From edfe5db411b2bf903c729c2d436c2c4972560424 Mon Sep 17 00:00:00 2001
From: MOshima-PIFSC <megumi.oshima@noaa.gov>
Date: Fri, 2 Feb 2024 13:24:48 -1000
Subject: [PATCH] remove download ss from R-CMD-check.yml and download in
 testthat.R

---
 .github/workflows/R-CMD-check.yaml | 38 ------------------------------
 tests/testthat.R                   |  4 ++--
 tests/testthat/SSmase_test.R       | 31 ------------------------
 tests/testthat/test-HCxval.R       |  3 ---
 4 files changed, 2 insertions(+), 74 deletions(-)
 delete mode 100644 tests/testthat/SSmase_test.R

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 7b9e768..55a2379 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.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
-
 
     
 
diff --git a/tests/testthat.R b/tests/testthat.R
index 54013a7..905f637 100644
--- a/tests/testthat.R
+++ b/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(
diff --git a/tests/testthat/SSmase_test.R b/tests/testthat/SSmase_test.R
deleted file mode 100644
index 893b116..0000000
--- a/tests/testthat/SSmase_test.R
+++ /dev/null
@@ -1,31 +0,0 @@
-## File is deprecated by MOshima 6/12/23
-
-# library(ss3diags)
-# Tests
-# sma = r4ss::SSsummarize(retro.sma)
-# Check joint MASE for indices
-# SSmase(retro.sma)
-# select indices
-# SSmase(retro.sma, indexselect = c(4))
-# check for length comps
-# smaL = ss3diags::SSretroComps(retro.sma)
-# SSmase(retro.sma, quants = "len", indexselect = 2:4)
-
-# check manually
-# mase <- SSmase(retro.sma, residuals = T)
-# Joint mase from index 1, 3,4
-# mae <- apply(
-#  mase$Residuals[c("Pred.Res", "Naive.Res")], 2,
-#  function(x) mean(abs(x))
-# )
-# MASE
-# mae[1] / mae[2]
-# compare
-# SSmase(retro.sma)
-
-# Check hake
-# phk= r4ss::SSsummarize(retro.phk)
-# SSmase(retro.phk, verbose = T, indexselect = 1)
-# check for age comps
-# phkA <- ss3diags::SSretroComps(retro.phk)
-# SSmase(retro.phk, quants = "age")
diff --git a/tests/testthat/test-HCxval.R b/tests/testthat/test-HCxval.R
index d86dc18..c983af2 100644
--- a/tests/testthat/test-HCxval.R
+++ b/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)