191 spawner recruit rebased

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

@@ -111,14 +111,15 @@ jobs:
             on.exit(system(paste0("cd ", wd)))
             # delete old starter files, rename forecast.ss_new and starter.ss_new files
             file.remove(file.path(dir, "starter.ss"))
-            file.remove(file.path("forecast.ss"))
+            file.remove(file.path(dir, "forecast.ss"))
             file.rename(file.path(dir, "starter.ss_new"), file.path(dir,"starter.ss"))
             file.rename(file.path(dir, "forecast.ss_new"), file.path(dir,"forecast.ss"))
             # rename control and data files to standardized names (from the starter files)
             start <- readLines(file.path(dir, "starter.ss"))
-            first_val_line <- grep("0=use init values in control file", start, fixed = TRUE)
-            datname <- start[first_val_line-2]
-            ctlname <- start[first_val_line-1]
+            datname <- start[grep("#_datfile", start, fixed = TRUE)]
+            datname <- gsub(" #_datfile", "", datname)
+            ctlname <- start[grep("#_ctlfile", start, fixed = TRUE)]
+            ctlname <- gsub(" #_ctlfile", "", ctlname)
             print(datname)
             print(ctlname)
             file.remove(file.path(dir, datname))

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

@@ -1,5 +1,4 @@
 # Build SS3 and run test models with estimation and hessian
-# Only runs manual run or if run-ss3-no-est.yml runs successfully
 name: run-ss3-with-est
 on:
   workflow_dispatch:
@@ -8,21 +7,20 @@ on:
   #     - '**.tpl'
   #   branches:
   #     - main
-  workflow_run:
-    workflows: ["run-ss3-no-est"]
-    types:
-      - completed
-  # pull_request:
-  #   types: ['opened', 'edited', 'reopened', 'synchronize', 'ready_for_review']
-  #   paths:
-  #     - '**.tpl'
-  #   branches:
-  #     - main
+  # workflow_run:
+  #   workflows: ["run-ss3-no-est"]
+  #   types:
+  #     - completed
+  pull_request:
+    paths:
+      - '**.tpl'
+    branches:
+      - main
 
 # Run fast running SS3 test models with estimation
 jobs:
   run-ss3-with-est:
-    if: ${{ github.event_name == 'workflow_dispatch' || (github.event.pull_request.draft == 'false' && github.event.workflow_run.conclusion == 'success') }}
+    # if: ${{ github.event_name == 'workflow_dispatch' || (github.event.pull_request.draft == 'false'}}
     runs-on: ubuntu-latest
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

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

@@ -52,7 +52,7 @@ jobs:
         run: Rscript -e 'install.packages(c("remotes","parallely", "furrr", "future"))'
 
       - name: Install r4ss
-        run: Rscript -e 'remotes::install_github("r4ss/r4ss")'
+        run: Rscript -e 'remotes::install_github("r4ss/r4ss@expanded_SR")'
 
       # - name: Get admb and put in path, linux
       #   run: |

.gitignore

@@ -7,10 +7,11 @@
 *.htp
 *.obj
 *.log
-ss.tpl
-ss3.tpl
-ss_opt.tpl
-ss_trans.tpl
+Compile/ss.tpl
+Compile/ss_opt.tpl
+Compile/ss_trans.tpl
+Compile/ss3.tpl
+Compile/Make_SS_warn.bat
 ~$*.*
 Compile/ss.log
 Compile/ss3.log

Compile/Make_SS_warn.bat

@@ -28,6 +28,6 @@ tpl2cpp ss3
 
 g++ -c -std=c++17 -O2 -D_FILE_OFFSET_BITS=64  -DUSE_ADMB_CONTRIBS -D_USE_MATH_DEFINES -I. -I"C:\ADMB-13.2\include" -I"C:\ADMB-13.2\include\contrib" -Wall -Wextra -o ss3.obj ss3.cpp
 
-g++ -static -o ss3.exe ss3.obj "C:\ADMB-13.2\lib\libadmb-contrib-mingw64-g++12.a"
+g++ -static -o ss3.exe ss3.obj "C:\ADMB-13.2\lib\libadmb-contrib-mingw64-g++13.a"
 
 dir *.exe