Update workflows admb docker

.github/workflows/build-ss3-warnings.yml

@@ -26,7 +26,7 @@ jobs:
       RSPM: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"
 
     steps:
-      - name: Checkout ss repo
+      - name: Checkout ss3 repo
         uses: actions/checkout@v3
 
       - name: Update Ubuntu packages
@@ -35,45 +35,50 @@ jobs:
       - name: setup R
         uses: r-lib/actions/setup-r@v2
 
-      - name: Get admb and put in path, linux
-        run: |
-          wget https://github.com/admb-project/admb/releases/download/admb-13.1/admb-13.1-linux.zip
-          sudo unzip admb-13.1-linux.zip -d /usr/local/bin
-          sudo chmod 755 /usr/local/bin/admb-13.1/bin/admb
-          echo "/usr/local/bin/admb-13.1/bin" >> $GITHUB_PATH
+      # - name: Get admb and put in path, linux
+        # run: |
+        #   wget https://github.com/admb-project/admb/releases/download/admb-13.1/admb-13.1-linux.zip
+        #   sudo unzip admb-13.1-linux.zip -d /usr/local/bin
+        #   sudo chmod 755 /usr/local/bin/admb-13.1/bin/admb
+        #   echo "/usr/local/bin/admb-13.1/bin" >> $GITHUB_PATH
 
-      - name: Build stock synthesis with warnings displayed in console
+      - name: Build stock synthesis with warnings displayed in console using admb docker image
         run: |
           rm -rf SS330
           rm -rf ss_osx.tar
           mkdir SS330
-          /bin/bash ./Make_SS_330_new.sh -a /usr/local/bin/admb-13.1 -b SS330 -w
+          chmod 777 SS330
+          /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330 -w
 
       - name: Build stock synthesis with warnings again to save to file
         run: |
           rm -rf SS330
           rm -rf ss_osx.tar
           mkdir SS330
-          /bin/bash ./Make_SS_330_new.sh -a /usr/local/bin/admb-13.1 -b SS330 -w &> warnings.txt
+          chmod 777 SS330
+          /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330 -w &> warnings.txt
 
       # Runs a set of commands using the runners shell
       - name: Use R to parse warnings output
         run: |
           txt <- readLines("warnings.txt", encoding = "UTF-8" )
-          warn_line <- grep(pattern = "compiling a second time to get warnings", x = txt, fixed = TRUE)
-          txt <- txt[(warn_line+1):length(txt)]
-          rm_warn_start_lines <- grep(pattern = "/usr/local/bin/admb-13.1", x = txt, fixed = TRUE)
+          warn_line <- grep(pattern = "g++ -c -std=c++17 -O3 -Wall -Wextra -D_USE_MATH_DEFINES -DUSE_ADMB_CONTRIBS", x = txt, fixed = TRUE)
+          end_warn_line <- grep(pattern = "*** Linking: ss.obj ", x = txt, fixed = TRUE)
+          txt <- txt[(warn_line+2):(end_warn_line-1)]
+          rm_warn_start_lines <- grep(pattern = "/usr/local/admb/include/admodel.h", x = txt, fixed = TRUE)
           all_warning_end_lines <- grep(pattern = "^", x = txt, fixed = TRUE)
           to_rm <- NULL
           for (l in rm_warn_start_lines) {
             tmp_end_line <- min(all_warning_end_lines[all_warning_end_lines > l])
             to_rm <- c(to_rm, l:tmp_end_line)
           }
           txt <- txt[-to_rm]
-          n_errors <- length(grep(pattern = "^", x = txt, fixed = TRUE))
+          n_errors <- length(grep(pattern = "^", x = txt))
           message("There are ", n_errors, " warning messages related to SS.")
           write.table(n_errors, "n_warn.txt")
           writeLines(txt, "warnings_ss.txt")
+        # warn_line <- grep(pattern = "compiling a second time to get warnings", x = txt, fixed = TRUE)
+        # txt <- txt[(warn_line+1):length(txt)]
         shell: Rscript {0}
 
       - name:  Print warnings
@@ -102,4 +107,4 @@ jobs:
         uses: actions/upload-artifact@main
         with:
           name: 'warnings_ss.txt'
-          path: warnings_ss.txt
+          path: warnings_ss.txt

.github/workflows/build-ss3.yml

@@ -34,69 +34,49 @@ jobs:
         if: matrix.config.os == 'ubuntu-latest'
         run: sudo apt-get update
 
-      - name: Build stock synthesis for linux with p flag and docker
-        if:  matrix.config.os == 'ubuntu-latest'
-        run: |
-          rm -rf SS330
-          rm -rf ss_osx.tar
-          mkdir SS330
-          chmod 777 SS330
-          /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330 -p
-          /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330 -o -p
-
-      - name: Build stock synthesis for mac with docker
-        if: matrix.config.os == 'macos-latest'
-        run: |
-          brew install docker
-          colima start
-          docker pull johnoel/admb:linux
-
-          rm -rf SS330
-          rm -rf ss_osx.tar
-          mkdir SS330
-          chmod 777 SS330
-          /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330
-          /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330 -o
-
-          colima stop
-
-      - name: checkout admb, mac
-        if: matrix.config.os == 'macos-latest'
-        uses: actions/checkout@v3
-        with:
-          repository: admb-project/admb
-          path: admb
-          ref: admb-13.1
-      - name: clean, mac
-        if: matrix.config.os == 'macos-latest'
-        run: cd admb && make clean
-      - name: see where admb is, mac
-        if: matrix.config.os == 'macos-latest'
-        run: |
-          ls
-          cd admb && ls
-      - name: compile admb, mac
-        if: matrix.config.os == 'macos-latest'
-        run: |
-          cd admb && make 
-      - name: see where admb is, mac
-        if: matrix.config.os == 'macos-latest'
-        run: |
-          cd admb && ls -l
-      - name: put admb in path, mac
-        if: matrix.config.os == 'macos-latest'
-        run: |
-          sudo mv admb /usr/local/bin
-          sudo chmod 755 /usr/local/bin/admb
-          echo "/usr/local/bin/admb" >> $GITHUB_PATH
+      # - name: Get admb and put in path, windows
+      #   if: matrix.config.os == 'windows-latest'
+      #   run: |
+      #     Invoke-WebRequest -Uri https://github.com/admb-project/admb/releases/download/admb-13.1/admb-13.1b-windows.zip -OutFile "D:\a\ss3-source-code\ss3-source-code\admb-13.1.zip"
+      #     Expand-Archive -LiteralPath "D:\a\ss3-source-code\ss3-source-code\admb-13.1.zip" -DestinationPath "D:\a\ss3-source-code\ss3-source-code\"
+      #     echo "D:\a\ss3-source-code\ss3-source-code\admb-13.1\bin" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
+      # - name: checkout admb, mac
+      #   if: matrix.config.os == 'macos-latest'
+      #   uses: actions/checkout@v3
+      #   with:
+      #     repository: admb-project/admb
+      #     path: admb
+      #     ref: admb-13.1
+      # - name: clean, mac
+      #   if: matrix.config.os == 'macos-latest'
+      #   run: cd admb && make clean
+      # - name: see where admb is, mac
+      #   if: matrix.config.os == 'macos-latest'
+      #   run: |
+      #     ls
+      #     cd admb && ls
+      # - name: compile admb, mac
+      #   if: matrix.config.os == 'macos-latest'
+      #   run: |
+      #     cd admb && make 
+      # - name: see where admb is, mac
+      #   if: matrix.config.os == 'macos-latest'
+      #   run: |
+      #     cd admb && ls -l
+      # - name: put admb in path, mac
+      #   if: matrix.config.os == 'macos-latest'
+      #   run: |
+      #     sudo mv admb /usr/local/bin
+      #     sudo chmod 755 /usr/local/bin/admb
+      #     echo "/usr/local/bin/admb" >> $GITHUB_PATH
 
-      - name: Get admb and put in path, linux
-        if: matrix.config.os == 'ubuntu-latest'
-        run: |
-          wget https://github.com/admb-project/admb/releases/download/admb-13.1/admb-13.1-linux.zip
-          sudo unzip admb-13.1-linux.zip -d /usr/local/bin
-          sudo chmod 755 /usr/local/bin/admb-13.1/bin/admb
-          echo "/usr/local/bin/admb-13.1/bin" >> $GITHUB_PATH
+      # - name: Get admb and put in path, linux
+      #   if: matrix.config.os == 'ubuntu-latest'
+      #   run: |
+      #     wget https://github.com/admb-project/admb/releases/download/admb-13.1/admb-13.1-linux.zip
+      #     sudo unzip admb-13.1-linux.zip -d /usr/local/bin
+      #     sudo chmod 755 /usr/local/bin/admb-13.1/bin/admb
+      #     echo "/usr/local/bin/admb-13.1/bin" >> $GITHUB_PATH
 
       - name: Set up R
         uses: r-lib/actions/setup-r@v2
@@ -214,28 +194,7 @@ jobs:
           writeLines(ver_info, "SS_versioninfo_330opt.tpl")
         shell: Rscript {0}
 
-      - name: Build stock synthesis for windows with docker
-        if: matrix.config.os == 'windows-latest'
-        run: |
-          pushd Compile
-          ./Make_SS_safe.bat
-          ./Make_SS_fast.bat
-          popd
-
-      - name: Get admb and put in path, windows
-        if: matrix.config.os == 'windows-latest'
-        run: |
-          Invoke-WebRequest -Uri https://github.com/admb-project/admb/releases/download/admb-13.1/admb-13.1b-windows.zip -OutFile "D:\a\ss3-source-code\ss3-source-code\admb-13.1.zip"
-          Expand-Archive -LiteralPath "D:\a\ss3-source-code\ss3-source-code\admb-13.1.zip" -DestinationPath "D:\a\ss3-source-code\ss3-source-code\"
-          echo "D:\a\ss3-source-code\ss3-source-code\admb-13.1\bin" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
-
-      - name: get info on gcc version and path
-        if: matrix.config.os == 'windows-latest'
-        run: |
-          g++ -v
-          echo $env:GITHUB_PATH
-
-      - name: Build stock synthesis for windows
+      - name: Build stock synthesis for windows with admb docker image
         if: matrix.config.os == 'windows-latest'
         run: |
           cd Compile
@@ -252,26 +211,22 @@ jobs:
           mv Compile/ss_opt.exe SS330/
           mv SS330/ss.exe SS330/ss3_win.exe
           mv SS330/ss_opt.exe SS330/ss3_opt_win.exe
-
-      - name: Build stock synthesis for mac
+  
+      - name: Build stock synthesis for mac with admb docker image
         if: matrix.config.os == 'macos-latest'
         run: |
+          brew install docker
+          colima start
+          docker pull johnoel/admb:linux
+
           rm -rf SS330
           rm -rf ss_osx.tar
           mkdir SS330
           chmod 777 SS330
-          /bin/bash ./Make_SS_330_new.sh -b SS330
-          /bin/bash ./Make_SS_330_new.sh -b SS330 -o
-
-      - name: Build stock synthesis for linux with p flag
-        if:  matrix.config.os == 'ubuntu-latest'
-        run: |
-          rm -rf SS330
-          rm -rf ss_osx.tar
-          mkdir SS330
-          chmod 777 SS330
-          /bin/bash ./Make_SS_330_new.sh -b SS330 -p
-          /bin/bash ./Make_SS_330_new.sh -b SS330 -o -p
+          /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330
+          /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330 -o
+
+          colima stop
 
       - name: Verify binary on mac
         if: matrix.config.os == 'macos-latest'
@@ -286,7 +241,17 @@ jobs:
           rm *.obj *.htp *.cpp ss_opt.tpl
           mv ss ss3_osx
           mv ss_opt ss3_opt_osx
-
+
+      - name: Build stock synthesis for linux with p flag and admb docker image
+        if:  matrix.config.os == 'ubuntu-latest'
+        run: |
+          rm -rf SS330
+          rm -rf ss_osx.tar
+          mkdir SS330
+          chmod 777 SS330
+          /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330 -p
+          /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330 -o -p   
+
       - name: Verify binary on linux
         if: matrix.config.os == 'ubuntu-latest'
         run: |

.github/workflows/reference_files/warnings_ss_ref.txt

@@ -1,2 +1,8 @@
 In file included from ss.cpp:7:
-In file included from ss.cpp:7:
+ss.cpp: In member function 'void model_parameters::evaluate_the_objective_function()':
+ss.cpp:27544:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
+27544 |         for (i = 1; i <= Svy_N_fleet(f); i++)
+      |         ^~~
+ss.cpp:27571:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
+27571 |           surv_like(f) = sum(Svy_like_I(f));
+      |           ^~~~~~~~~

.github/workflows/run-ss3-bootstrap.yml

@@ -42,26 +42,34 @@ jobs:
       - name: setup R
         uses: r-lib/actions/setup-r@v2
 
-      - name: Get admb and put in path, linux
-        run: |
-          wget https://github.com/admb-project/admb/releases/download/admb-13.1/admb-13.1-linux.zip
-          sudo unzip admb-13.1-linux.zip -d /usr/local/bin
-          sudo chmod 755 /usr/local/bin/admb-13.1/bin/admb
-          echo "/usr/local/bin/admb-13.1/bin" >> $GITHUB_PATH
-
-      - name: Build stock synthesis
+      # - name: Get admb and put in path, linux
+      #   run: |
+      #     wget https://github.com/admb-project/admb/releases/download/admb-13.1/admb-13.1-linux.zip
+      #     sudo unzip admb-13.1-linux.zip -d /usr/local/bin
+      #     sudo chmod 755 /usr/local/bin/admb-13.1/bin/admb
+      #     echo "/usr/local/bin/admb-13.1/bin" >> $GITHUB_PATH
+
+      # - name: Build stock synthesis
+      #   run: |
+      #     rm -rf SS330
+      #     mkdir SS330
+      #     /bin/bash ./Make_SS_330_new.sh -b SS330
+
+      - name: Build stock synthesis with admb docker image
         run: |
           rm -rf SS330
+          rm -rf ss_osx.tar
           mkdir SS330
-          /bin/bash ./Make_SS_330_new.sh -b SS330
+          chmod 777 SS330
+          /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330
 
       - name: move exes, scripts to needed locations
         run: |
           mv test-models-repo/models test-models-repo/model_runs
           mv SS330/ss test-models-repo/model_runs/Simple_with_DM_sizefreq/ss3
 
       - name: change permissions on ss3 exes
-        run: chmod a+x test-models-repo/model_runs/Simple_with_DM_sizefreq/ss3
+        run: sudo chmod a+x test-models-repo/model_runs/Simple_with_DM_sizefreq/ss3
 
       - name: download R packages
         run: Rscript -e 'install.packages(c("remotes", "purrr", "arsenal", "utils"))'

.github/workflows/run-ss3-mcmc.yml

@@ -40,18 +40,26 @@ jobs:
       - name: setup R
         uses: r-lib/actions/setup-r@v2
 
-      - name: Get admb and put in path, linux
-        run: |
-          wget https://github.com/admb-project/admb/releases/download/admb-13.1/admb-13.1-linux.zip
-          sudo unzip admb-13.1-linux.zip -d /usr/local/bin
-          sudo chmod 755 /usr/local/bin/admb-13.1/bin/admb
-          echo "/usr/local/bin/admb-13.1/bin" >> $GITHUB_PATH
+      # - name: Get admb and put in path, linux
+      #   run: |
+      #     wget https://github.com/admb-project/admb/releases/download/admb-13.1/admb-13.1-linux.zip
+      #     sudo unzip admb-13.1-linux.zip -d /usr/local/bin
+      #     sudo chmod 755 /usr/local/bin/admb-13.1/bin/admb
+      #     echo "/usr/local/bin/admb-13.1/bin" >> $GITHUB_PATH
+
+      # - name: Build stock synthesis
+      #   run: |
+      #     rm -rf SS330
+      #     mkdir SS330
+      #     /bin/bash ./Make_SS_330_new.sh -b SS330
 
-      - name: Build stock synthesis
+      - name: Build stock synthesis with admb docker image
         run: |
           rm -rf SS330
+          rm -rf ss_osx.tar
           mkdir SS330
-          /bin/bash ./Make_SS_330_new.sh -b SS330
+          chmod 777 SS330
+          /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330
 
       - name: move exes, scripts to needed locations
         run: |
@@ -63,7 +71,7 @@ jobs:
           ls
 
       - name: change permissions on ss exe
-        run: chmod a+x ss3
+        run: sudo chmod a+x ss3
 
       - name: run models without estimation
         run: |