Resolve "Gitlab-CI: correctly handle WARNING and NOTE in checks"

Closes #86 (closed)

R/CreateInputsModel.R

@@ -5,6 +5,7 @@ CreateInputsModel <- function(FUN_MOD,
                               TempMean = NULL, TempMin = NULL, TempMax = NULL,
                               ZInputs = NULL, HypsoData = NULL, NLayers = 5,
                               Qupstream = NULL, LengthHydro = NULL, BasinAreas = NULL,
+                              QupstrUnit = "mm",
                               verbose = TRUE) {
 
 
@@ -215,6 +216,8 @@ CreateInputsModel <- function(FUN_MOD,
     if(any(LengthHydro > 1000)) {
       warning("The unit of 'LengthHydro' has changed from m to km in v1.7 of airGR: values superior to 1000 km seem unrealistic")
     }
+    QupstrUnit <- tolower(QupstrUnit)
+    QupstrUnit <- match.arg(arg = QupstrUnit, choices = c("mm", "m3", "m3/s", "l/s"))
   }
 
   ##check_NA_values
@@ -330,6 +333,16 @@ CreateInputsModel <- function(FUN_MOD,
                                        ZLayers              = RESULT$ZLayers))
   }
   if ("SD" %in% ObjectClass) {
+    # Qupstream is internally stored in m3/time step
+    if (QupstrUnit == "mm") {
+      iConvBasins <- which(!is.na(BasinAreas[seq.int(length(LengthHydro))]))
+      Qupstream[,iConvBasins] <-
+        Qupstream[,iConvBasins] * rep(BasinAreas[iConvBasins], each = LLL) * 1e3
+    } else if (QupstrUnit == "m3/s") {
+      Qupstream <- Qupstream * TimeStep
+    } else if (QupstrUnit == "l/s") {
+      Qupstream <- Qupstream * TimeStep / 1e3
+    }
     InputsModel <- c(InputsModel, list(Qupstream = Qupstream,
                                        LengthHydro   = LengthHydro,
                                        BasinAreas = BasinAreas))

R/RunModel_Lag.R

@@ -48,7 +48,7 @@ RunModel_Lag <- function(InputsModel, RunOptions, Param, QcontribDown) {
 
   NbUpBasins <- length(InputsModel$LengthHydro)
   LengthTs <- length(OutputsModel$QsimDown)
-  OutputsModel$Qsim <- OutputsModel$QsimDown * InputsModel$BasinAreas[length(InputsModel$BasinAreas)] * 1e3
+  OutputsModel$Qsim_m3 <- OutputsModel$QsimDown * InputsModel$BasinAreas[length(InputsModel$BasinAreas)] * 1e3
 
   IniSD <- RunOptions$IniStates[grep("SD", names(RunOptions$IniStates))]
   if (length(IniSD) > 0) {
@@ -78,15 +78,15 @@ RunModel_Lag <- function(InputsModel, RunOptions, Param, QcontribDown) {
   for (upstream_basin in seq_len(NbUpBasins)) {
     Qupstream <- c(IniStates[[upstream_basin]],
                    InputsModel$Qupstream[RunOptions$IndPeriod_Run, upstream_basin])
-    if (!is.na(InputsModel$BasinAreas[upstream_basin])) {
-      # Upstream flow with area needs to be converted to m3 by time step
-      Qupstream <- Qupstream * InputsModel$BasinAreas[upstream_basin] * 1e3
-    }
     # message("Qupstream[", upstream_basin, "]: ", paste(Qupstream, collapse = ", "))
-    OutputsModel$Qsim <- OutputsModel$Qsim +
+    OutputsModel$Qsim_m3 <- OutputsModel$Qsim_m3 +
       Qupstream[2:(1 + LengthTs)] * HUTRANS[1, upstream_basin] +
       Qupstream[1:LengthTs] * HUTRANS[2, upstream_basin]
   }
+  # Convert back Qsim to mm
+  OutputsModel$Qsim <- OutputsModel$Qsim_m3 / sum(InputsModel$BasinAreas, na.rm = TRUE) / 1e3
+  # message("Qsim: ", paste(OutputsModel$Qsim, collapse = ", "))
+
   # Warning for negative flows or NAs only in extended outputs
   if(length(RunOptions$Outputs_Sim) > 2) {
     if (any(OutputsModel$Qsim[!is.na(OutputsModel$Qsim)] < 0)) {
@@ -98,9 +98,6 @@ RunModel_Lag <- function(InputsModel, RunOptions, Param, QcontribDown) {
       warning(length(which(is.na(OutputsModel$Qsim))), " time steps with NA values")
     }
   }
-  # Convert back Qsim to mm
-  OutputsModel$Qsim <- OutputsModel$Qsim / sum(InputsModel$BasinAreas, na.rm = TRUE) / 1e3
-  # message("Qsim: ", paste(OutputsModel$Qsim, collapse = ", "))
 
   if ("StateEnd" %in% RunOptions$Outputs_Sim) {
     OutputsModel$StateEnd$SD <- lapply(seq(NbUpBasins), function(x) {

man/Calibration_Michel.Rd

@@ -40,7 +40,7 @@ Calibration_Michel(InputsModel, RunOptions, InputsCrit, CalibOptions,
 
 \item{verbose}{(optional) [boolean] boolean indicating if the function is run in verbose mode or not, default = \code{TRUE}}
 
-\item{...}{Further arguments to pass to \code{\link{RunModel}}}
+\item{...}{(optional) arguments to pass to \code{\link{RunModel}}}
 }
 
 

man/CreateInputsModel.Rd

@@ -19,7 +19,7 @@ CreateInputsModel(FUN_MOD, DatesR, Precip, PrecipScale = TRUE, PotEvap = NULL,
                   TempMean = NULL, TempMin = NULL, TempMax = NULL,
                   ZInputs = NULL, HypsoData = NULL, NLayers = 5,
                   Qupstream = NULL, LengthHydro = NULL, BasinAreas = NULL,
-                  verbose = TRUE)
+                  QupstrUnit = "mm", verbose = TRUE)
 
 \method{[}{InputsModel}(x, i)
 }
@@ -50,12 +50,14 @@ CreateInputsModel(FUN_MOD, DatesR, Precip, PrecipScale = TRUE, PotEvap = NULL,
 
 \item{verbose}{(optional) [boolean] boolean indicating if the function is run in verbose mode or not, default = \code{TRUE}}
 
-\item{Qupstream}{(optional) [numerical matrix] time series of upstream flows (catchment average) [mm/time step or m3/time step, see details], required to create the SD model inputs . See details}
+\item{Qupstream}{(optional) [numerical matrix] time series of upstream flows (catchment average), its unit is defined by the \code{QupstrUnit} parameter, required to create the SD model inputs. See details}
 
 \item{LengthHydro}{(optional) [numeric] real giving the distance between the downstream outlet and each upstream inlet of the sub-catchment [km], required to create the SD model inputs . See details}
 
 \item{BasinAreas}{(optional) [numeric] real giving the area of each upstream sub-catchment [km2] and the area of the downstream sub-catchment in the last item, required to create the SD model inputs . See details}
 
+\item{QupstrUnit}{(optional) [character] unit of the flow in the argument \code{Qupstream}, available units are: "mm" for mm/time-step (default), "m3" for m3/time-step, "m3/s" and "l/s". See details}
+
 \item{x}{[InputsModel] object of class InputsModel}
 
 \item{i}{[integer] of the indices to subset a time series or [character] names of the elements to extract}
@@ -80,9 +82,11 @@ Users wanting to use \code{FUN_MOD} functions that are not included in
 the package must create their own InputsModel object accordingly. \cr
 Please note that if CemaNeige is used, and \code{ZInputs} is different than \code{HypsoData}, then precipitation and temperature are interpolated with the \code{DataAltiExtrapolation_Valery} function.
 
-Users wanting to use a semi-distributed (SD) lag model should provide valid \code{Qupstream}, \code{LengthHydro}, and \code{BasinAreas} parameters. Each upstream sub-catchment is described by an upstream flow time series (one column in \code{Qupstream} matrix), a distance between the downstream outlet and the upstream inlet (one item in \code{LengthHydro}) and an area (one item in \code{BasinAreas}).
-The order of the columns or of the items should be consistent for all these parameters. \code{BasinAreas} should contain one extra information (stored in the last item) which is the area of the downstream sub-catchment.
-Upstream flows that are not related to a sub-catchment such as a release or withdraw spot are identified by an area equal to \code{NA} and an upstream flow expressed in m3/time step instead of mm/time step.
+Users wanting to use a semi-distributed (SD) model should provide valid \code{Qupstream}, \code{LengthHydro}, and \code{BasinAreas} arguments. Each upstream sub-catchment is described by an upstream flow time series (one column in \code{Qupstream} matrix), a distance between the downstream outlet and the upstream inlet (one item in \code{LengthHydro}) and an area (one item in \code{BasinAreas}).
+The order of the columns or of the items should be consistent for all these parameters.
+\code{BasinAreas} should contain one extra information (stored in the last item) which is the area of the downstream sub-catchment.
+Upstream flows that are not related to a sub-catchment such as release or withdraw spots are identified by an area equal to \code{NA}, and if \code{unit="mm"} the upstream flow must be expressed in m3/time step instead of mm/time step which is not possible in absence of a related area.
+Please note that the use of SD model requires to use the \code{\link{RunModel}} function instead of \code{\link{RunModel_GR4J}} or the other \code{RunModel_*} functions.
 }
 
 \examples{

man/RunModel.Rd

@@ -3,7 +3,6 @@
 
 \name{RunModel}
 \alias{RunModel}
-%\alias{[.OutputsModel}
 
 
 \title{Run with the provided hydrological model function}
@@ -16,8 +15,6 @@ Function which performs a single model run with the provided function over the s
 
 \usage{
 RunModel(InputsModel, RunOptions, Param, FUN_MOD, ...)
-%
-%\method{[}{OutputsModel}(x, i)
 }
 
 
@@ -29,11 +26,8 @@ RunModel(InputsModel, RunOptions, Param, FUN_MOD, ...)
 \item{Param}{[numeric] vector of model parameters (See details for SD lag model)}
 
 \item{FUN_MOD}{[function] hydrological model function (e.g. \code{\link{RunModel_GR4J}}, \code{\link{RunModel_CemaNeigeGR4J}})}
-%
-%\item{x}{[InputsModel] object of class InputsModel}
-%
-%\item{i}{[integer] of the indices to subset a time series or [character] names of the elements to extract}
-\item{...}{Further arguments to pass to the hydrological model function. See \code{\link{RunModel_Lag}} for example}
+
+\item{...}{(optional) arguments to pass to \code{FUN_MOD}}
 }
 
 

tests/testthat/test-RunModel_Lag.R

@@ -39,6 +39,22 @@ RunOptions <- suppressWarnings(CreateRunOptions(FUN_MOD = RunModel_GR4J,
                                                 InputsModel = InputsModel,
                                                 IndPeriod_Run = Ind_Run))
 
+test_that("'QupstrUnit' must correspond to one possible value", {
+  expect_error(
+    InputsModel <- CreateInputsModel(
+      FUN_MOD = RunModel_GR4J,
+      DatesR = BasinObs$DatesR,
+      Precip = BasinObs$P,
+      PotEvap = BasinObs$E,
+      Qupstream = matrix(Qupstream, ncol = 1),
+      LengthHydro = 1,
+      BasinAreas = BasinAreas,
+      QupstrUnit = "m3/h"
+    ),
+    regexp = "'arg' should be one of \"mm\", \"m3\", \"m3/s\", \"l/s\""
+  )
+})
+
 test_that("QcontribDown parameter should be a numeric vector or an OutputModel object", {
   regexp = "'QcontribDown' must be a numeric vector or a 'OutputsModel' object"
   expect_error(
@@ -125,8 +141,15 @@ test_that("'Qupstream' contain NA values", {
 })
 
 test_that("Upstream basin with nil area should return same Qdown as GR4J alone", {
-  UpstBasinArea <- InputsModel$BasinAreas[1L]
-  InputsModel$BasinAreas[1L] <- 0
+  InputsModel <- CreateInputsModel(
+    FUN_MOD = RunModel_GR4J,
+    DatesR = BasinObs$DatesR,
+    Precip = BasinObs$P,
+    PotEvap = BasinObs$E,
+    Qupstream = matrix(Qupstream, ncol = 1),
+    LengthHydro = 1,
+    BasinAreas = c(0,BasinAreas[2])
+  )
   OutputsSD <- RunModel(InputsModel,
                         RunOptions,
                         Param = c(1, Param),
@@ -135,8 +158,15 @@ test_that("Upstream basin with nil area should return same Qdown as GR4J alone",
 })
 
 test_that("Downstream basin with nil area and nul upstream length should return same Qdown as Qupstream alone", {
-  InputsModel$LengthHydro <- 0
-  InputsModel$BasinAreas <- c(BasinInfo$BasinArea, 0)
+  InputsModel <- CreateInputsModel(
+    FUN_MOD = RunModel_GR4J,
+    DatesR = BasinObs$DatesR,
+    Precip = BasinObs$P,
+    PotEvap = BasinObs$E,
+    Qupstream = matrix(Qupstream, ncol = 1),
+    LengthHydro = 0,
+    BasinAreas = c(BasinInfo$BasinArea, 0)
+  )
   OutputsSD <- RunModel(InputsModel,
                         RunOptions,
                         Param = c(1, Param),
@@ -146,22 +176,72 @@ test_that("Downstream basin with nil area and nul upstream length should return
 
 ParamSD <- c(InputsModel$LengthHydro * 1e3 / (24 * 60 * 60), Param) # Speed corresponding to one time step delay
 
-QlsGR4Only <- OutputsGR4JOnly$Qsim * InputsModel$BasinAreas[2L] * 1e6 / 86400
+Qm3GR4Only <- OutputsGR4JOnly$Qsim * InputsModel$BasinAreas[2L] * 1e3
 
 test_that("1 input with lag of 1 time step delay out gives an output delayed of one time step", {
   OutputsSD <- RunModel(InputsModel, RunOptions, Param = ParamSD, FUN_MOD = RunModel_GR4J)
-  QlsSdSim <- OutputsSD$Qsim * sum(InputsModel$BasinAreas) * 1e6 / 86400
-  QlsUpstLagObs <- c(0, Qupstream[Ind_Run[1:(length(Ind_Run) - 1)]]) * InputsModel$BasinAreas[1L] * 1e6 / 86400
-  expect_equal(QlsSdSim - QlsGR4Only, QlsUpstLagObs)
+  Qm3SdSim <- OutputsSD$Qsim_m3
+  Qm3UpstLagObs <- c(0, Qupstream[Ind_Run[1:(length(Ind_Run) - 1)]]) * InputsModel$BasinAreas[1] * 1e3
+  expect_equal(Qm3SdSim - Qm3GR4Only, Qm3UpstLagObs)
 })
 
 test_that("1 input with lag of 0.5 time step delay out gives an output delayed of 0.5 time step", {
   OutputsSD <- RunModel(InputsModel, RunOptions,
                         Param = c(InputsModel$LengthHydro * 1e3 / (12 * 3600), Param),
                         FUN_MOD = RunModel_GR4J)
-  QlsSdSim <- OutputsSD$Qsim * sum(InputsModel$BasinAreas) * 1e6 / 86400
-  QlsUpstLagObs <- (Qupstream[Ind_Run] + c(0, Qupstream[Ind_Run[1:(length(Ind_Run) - 1)]]))/2 * InputsModel$BasinAreas[1L] * 1e6 / 86400
-  expect_equal(QlsSdSim - QlsGR4Only, QlsUpstLagObs)
+  Qm3SdSim <- OutputsSD$Qsim_m3
+  Qm3UpstLagObs <- (Qupstream[Ind_Run] + c(0, Qupstream[Ind_Run[1:(length(Ind_Run) - 1)]])) / 2 * InputsModel$BasinAreas[1] * 1e3
+  expect_equal(Qm3SdSim - Qm3GR4Only, Qm3UpstLagObs)
+})
+
+test_that("Qupstream in different units should return the same result", {
+  OutputsSD_mm <- RunModel(InputsModel, RunOptions,
+                        Param = ParamSD,
+                        FUN_MOD = RunModel_GR4J)
+  InputsModel_m3 <- CreateInputsModel(
+    FUN_MOD = RunModel_GR4J,
+    DatesR = BasinObs$DatesR,
+    Precip = BasinObs$P,
+    PotEvap = BasinObs$E,
+    Qupstream = matrix(Qupstream, ncol = 1) * BasinAreas[1] * 1e3,
+    LengthHydro = 1,
+    BasinAreas = BasinAreas,
+    QupstrUnit = "m3"
+  )
+  OutputsSD_m3 <- RunModel(InputsModel_m3, RunOptions,
+                           Param = ParamSD,
+                           FUN_MOD = RunModel_GR4J)
+  expect_equal(OutputsSD_mm$Qsim, OutputsSD_m3$Qsim)
+
+  InputsModel_m3s <- CreateInputsModel(
+    FUN_MOD = RunModel_GR4J,
+    DatesR = BasinObs$DatesR,
+    Precip = BasinObs$P,
+    PotEvap = BasinObs$E,
+    Qupstream = matrix(Qupstream, ncol = 1) * BasinAreas[1] * 1e3 / 86400,
+    LengthHydro = 1,
+    BasinAreas = BasinAreas,
+    QupstrUnit = "m3/s"
+  )
+  OutputsSD_m3s <- RunModel(InputsModel_m3s, RunOptions,
+                           Param = ParamSD,
+                           FUN_MOD = RunModel_GR4J)
+  expect_equal(OutputsSD_mm$Qsim, OutputsSD_m3s$Qsim)
+
+  InputsModel_ls <- CreateInputsModel(
+    FUN_MOD = RunModel_GR4J,
+    DatesR = BasinObs$DatesR,
+    Precip = BasinObs$P,
+    PotEvap = BasinObs$E,
+    Qupstream = matrix(Qupstream, ncol = 1) * BasinAreas[1] * 1e6 / 86400,
+    LengthHydro = 1,
+    BasinAreas = BasinAreas,
+    QupstrUnit = "L/s"
+  )
+  OutputsSD_ls <- RunModel(InputsModel_ls, RunOptions,
+                           Param = ParamSD,
+                           FUN_MOD = RunModel_GR4J)
+  expect_equal(OutputsSD_mm$Qsim, OutputsSD_ls$Qsim)
 })
 
 InputsCrit <- CreateInputsCrit(
@@ -218,7 +298,7 @@ test_that("1 no area input with lag of 1 time step delay out gives an output del
 
   expect_false(any(is.na(OutputsSD$Qsim)))
 
-  Qm3SdSim <- OutputsSD$Qsim * sum(InputsModel$BasinAreas, na.rm = TRUE) * 1e3
+  Qm3SdSim <- OutputsSD$Qsim_m3
   Qm3UpstLagObs <- c(0, InputsModel$Qupstream[Ind_Run[1:(length(Ind_Run) - 1)]])
 
   expect_equal(Qm3SdSim - Qm3GR4Only, Qm3UpstLagObs)

.gitlab-ci.yml

 stages:
-  - build
+  - check
   - regression
-  - tests
-
-variables:
-  R_LIBS_USER: "$CI_PROJECT_DIR/ci/lib"
-  CHECK_DIR: "$CI_PROJECT_DIR/ci/logs"
-  BUILD_LOGS_DIR: "$CI_PROJECT_DIR/ci/logs/$CI_PROJECT_NAME.Rcheck"
+  - revdepcheck
 
 default:
   before_script:
     - echo "setwd(\"$(pwd)\")" > .Rprofile
+    - echo ".libPaths <- c(Sys.getenv(\"R_LIBS_USER\"), .libPaths())" >> .Rprofile
     - PATH=~/R/sources/R-${R_VERSION}/bin:$PATH
-    - rename "s/${R_VERSION}.airGR/airGR/" *.tar.gz
-
-.build:
-  stage: build
-  script:
-    - cd ..
-    - echo "setwd(\"$(pwd)\")" > .Rprofile
-    - R -e 'utils::install.packages("usethis", repo = "https://cloud.r-project.org/")'
-    - R -e 'remotes::install_deps(pkgdir = "airgr", dep = T)'
-    - R CMD build airgr
-    - rename "s/airGR/${R_VERSION}.airGR/" airGR_*.tar.gz
-    - mv *.tar.gz airgr/
-  artifacts:
-    untracked: true
-    expire_in: 1 week
+    - R -e 'remotes::install_deps(dep = T)'
 
 .regression:
   stage: regression
@@ -37,28 +19,20 @@ default:
     - Rscript tests/testthat/regression_tests.R compare
 
 .check:
-  stage: tests
+  stage: check
   script:
-  - R -e 'devtools::check(check_dir = Sys.getenv("CHECK_DIR"), cran = !as.logical(Sys.getenv("AS_CRAN")))'
-  - R -e 'if (length(devtools::check_failures(path = Sys.getenv("BUILD_LOGS_DIR"), note = FALSE)) > 0) stop()'
+  - R -e ' rcmdcheck::rcmdcheck(args = ifelse(as.logical(Sys.getenv("NOT_CRAN")), "", "--as-cran"), error_on = "warning")'
 
 .check_not_cran:
   variables:
     NOT_CRAN: "true"
-    AS_CRAN: "false"
   extends: .check
 
 .check_as_cran:
   variables:
     NOT_CRAN: "false"
-    AS_CRAN: "true"
   extends: .check
 
-build_patched:
-  variables:
-    R_VERSION: "patched"
-  extends: .build
-
 regression_patched:
   variables:
     R_VERSION: "patched"
@@ -90,15 +64,6 @@ check_as_cran_patched:
     R_VERSION: "patched"
   extends: .check_as_cran
 
-build_devel:
-  only:
-    refs:
-      - tags
-      - schedules
-  variables:
-    R_VERSION: "devel"
-  extends: .build
-
 check_not_cran_devel:
   only:
     refs:
@@ -117,29 +82,39 @@ check_as_cran_devel:
     R_VERSION: "devel"
   extends: .check_as_cran
 
-build_oldrel:
+check_not_cran_oldrel:
   only:
     refs:
       - tags
       - schedules
   variables:
     R_VERSION: "oldrel"
-  extends: .build
+  extends: .check_not_cran
 
-check_not_cran_oldrel:
+check_as_cran_oldrel:
   only:
     refs:
       - tags
       - schedules
   variables:
     R_VERSION: "oldrel"
-  extends: .check_not_cran
+  extends: .check_as_cran
 
-check_as_cran_oldrel:
+revdepcheck_patched:
+  stage: revdepcheck
   only:
     refs:
       - tags
       - schedules
   variables:
-    R_VERSION: "oldrel"
-  extends: .check_as_cran
+    R_VERSION: "patched"
+  script:
+    - R -e 'remotes::install_github("https://github.com/r-lib/revdepcheck")'
+    - R -e 'revdepcheck::revdep_check(num_workers = 2)'
+    - R -e 'if (any(sapply(revdepcheck::revdep_summary(), function(x) {any(x$cmp$change == 1)}))) stop()'
+  artifacts:
+    paths:
+      - revdep/README.md
+      - revdep/problems.md
+      - revdep/failures.md
+      - revdep/cran.md