Merge pull request #98 from PIFSCstockassessments/97-bug-tests-are-fa…

…iling

remove download ss from R-CMD-check.yml and download in testthat.R

.github/workflows/R-CMD-check.yaml

@@ -28,35 +28,6 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
-
-      - name: Get the latest SS3 executable for linux and move to expected location
-        if: matrix.config.os == 'ubuntu-latest'
-        run: |
-          curl https://api.github.com/repos/nmfs-stock-synthesis/stock-synthesis/releases/latest | grep "browser_download_url" | grep -Eo 'https://[^\"]*' | grep "ss_linux" | xargs wget
-          mv ss_linux ss
-          sudo chmod a+x ss
-          cp ss inst/extdata/ss
-          rm ss
-
-      - name: Get the latest SS3 executable for windows and move to expected location
-        if: matrix.config.os == 'windows-latest' 
-        run:  |
-          Invoke-WebRequest -Uri https://github.com/nmfs-stock-synthesis/stock-synthesis/releases/download/v3.30.21/ss_win.exe -Outfile "D:\a\ss3diags\ss3diags\ss_win.exe"
-          mv ss_win.exe ss.exe
-          cp ss.exe inst/extdata/ss.exe
-
-      - uses: nick-fields/retry@v2
-        if: matrix.config.os == 'macOS-latest' 
-        with:
-          timeout_minutes: 3
-          max_attempts: 3
-          retry_on: error
-          command:  |
-            curl https://api.github.com/repos/nmfs-stock-synthesis/stock-synthesis/releases/latest | grep "browser_download_url" | grep -Eo 'https://[^\"]*' | grep "ss_osx" | xargs wget
-            mv ss_osx ss
-            sudo chmod a+x ss
-            cp ss inst/extdata/ss
-            rm ss
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -76,15 +47,6 @@ jobs:
         with: 
           error-on: '"error"'
 
-      - name: remove ss executable
-        run: |
-          if ["$RUNNER_OS" == "Linux" ]; then
-            rm inst/extdata/ss.exe
-          else 
-            rm inst/extdata/ss
-          fi
-        shell: bash
-
 
 
 

DESCRIPTION

@@ -39,4 +39,4 @@ Encoding: UTF-8
 LazyData: True
 LazyDataCompression: gzip
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1

tests/testthat.R

@@ -7,9 +7,9 @@ files_path <- system.file("extdata", package = "ss3diags")
 run_tmp <- file.path(tempdir(check = TRUE), "test-runs")
 dir.create(run_tmp, showWarnings = FALSE)
 file.copy(from = list.files(files_path, full.names = TRUE), to = run_tmp)
-
+r4ss::get_ss3_exe(dir = run_tmp, version = "v3.30.21")
 ## Run retrospectives
-if (file.exists(file.path(files_path, "ss")) | file.exists(file.path(files_path, "ss.exe"))) {
+if (file.exists(file.path(run_tmp, "ss3")) | file.exists(file.path(run_tmp, "ss3.exe"))) {
   r4ss::retro(dir = run_tmp, oldsubdir = "", newsubdir = "retrospectives", years = 0:-3, show_in_console = FALSE)
   # Creating retrospective object here so that multiple test files can access it without having to re-run retrospective for each test
   retroModels <- r4ss::SSgetoutput(

tests/testthat/test-HCxval.R

@@ -1,8 +1,5 @@
 ## Test script for hindcast cross validation and MASE
 
-# retroSimple <- ss3diags::retroSimple
-# retrosum.simple <- r4ss::SSsummarize(retroSimple)
-
 path <- file.path(tempdir(), "test_runs")
 dir.create(path, showWarnings = FALSE)