R)
+            && github.event.schedule == '30 1 * * 1')
         run: |
           BRANCH=${GITHUB_REF##*/}
           echo "GITHUB_BRANCH=${BRANCH}" >> $GITHUB_ENV

CHANGELOG.md

@@ -45,6 +45,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 - Added new feature of preparing initial conditions for MODIS LAI, AGB, ISCN SOC, and soil moisture across NA anchor sites.
 - Added GEDI AGB preparation workflow.
 - Added new feature of downloading datasets from the NASA DAAC ORNL database.
+- Extended downscale function and created 'downscale_hrly' so that it handles more frequent data
 - Added 'aggregate' as a new feature for downscaled data
 
 ### Fixed

CODE_OF_CONDUCT.md

@@ -0,0 +1,45 @@
+# Contributor Covenant Code of Conduct
+
+**Our Pledge**
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+**Our Standards**
+
+Examples of behavior that contributes to creating a positive environment include:
+
+   * Using welcoming and inclusive language
+   * Being respectful of differing viewpoints and experiences
+   * Gracefully accepting constructive criticism
+   * Focusing on what is best for the community
+   * Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+
+
+**Our Responsibilities**
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+**Scope**
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+**Enforcement**
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at pecanproj[at]gmail.com. All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+
+**Attribution**
+
+This Code of Conduct is adapted from the [Contributor Covenant](http://contributor-covenant.org/)  version 1.4, available at [http://contributor-covenant.org/version/1/4](http://contributor-covenant.org/version/1/4/).

DEV-INTRO.md

@@ -78,7 +78,6 @@ You can copy the [`docker/env.example`](docker/env.example) file as .env in your
 cp docker/env.example .env
 ```
 
-
 The variables we want to modify are:
 
 - `COMPOSE_PROJECT_NAME`, the prefix for all containers. Set this to "pecan".
@@ -181,13 +180,13 @@ Next copy the R packages from a container to volume `pecan_lib`. This is not rea
 
 You can copy all the data using the following command. This will copy all compiled packages to your local machine.
 
-```
+```bash
 docker run -ti --rm -v pecan_R_library:/rlib pecan/base:develop cp -a /usr/local/lib/R/site-library/. /rlib/
 ```
 
 If you have set a custom UID or GID in your `.env`, change ownership of these files as described above for the data volume. E.g. if you use the same UID in the containers as on your host machine, run:
 
-```
+```bash
 docker run -ti --rm -v pecan_R_library:/rlib pecan/base:develop chown -R "$(id -u):$(id -g)" /rlib/
 ```
 
@@ -210,7 +209,7 @@ For Windows
 copy docker\web\config.docker.php web\config.php
 ```
 
-## PEcAn Development
+## PEcAn Development Setup
 
 To begin development we first have to bring up the full PEcAn stack. This assumes you have done once the steps above. You don\'t need to stop any running containers, you can use the following command to start all containers. At this point you have PEcAn running in docker.
 
@@ -239,13 +238,13 @@ R CMD ../web/workflow.R --settings docker.sipnet.xml
 
 A better way of doing this is developed as part of GSOC, in which case you can leverage of the restful interface defined, or using the new R PEcAn API package.
 
-# PEcAn URLs
+## PEcAn URLs
 
 You can check the RabbitMQ server used by pecan using <https://rabbitmq.pecan.localhost> on the same server that the docker stack is running on. You can use rstudio either with <http://server/rstudio> or at <http://rstudio.pecan.localhost>. To check the traefik dashboard you can use <http://traefik.pecan.localhost>.
 
 If the stack is running on a remote machine, you can use ssh and port forwarding to connect to the server. For example `ssh -L 8000:localhost:80` will allow you to use <http://rabbitmq.pecan.localhost:8000/> in your browser to connect to the remote PEcAn server RabbitMQ.
 
-# Directory Structure
+## Directory Structure
 
 Following are the main folders inside the pecan repository.
 
@@ -281,9 +280,9 @@ Some of the docker build files. The Dockerfiles for each model are placed in the
 
 Small scripts that are used as part of the development and installation of PEcAn.
 
-# Advanced Development Options
+## Advanced Development Options
 
-## Reset all containers/database
+### Reset all containers/database
 
 If you want to start from scratch and remove all old data, but keep your pecan checked out folder, you can remove the folders where you have written the data (see `folders` below). You will also need to remove any of the docker managed volumes. To see all volumes you can do `docker volume ls -q -f name=pecan`. If you are sure, you can either remove them one by one, or remove them all at once using the command below. **THIS DESTROYS ALL DATA IN DOCKER MANAGED VOLUMES.**.
 

base/db/tests/Rcheck_reference.log

@@ -62,7 +62,8 @@ The Date field is over a month old.
 * checking package directory ... OK
 * checking for future file timestamps ... OK
 * checking ‘build’ directory ... OK
-* checking DESCRIPTION meta-information ... OK
+* checking DESCRIPTION meta-information ... NOTE
+License stub is invalid DCF.
 * checking top-level files ... OK
 * checking for left-over files ... OK
 * checking index information ... OK

base/qaqc/tests/Rcheck_reference.log

@@ -24,6 +24,7 @@ Malformed Description field: should contain one or more complete sentences.
 Authors@R field gives no person with name and roles.
 Authors@R field gives no person with maintainer role, valid email
 address and non-empty name.
+License stub is invalid DCF.
 * checking top-level files ... NOTE
 Non-standard file/directory found at top level:
   ‘README.Rmd’

base/remote/tests/Rcheck_reference.log

@@ -19,7 +19,8 @@
 * checking whether package ‘PEcAn.remote’ can be installed ... OK
 * checking installed package size ... OK
 * checking package directory ... OK
-* checking DESCRIPTION meta-information ... OK
+* checking DESCRIPTION meta-information ... NOTE
+License stub is invalid DCF.
 * checking top-level files ... OK
 * checking for left-over files ... OK
 * checking index information ... OK

base/settings/R/check.all.settings.R

@@ -936,9 +936,10 @@ check.model.settings <- function(settings, dbcon = NULL) {
   return(settings)
 }
 
-#' @title Check Workflow Settings
+#' Check Workflow Settings
 #' @param settings settings file
-#' @export check.workflow.settings
+#' @param dbcon database connection
+#' @export
 check.workflow.settings <- function(settings, dbcon = NULL) {
   # check for workflow defaults
   fixoutdir <- FALSE

base/settings/tests/Rcheck_reference.log

@@ -73,7 +73,8 @@ The Date field is over a month old.
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK
-* checking DESCRIPTION meta-information ... OK
+* checking DESCRIPTION meta-information ... NOTE
+License stub is invalid DCF.
 * checking top-level files ... NOTE
 Non-standard file/directory found at top level:
   ‘examples’
@@ -140,36 +141,7 @@ All user-level objects in a package should have documentation entries.
 See chapter ‘Writing R documentation files’ in the ‘Writing R
 Extensions’ manual.
 * checking for code/documentation mismatches ... OK
-* checking Rd \usage sections ... WARNING
-Undocumented arguments in documentation object 'addSecrets'
-  ‘force’
-
-Undocumented arguments in documentation object 'check.model.settings'
-  ‘dbcon’
-
-Undocumented arguments in documentation object 'check.run.settings'
-  ‘dbcon’
-
-Undocumented arguments in documentation object 'check.settings'
-  ‘force’
-
-Undocumented arguments in documentation object 'check.workflow.settings'
-  ‘dbcon’
-
-Undocumented arguments in documentation object 'clean.settings'
-  ‘write’
-
-Undocumented arguments in documentation object 'fix.deprecated.settings'
-  ‘force’
-
-Undocumented arguments in documentation object 'update.settings'
-  ‘force’
-
-Functions with \usage entries need to have the appropriate \alias
-entries, and all their arguments documented.
-The \usage entries must correspond to syntactically valid R code.
-See chapter ‘Writing R documentation files’ in the ‘Writing R
-Extensions’ manual.
+* checking Rd \usage sections ... OK
 * checking Rd contents ... OK
 * checking for unstated dependencies in examples ... OK
 * checking examples ... OK
@@ -179,4 +151,4 @@ Extensions’ manual.
 * checking for detritus in the temp directory ... OK
 * DONE
 
-Status: 5 WARNINGs, 3 NOTEs
+Status: 3 WARNINGs, 2 NOTEs

base/utils/tests/Rcheck_reference.log

@@ -71,7 +71,8 @@ The Date field is over a month old.
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK
-* checking DESCRIPTION meta-information ... OK
+* checking DESCRIPTION meta-information ... NOTE
+License stub is invalid DCF.
 * checking top-level files ... OK
 * checking for left-over files ... OK
 * checking index information ... OK

base/visualization/DESCRIPTION

@@ -38,9 +38,11 @@ Imports:
     stringr(>= 1.1.0)
 Suggests:
     grid,
+    knitr,
     mockery,
     png,
     raster,
+    rmarkdown,
     sp,
     testthat (>= 1.0.2),
     withr
@@ -49,5 +51,6 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
+VignetteBuilder: knitr
 RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)

base/visualization/R/plots.R

@@ -263,7 +263,7 @@ plot_data <- function(trait.data, base.plot = NULL, ymax) {
 ##' 
 ##' @return adds borders to ggplot as a side effect
 ##' @author Rudolf Cardinal
-##' @author \url{ggplot2 google group}{https://groups.google.com/forum/?fromgroups#!topic/ggplot2/-ZjRE2OL8lE}
+##' @author [ggplot2 google group](https://groups.google.com/forum/?fromgroups#!topic/ggplot2/-ZjRE2OL8lE)
 ##' @examples
 ##' \dontrun{
 ##' df = data.frame( x=c(1,2,3), y=c(4,5,6) )

base/visualization/tests/Rcheck_reference.log

@@ -71,7 +71,8 @@ The Date field is over a month old.
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK
-* checking DESCRIPTION meta-information ... OK
+* checking DESCRIPTION meta-information ... NOTE
+License stub is invalid DCF.
 * checking top-level files ... OK
 * checking for left-over files ... OK
 * checking index information ... OK

base/visualization/vignettes/usmap.Rmd

@@ -1,7 +1,19 @@
+---
+title: "Maps"
+output: html_vignette
+vignette: >
+   %\VignetteIndexEntry{Maps}
+   %\VignetteEngine{knitr::rmarkdown}
+---
+
+
+
 Map
 ========================================================
 
-```{r}
+(all code chunks are disabled because vignette build was throwing errors. TODO: debug and re-enable.)
+
+```{r,eval=FALSE}
 require(raster)
 require(sp)
 require(ggplot2)
@@ -20,7 +32,7 @@ spplot(spdf)
 
 ### Plot all maps for BETYdb
 
-```{r}
+```{r,eval=FALSE}
 files <- dir("~/dev/bety/local/modelout", pattern="grid.csv", full.names=TRUE)
 yieldfiles <- files[!grepl("evapotranspiration", files)]
 etfiles <- files[grepl("evapotranspiration", files)]
@@ -42,7 +54,7 @@ for(file in etfiles){
 ```
 
 ### Misc additional code
-```{r}
+```{r,eval=FALSE}
 # Make an evenly spaced raster, the same extent as original data
 e <- extent( spdf )
 
@@ -63,7 +75,7 @@ ggplot( NULL ) + geom_raster( data = rdf , aes( x , y , fill = layer ) )
 
 ```
 
-```{r}
+```{r,eval=FALSE}
 # from http://gis.stackexchange.com/a/20052/3218
 require(rgdal)
 proj4string(spdf) <- CRS("+init=epsg:4326")

base/workflow/tests/Rcheck_reference.log

@@ -70,7 +70,7 @@ Author field differs from that derived from Authors@R
 Maintainer field differs from that derived from Authors@R
   Maintainer: ‘David LeBauer <[email protected]>’
   Authors@R:  ‘David LeBauer <[email protected]>’
-
+License stub is invalid DCF.
 * checking top-level files ... OK
 * checking for left-over files ... OK
 * checking index information ... OK