Merge pull request #365 from morungos/testing

Add basic testing, fix a few check issues (take 2)

.github/workflows/pkgdown.yaml

@@ -52,38 +52,41 @@ jobs:
 
       - name: Build data and configuration archive for AMAP/external
         run: |
+          set +f
           mkdir -p $TEMP_DIR/external
           cp -R data/example_external_data $TEMP_DIR/external/
           mv $TEMP_DIR/external/example_external_data $TEMP_DIR/external/data
           cp -R information/AMAP $TEMP_DIR/external/
           mv $TEMP_DIR/external/AMAP $TEMP_DIR/external/information
-          mv $TEMP_DIR/external/information/README*.* $TEMP_DIR/external/
+          mv $TEMP_DIR/external/data/README*.* $TEMP_DIR/external/
           cd $TEMP_DIR
           zip -r $WORK_DIR/docs/external.zip external
           cd $WORK_DIR
         continue-on-error: true
 
       - name: Build data and configuration archive for OSPAR 2022
         run: |
+          set +f
           mkdir -p $TEMP_DIR/ospar
           cp -R data/example_OSPAR $TEMP_DIR/ospar/
           mv $TEMP_DIR/ospar/example_OSPAR $TEMP_DIR/ospar/data
           cp -R information/OSPAR_2022 $TEMP_DIR/ospar/
           mv $TEMP_DIR/ospar/OSPAR_2022 $TEMP_DIR/ospar/information
-          mv $TEMP_DIR/ospar/information/README*.* $TEMP_DIR/ospar/
+          mv $TEMP_DIR/ospar/data/README*.* $TEMP_DIR/ospar/
           cd $TEMP_DIR
           zip -r $WORK_DIR/docs/ospar.zip ospar
           cd $WORK_DIR
         continue-on-error: true
 
       - name: Build data and configuration archive for HELCOM 2023
         run: |
+          set +f
           mkdir -p $TEMP_DIR/helcom
           cp -R data/example_HELCOM $TEMP_DIR/helcom/
           mv $TEMP_DIR/helcom/example_HELCOM $TEMP_DIR/helcom/data
           cp -R information/HELCOM_2023 $TEMP_DIR/helcom/
           mv $TEMP_DIR/helcom/HELCOM_2023 $TEMP_DIR/helcom/information
-          mv $TEMP_DIR/helcom/information/README*.* $TEMP_DIR/helcom/
+          mv $TEMP_DIR/helcom/data/README*.* $TEMP_DIR/helcom/
           cd $TEMP_DIR
           zip -r $WORK_DIR/docs/helcom.zip helcom
           cd $WORK_DIR

.gitignore

@@ -4,7 +4,7 @@
 .Ruserdata
 .build.timestamp
 HARSAT.RProj
-HARSAT.Rcheck
+harsat.Rcheck
 harsat_*.tar.gz
 oddities/
 output/

CONTRIBUTING.md

@@ -100,7 +100,8 @@ Let's assume the current version is `x.y.z`
 ```
 git checkout develop
 git flow release start x.y.z+1
-emacs DESCRIPTION ## Update version x.y.z-9000 -> x.y.z+1
+emacs DESCRIPTION     ## Update version x.y.z-9000 -> x.y.z+1
+emacs CHANGES.md      ## Update the change log, as appropriate
 R --quiet --vanilla < vignettes/precompile.R
 R CMD build .
 R CMD check --no-manual harsat_x.y.z+1.tar.gz
@@ -113,7 +114,7 @@ git push --tags
 git push upstream
 git push --tags upstream
 git checkout develop
-emacs DESCRIPTION ## Bump version to x.y.(z+1)-9000
+emacs DESCRIPTION      ## Bump version to x.y.(z+1)-9000
 git commit -am "Bump develop version [ci skip]"
 git push
 git push upstream

NAMESPACE

@@ -45,3 +45,45 @@ export(run_assessment)
 export(tidy_data)
 export(update_assessment)
 export(write_summary_table)
+importFrom(grDevices,dev.off)
+importFrom(grDevices,extendrange)
+importFrom(grDevices,grey)
+importFrom(grDevices,pdf)
+importFrom(grDevices,png)
+importFrom(graphics,par)
+importFrom(stats,AIC)
+importFrom(stats,as.formula)
+importFrom(stats,complete.cases)
+importFrom(stats,dmultinom)
+importFrom(stats,dnorm)
+importFrom(stats,filter)
+importFrom(stats,glm)
+importFrom(stats,glm.control)
+importFrom(stats,integrate)
+importFrom(stats,lm)
+importFrom(stats,logLik)
+importFrom(stats,median)
+importFrom(stats,na.omit)
+importFrom(stats,optim)
+importFrom(stats,pbinom)
+importFrom(stats,pf)
+importFrom(stats,plogis)
+importFrom(stats,pnorm)
+importFrom(stats,predict)
+importFrom(stats,pt)
+importFrom(stats,qf)
+importFrom(stats,qlogis)
+importFrom(stats,qnorm)
+importFrom(stats,qt)
+importFrom(stats,quasi)
+importFrom(stats,reshape)
+importFrom(stats,rnorm)
+importFrom(stats,sd)
+importFrom(stats,setNames)
+importFrom(stats,uniroot)
+importFrom(stats,update)
+importFrom(utils,head)
+importFrom(utils,modifyList)
+importFrom(utils,read.csv)
+importFrom(utils,read.delim)
+importFrom(utils,tail)

R/harsat-package.R

@@ -1,6 +1,15 @@
 #' @keywords internal
 "_PACKAGE"
 
+#' @importFrom grDevices dev.off extendrange grey pdf png
+#' @importFrom graphics par
+#' @importFrom utils head tail modifyList read.csv read.delim
+#' @importFrom stats AIC as.formula complete.cases dmultinom dnorm filter 
+#'   glm glm.control integrate lm logLik median na.omit 
+#'   optim pbinom pf plogis pnorm predict pt qf qlogis qnorm
+#'   qt quasi reshape rnorm sd setNames
+#'   uniroot update
+
 ## usethis namespace: start
 ## usethis namespace: end
 NULL

R/import_functions.R

@@ -65,13 +65,12 @@ library(readxl)
 #'   `retain == FALSE` are deleted later in `tidy_data`
 #' * `stations`
 #'
-#' @section Control parameters
-#'
-#'   Many aspects of the assessment process can be controlled through the
-#'   parameters stored in `info$control`. This is a list populated with default
-#'   values which can then be overwritten, if required, using the `control`
-#'   argument.
+#' ## Control parameters
 #'
+#' Many aspects of the assessment process can be controlled through the
+#' parameters stored in `info$control`. This is a list populated with default
+#' values which can then be overwritten, if required, using the `control`
+#' argument.
 #'
 #' @export
 read_data <- function(
@@ -190,7 +189,8 @@ read_data <- function(
     info$max_year <- max(data$year)
     cat(
       "\nArgument max_year taken to be the maximum year in the data:", 
-      info$max_year
+      info$max_year,
+      "\n"
     )
   }
 
@@ -427,7 +427,7 @@ locate_information_file <- function(name, path) {
   for(directory in path) {
     search <- normalizePath(file.path(directory, name), mustWork = FALSE)
     if(file.exists(search)) {
-      print(paste("found in path", name, search, path))
+      cat(paste("Found in path", name, search, "\n"))
       return(search)
     }
   }
@@ -437,10 +437,10 @@ locate_information_file <- function(name, path) {
   search_file <- file.path("information", name)
   search <- system.file(search_file, package = "harsat", mustWork = FALSE)
   if(file.exists(search)) {
-    print(paste("found in package", name, search, path))
+    cat(paste("Found in package", name, search, "\n"))
     return(search)
   }
-    print(paste("missing", name, path))
+    warning(paste("Missing file in path:", name, path))
   return(NULL)
 }
 

_pkgdown.yml

@@ -22,6 +22,10 @@ navbar:
       - text: External file format
         href: articles/external-file-format.html
       - text: -------
+      - text: "Resources"
+      - text: Datasets
+        href: articles/datasets.html
+      - text: -------
       - text: "Examples"
       - text: HELCOM (read first)
         href: articles/example_HELCOM.html

test_parallel.r

@@ -7,8 +7,7 @@
 ## system, but we check serial too to be safe.
 
 library(harsat)
-library(here)
-working.directory <- here()
+working.directory <- getwd()
 
 
 water_data <- read_data(

tests/datasets/external-1/EXTERNAL_AMAP_STATIONS.csv

@@ -0,0 +1,56 @@
+station_code,country,station_name,station_latitude,station_longitude,station_governance,AMAP_region,station_longname,station_type,waterbody_type
+A1,Canada,Southern Labrador Sea,56.54,-61.7,AMAP,Labrador Sea,,,
+A2,Canada,Cumberland Sound,66.15,-65.7,AMAP,Labrador Sea,,,
+A3,Canada,Southern Hudson Bay,56.54,-79.22,AMAP,Hudson Bay,,,
+A4,Canada,Digges Island,62.56,-77.96,AMAP,Hudson Bay,,,
+A5,Canada,Coats Island,62.47,-83.1,AMAP,Hudson Bay,,,
+A6,Canada,Western Hudson Bay,61.11,-94.06,AMAP,Hudson Bay,,,
+A7,Canada,Queen Maud Gulf,69.12,-105.06,AMAP,Queen Maud Gulf,,,
+A8,Canada,Eastern Beaufort Sea,71.99,-125.25,AMAP,Beaufort Sea,,,
+A9,Canada,Southern Beaufort Sea,69.5,-133.58,AMAP,Beaufort Sea,,,
+A10,Canada,GSL-West Basin,60.82,-115.79,AMAP,Great Slave Lake,,,
+A11,Canada,GSL-East Arm,62.41,-110.74,AMAP,Great Slave Lake,,,
+A12,Canada,Fort Good Hope,61.34,-135.65,AMAP,Mackenzie River,,,
+A13,Canada,Little Fox Lake,66.26,-128.63,AMAP,Little Fox Lake,,,
+A14,Canada,Lake Laberge,61.06,-135.11,AMAP,Lake Laberge,,,
+A15,Canada,Lake Kusawa,60.41,-136.26,AMAP,Lake Kusawa,,,
+A16,Canada,Old Crow,67.57,-139.83,AMAP,Northern Yukon,,,
+A17,Canada,Alert,82.5,-62.35,AMAP,Ellesmere Island,,,
+A18,Canada,Lake Hazen,81.8,-71,AMAP,Ellesmere Island,,,
+A19,Canada,Prince Leopold Island,74.04,-90.03,AMAP,Lancaster Sound,,,
+A20,Canada,Resolute Passage,74.7,-94.83,AMAP,Lancaster Sound,,,
+A21,Canada,Amituk Lake,75.05,-93.75,AMAP,Cornwallis Island,,,
+A22,Canada,Char Lake,74.71,-94.9,AMAP,Cornwallis Island,,,
+A23,Canada,Meretta Lake,74.68,-94.92,AMAP,Cornwallis Island,,,
+A24,Canada,Resolute Lake,74.69,-94.94,AMAP,Cornwallis Island,,,
+A25,Canada,Small Lake,74.76,-95.06,AMAP,Cornwallis Island,,,
+A26,Canada,North Lake,74.78,-95.09,AMAP,Cornwallis Island,,,
+A27,Canada,SW Beaufort Sea,70,-150,AMAP,Beaufort Sea,,,
+A28,Canada,Kuujjuaq,58.1,-68.42,AMAP,Nunavik,,,
+A31,Canada,Arviat,61.1078,-94.0624,AMAP,Nunavut,,,
+A32,Canada,Nain,56.5417,-61.6969,AMAP,Newfoundland,,,
+A33,Canada,Resolute,74.6973,-94.8297,AMAP,Nunavut,,,
+A34,Canada,SachsHarbour,71.9851,-125.2465,AMAP,NWT,,,
+A29,Greenland,Disko Bay,69.03,-52.04,AMAP,Greenland,,,
+A90,Greenland,Ittoqqortoormiit AMAP,70.29,-21.58,AMAP~OSPAR,East Greenland,,,
+A95,Greenland,Nanortalik AMAP,60.1425,-45.2395,AMAP~OSPAR,South Greenland,,,
+A100,Greenland,Avanersuaq AMAP,77.28,-69.14,AMAP,Northwest Greenland,,,
+A110,Greenland,Qeqertarsuaq AMAP,69.15,-53.32,AMAP,Central-West Greenland,,,
+A120,Greenland,Isortoq AMAP,60.54,-47.33,AMAP,Southwest Greenland,,,
+A130,Greenland,Ittoqqortoormiit Ukaleqarteq,70.72,-21.55,AMAP,East Greenland,,,
+A902,Faroe Islands,Føroyskar hvalvágir ,62,-7,AMAP,Greenland-Scotland ridge,,,
+A911,Faroe Islands,Mýlingsgrunnur,62.38333,-7.41667,OSPAR~AMAP,Greenland-Scotland ridge,,,
+A912,Faroe Islands,Á Mýrunum,62.16914,-7.08579,AMAP,Greenland-Scotland ridge,,,
+A919,Faroe Islands,Tindhólmur,62.079,-7.43217,AMAP,Greenland-Scotland ridge,,,
+A921,Faroe Islands,Vestmanna,62.15383,-7.15983,AMAP,Greenland-Scotland ridge,,,
+A917,Faroe Islands,Sveipur,61.95,-6.71667,AMAP,Greenland-Scotland ridge,,,
+A909,Faroe Islands,Koltur,61.99447,-6.99343,AMAP,Greenland-Scotland ridge,,,
+A916,Faroe Islands,Skúvoy,61.76833,-6.80167,AMAP,Greenland-Scotland ridge,,,
+A12429,Faroe Islands,Leitisvatn,62.04803,-7.23487,AMAP,Greenland-Scotland ridge,,,
+A12434,Faroe Islands,Mjáuvøtn,62.12789,-7.00171,AMAP,Greenland-Scotland ridge,,,
+A400,Sweden,Storvindeln,65.7,17.13,AMAP~OSPAR,Barents Sea,,,
+A401,Sweden,Abiskojaure AMAP,68.28789,18.58575,AMAP~OSPAR,Barents Sea,,,
+A47001,Norway,Svalbard,77.875,20.975,AMAP,Barents Sea,,,
+A47002,Norway,Svalbard-Kongsfjorden area,79,11.6667,AMAP,Barents Sea,,,
+A47010,Norway,Bjørnøya,74.452,19.115,AMAP,Barents Sea,,,
+A47011,Norway,Bjørnøya-Ellasjoen,74.388,19.031,AMAP,Barents Sea,,,