From 6f623c0950e40c856877cc31aa308073689457f3 Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Tue, 28 Jun 2022 09:15:10 +0200
Subject: [PATCH 1/9] Create the folders and necessary file for automatic unit
 testing

---
 .gitlab-ci.yml                        | 9 +++++++++
 tests/testthat.R                      | 7 +++++++
 tests/testthat/test-decadal_monthly.R | 6 ++++++
 3 files changed, 22 insertions(+)
 create mode 100644 .gitlab-ci.yml
 create mode 100644 tests/testthat.R
 create mode 100644 tests/testthat/test-decadal_monthly.R

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 00000000..c1e690c2
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,9 @@
+stages:
+  - build
+build:
+  stage: build
+  script:
+    - module load R/3.6.1-foss-2015a-bare
+    - module load CDO/1.9.8-foss-2015a
+    - R CMD build --resave-data .
+    - R CMD check --as-cran --no-manual --run-donttest startR_*.tar.gz
diff --git a/tests/testthat.R b/tests/testthat.R
new file mode 100644
index 00000000..3d7dd459
--- /dev/null
+++ b/tests/testthat.R
@@ -0,0 +1,7 @@
+library(testthat)
+library(startR)
+library(SpecsVerification)
+library(s2dv)
+library(CSTools)
+
+test_check("auto-S2S")
diff --git a/tests/testthat/test-decadal_monthly.R b/tests/testthat/test-decadal_monthly.R
new file mode 100644
index 00000000..6d342bf9
--- /dev/null
+++ b/tests/testthat/test-decadal_monthly.R
@@ -0,0 +1,6 @@
+context("Decadal monthly data")
+
+test_that("1. ", {
+
+
+})
-- 
GitLab


From fd5535fc91410baaa705db3361386b7b14892611 Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Wed, 29 Jun 2022 14:48:22 +0200
Subject: [PATCH 2/9] Create CI/CD

---
 .gitlab-ci.yml                        | 25 ++++++++++++++++++++-----
 tests/testthat.R                      |  3 ++-
 tests/testthat/test-decadal_monthly.R | 13 ++++++++++++-
 3 files changed, 34 insertions(+), 7 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c1e690c2..3000e522 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,9 +1,24 @@
-stages:
+default:
+#  before_script:
+#    - R --version     
+#    - cdo --version
+#  after_script:
+#  - echo "After script section"
+#  - echo "For example you might do some cleanup here"
+
+stages:  # List of stages for jobs, and their order of execution
   - build
-build:
+  - test
+
+build-job:
   stage: build
   script:
-    - module load R/3.6.1-foss-2015a-bare
+    - echo "Build: Loading modules..."
+    - module load R/4.1.2-foss-2015a-bare
     - module load CDO/1.9.8-foss-2015a
-    - R CMD build --resave-data .
-    - R CMD check --as-cran --no-manual --run-donttest startR_*.tar.gz
+
+unit-test-job:  # This job runs in the test stage.
+  stage: test  # It only starts when the job in the build stage completes successfully.
+  script:
+    - echo "Test: Running unit tests..."
+    - Rscript ./tests/testthat.R #/test-decadal_monthly.R
diff --git a/tests/testthat.R b/tests/testthat.R
index 3d7dd459..9e9b5a21 100644
--- a/tests/testthat.R
+++ b/tests/testthat.R
@@ -4,4 +4,5 @@ library(SpecsVerification)
 library(s2dv)
 library(CSTools)
 
-test_check("auto-S2S")
+print('In testthat.R. Running...')
+source('./tests/testthat/test-decadal_monthly.R')
diff --git a/tests/testthat/test-decadal_monthly.R b/tests/testthat/test-decadal_monthly.R
index 6d342bf9..e3f85290 100644
--- a/tests/testthat/test-decadal_monthly.R
+++ b/tests/testthat/test-decadal_monthly.R
@@ -1,6 +1,17 @@
 context("Decadal monthly data")
 
-test_that("1. ", {
+source("modules/Loading/Loading_decadal.R")
+source("modules/Calibration/Calibration.R")
+source("modules/Skill/Skill.R")
+source("modules/Saving/Save_data.R")
 
+recipe_file <- "modules/Loading/testing_recipes/recipe_decadal.yml"
+
+test_that("1. Loading", {
+
+print('In test_that 1.')
+#suppressWarnings(
+#data <- load_datasets(recipe_file)
+#)
 
 })
-- 
GitLab


From 9c81ee9c1533cc55d31445a6a958d6876466e2b8 Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Wed, 29 Jun 2022 14:56:59 +0200
Subject: [PATCH 3/9] Syntax fix

---
 .gitlab-ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 3000e522..36590a09 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -13,12 +13,12 @@ stages:  # List of stages for jobs, and their order of execution
 build-job:
   stage: build
   script:
-    - echo "Build: Loading modules..."
+    - echo "Build Loading modules..."
     - module load R/4.1.2-foss-2015a-bare
     - module load CDO/1.9.8-foss-2015a
 
 unit-test-job:  # This job runs in the test stage.
   stage: test  # It only starts when the job in the build stage completes successfully.
   script:
-    - echo "Test: Running unit tests..."
+    - echo "Test Running unit tests..."
     - Rscript ./tests/testthat.R #/test-decadal_monthly.R
-- 
GitLab


From 765495dc15e13d52017d34db8e19ddcb4f9e2bf7 Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Wed, 29 Jun 2022 15:14:35 +0200
Subject: [PATCH 4/9] Try fixing bugs

---
 .gitlab-ci.yml   | 2 +-
 tests/testthat.R | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 36590a09..8707fee2 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -14,7 +14,7 @@ build-job:
   stage: build
   script:
     - echo "Build Loading modules..."
-    - module load R/4.1.2-foss-2015a-bare
+    - module load R/3.6.1-foss-2015a-bare #R/4.1.2-foss-2015a-bare
     - module load CDO/1.9.8-foss-2015a
 
 unit-test-job:  # This job runs in the test stage.
diff --git a/tests/testthat.R b/tests/testthat.R
index 9e9b5a21..e803bbe4 100644
--- a/tests/testthat.R
+++ b/tests/testthat.R
@@ -1,8 +1,8 @@
-library(testthat)
 library(startR)
 library(SpecsVerification)
 library(s2dv)
 library(CSTools)
+library(testthat)
 
 print('In testthat.R. Running...')
 source('./tests/testthat/test-decadal_monthly.R')
-- 
GitLab


From f8b52a17edb32042030a3ae9e608db92ff5f50cd Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Wed, 29 Jun 2022 15:16:07 +0200
Subject: [PATCH 5/9] Try fixing CI/CD bugs - 2

---
 .gitlab-ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8707fee2..80dcde6d 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -21,4 +21,5 @@ unit-test-job:  # This job runs in the test stage.
   stage: test  # It only starts when the job in the build stage completes successfully.
   script:
     - echo "Test Running unit tests..."
+    - module list
     - Rscript ./tests/testthat.R #/test-decadal_monthly.R
-- 
GitLab


From 38f4694ee7cee346af46745508e7ad5ca3255de9 Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Wed, 29 Jun 2022 15:18:48 +0200
Subject: [PATCH 6/9] Try fixing CI/CD bugs - 3

---
 .gitlab-ci.yml | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 80dcde6d..320ff66e 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -7,19 +7,22 @@ default:
 #  - echo "For example you might do some cleanup here"
 
 stages:  # List of stages for jobs, and their order of execution
-  - build
+#  - build
   - test
 
-build-job:
-  stage: build
-  script:
-    - echo "Build Loading modules..."
-    - module load R/3.6.1-foss-2015a-bare #R/4.1.2-foss-2015a-bare
-    - module load CDO/1.9.8-foss-2015a
+#build-job:
+#  stage: build
+#  script:
+#    - echo "Build Loading modules..."
+#    - module load R/3.6.1-foss-2015a-bare #R/4.1.2-foss-2015a-bare
+#    - module load CDO/1.9.8-foss-2015a
 
 unit-test-job:  # This job runs in the test stage.
   stage: test  # It only starts when the job in the build stage completes successfully.
   script:
+    - echo "Build Loading modules..."
+    - module load R/4.1.2-foss-2015a-bare
+    - module load CDO/1.9.8-foss-2015a
     - echo "Test Running unit tests..."
     - module list
     - Rscript ./tests/testthat.R #/test-decadal_monthly.R
-- 
GitLab


From f2113ec931c660ee40ff65d3aca8fc5521539c89 Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Wed, 29 Jun 2022 15:45:26 +0200
Subject: [PATCH 7/9] Try having two test jobs

---
 .gitlab-ci.yml                         | 34 +++++++++++---------------
 tests/test_decadal.R                   |  3 +++
 tests/test_seasonal.R                  |  3 +++
 tests/testthat.R                       |  8 ------
 tests/testthat/test-seasonal_monthly.R | 17 +++++++++++++
 5 files changed, 37 insertions(+), 28 deletions(-)
 create mode 100644 tests/test_decadal.R
 create mode 100644 tests/test_seasonal.R
 delete mode 100644 tests/testthat.R
 create mode 100644 tests/testthat/test-seasonal_monthly.R

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 320ff66e..4ea4685f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,28 +1,22 @@
-default:
-#  before_script:
-#    - R --version     
-#    - cdo --version
-#  after_script:
-#  - echo "After script section"
-#  - echo "For example you might do some cleanup here"
-
 stages:  # List of stages for jobs, and their order of execution
-#  - build
   - test
 
-#build-job:
-#  stage: build
-#  script:
-#    - echo "Build Loading modules..."
-#    - module load R/3.6.1-foss-2015a-bare #R/4.1.2-foss-2015a-bare
-#    - module load CDO/1.9.8-foss-2015a
-
 unit-test-job:  # This job runs in the test stage.
-  stage: test  # It only starts when the job in the build stage completes successfully.
+  stage: test 
+  script:
+    - echo "Loading modules..."
+    - module load R/4.1.2-foss-2015a-bare
+    - module load CDO/1.9.8-foss-2015a
+    - module list
+    - echo "Running unit tests..."
+    - Rscript ./tests/test_seasonal.R
+
+unit-test-decadal:  # This job runs in the test stage.
+  stage: test
   script:
-    - echo "Build Loading modules..."
+    - echo "Loading modules..."
     - module load R/4.1.2-foss-2015a-bare
     - module load CDO/1.9.8-foss-2015a
-    - echo "Test Running unit tests..."
     - module list
-    - Rscript ./tests/testthat.R #/test-decadal_monthly.R
+    - echo "Running decadal unit tests..."
+    - Rscript ./tests/test_decadal.R
diff --git a/tests/test_decadal.R b/tests/test_decadal.R
new file mode 100644
index 00000000..26bc856e
--- /dev/null
+++ b/tests/test_decadal.R
@@ -0,0 +1,3 @@
+library(testthat)
+
+source('./tests/testthat/test-decadal_monthly.R')
diff --git a/tests/test_seasonal.R b/tests/test_seasonal.R
new file mode 100644
index 00000000..37aa3ee4
--- /dev/null
+++ b/tests/test_seasonal.R
@@ -0,0 +1,3 @@
+library(testthat)
+
+source('./tests/testthat/test-seasonal_monthly.R')
diff --git a/tests/testthat.R b/tests/testthat.R
deleted file mode 100644
index e803bbe4..00000000
--- a/tests/testthat.R
+++ /dev/null
@@ -1,8 +0,0 @@
-library(startR)
-library(SpecsVerification)
-library(s2dv)
-library(CSTools)
-library(testthat)
-
-print('In testthat.R. Running...')
-source('./tests/testthat/test-decadal_monthly.R')
diff --git a/tests/testthat/test-seasonal_monthly.R b/tests/testthat/test-seasonal_monthly.R
new file mode 100644
index 00000000..b4147fbf
--- /dev/null
+++ b/tests/testthat/test-seasonal_monthly.R
@@ -0,0 +1,17 @@
+context("Decadal monthly data")
+
+source("modules/Loading/Loading_decadal.R")
+source("modules/Calibration/Calibration.R")
+source("modules/Skill/Skill.R")
+source("modules/Saving/Save_data.R")
+
+recipe_file <- "modules/Loading/testing_recipes/recipe_4.yml"
+
+test_that("1. Loading", {
+
+print('In test_that 1.')
+#suppressWarnings(
+#data <- load_datasets(recipe_file)
+#)
+
+})
-- 
GitLab


From 51b9a5a980e2abb6e7a2b68f6b2d30fd15231407 Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Wed, 29 Jun 2022 17:31:14 +0200
Subject: [PATCH 8/9] Set up unit test structure and add first decadal monthly
 case

---
 .gitlab-ci.yml                             |   4 +-
 modules/Loading/Loading_decadal.R          |   4 +-
 tests/recipes/recipe-decadal_monthly_1.yml |  46 +++++
 tests/test_decadal.R                       |   7 +-
 tests/testthat/test-decadal_monthly.R      | 192 ++++++++++++++++++++-
 5 files changed, 242 insertions(+), 11 deletions(-)
 create mode 100644 tests/recipes/recipe-decadal_monthly_1.yml

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 4ea4685f..8c720372 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,14 +1,14 @@
 stages:  # List of stages for jobs, and their order of execution
   - test
 
-unit-test-job:  # This job runs in the test stage.
+unit-test-seasonal:  # This job runs in the test stage.
   stage: test 
   script:
     - echo "Loading modules..."
     - module load R/4.1.2-foss-2015a-bare
     - module load CDO/1.9.8-foss-2015a
     - module list
-    - echo "Running unit tests..."
+    - echo "Running seasonal unit tests..."
     - Rscript ./tests/test_seasonal.R
 
 unit-test-decadal:  # This job runs in the test stage.
diff --git a/modules/Loading/Loading_decadal.R b/modules/Loading/Loading_decadal.R
index fe615594..f94d1343 100644
--- a/modules/Loading/Loading_decadal.R
+++ b/modules/Loading/Loading_decadal.R
@@ -2,11 +2,11 @@
 # 1. archive.yml
 # 2. recipe.yml
 # 3. Load_decadal.R (V)
-setwd('/esarchive/scratch/aho/git/auto-s2s/')
+#setwd('/esarchive/scratch/aho/git/auto-s2s/')
 
 ## TODO: remove paths to personal scratchs 
 source("/esarchive/scratch/vagudets/repos/csoperational/R/get_regrid_params.R")
-source("/esarchive/scratch/vagudets/repos/cstools/R/s2dv_cube.R")
+#source("/esarchive/scratch/vagudets/repos/cstools/R/s2dv_cube.R")
 # Load required libraries/funs
 source("modules/Loading/get_daily_time_ind.R")
 source("modules/Loading/check_latlon.R")
diff --git a/tests/recipes/recipe-decadal_monthly_1.yml b/tests/recipes/recipe-decadal_monthly_1.yml
new file mode 100644
index 00000000..5acd642d
--- /dev/null
+++ b/tests/recipes/recipe-decadal_monthly_1.yml
@@ -0,0 +1,46 @@
+Description:
+  Author: An-Chi Ho
+  '': split version
+Analysis:
+  Horizon: Decadal
+  Variables:
+    name: tas
+    freq: monthly_mean
+  Datasets:
+    System: 
+      name: EC-Earth3-i4 #CanESM5 
+      member: r1i4p1f1,r2i4p1f1
+    Multimodel: no
+    Reference:
+      name: ERA5 #JRA-55
+  Time:
+    sdate:
+    fcst:  2021
+#      fcst_sday: '1101'
+    hcst_start: 1991 #'1993'
+    hcst_end: 1994 #'2016'
+#    season: 'Annual'
+    leadtimemin: 0
+    leadtimemax: 2
+  Region:
+    latmin: 17 #-90
+    latmax: 20 #90
+    lonmin: 12
+    lonmax: 15 #359.9
+  Regrid:
+    method: bilinear
+    type: to_system #to_reference
+  Workflow:
+    Calibration:
+      method: bias
+    Skill:
+      metric: RPSS
+    Indicators:
+      index: FALSE
+  Output_format: S2S4E
+Run:
+  Loglevel: INFO
+  Terminal: yes
+  output_dir: /esarchive/scratch/aho/git/auto-s2s/out-logs/
+  code_dir: /esarchive/scratch/aho/git/auto-s2s/
+
diff --git a/tests/test_decadal.R b/tests/test_decadal.R
index 26bc856e..84a23b62 100644
--- a/tests/test_decadal.R
+++ b/tests/test_decadal.R
@@ -1,3 +1,8 @@
 library(testthat)
 
-source('./tests/testthat/test-decadal_monthly.R')
+path_testthat <- file.path('./tests/testthat/') 
+files_testthat <- list.files('./tests/testthat/', pattern = 'decadal')
+
+for (i_file in 1:length(files_testthat)) {
+  source(paste0('./tests/testthat/', files_testthat[i_file]))
+}
diff --git a/tests/testthat/test-decadal_monthly.R b/tests/testthat/test-decadal_monthly.R
index e3f85290..19560921 100644
--- a/tests/testthat/test-decadal_monthly.R
+++ b/tests/testthat/test-decadal_monthly.R
@@ -1,17 +1,197 @@
-context("Decadal monthly data")
+context("Decadal monthly data - 1")
+
+###########################################
 
 source("modules/Loading/Loading_decadal.R")
 source("modules/Calibration/Calibration.R")
 source("modules/Skill/Skill.R")
 source("modules/Saving/Save_data.R")
 
-recipe_file <- "modules/Loading/testing_recipes/recipe_decadal.yml"
+recipe_file <- "tests/recipes/recipe-decadal_monthly_1.yml"
+
+# Load datasets
+suppressWarnings({invisible(capture.output(
+data <- load_datasets(recipe_file)
+))})
+
+recipe <- read_yaml(recipe_file)
+# Calibrate datasets
+suppressWarnings({invisible(capture.output(
+  calibrated_data <- calibrate_datasets(data, recipe)
+))})
+
+# Compute skill metrics
+suppressWarnings({invisible(capture.output(
+skill_metrics <- compute_skill_metrics(calibrated_data$hcst, data$obs,
+                                       recipe, na.rm = T, ncores = 4)
+))})
+
+#======================================
 
 test_that("1. Loading", {
 
-print('In test_that 1.')
-#suppressWarnings(
-#data <- load_datasets(recipe_file)
-#)
+expect_equal(
+is.list(data),
+TRUE
+)
+expect_equal(
+names(data),
+c("hcst", "fcst", "obs")
+)
+expect_equal(
+class(data$hcst),
+"s2dv_cube"
+)
+expect_equal(
+class(data$fcst),
+"s2dv_cube"
+)
+expect_equal(
+class(data$obs),
+"s2dv_cube"
+)
+expect_equal(
+names(data$hcst),
+c("data", "Variable", "Datasets", "Dates", "when", "source_files", "load_parameters")
+)
+expect_equal(
+names(data$hcst),
+names(data$fcst)
+)
+expect_equal(
+names(data$hcst),
+names(data$obs)
+)
+expect_equal(
+dim(data$hcst$data),
+c(dat = 1, var = 1, ensemble = 2, sday = 1, sweek = 1, syear = 4, time = 3, latitude = 5, longitude = 4)
+)
+expect_equal(
+dim(data$fcst$data),
+c(dat = 1, var = 1, ensemble = 2, sday = 1, sweek = 1, syear = 1, time = 3, latitude = 5, longitude = 4)
+)
+expect_equal(
+dim(data$hcst$Dates$start),
+c(sday = 1, sweek = 1, syear = 4, time = 3)
+)
+expect_equal(
+as.vector(drop(data$hcst$data)[,1:2,1,2,3]),
+c(291.3831, 291.6227, 292.3012, 290.9779),
+tolerance = 0.0001
+)
+expect_equal(
+mean(data$hcst$data),
+287.3804,
+tolerance = 0.0001
+)
+expect_equal(
+range(data$hcst$data),
+c(281.7395, 294.2467),
+tolerance = 0.0001
+)
+expect_equal(
+(data$hcst$Dates$start)[1],
+as.POSIXct("1991-11-16", tz = 'UTC')
+)
+expect_equal(
+(data$hcst$Dates$start)[2],
+as.POSIXct("1992-11-16", tz = 'UTC')
+)
+expect_equal(
+(data$hcst$Dates$start)[5],
+as.POSIXct("1991-12-16 12:00:00", tz = 'UTC')
+)
+expect_equal(
+(data$hcst$Dates$start)[10],
+as.POSIXct("1993-01-16 12:00:00", tz = 'UTC')
+)
+
+})
+
+#======================================
+test_that("2. Calibration", {
+
+expect_equal(
+is.list(calibrated_data),
+TRUE
+)
+expect_equal(
+names(calibrated_data),
+c("hcst", "fcst")
+)
+expect_equal(
+class(calibrated_data$hcst),
+"s2dv_cube"
+)
+expect_equal(
+class(calibrated_data$fcst),
+"s2dv_cube"
+)
+expect_equal(
+dim(calibrated_data$hcst$data),
+c(dat = 1, var = 1, ensemble = 2, sday = 1, sweek = 1, syear = 4, time = 3, latitude = 5, longitude = 4)
+)
+expect_equal(
+dim(calibrated_data$fcst$data),
+c(dat = 1, var = 1, ensemble = 2, sday = 1, sweek = 1, syear = 1, time = 3, latitude = 5, longitude = 4)
+)
+expect_equal(
+mean(calibrated_data$fcst$data),
+291.8375,
+tolerance = 0.0001
+)
+expect_equal(
+mean(calibrated_data$hcst$data),
+289.6679,
+tolerance = 0.0001
+)
+expect_equal(
+as.vector(drop(calibrated_data$hcst$data)[1, , 2, 3, 4]),
+c(286.3895, 286.6408, 290.6652, 288.3759),
+tolerance = 0.0001
+)
+expect_equal(
+range(calibrated_data$fcst$data),
+c(287.2173, 297.4578),
+tolerance = 0.0001
+)
+
+})
+
+
+#======================================
+test_that("3. Metrics", {
+
+expect_equal(
+is.list(skill_metrics),
+TRUE
+)
+expect_equal(
+names(skill_metrics),
+c("rpss", "rpss_significance")
+)
+expect_equal(
+class(skill_metrics$rpss[[1]]),
+"array"
+)
+expect_equal(
+dim(skill_metrics$rpss[[1]]),
+c(dat = 1, var = 1, sday = 1, sweek = 1, time = 3, latitude = 5, longitude = 4)
+)
+expect_equal(
+dim(skill_metrics$rpss_significance[[1]]),
+dim(skill_metrics$rpss[[1]])
+)
+expect_equal(
+as.vector(drop(skill_metrics$rpss[[1]])[, 2, 3]),
+c(-0.2857143, -1.2500000, -1.8928571),
+tolerance = 0.0001
+)
+expect_equal(
+as.vector(drop(skill_metrics$rpss_significance[[1]])[, 2, 3]),
+rep(FALSE, 3)
+)
 
 })
+
+
-- 
GitLab


From 580bb08123274aca8b3c06642b75dd4702cda9eb Mon Sep 17 00:00:00 2001
From: Victoria Agudetse Roures <victoria.agudetse@bsc.es>
Date: Tue, 5 Jul 2022 11:26:30 +0200
Subject: [PATCH 9/9] Add monthly seasonal tests to CI/CD

---
 tests/recipes/recipe-seasonal_monthly_1.yml |  43 +++++
 tests/test_seasonal.R                       |   8 +-
 tests/testthat/test-seasonal_monthly.R      | 187 +++++++++++++++++++-
 3 files changed, 230 insertions(+), 8 deletions(-)
 create mode 100644 tests/recipes/recipe-seasonal_monthly_1.yml

diff --git a/tests/recipes/recipe-seasonal_monthly_1.yml b/tests/recipes/recipe-seasonal_monthly_1.yml
new file mode 100644
index 00000000..3631c783
--- /dev/null
+++ b/tests/recipes/recipe-seasonal_monthly_1.yml
@@ -0,0 +1,43 @@
+Description:
+  Author: V. Agudetse
+
+Analysis:
+  Horizon: Seasonal
+  Variables:
+    name: tas
+    freq: monthly_mean
+  Datasets:
+    System:
+      name: system7c3s
+    Multimodel: False
+    Reference:
+      name: era5
+  Time:
+    sdate:
+      fcst_syear: '2020'
+      fcst_sday: '1101'
+    hcst_start: '1993'
+    hcst_end: '1996'
+    leadtimemin: 0
+    leadtimemax: 2
+  Region:
+    latmin: 17
+    latmax: 20
+    lonmin: 12
+    lonmax: 15
+  Regrid:
+    method: bilinear
+    type: to_system
+  Workflow:
+    Calibration:
+      method: mse_min
+    Skill:
+      metric: RPSS
+    Indicators:
+      index: no
+  Output_format: S2S4E
+Run:
+  Loglevel: INFO
+  Terminal: yes
+  output_dir: /esarchive/scratch/vagudets/repos/auto-s2s/out-logs/
+  code_dir: /esarchive/scratch/vagudets/repos/auto-s2s/
diff --git a/tests/test_seasonal.R b/tests/test_seasonal.R
index 37aa3ee4..4718e3d4 100644
--- a/tests/test_seasonal.R
+++ b/tests/test_seasonal.R
@@ -1,3 +1,9 @@
 library(testthat)
 
-source('./tests/testthat/test-seasonal_monthly.R')
+path_testthat <- file.path('./tests/testthat/')
+files_testthat <- list.files('./tests/testthat/', pattern = 'seasonal')
+
+for (i_file in 1:length(files_testthat)) {
+  source(paste0('./tests/testthat/', files_testthat[i_file]))
+}
+
diff --git a/tests/testthat/test-seasonal_monthly.R b/tests/testthat/test-seasonal_monthly.R
index b4147fbf..4bdf833d 100644
--- a/tests/testthat/test-seasonal_monthly.R
+++ b/tests/testthat/test-seasonal_monthly.R
@@ -1,17 +1,190 @@
-context("Decadal monthly data")
+context("Seasonal monthly data")
 
-source("modules/Loading/Loading_decadal.R")
+source("modules/Loading/Loading.R")
 source("modules/Calibration/Calibration.R")
 source("modules/Skill/Skill.R")
 source("modules/Saving/Save_data.R")
 
-recipe_file <- "modules/Loading/testing_recipes/recipe_4.yml"
+recipe_file <- "tests/recipes/recipe-seasonal_monthly_1.yml"
+
+# Load datasets
+suppressWarnings({invisible(capture.output(
+data <- load_datasets(recipe_file)
+))})
+
+recipe <- read_yaml(recipe_file)
+
+suppressWarnings({invisible(capture.output(
+calibrated_data <- calibrate_datasets(data, recipe)
+))})
+
+# Compute skill metrics
+suppressWarnings({invisible(capture.output(
+skill_metrics <- compute_skill_metrics(calibrated_data$hcst, data$obs,
+                                       recipe, na.rm = T, ncores = 4)
+))})
 
 test_that("1. Loading", {
 
-print('In test_that 1.')
-#suppressWarnings(
-#data <- load_datasets(recipe_file)
-#)
+expect_equal(
+is.list(data),
+TRUE
+)
+expect_equal(
+names(data),
+c("hcst", "fcst", "obs")
+)
+expect_equal(
+class(data$hcst),
+"s2dv_cube"
+)
+expect_equal(
+class(data$fcst),
+"s2dv_cube"
+)
+expect_equal(
+class(data$obs),
+"s2dv_cube"
+)
+expect_equal(
+names(data$hcst),
+c("data", "lon", "lat", "Variable", "Datasets", "Dates", "when", "source_files", "load_parameters")
+)
+expect_equal(
+names(data$hcst),
+names(data$fcst)
+)
+expect_equal(
+names(data$hcst),
+names(data$obs)
+)
+expect_equal(
+dim(data$hcst$data),
+c(dat = 1, var = 1, sday = 1, sweek = 1, syear = 4, time = 3, latitude = 3, longitude = 3, ensemble = 25)
+)
+expect_equal(
+dim(data$fcst$data),
+c(dat = 1, var = 1, sday = 1, sweek = 1, syear = 1, time = 3, latitude = 3, longitude = 3, ensemble = 51)
+)
+expect_equal(
+dim(data$hcst$Dates$start),
+c(sday = 1, sweek = 1, syear = 4, time = 3)
+)
+expect_equal(
+as.vector(drop(data$hcst$data)[1:2,1:2,1,2,3]),
+c(293.9651, 295.9690, 290.6771, 290.7957),
+tolerance = 0.0001
+)
+expect_equal(
+mean(data$hcst$data),
+290.8758,
+tolerance = 0.0001
+)
+expect_equal(
+range(data$hcst$data),
+c(284.7413, 299.6219),
+tolerance = 0.0001
+)
+expect_equal(
+(data$hcst$Dates$start)[1],
+as.POSIXct("1993-12-01", tz = 'UTC')
+)
+expect_equal(
+(data$hcst$Dates$start)[2],
+as.POSIXct("1994-12-01", tz = 'UTC')
+)
+expect_equal(
+(data$hcst$Dates$start)[5],
+as.POSIXct("1994-01-01", tz = 'UTC')
+)
+expect_equal(
+(data$obs$Dates$start)[10],
+as.POSIXct("1995-02-14", tz = 'UTC')
+)
+
+})
+
+test_that("2. Calibration", {
+
+expect_equal(
+is.list(calibrated_data),
+TRUE
+)
+expect_equal(
+names(calibrated_data),
+c("hcst", "fcst")
+)
+expect_equal(
+class(calibrated_data$hcst),
+"s2dv_cube"
+)
+expect_equal(
+class(calibrated_data$fcst),
+"s2dv_cube"
+)
+expect_equal(
+dim(calibrated_data$hcst$data),
+c(dat = 1, var = 1, sday = 1, sweek = 1, syear = 4, time = 3, latitude = 3, longitude = 3, ensemble = 25)
+)
+expect_equal(
+dim(calibrated_data$fcst$data),
+c(dat = 1, var = 1, sday = 1, sweek = 1, syear = 1, time = 3, latitude = 3, longitude = 3, ensemble = 51)
+)
+expect_equal(
+mean(calibrated_data$fcst$data),
+291.1218,
+tolerance = 0.0001
+)
+expect_equal(
+mean(calibrated_data$hcst$data),
+289.8596,
+tolerance = 0.0001
+)
+expect_equal(
+as.vector(drop(calibrated_data$hcst$data)[1, , 2, 3, 4]),
+c(287.7982, 287.0422, 290.4297),
+tolerance = 0.0001
+)
+expect_equal(
+range(calibrated_data$fcst$data),
+c(283.5374, 306.2353),
+tolerance = 0.0001
+)
+
+})
+
+
+#======================================
+test_that("3. Metrics", {
+
+expect_equal(
+is.list(skill_metrics),
+TRUE
+)
+expect_equal(
+names(skill_metrics),
+c("rpss", "rpss_significance")
+)
+expect_equal(
+class(skill_metrics$rpss[[1]]),
+"array"
+)
+expect_equal(
+dim(skill_metrics$rpss[[1]]),
+c(dat = 1, var = 1, sday = 1, sweek = 1, time = 3, latitude = 3, longitude = 3)
+)
+expect_equal(
+dim(skill_metrics$rpss_significance[[1]]),
+dim(skill_metrics$rpss[[1]])
+)
+expect_equal(
+as.vector(drop(skill_metrics$rpss[[1]])[, 2, 3]),
+c(-1.153829, -1.114743, -1.392457),
+tolerance = 0.0001
+)
+expect_equal(
+as.vector(drop(skill_metrics$rpss_significance[[1]])[, 2, 3]),
+rep(FALSE, 3)
+)
 
 })
-- 
GitLab