Add tests and github actions

.github/workflows/build.yml

@@ -0,0 +1,47 @@
+name: build
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  R-CMD:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+        - { os: ubuntu-latest, r: 'devel', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      GITHUB_PAT: ${{ secrets.GH_RFASSTUI_TOKEN}}
+
+    steps:
+      - uses: actions/checkout@v1
+      - uses: r-lib/actions/setup-r@v2-branch
+        with:
+          r-version: '3.6'
+      - uses: r-lib/actions/setup-pandoc@v2-branch
+      - uses: r-lib/actions/setup-tinytex@v2-branch
+
+      - name: Install libraries
+        if: startsWith(matrix.config.os, 'ubuntu')
+        run: |
+          sudo apt-add-repository ppa:ubuntugis/ubuntugis-unstable
+          sudo apt-get update
+          sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev libudunits2-dev libgdal-dev libgeos-dev libproj-dev libmagick++-dev libavfilter-dev libharfbuzz-dev libfribidi-dev
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes","rcmdcheck"), repos = "https://cloud.r-project.org")
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_github("JGCRI/rpackageutils")
+        shell: Rscript {0}
+
+      - name: Check
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--ignore-vignettes", "--no-build-vignettes"), build_args = c("--no-manual", "--ignore-vignettes", "--no-build-vignettes"), error_on = "error")
+        shell: Rscript {0}

.github/workflows/codecov.yml

@@ -0,0 +1,48 @@
+name: test-coverage
+
+on:
+  push:
+    branches:
+      - main
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      GITHUB_PAT: ${{secrets.GH_GCAMREPORT_TOKEN}}
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-r@v2-branch
+        with:
+          r-version: '4.1.0'
+      - uses: r-lib/actions/setup-pandoc@v2-branch
+      - uses: r-lib/actions/setup-tinytex@v2-branch
+      - uses: actions/download-artifact@v2
+
+      - name: Cache R packages
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Ubuntu config
+        run: |
+          sudo apt-add-repository ppa:ubuntugis/ubuntugis-unstable
+          sudo apt-get update
+          sudo apt-get install -y libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev libssl-dev libxml2-dev libudunits2-dev libgdal-dev libgeos-dev libproj-dev libmagick++-dev libavfilter-dev
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes","rcmdcheck","covr"), repos = "https://cloud.r-project.org")
+          remotes::install_github("JGCRI/rpackageutils")
+          remotes::install_deps(dependencies = TRUE)
+        shell: Rscript {0}
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/[email protected]
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: bc3LC/rfasstui

NAMESPACE

@@ -1,7 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export(data_query)
-export(fill_queries)
 export(get_example_prj)
 export(get_globalCapabilities)
 export(get_globalCustomColorScales)

R/set_globals.R

@@ -103,10 +103,6 @@ get_globalCapabilities <- function() {
   globalCapabilities[['agriculture_rev_loss']] <- 'agriculture_rev_loss'
   attr(globalCapabilities[['agriculture_rev_loss']], 'longName') <- "Agriculture revenue loss"
 
-  # # "Economic impacts" TODO
-  # globalCapabilities[['economy']] <- c('VSL')
-  # attr(globalCapabilities[['economy']], 'longName') <- "Economic imipacts"
-
 
   return(globalCapabilities)
 }

inst/rfasstui/server.R

@@ -183,11 +183,11 @@ server <- function(input, output, session)
 
 
     # Add nonCO2 query manually (it is too big to use the usual method)
-    prj <- rfasstui::fill_queries(prj, db_path, db_name, prj_name, scen_name,
-                                  query_path, query_file)
+    prj <- rfasst::fill_queries(prj, db_path, db_name, prj_name, scenarios,
+                                query_path, queries = 'queries_rfasst_nonCO2.xml')
 
     # Save the project
-    rgcam::saveProject(prj, file = file.path('output',prj_name))")
+    rgcam::saveProject(prj, file = prj_name)")
   })
 
 

tests/testthat.R

@@ -0,0 +1,4 @@
+library(testthat)
+library(rfasstui)
+
+test_check("rfasstui")

tests/testthat/test-globals.R

@@ -0,0 +1,91 @@
+library(rfasst)
+
+
+context("globals")
+
+
+test_that("globals:  color SSP scale", {
+
+  globalSSPColorScales <- get_globalSSPColorScales()
+
+  testthat::expect_equal(globalSSPColorScales,
+                         c("GCAM_SSP1" = "#5DBFDE", "GCAM_SSP2" = "#5CB95C", "GCAM_SSP3" = "#FBAB33",
+                                       "GCAM_SSP4" ="#D7534E", "GCAM_SSP5" ="#9E49D1"))
+
+})
+
+test_that("globals:  color custom scale", {
+
+  globalCustomColorScales <- get_globalCustomColorScales()
+
+  testthat::expect_equal(globalCustomColorScales,
+                         c("#5DBFDE","#5CB95C","#FBAB33","#D7534E","#9E49D1"))
+
+})
+
+
+test_that("globals:  get example prj", {
+
+  globalExamplePrj <- get_example_prj()
+
+  testthat::expect_equal(globalExamplePrj,
+                         get(load(file.path(rprojroot::find_root(rprojroot::is_testthat),"test_results","globalExamplePrj.RData"))))
+
+})
+
+test_that("globals:  get queries", {
+
+  globalQueries <- get_queries()
+
+  testthat::expect_equal(globalQueries,
+                         get(load(file.path(rprojroot::find_root(rprojroot::is_testthat),"test_results","globalQueries.RData"))))
+
+})
+
+
+test_that("globals:  global capabilities", {
+
+  globalCapabilities <- get_globalCapabilities()
+
+  expect_equal(globalCapabilities[['emissions_bc']][1], 'emissions_bc')
+  expect_equal(attributes(globalCapabilities[['emissions_bc']])$longName, 'BC emissions')
+
+  expect_equal(globalCapabilities[['emissions_nh3']][1], 'emissions_nh3')
+  expect_equal(attributes(globalCapabilities[['emissions_nh3']])$longName, 'NH3 emissions')
+
+  expect_equal(globalCapabilities[['emissions_nmvoc']][1], 'emissions_nmvoc')
+  expect_equal(attributes(globalCapabilities[['emissions_nmvoc']])$longName, 'NMVOC emissions')
+
+  expect_equal(globalCapabilities[['emissions_nox']][1], 'emissions_nox')
+  expect_equal(attributes(globalCapabilities[['emissions_nox']])$longName, 'NOx emissions')
+
+  expect_equal(globalCapabilities[['emissions_pom']][1], 'emissions_pom')
+  expect_equal(attributes(globalCapabilities[['emissions_pom']])$longName, 'POM emissions')
+
+  expect_equal(globalCapabilities[['emissions_so2']][1], 'emissions_so2')
+  expect_equal(attributes(globalCapabilities[['emissions_so2']])$longName, 'SO2 emissions')
+
+  expect_equal(globalCapabilities[['concentration_pm25']][1], 'concentration_pm25')
+  expect_equal(attributes(globalCapabilities[['concentration_pm25']])$longName, 'PM25 concentration')
+
+  expect_equal(globalCapabilities[['concentration_o3']][1], 'concentration_o3')
+  expect_equal(attributes(globalCapabilities[['concentration_o3']])$longName, 'O3 concentration')
+
+  expect_equal(globalCapabilities[['health_deaths_pm25']][1], 'health_deaths_pm25')
+  expect_equal(attributes(globalCapabilities[['health_deaths_pm25']])$longName, 'Premature deaths due to PM25')
+
+  expect_equal(globalCapabilities[['health_deaths_o3']][1], 'health_deaths_o3')
+  expect_equal(attributes(globalCapabilities[['health_deaths_o3']])$longName, 'Premature deaths due to O3')
+
+  expect_equal(globalCapabilities[['health_deaths_total']][1], 'health_deaths_total')
+  expect_equal(attributes(globalCapabilities[['health_deaths_total']])$longName, 'Total premature deaths')
+
+  expect_equal(globalCapabilities[['agriculture_ryl_mi']][1], 'agriculture_ryl_mi')
+  expect_equal(attributes(globalCapabilities[['agriculture_ryl_mi']])$longName, 'Agriculture relative yield loss')
+
+  expect_equal(globalCapabilities[['agriculture_prod_loss']][1], 'agriculture_prod_loss')
+  expect_equal(attributes(globalCapabilities[['agriculture_prod_loss']])$longName, 'Agriculture production loss')
+
+  expect_equal(globalCapabilities[['agriculture_rev_loss']][1], 'agriculture_rev_loss')
+  expect_equal(attributes(globalCapabilities[['agriculture_rev_loss']])$longName, 'Agriculture revenue loss')
+})