update all files to make ss3 to be ss3 and ss3_opt

nmfs-ost · Feb 15, 2024 · cf4c3b5 · cf4c3b5
1 parent 83a70eb
commit cf4c3b5
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Showing 11 changed files with 75 additions and 75 deletions.
diff --git a/.github/workflows/build-ss3-warnings.yml b/.github/workflows/build-ss3-warnings.yml
@@ -45,15 +45,15 @@ 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

diff --git a/.github/workflows/build-ss3.yml b/.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
+          mv ss3 ss3_linux
+          mv ss3_opt ss3_opt_linux
 
       - name: Archive binaries
         if: success()

diff --git a/.github/workflows/run-ss3-bootstrap.yml b/.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

diff --git a/.github/workflows/run-ss3-mcmc.yml b/.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

diff --git a/.github/workflows/run-ss3-no-est.yml b/.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
 

diff --git a/.github/workflows/run-ss3-with-est.yml b/.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

diff --git a/.github/workflows/test-r4ss-with-ss3.yml b/.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
 

diff --git a/Compile/Make_SS_fast.bat b/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
 )
diff --git a/Compile/Make_SS_safe.bat b/Compile/Make_SS_safe.bat
@@ -20,37 +20,37 @@ 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
 )
diff --git a/GNUmakefile b/GNUmakefile
@@ -16,53 +16,53 @@
 export CXXFLAGS=-Wall -Wextra
 
 all: clean
-	$(MAKE) ss
-	$(MAKE) ss_opt
+	$(MAKE) ss3
+	$(MAKE) ss3_opt
 
 docker:
 	chmod -R 777 $(CURDIR)
 	$(MAKE) USE_DOCKER=yes all
 
-ss: ss.tpl
+ss3: ss3.tpl
 ifdef USE_DOCKER
   ifeq ($(OS),Windows_NT)
-	docker run --rm --volume $(CURDIR):C:\\workdir\\ss --workdir C:\\workdir\\ss johnoel/admb:windows-ltsc2022-winlibs ss.tpl
+	docker run --rm --volume $(CURDIR):C:\\workdir\\ss --workdir C:\\workdir\\ss johnoel/admb:windows-ltsc2022-winlibs ss3.tpl
   else
-	docker run --rm --volume $(CURDIR):/workdir/ss:rw --workdir /workdir/ss johnoel/admb:linux ss.tpl
+	docker run --rm --volume $(CURDIR):/workdir/ss:rw --workdir /workdir/ss johnoel/admb:linux ss3.tpl
   endif
 else
-	$(MY_ADMB_HOME)admb $(DEBUG)$(STATIC_BUILD) ss.tpl
+	$(MY_ADMB_HOME)admb $(DEBUG)$(STATIC_BUILD) ss3.tpl
 endif
 
-ss_opt: ss_opt.tpl
+ss3_opt: ss3_opt.tpl
 ifdef USE_DOCKER
   ifeq ($(OS),Windows_NT)
-	docker run --rm --volume $(CURDIR):C:\\workdir\\ss_opt --workdir C:\\workdir\\ss_opt johnoel/admb:windows-ltsc2022-winlibs ss_opt.tpl
+	docker run --rm --volume $(CURDIR):C:\\workdir\\ss_opt --workdir C:\\workdir\\ss_opt johnoel/admb:windows-ltsc2022-winlibs ss3_opt.tpl
   else
-	docker run --rm --volume $(CURDIR):/workdir/ss_opt:rw --workdir /workdir/ss_opt johnoel/admb:linux ss_opt.tpl
+	docker run --rm --volume $(CURDIR):/workdir/ss_opt:rw --workdir /workdir/ss_opt johnoel/admb:linux ss3_opt.tpl
   endif
 else
-	$(MY_ADMB_HOME)admb -f $(DEBUG)$(STATIC_BUILD) ss_opt.tpl
+	$(MY_ADMB_HOME)admb -f $(DEBUG)$(STATIC_BUILD) ss3_opt.tpl
 endif
 
-ss.tpl: SS_functions.temp
-	cat 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 > ss.tpl
+ss3.tpl: SS_functions.temp
+	cat 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 > ss3.tpl
 
-ss_opt.tpl: SS_functions.temp
-	cat 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 > ss_opt.tpl
+ss3_opt.tpl: SS_functions.temp
+	cat 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 > ss3_opt.tpl
 
 SS_functions.temp:
 	cat 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
 
 clean:
-	@rm -vf ss
-	@rm -vf ss_opt
-	@rm -vf ss.tpl
-	@rm -vf ss_opt.tpl
+	@rm -vf ss3
+	@rm -vf ss3_opt
+	@rm -vf ss3.tpl
+	@rm -vf ss3_opt.tpl
 	@rm -vf SS_functions.temp
-	@rm -vf ss.cpp
-	@rm -vf ss.htp
-	@rm -vf ss.obj
-	@rm -vf ss_opt.cpp
-	@rm -vf ss_opt.htp
-	@rm -vf ss_opt.obj
+	@rm -vf ss3.cpp
+	@rm -vf ss3.htp
+	@rm -vf ss3.obj
+	@rm -vf ss3_opt.cpp
+	@rm -vf ss3_opt.htp
+	@rm -vf ss3_opt.obj