Merge pull request #127 from orichters/master

add orange 'no mif', don't fail on run folder with blanks

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '4548250'
+ValidationKey: '4569964'
 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: 0.22.6
-date-released: '2025-02-06'
+version: 0.22.7
+date-released: '2025-02-13'
 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: 0.22.6
-Date: 2025-02-06
+Version: 0.22.7
+Date: 2025-02-13
 Authors@R: c(
     person("Anastasis", "Giannousakis", email = "giannou@pik-potsdam.de", role = c("aut","cre")),
     person("Oliver", "Richters", role = "aut")

R/getRunStatus.R

@@ -149,17 +149,17 @@ getRunStatus <- function(mydir = dir(), sort = "nf", user = NULL) {
     cm_iteration_max <- cfg$gms$cm_iteration_max
     if (isTRUE(cfg$gms$cm_nash_autoconverge > 0) && grepl("nash", out[i, "RunType"])) {
       if (file.exists(fullgms)) {
-        cm_iteration_max <- suppressWarnings(system(paste0("tac ", fullgms, "| grep -m 1 'cm_iteration_max = [1-9].*.;[ ]*$'"), intern = TRUE))
+        cm_iteration_max <- suppressWarnings(system(paste0("tac '", fullgms, "' | grep -m 1 'cm_iteration_max = [1-9].*.;[ ]*$'"), intern = TRUE))
         cm_iteration_max <- sub(";[ ]*", "", sub("^.*.= ", "", cm_iteration_max))
       }
     }
     out[i, "Iter"] <- "NA"
     out[i, "RunStatus"] <- "NA"
     if (file.exists(fulllog)) {
-      suppressWarnings(try(loop <- sub("^.*.= ", "", system(paste0("grep 'LOOPS' ", fulllog, " | tail -1"), intern = TRUE)), silent = TRUE))
+      suppressWarnings(try(loop <- sub("^.*.= ", "", system(paste0("grep 'LOOPS' '", fulllog, "' | tail -1"), intern = TRUE)), silent = TRUE))
       if (length(loop) > 0) out[i, "Iter"] <- loop
       if (length(cm_iteration_max) > 0) out[i, "Iter"] <- paste0(out[i, "Iter"], "/", cm_iteration_max)
-      suppressWarnings(try(out[i, "RunStatus"] <- substr(sub("\\(s\\)", "", sub("\\*\\*\\* Status: ", "", system(paste0("grep '*** Status: ' ", fulllog), intern = TRUE))), start = 1, stop = 17), silent = TRUE))
+      suppressWarnings(try(out[i, "RunStatus"] <- substr(sub("\\(s\\)", "", sub("\\*\\*\\* Status: ", "", system(paste0("grep '*** Status: ' '", fulllog, "'"), intern = TRUE))), start = 1, stop = 17), silent = TRUE))
       if (onCluster && out[i, "RunStatus"] == "NA") {
         if (out[i, "jobInSLURM"] == "no" || grepl("pending$", out[i, "jobInSLURM"])) {
           if (file.exists(logtxt)) {
@@ -193,8 +193,8 @@ getRunStatus <- function(mydir = dir(), sort = "nf", user = NULL) {
         if (out[i, "RunStatus"] == "NA") out[i, "RunStatus"] <- "Run interrupted"
       }
       if (out[i, "RunStatus"] == "Normal completion" && file.exists(logtxt) && out[i, "jobInSLURM"] != "no") {
-        startrep <- suppressWarnings(system(paste0("tac ", logtxt, " | grep -m 1 'Starting output generation for'"), intern = TRUE))
-        endrep <- suppressWarnings(system(paste0("tac ", logtxt, " | grep -m 1 'Finished output generation for'"), intern = TRUE))
+        startrep <- suppressWarnings(system(paste0("tac '", logtxt, "' | grep -m 1 'Starting output generation for'"), intern = TRUE))
+        endrep <- suppressWarnings(system(paste0("tac '", logtxt, "' | grep -m 1 'Finished output generation for'"), intern = TRUE))
         if (length(startrep) > length(endrep) && out[i, "jobInSLURM"] != "no") {
           out[i, "RunStatus"] <- "Running reporting"
         }
@@ -212,16 +212,16 @@ getRunStatus <- function(mydir = dir(), sort = "nf", user = NULL) {
         }
       }
       if (file.exists(logmagtxt) && out[i, "jobInSLURM"] != "no" && (out[i, "RunStatus"] == "Normal completion" || grepl("log-mag.txt", logmagtxt))) {
-        startmag <- suppressWarnings(system(paste0("tac ", logmagtxt, " | grep -m 1 'Preparing MAgPIE'"), intern = TRUE))
-        endmag <- suppressWarnings(system(paste0("tac ", logmagtxt, " | grep -m 1 'MAgPIE output was stored'"), intern = TRUE))
+        startmag <- suppressWarnings(system(paste0("tac '", logmagtxt, "' | grep -m 1 'Preparing MAgPIE'"), intern = TRUE))
+        endmag <- suppressWarnings(system(paste0("tac '", logmagtxt, "' | grep -m 1 'MAgPIE output was stored'"), intern = TRUE))
         if (length(startmag) > length(endmag)) {
           fulllogmag <- gsub("-rem-", "-mag-", gsub("output", file.path("magpie", "output"), fulllog))
           if (! file.exists(fulllogmag)) fulllogmag <- gsub("-rem-", "-mag-", gsub("output", file.path("..", "magpie", "output"), fulllog))
           loopmag <- NULL
           if (file.exists(fulllogmag)) {
-            suppressWarnings(try(loopmag <- sub("^.*.= ", "", system(paste0("grep 'LOOPS' ", fulllogmag, " | tail -1"), intern = TRUE)), silent = TRUE))
+            suppressWarnings(try(loopmag <- sub("^.*.= ", "", system(paste0("grep 'LOOPS' '", fulllogmag, "' | tail -1"), intern = TRUE)), silent = TRUE))
           }
-          if (length(suppressWarnings(system(paste0("tac ", logmagtxt, " | grep -m 1 'Start getReport'"), intern = TRUE)) > 0)) loopmag <- "report"
+          if (length(suppressWarnings(system(paste0("tac '", logmagtxt, "' | grep -m 1 'Start getReport'"), intern = TRUE)) > 0)) loopmag <- "report"
           out[i, "RunStatus"] <- paste("Run MAgPIE", loopmag)
         }
         if (isTRUE(grepl("try to acquire model lock", try(system(paste("tail -1", logmagtxt), intern = TRUE), silent = TRUE)))) {
@@ -257,7 +257,7 @@ getRunStatus <- function(mydir = dir(), sort = "nf", user = NULL) {
 
     # Calib Iter
     if ((isTRUE(grepl("Calib", out[i, "RunType"])) || isTRUE(cfg$gms$CES_parameters == "calibrate")) && file.exists(logtxt)) {
-      calibiter <- tail(suppressWarnings(system(paste0("grep 'CES calibration iteration' ", logtxt, " |  grep -Eo  '[0-9]{1,2}'"), intern = TRUE)), n = 1)
+      calibiter <- tail(suppressWarnings(system(paste0("grep 'CES calibration iteration' '", logtxt, "' |  grep -Eo  '[0-9]{1,2}'"), intern = TRUE)), n = 1)
       if (isTRUE(as.numeric(calibiter) > 0)) out[i, "Iter"] <- paste0(out[i, "Iter"], " ", "Clb: ", calibiter)
       if (isTRUE(out[i, "Conv"] %in% c("converged", "converged (had INFES)")) &&
           (length(system(paste0("find ", ii, " -name 'fulldata_*.gdx'"), intern = TRUE)) > 10 ||

R/loopRuns.R

@@ -24,9 +24,10 @@ loopRuns <- function(mydir, user = NULL, colors = TRUE, sortbytime = TRUE) {
   if (mydir[[1]] == "exit") return(NULL)
 
   red <- make_style("orangered")
+  orange <- make_style("orange")
   if (colors) {
     cat("# Color code: ", yellow("pending"), "/", yellow("startup"), ", ", cyan("running"), ", ",
-        underline(green("converged")), ", ", blue("converged (had INFES)"), ", ",
+        underline(green("converged")), ", ", blue("converged (had INFES)"), ", ", orange("no mif"), ", ",
         green("finished"), ", ", magenta("conopt stalled?"), ", ", red("error"), ".\n\n", sep = "")
   }
   a <- file.info(mydir)
@@ -109,14 +110,16 @@ loopRuns <- function(mydir, user = NULL, colors = TRUE, sortbytime = TRUE) {
         cat(magenta(out))
       } else if (! status[["jobInSLURM"]] == "no") {
         cat(cyan(out))
-      } else if (status[["Conv"]] == "converged (had INFES)") {
+      } else if (status[["Conv"]] == "converged (had INFES)" && ! status[["Mif"]] == "no") {
         cat(blue(out))
       } else if (grepl("not_converged|Execution erro|Compilation er|interrupted|Intermed Infes", status[["RunStatus"]])) {
         cat(red(out))
-      } else if (status[["Conv"]] %in% c("converged", "Clb_converged")) {
+      } else if (status[["Conv"]] %in% c("converged", "Clb_converged") && ! status[["Mif"]] == "no") {
         cat(underline(green(out)))
       } else if (grepl("2: Locally Optimal", status[["modelstat"]]) && ! grepl("nash", status[["RunType"]])) {
         cat(green(out))
+      } else if (status[["Mif"]] == "no" && status[["Conv"]] %in% c("converged", "Clb_converged", "converged (had INFES)")) {
+        cat(orange(out))
       } else if (status[["jobInSLURM"]] == "no") {
         cat(red(out))
       } else {

README.md

@@ -1,6 +1,6 @@
 # Run Analysis Tools
 
-R package **modelstats**, version **0.22.6**
+R package **modelstats**, version **0.22.7**
 
 [![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)
 
@@ -47,17 +47,17 @@ In case of questions / problems please contact Anastasis Giannousakis <giannou@p
 
 To cite package **modelstats** in publications use:
 
-Giannousakis A, Richters O (2025). "modelstats: Run Analysis Tools." Version: 0.22.6, <https://github.com/pik-piam/modelstats>.
+Giannousakis A, Richters O (2025). "modelstats: Run Analysis Tools." Version: 0.22.7, <https://github.com/pik-piam/modelstats>.
 
 A BibTeX entry for LaTeX users is
 
  ```latex
 @Misc{,
   title = {modelstats: Run Analysis Tools},
   author = {Anastasis Giannousakis and Oliver Richters},
-  date = {2025-02-06},
+  date = {2025-02-13},
   year = {2025},
   url = {https://github.com/pik-piam/modelstats},
-  note = {Version: 0.22.6},
+  note = {Version: 0.22.7},
 }
 ```