Merge pull request #95 from dklein-pik/master

Remove `iamCheck`

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '3760100'
+ValidationKey: '3780463'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

CITATION.cff

@@ -2,8 +2,8 @@ cff-version: 1.2.0
 message: If you use this software, please cite it using the metadata from this file.
 type: software
 title: 'modelstats: Run Analysis Tools'
-version: 0.19.0
-date-released: '2024-03-08'
+version: 0.19.1
+date-released: '2024-03-11'
 abstract: A collection of tools to analyze model runs.
 authors:
 - family-names: Giannousakis

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: modelstats
 Type: Package
 Title: Run Analysis Tools
-Version: 0.19.0
-Date: 2024-03-08
+Version: 0.19.1
+Date: 2024-03-11
 Authors@R: c(
     person("Anastasis", "Giannousakis", email = "[email protected]", role = c("aut","cre")),
     person("Oliver", "Richters", role = "aut")
@@ -14,7 +14,6 @@ Imports:
     crayon,
     gdx,
     gtools,
-    piamModelTests,
     lubridate,
     lucode2,
     utils,

NAMESPACE

@@ -19,7 +19,6 @@ importFrom(lucode2,sendmail)
 importFrom(magclass,collapseNames)
 importFrom(magclass,read.report)
 importFrom(magclass,write.report)
-importFrom(piamModelTests,iamCheck)
 importFrom(quitte,read.quitte)
 importFrom(remind2,compareScenarios2)
 importFrom(rlang,.data)

R/modeltests.R

@@ -12,7 +12,6 @@
 #' @param model Model name
 #' @param test Use this option to run a test of the workflow (no runs will be submitted)
 #' The test parameter needs to be of the form "YY-MM-DD"
-#' @param iamccheck Use this option to turn iamc-style checks on and off
 #' @param email whether an email notification will be send or not
 #' @param mattermostToken token used for mattermost notifications
 #' @param compScen whether compScen has to run or not
@@ -22,7 +21,6 @@
 #' @seealso \code{\link{package2readme}}
 #' @importFrom utils read.csv2
 #' @importFrom dplyr filter %>%
-#' @importFrom piamModelTests iamCheck
 #' @importFrom quitte read.quitte
 #' @importFrom lucode2 sendmail
 #' @importFrom remind2 compareScenarios2
@@ -35,7 +33,6 @@ modeltests <- function(
     model = NULL,
     user = NULL,
     test = NULL,
-    iamccheck = TRUE,
     email = TRUE,
     compScen = TRUE,
     mattermostToken = NULL,
@@ -57,7 +54,7 @@ modeltests <- function(
     message("Found 'end' in ", normalizePath("../.testsstatus"), "\nCalling 'evaluateRuns'")
     withr::with_dir("output", {
       evaluateRuns(model = model, mydir = mydir, gitPath = gitPath, compScen = compScen, email = email,
-                   mattermostToken = mattermostToken, gitdir = gitdir, iamccheck = iamccheck, user = user)
+                   mattermostToken = mattermostToken, gitdir = gitdir, user = user)
                    })
     # make sure next call will start runs
     message("Writing 'start' to ", normalizePath("../.testsstatus"))
@@ -178,7 +175,7 @@ startRuns <- function(test, model, mydir, gitPath, user) {
   message("Function 'startRuns' finished.")
 }
 
-evaluateRuns <- function(model, mydir, gitPath, compScen, email, mattermostToken, gitdir, iamccheck, user, test = NULL) {
+evaluateRuns <- function(model, mydir, gitPath, compScen, email, mattermostToken, gitdir, user, test = NULL) {
   message("Current working directory ", normalizePath("."))
   if (is.null(test)) test <- readRDS(paste0(mydir, "/test.rds"))
   if (!test) {
@@ -391,25 +388,6 @@ evaluateRuns <- function(model, mydir, gitPath, compScen, email, mattermostToken
     }
   }
 
-  if (iamccheck) {
-    a <- NULL
-    if (length(runsStarted) > 0) {
-      mifs <- paste0(runsStarted, "/REMIND_generic_", sub("_20[0-9][0-9].*.$", "", runsStarted), ".mif")
-      mifs <- mifs[file.exists(mifs)]
-      try(a <- read.quitte(mifs))
-      if (!is.null(a)) {
-        out[["iamCheck"]] <- iamCheck(a, cfg = model)
-        if (!test) {
-          saveRDS(out[["iamCheck"]], file = paste0("iamccheck-", commitTested, ".rds"))
-        } else {
-          saveRDS(out[["iamCheck"]], file = paste0("iamccheck-", test, ".rds"))
-        }
-      }
-    }
-    write(paste0("The IAMC check of these runs can be found in /p/projects/remind/modeltests/remind/output/iamccheck-",
-                 commitTested, ".rds", "\n"), myfile, append = TRUE)
-  }
-
   if(length(runsStarted) < 1) errorList <- c(errorList, "No runs started")
 
   if(is.null(errorList)) {

README.md

@@ -1,6 +1,6 @@
 # Run Analysis Tools
 
-R package **modelstats**, version **0.19.0**
+R package **modelstats**, version **0.19.1**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/modelstats)](https://cran.r-project.org/package=modelstats)  [![R build status](https://github.com/pik-piam/modelstats/workflows/check/badge.svg)](https://github.com/pik-piam/modelstats/actions) [![codecov](https://codecov.io/gh/pik-piam/modelstats/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/modelstats) [![r-universe](https://pik-piam.r-universe.dev/badges/modelstats)](https://pik-piam.r-universe.dev/builds)
 
@@ -47,7 +47,7 @@ In case of questions / problems please contact Anastasis Giannousakis <giannou@p
 
 To cite package **modelstats** in publications use:
 
-Giannousakis A, Richters O (2024). _modelstats: Run Analysis Tools_. R package version 0.19.0, <https://github.com/pik-piam/modelstats>.
+Giannousakis A, Richters O (2024). _modelstats: Run Analysis Tools_. R package version 0.19.1, <https://github.com/pik-piam/modelstats>.
 
 A BibTeX entry for LaTeX users is
 
@@ -56,7 +56,7 @@ A BibTeX entry for LaTeX users is
   title = {modelstats: Run Analysis Tools},
   author = {Anastasis Giannousakis and Oliver Richters},
   year = {2024},
-  note = {R package version 0.19.0},
+  note = {R package version 0.19.1},
   url = {https://github.com/pik-piam/modelstats},
 }
 ```

modelstats.Rproj

@@ -18,3 +18,4 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

vignettes/testingSuite.R

@@ -1,3 +1,3 @@
-## ----setup, include=FALSE-----------------------------------------------------
+## ----setup, include=FALSE-----------------------------------------------------------------------------------------------------------------------------------
 knitr::opts_chunk$set(echo = TRUE)
 

vignettes/testingSuite.Rmd

@@ -25,22 +25,12 @@ It is fully automated (runs every weekend), documents its findings in a gitlab p
 
 ## How it works:
 
-A scheduled and recurring job runs on the cluster every weekend, starting model runs according to a predefined set of scenarios. Once the runs are finished the job creates an overview of the results using [rs2](http://htmlpreview.github.io/?https://github.com/pik-piam/modelstats/blob/master/vignettes/rs2.html), and (optionally) additionally runs [compareScenarios](https://github.com/pik-piam/remind2/blob/master/R/compareScenarios.R) comparing each run with the previous run with the same scenario name (the comparison PDF files are found in each scenario folder, they also contain comparisons with historical data). It also uploads all runs to the [shinyResults::appResults](https://github.com/pik-piam/shinyresults/blob/master/R/appResults.R) app for easy and interactive viewing. Also here a comparison with historical data is found. Further, the results of all runs are gathered, passed through an [IAMC-style](https://github.com/IAMconsortium/iamc) check for consistency, and archived. These checks include:
-
-  *  non-standard variable names
-  *  missing variables
-  *  min and max values
-  *  summation groups (using the |+| notation)
-  *  units
-
-Finally, using a gitlab integration hook an overview of the results is automatically reported to the developer team via email.
+A scheduled and recurring job runs on the cluster every weekend, starting model runs according to a predefined set of scenarios. Once the runs are finished the job creates an overview of the results using [rs2](http://htmlpreview.github.io/?https://github.com/pik-piam/modelstats/blob/master/vignettes/rs2.html), and (optionally) additionally runs [compareScenarios](https://github.com/pik-piam/remind2/blob/master/R/compareScenarios.R) comparing each run with the previous run with the same scenario name (the comparison PDF files are found in each scenario folder, they also contain comparisons with historical data). It also uploads all runs to the [shinyResults::appResults](https://github.com/pik-piam/shinyresults/blob/master/R/appResults.R) app for easy and interactive viewing. Also here a comparison with historical data is found. Finally, using a gitlab integration hook an overview of the results is automatically reported to the developer team via email.
 
 ## How to use/contribute:
 
 If the report contains runs that failed, or output that looks wrong (or has not been generated at all) someone has to take action. If there are cases for which you feel responsible or in the position to fix, please do so. This early warning system ensures stable workflows for all members of the team.
 
 If you want your own scenarios to be included in future tests: For REMIND, add your scenarios to the `scenario_config.csv`, add `AMT` in the `start` column and simply commit it to the model's develop branch (similar for MAgPIE). They will be automatically executed the next time the tests are run.
 
-Tailor the IAMC-style checks to your needs or add further IAMC-style checks here (read the vignette to see how this is done): http://htmlpreview.github.io/?https://github.com/pik-piam/piamModelTests/blob/master/vignettes/iamc.html
-
 For wishes, changes etc, please contact RSE or open a new issue here: https://github.com/pik-piam/modelstats/issues