Update makefile

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

@@ -45,37 +45,33 @@ jobs:
       - name: Build stock synthesis with warnings displayed in console using admb docker image
         run: |
           rm -rf SS330
-          rm -rf ss_osx.tar
+          rm -rf ss3_osx.tar
           mkdir SS330
           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
+          rm -rf ss3_osx.tar
           mkdir SS330
           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" )
+          txt <- readLines("warnings.txt", encoding = "UTF-8")
           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))
-          message("There are ", n_errors, " warning messages related to SS.")
-          write.table(n_errors, "n_warn.txt")
+          end_warn_line <- grep(pattern = "*** Linking: ss3.obj ", x = txt, fixed = TRUE)
+          if (length(warn_line) == 1 & length(end_warn_line) == 1) {
+            txt <- txt[(warn_line+3):(end_warn_line-1)]
+            rm_warn_start_lines <- grep(pattern = "/usr/local/admb/include/admodel.h: ", x = txt, fixed = TRUE, invert = TRUE)
+            txt <- txt[rm_warn_start_lines]
+            n_errors <- length(grep(pattern = "^ [0-9]", x = txt))
+            message("There are ", n_errors, " warning messages related to SS3.")
+            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)]

.github/workflows/build-ss3.yml

@@ -207,10 +207,10 @@ jobs:
         run: |
           mkdir SS330
           chmod 777 SS330
-          mv Compile/ss.exe SS330/
-          mv Compile/ss_opt.exe SS330/
-          mv SS330/ss.exe SS330/ss3_win.exe
-          mv SS330/ss_opt.exe SS330/ss3_opt_win.exe
+          mv Compile/ss3.exe SS330/
+          mv Compile/ss3_opt.exe SS330/
+          mv SS330/ss3.exe SS330/ss3_win.exe
+          mv SS330/ss3_opt.exe SS330/ss3_opt_win.exe
 
       - name: Build stock synthesis for mac with admb docker image
         if: matrix.config.os == 'macos-latest'
@@ -220,7 +220,7 @@ jobs:
           docker pull johnoel/admb:linux
 
           rm -rf SS330
-          rm -rf ss_osx.tar
+          rm -rf ss3_osx.tar
           mkdir SS330
           chmod 777 SS330
           /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330
@@ -231,22 +231,22 @@ jobs:
       - name: Verify binary on mac
         if: matrix.config.os == 'macos-latest'
         run: |
-          shasum -a 256 SS330/ss
-          shasum -a 256 SS330/ss_opt
+          shasum -a 256 SS330/ss3
+          shasum -a 256 SS330/ss3_opt
 
       - name: Delete unneeded files and change exe names on mac
         if: matrix.config.os == 'macos-latest'
         run: |
           cd SS330
-          rm *.obj *.htp *.cpp ss_opt.tpl
-          mv ss ss3_osx
-          mv ss_opt ss3_opt_osx
+          rm *.obj *.htp *.cpp ss3_opt.tpl
+          mv ss3 ss3_osx
+          mv ss3_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
+          rm -rf ss3_osx.tar
           mkdir SS330
           chmod 777 SS330
           /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330 -p
@@ -255,16 +255,16 @@ jobs:
       - name: Verify binary on linux
         if: matrix.config.os == 'ubuntu-latest'
         run: |
-          sha256sum SS330/ss
-          sha256sum SS330/ss_opt
+          sha256sum SS330/ss3
+          sha256sum SS330/ss3_opt
 
       - name: Delete unneeded files and change exe names on linux
         if: matrix.config.os == 'ubuntu-latest'
         run: |
           cd SS330
-          rm *.obj *.htp *.cpp ss_opt.tpl ss.tpl
-          mv ss ss3_linux
-          mv ss_opt ss3_opt_linux
+          rm *.obj *.htp *.cpp ss3_opt.tpl ss3.tpl
+          mv ss3 ss3_linux
+          mv ss3_opt ss3_opt_linux
 
       - name: Archive binaries
         if: success()

.github/workflows/reference_files/warnings_ss_ref.txt

@@ -1,8 +1,12 @@
-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));
-      |           ^~~~~~~~~
+/usr/local/admb/include/admodel.h:1915:38: warning: unused parameter 'gradients' [-Wunused-parameter]
+ 1915 |   virtual void report(const dvector& gradients){;};
+      |                       ~~~~~~~~~~~~~~~^~~~~~~~~
+/usr/local/admb/include/admodel.h:2501:43: warning: unused parameter 'ofs' [-Wunused-parameter]
+ 2501 |   virtual void save_value(const ofstream& ofs, int prec,const dvector&,
+      |                           ~~~~~~~~~~~~~~~~^~~
+/usr/local/admb/include/admodel.h:2501:52: warning: unused parameter 'prec' [-Wunused-parameter]
+ 2501 |   virtual void save_value(const ofstream& ofs, int prec,const dvector&,
+      |                                                ~~~~^~~~
+/usr/local/admb/include/admodel.h:2502:10: warning: unused parameter 'offset' [-Wunused-parameter]
+ 2502 |     int& offset){}
+      |     ~~~~~^~~~~~

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

@@ -58,15 +58,15 @@ jobs:
       - name: Build stock synthesis with admb docker image
         run: |
           rm -rf SS330
-          rm -rf ss_osx.tar
+          rm -rf ss3_osx.tar
           mkdir 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
+          mv SS330/ss3 test-models-repo/model_runs/Simple_with_DM_sizefreq/ss3
 
       - name: change permissions on ss3 exes
         run: sudo chmod a+x test-models-repo/model_runs/Simple_with_DM_sizefreq/ss3

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

@@ -56,7 +56,7 @@ jobs:
       - name: Build stock synthesis with admb docker image
         run: |
           rm -rf SS330
-          rm -rf ss_osx.tar
+          rm -rf ss3_osx.tar
           mkdir SS330
           chmod 777 SS330
           /bin/bash ./Make_SS_330_new.sh --admb docker -b SS330
@@ -67,7 +67,7 @@ jobs:
           mv test-models-repo/models/Simple/forecast.ss forecast.ss
           mv test-models-repo/models/Simple/control.ss control.ss
           mv test-models-repo/models/Simple/data.ss data.ss
-          mv SS330/ss ss3
+          mv SS330/ss3 ss3
           ls
 
       - name: change permissions on ss exe

.github/workflows/run-ss3-no-est.yml

@@ -62,15 +62,15 @@ jobs:
       - name: Build stock synthesis with admb docker image
         run: |
           rm -rf SS330
-          rm -rf ss_osx.tar
+          rm -rf ss3_osx.tar
           mkdir 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/ss3
+          mv SS330/ss3 test-models-repo/model_runs/ss3
           mv test-models-repo/.github/r_scripts/run_from_par.R test-models-repo/run_from_par.R
           mv test-models-repo/.github/r_scripts/run_compare_noest.R test-models-repo/run_compare_noest.R
 

.github/workflows/run-ss3-with-est.yml

@@ -52,15 +52,15 @@ jobs:
       - name: Build stock synthesis with admb docker image
         run: |
           rm -rf SS330
-          rm -rf ss_osx.tar
+          rm -rf ss3_osx.tar
           mkdir 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/ss3
+          mv SS330/ss3 test-models-repo/model_runs/ss3
 
       - name: change permissions on ss3 exes
         run: sudo chmod a+x test-models-repo/model_runs/ss3

.github/workflows/test-r4ss-with-ss3.yml

@@ -64,15 +64,15 @@ jobs:
       - name: Build stock synthesis with admb docker image
         run: |
           rm -rf SS330
-          rm -rf ss_osx.tar
+          rm -rf ss3_osx.tar
           mkdir 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/ss3
+          mv SS330/ss3 test-models-repo/model_runs/ss3
           mv test-models-repo/.github/r_scripts/run_from_par.R test-models-repo/run_from_par.R
           mv test-models-repo/.github/r_scripts/run_compare_noest.R test-models-repo/run_compare_noest.R
 

.gitignore

@@ -8,12 +8,14 @@
 *.obj
 *.log
 ss.tpl
+ss3.tpl
 ss_opt.tpl
 ss_trans.tpl
 ~$*.*
 Compile/ss.log
+Compile/ss3.log
 .Rproj.user
 *.Rproj
 .Rhistory
-Compile/ssFileLabels.txt
-StockSynthesis.code-workspace
+Compile/ssFileLabels.txt
+StockSynthesis.code-workspace

.vscode/settings.json

@@ -0,0 +1,6 @@
+{
+    "files.associations": {
+        "*.tpl": "c",
+        "*.htp": "c"
+    }
+}

CONTRIBUTING.md

@@ -27,7 +27,7 @@ All code contributions should be submitted as pull requests to be reviewed by an
 3. Add ADMB to the PATH or use the ADMB command window for the following commands.
 4. On Linux or Mac:
     - Change directory to the cloned Stock Synthesis repository and use the script [Make_SS_330_new.sh](https://github.com/nmfs-ost/ss3-source-code/blob/main/Make_SS_330_new.sh) by calling `./Make_SS_330_new.sh`. To see all options for the function, use `./Make_SS_330_new.sh --help`.
-    - Follow the instructions found in the [GNUmakefile](https://github.com/nmfs-ost/ss3-source-code/blob/main/GNUmakefile) which will allow you to compile Stock Synthesis using the command `~/stock-synthesis$ make` within a command line opened in the cloned Stock Synthesis repository folder.
+    - Follow the instructions found in the [GNUmakefile](https://github.com/nmfs-ost/ss3-source-code/blob/main/GNUmakefile) which will allow you to compile Stock Synthesis using the command `~/ss3-source-code$ make` within a command line opened in the cloned Stock Synthesis repository folder.
 6. On Windows: Change directory to the cloned Stock Synthesis repository's [Compile](https://github.com/nmfs-ost/ss3-source-code/tree/main/Compile) subfolder and call the [Make_SS_safe batch script](https://github.com/nmfs-ost/ss3-source-code/blob/main/Compile/Make_SS_safe.bat) to build the "safe" version of Stock Synthesis. (to build the fast (aka optimized) version of Stock Synthesis, call the Make_SS_fast.bat batch scripts instead). Upon calling the batch script, SS3 will be built in the Compile subfolder.
 
 # Still have a question on the contributing workflow?

Compile/Make_SS_fast.bat

@@ -12,16 +12,16 @@ del SS_functions.temp
 @REM create SS_functions.temp file combining various functions
 copy/b SS_biofxn.tpl+SS_miscfxn.tpl+SS_selex.tpl+SS_popdyn.tpl+SS_recruit.tpl+SS_benchfore.tpl+SS_expval.tpl+SS_objfunc.tpl+SS_write.tpl+SS_write_ssnew.tpl+SS_write_report.tpl+SS_ALK.tpl+SS_timevaryparm.tpl+SS_tagrecap.tpl SS_functions.temp
 
-@REM combine remaining files to create ss.tpl
-copy/b SS_versioninfo_330opt.tpl+SS_readstarter.tpl+SS_readdata_330.tpl+SS_readcontrol_330.tpl+SS_param.tpl+SS_prelim.tpl+SS_global.tpl+SS_proced.tpl+SS_functions.temp "Compile\ss_opt.tpl"
+@REM combine remaining files to create ss3_opt.tpl
+copy/b SS_versioninfo_330opt.tpl+SS_readstarter.tpl+SS_readdata_330.tpl+SS_readcontrol_330.tpl+SS_param.tpl+SS_prelim.tpl+SS_global.tpl+SS_proced.tpl+SS_functions.temp "Compile\ss3_opt.tpl"
 
 cd Compile
 
 if defined ADMB_HOME (
   if exist "%ADMB_HOME%\\admb.cmd" (
     @echo "-- Building ss_opt.exe with %ADMB_HOME%\admb.cmd in '%CD%' --"
     set CXX=g++
-    %ADMB_HOME%\\admb.cmd -f ss_opt
+    %ADMB_HOME%\\admb.cmd -f ss3_opt
     goto CHECK
   )
 )
@@ -30,7 +30,7 @@ if defined ADMB_HOME (
 for /f "tokens=*" %%i in ('where admb.cmd 2^>^&1 ^| findstr "admb.cmd"') do (
   @echo "-- Building ss_opt.exe with admb.cmd in '%CD%' --"
   set CXX=g++
-  admb -f ss_opt.tpl
+  admb -f ss3_opt.tpl
   goto CHECK
 )
 
@@ -41,15 +41,15 @@ for /f "tokens=*" %%i in ('where docker.exe 2^>^&1 ^| findstr "docker.exe"') do
     set "ISWINDOWS10=found"
   )
   if defined ISWINDOWS10 (
-    docker run --rm --mount source=%CD%,destination=C:\compile,type=bind --workdir C:\\compile johnoel/admb:windows-ltsc2019-winlibs -f ss_opt.tpl
+    docker run --rm --mount source=%CD%,destination=C:\compile,type=bind --workdir C:\\compile johnoel/admb:windows-ltsc2019-winlibs -f ss3_opt.tpl
   ) else (
-    docker run --rm --mount source=%CD%,destination=C:\compile,type=bind --workdir C:\\compile johnoel/admb:windows-ltsc2022-winlibs -f ss_opt.tpl
+    docker run --rm --mount source=%CD%,destination=C:\compile,type=bind --workdir C:\\compile johnoel/admb:windows-ltsc2022-winlibs -f ss3_opt.tpl
   )
   goto CHECK
 )
 
 :CHECK
-if not exist ss_opt.exe (
-  @echo "Error: Unable to build ss_opt.exe"
+if not exist ss3_opt.exe (
+  @echo "Error: Unable to build ss3_opt.exe"
   exit /b 1
 )

Compile/Make_SS_safe.bat

@@ -11,46 +11,46 @@ del SS_functions.temp
 ::create SS_functions.temp file combining various functions
 copy/b SS_biofxn.tpl+SS_miscfxn.tpl+SS_selex.tpl+SS_popdyn.tpl+SS_recruit.tpl+SS_benchfore.tpl+SS_expval.tpl+SS_objfunc.tpl+SS_write.tpl+SS_write_ssnew.tpl+SS_write_report.tpl+SS_ALK.tpl+SS_timevaryparm.tpl+SS_tagrecap.tpl SS_functions.temp
 
-::combine remaining files to create ss.tpl
-copy/b SS_versioninfo_330safe.tpl+SS_readstarter.tpl+SS_readdata_330.tpl+SS_readcontrol_330.tpl+SS_param.tpl+SS_prelim.tpl+SS_global.tpl+SS_proced.tpl+SS_functions.temp "Compile\ss.tpl"
+::combine remaining files to create ss3.tpl
+copy/b SS_versioninfo_330safe.tpl+SS_readstarter.tpl+SS_readdata_330.tpl+SS_readcontrol_330.tpl+SS_param.tpl+SS_prelim.tpl+SS_global.tpl+SS_proced.tpl+SS_functions.temp "Compile\ss3.tpl"
 
 ::path=c:\admb;C:\rtools40\mingw64\bin;%path%
 
 cd Compile
 
 if defined ADMB_HOME (
   if exist "%ADMB_HOME%\\admb.cmd" (
-    @echo "-- Building ss.exe with %ADMB_HOME%\admb.cmd in '%CD%' --"
+    @echo "-- Building ss3.exe with %ADMB_HOME%\admb.cmd in '%CD%' --"
     set CXX=g++
-    %ADMB_HOME%\\admb.cmd ss
+    %ADMB_HOME%\\admb.cmd ss3
     goto CHECK
   )
 )
 
 @REM check if admb.cmd is in path
 for /f "tokens=*" %%i in ('where admb.cmd 2^>^&1 ^| findstr "admb.cmd"') do (
-  @echo "-- Building ss.exe with admb.cmd in '%CD%' --"
+  @echo "-- Building ss3.exe with admb.cmd in '%CD%' --"
   set CXX=g++
-  admb ss.tpl
+  admb ss3.tpl
   goto CHECK
 )
 
 @REM compile executable
 for /f "tokens=*" %%i in ('where docker.exe 2^>^&1 ^| findstr "docker.exe"') do (
-  @echo "-- Building ss.exe with docker in '%CD%' --"
+  @echo "-- Building ss3.exe with docker in '%CD%' --"
   for /f "tokens=*" %%j in ('ver ^| findstr "10.0.1"') do (
     set "ISWINDOWS10=found"
   )
   if defined ISWINDOWS10 (
-    docker run --rm --mount source=%CD%,destination=C:\compile,type=bind --workdir C:\\compile johnoel/admb:windows-ltsc2019-winlibs ss.tpl
+    docker run --rm --mount source=%CD%,destination=C:\compile,type=bind --workdir C:\\compile johnoel/admb:windows-ltsc2019-winlibs ss3.tpl
   ) else (
-    docker run --rm --mount source=%CD%,destination=C:\compile,type=bind --workdir C:\\compile johnoel/admb:windows-ltsc2022-winlibs ss.tpl
+    docker run --rm --mount source=%CD%,destination=C:\compile,type=bind --workdir C:\\compile johnoel/admb:windows-ltsc2022-winlibs ss3.tpl
   )
   goto CHECK
 )
 
 :CHECK
-if not exist ss.exe (
-  @echo "Error: Unable to build ss.exe"
+if not exist ss3.exe (
+  @echo "Error: Unable to build ss3.exe"
   exit /b 1
 )