Merge branch 'main' into try-codespace-merge

.github/ISSUE_TEMPLATE/ss3-release-template.md

@@ -8,36 +8,41 @@ assignees:
   - chantelwetzel-noaa
   - iantaylor-NOAA
   - kellijohnson-NOAA
-  - e-gugliotti-NOAA
+  - shcaba
+  - e-perl-NOAA
 ---
 
 # Release checklist
 
 <!---Note all instances of xx should be replaced with the version number (e.g., the release for v3.30.20 would replace xx with 20)-->
 
-## Checklist for before prerelease
-- [ ] SS3 testing and debugging completed (RM and IT)
-- [ ] Check artifact from the `call-build-ss3-warnings` GitHub action for useful warnings (RM and IT)
-- [ ] r4ss updated (IT)
+## General checklist before pre-release and release
+- [ ] SS3 testing and debugging completed (RM/IT)
+- [ ] Check artifact from the `call-build-ss3-warnings` GitHub action for useful warnings (RM/IT/EP)
+- [ ] r4ss updated (IT/EP)
+
+<!---## Checklist for before pre-release (if pre-release is being done)
 - [ ] Put together pre-release announcement (RM)
 - [ ] code committed and tagged in repo as `v3.30.xx-prerel` (RM)
 - [ ] All exes added to GitHub releases as `v3.30.xx-prerel` (RM)
-- [ ] Announce prerelease (RM)
+- [ ] Announce prerelease (RM)-->
 
 ## Checklist for before release
-- [ ] Manual updated and tagged in repo (EG) - address at least issues with the [`v3.30.xx` release label](add correct link to GitHub issues using filter: is:issue is:open label:"3.30.xx release" when available)
-- [ ] Manual added to a GitHub release, include attaching a pdf version (EG)
-- [ ] Manual release version on website updated once pdf and html built (EG) (update https://github.com/nmfs-ost/ss3-doc/blob/main/docs/SS330_User_Manual_release.html to the `v3.30.xx` version; update links to link to `v3.30.xx` in https://github.com/nmfs-ost/ss3-doc/blob/main/docs/index.md#links-to-documentation)
+- [ ] The following steps should be encompassed in the new manual [release workflow](https://github.com/nmfs-ost/ss3-doc/actions/workflows/release.yml) and [bug fix release workflow](https://github.com/nmfs-ost/ss3-doc/actions/workflows/release_bug_fix.yml) and can be deleted at a future time once the new manual release workflows have been used for a couple releases (EP). **Note that the branch protection rules must be briefly turned off to allow this workflow to run**
+  - [ ] Manual updated and tagged in repo (EP) - address at least issues with the [`v3.30.xx` release label](add correct link to GitHub issues using filter: is:issue is:open label:"3.30.xx release" when available)
+  - [ ] Manual added to a GitHub release, include attaching a pdf version (EP)
+  - [ ] Manual release version on website updated once pdf and html built (EP) (update https://github.com/nmfs-ost/ss3-doc/blob/main/docs/SS330_User_Manual_release.html to the `v3.30.xx` version; update links to link to `v3.30.xx` in https://github.com/nmfs-ost/ss3-doc/blob/main/docs/index.md#links-to-documentation)
 - [ ] Make changes to SS3 if any bugs caught in prerelease (RM)
 - [ ] [Change log project board](https://github.com/orgs/nmfs-ost/projects/11) updated with any issues labelled "change log" (RM)
-- [ ] Code committed and tagged in repo as `v3.30.xx`, which will trigger a GHA to build the release executables (EG) (Instructions on [how to push a a local tag to a remote](https://github.com/nmfs-ost/ss3-source-code/wiki/Stock-Synthesis:-practices-for-maintainers#how-to-push-a-local-tag-up-to-github))
-- [ ] Exe and .tpl archived on [Google drive](https://drive.google.com/drive/folders/1Gh_dXi8v3rqawpwn2N6yaaEXZPq6G2io) (EG)
-- [ ] All exes added to GitHub releases as `v3.30.xx` (EG) (get exes in the artifacts of the GHA that built the release exes)
-- [ ] Send out release announcement msg (RM)
-- [ ] Add to release discussion on GitHub repository (EG)
+- [ ] Code committed and tagged in repo as `v3.30.xx`, which will trigger a GHA to build the release executables (EP) (Instructions on [how to push a a local tag to a remote](https://github.com/nmfs-ost/ss3-source-code/wiki/Stock-Synthesis:-practices-for-maintainers#how-to-push-a-local-tag-up-to-github))
+- [ ] Exe and .tpl archived on [Google drive](https://drive.google.com/drive/folders/1Gh_dXi8v3rqawpwn2N6yaaEXZPq6G2io) (EP)
+- [ ] All exes added to GitHub releases as `v3.30.xx` (EP) (get exes in the artifacts of the GHA that built the release exes)
+- [ ] Send out release announcement message to the [SS3 forum](https://groups.google.com/g/ss3-forum) (RM)
+- [ ] Add to release discussion on GitHub repository (EP)
 
 ## Checklist for after release
-- [ ] Update user-example models using [this github action](https://github.com/nmfs-ost/ss3-user-examples/blob/main/R/update_examples.R) and tag with new release number after updating (EG)
-- [ ] Update test models using [this github action](https://github.com/nmfs-ost/ss3-test-models/actions/workflows/update-ss3-models.yml) and tag with new release number after updating (EG)
+- [ ] Update user-example models using [this github action](https://github.com/nmfs-ost/ss3-user-examples/blob/main/R/update_examples.R) and tag with new release number after updating (EP)
+- [ ] Update test models using [this github action](https://github.com/nmfs-ost/ss3-test-models/actions/workflows/update-ss3-models.yml) and tag with new release number after updating (EP)
+- [ ] Update executables in the [SAC tool](https://github.com/shcaba/SS-DL-tool) (also suggest updating the input files to the .ss_new files (EP/JC)
 - [ ] Removed "resolved" tag and close all issues worked in the milestone for this release (RM)
 - [ ] Move unworked issues for the release milestone to the next milestone (RM)

.github/workflows/add-exe-build-artifacts-to-PR.yml

@@ -0,0 +1,21 @@
+name: add-exe-build-artifacts-to-PR
+on:
+  workflow_run:
+    workflows: [build-ss3]
+    types: [completed]
+  workflow_dispatch:
+
+jobs:
+  artifacts-url-comments:
+    name: add artifact links to pull request and related issues job
+    runs-on: ubuntu-latest
+    if: ${{ github.event.workflow_run.conclusion == 'success'}}
+    steps:
+      - name: add artifact links to PR and issues
+        uses: tonyhallett/[email protected]
+        env:
+            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+            prefix: 'Here are the successful executable builds from your PR:'
+            format: name
+            addTo: pullandissues

.github/workflows/build-admb-and-ss3-from-source.yml

@@ -1,6 +1,7 @@
-# Builds the stock synthesis executables for testing and distribution.
-# for mac, linux, windows
-# Runs on every push and PR (even draft PRs)
+# Builds admb from source and then builds the stock synthesis executables from source for testing and distribution.
+# for macOS 13 (couldn't get this to run on macOS 12), macOS latest (arm64 architecture), linux, Windows
+# Runs on a scheduled basis weekly to ensure that this workflow will work IF the build-ss3.yml workflow stops
+# working due to issues with the admb docker image.
 name: build-admb-and-ss3-from-source
 
 on:
@@ -16,7 +17,7 @@ jobs:
       matrix:
         config:
           - {os: windows-latest}
-          - {os: macos-14}
+          - {os: macos-latest}
           - {os: macos-13}
           - {os: ubuntu-latest}
     # Limit run time to 90 min to avoid wasting action minutes.
@@ -28,7 +29,7 @@ jobs:
       - uses: actions/checkout@v4
 
     # Set up R
-      - name: Set up R, specify rtools version and path for windows
+      - name: Set up R, specify rtools version and path for Windows
         uses: r-lib/actions/setup-r@v2
         with: 
           r-version: 'release'
@@ -37,50 +38,50 @@ jobs:
           update-rtools: TRUE
 
     # Checkout ADMB repository
-      - name: checkout admb and build from source, windows
+      - name: Checkout admb
         uses: actions/checkout@v4
         with:
           repository: admb-project/admb
           path: admb
           ref: admb-13.2
 
     # Build ADMB for Windows
-      - name: build admb, windows using rtools 42
+      - name: Build admb for Windows using rtools 42
         if: matrix.config.os == 'windows-latest'
         run: |
           cd admb
           make -j 4
         shell: cmd
 
-      - name: But admb in path
+      - name: Put admb in path, Windows
         if: matrix.config.os == 'windows-latest'
         run: |
           echo "D:\a\ss3-source-code\ss3-source-code\admb\build\admb\bin" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
           echo $env:GITHUB_PATH
 
     # Build ADMB for macOS
-      - name: clean, mac
-        if: matrix.config.os == 'macos-14' || matrix.config.os == 'macos-13'
+      - name: Clean, macOS
+        if: matrix.config.os == 'macos-latest' || matrix.config.os == 'macos-13'
         run: cd admb && make clean
 
-      - name: see where admb is, mac
-        if: matrix.config.os == 'macos-14' || matrix.config.os == 'macos-13'
+      - name: See where admb is, macOS
+        if: matrix.config.os == 'macos-latest' || matrix.config.os == 'macos-13'
         run: |
           ls
           cd admb && ls
 
-      - name: compile admb, mac
-        if: matrix.config.os == 'macos-14' || matrix.config.os == 'macos-13'
+      - name: Compile admb, macOS
+        if: matrix.config.os == 'macos-latest' || matrix.config.os == 'macos-13'
         run: |
           cd admb && make -j 4
 
-      - name: see where admb is, mac
-        if: matrix.config.os == 'macos-14' || matrix.config.os == 'macos-13'
-        run: |
-          cd admb && ls -l
+      # - name: See where admb is, mac
+      #   if: matrix.config.os == 'macos-latest' || matrix.config.os == 'macos-13'
+      #   run: |
+      #     cd admb && ls -l
 
-      - name: put admb in path, mac
-        if: matrix.config.os == 'macos-14' || matrix.config.os == 'macos-13'
+      - name: Change permissions of admb and put in path, macOS
+        if: matrix.config.os == 'macos-latest' || matrix.config.os == 'macos-13'
         run: |
           sudo mv admb /usr/local/bin
           sudo chmod 755 /usr/local/bin/admb
@@ -91,7 +92,7 @@ jobs:
         if: matrix.config.os == 'ubuntu-latest'
         run: sudo apt-get update
 
-      - name: Get admb and put in path, linux
+      - name: Change permissions of admb and put in path, linux
         if: matrix.config.os == 'ubuntu-latest'
         run: |
           cd admb && make clean
@@ -104,12 +105,12 @@ jobs:
           echo "/usr/local/bin/admb" >> $GITHUB_PATH
     
     # Fetch Tags
-      - name: Fetch tags
+      - name: Fetch git tags
         run: |
           git fetch --tags
           git fetch --prune --unshallow || true
 
-      - name: Get the last tag on windows
+      - name: Get the last tag on Windows
         id: get-latest-tag-win
         if: matrix.config.os == 'windows-latest'
         run: |
@@ -121,17 +122,17 @@ jobs:
           echo "tag_commit=${latest_tag_commit}" >> $env:GITHUB_OUTPUT
           echo "commit=${latest_commit}" >> $env:GITHUB_OUTPUT
 
-      - name: pull the last tag value to use in the Rscript on windows
+      - name: Pull the last tag value to use in the Rscript on Windows
         id: get-version-win
         if: matrix.config.os == 'windows-latest'
         run: |
           Out-File -InputObject ${{ steps.get-latest-tag-win.outputs.tag }} -FilePath .github/last_tag.txt
           Out-File -InputObject ${{ steps.get-latest-tag-win.outputs.tag_commit }} -FilePath .github/last_tag_commit.txt
           Out-File -InputObject ${{ steps.get-latest-tag-win.outputs.commit}} -FilePath .github/last_commit.txt
 
-      - name: Get the last tag on unix
+      - name: Get the last tag on unix (macOS and linux)
         id: get-latest-tag-unix
-        if: matrix.config.os == 'macos-14' || matrix.config.os == 'macos-13' || matrix.config.os == 'ubuntu-latest'
+        if: matrix.config.os == 'macos-latest' || matrix.config.os == 'macos-13' || matrix.config.os == 'ubuntu-latest'
         run: |
           git tag
           latest_tag=$(git describe --abbrev=0 --tags)
@@ -141,9 +142,9 @@ jobs:
           echo "tag_commit=${latest_tag_commit}" >> $GITHUB_OUTPUT
           echo "commit=${latest_commit}" >> $GITHUB_OUTPUT
 
-      - name: pull the last tag value to use in the Rscript on unix
+      - name: Pull the last tag value to use in the Rscript on unix (macOS and linux)
         id: get-version-unix
-        if: matrix.config.os == 'macos-14' || matrix.config.os == 'macos-13' || matrix.config.os == 'ubuntu-latest'
+        if: matrix.config.os == 'macos-latest' || matrix.config.os == 'macos-13' || matrix.config.os == 'ubuntu-latest'
         run: |
           echo "${{ steps.get-latest-tag-unix.outputs.tag }}" > .github/last_tag.txt
           echo "${{ steps.get-latest-tag-unix.outputs.tag_commit }}" > .github/last_tag_commit.txt
@@ -215,7 +216,7 @@ jobs:
         shell: Rscript {0}
 
     # Build SS3 for Windows
-      - name: Build stock synthesis for windows with admb docker image
+      - name: Build stock synthesis for Windows
         if: matrix.config.os == 'windows-latest'
         run: |
           cd Compile
@@ -234,8 +235,8 @@ jobs:
           mv SS330/ss3_opt.exe SS330/ss3_opt_win.exe
 
     # Build SS3 for macOS
-      - name: Build stock synthesis for mac with admb docker image
-        if: matrix.config.os == 'macos-14' || matrix.config.os == 'macos-13'
+      - name: Build stock synthesis for macOS
+        if: matrix.config.os == 'macos-latest' || matrix.config.os == 'macos-13'
         run: |
           rm -rf SS330
           rm -rf ss3_osx.tar
@@ -244,22 +245,22 @@ jobs:
           /bin/bash ./Make_SS_330_new.sh -b SS330
           /bin/bash ./Make_SS_330_new.sh -b SS330 -o
 
-      - name: Verify binary on mac
-        if: matrix.config.os == 'macos-14' || matrix.config.os == 'macos-13'
+      - name: Verify binary on macOS
+        if: matrix.config.os == 'macos-latest' || matrix.config.os == 'macos-13'
         run: |
           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-14' || matrix.config.os == 'macos-13'
+      - name: Delete unnecessary files and change exe names on macOS
+        if: matrix.config.os == 'macos-latest' || matrix.config.os == 'macos-13'
         run: |
           cd SS330
           rm *.obj *.htp *.cpp ss3_opt.tpl
           mv ss3 ss3_osx
           mv ss3_opt ss3_opt_osx
 
     # Build SS3 for Linux
-      - name: Build stock synthesis for linux with p flag and admb docker image
+      - name: Build stock synthesis for linux with p flag
         if:  matrix.config.os == 'ubuntu-latest'
         run: |
           rm -rf SS330

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

@@ -1,5 +1,7 @@
-# Build stock synthesis with all c++ compiler warnings, and fail job if the
-# number of warnings has increased.
+# Build stock synthesis on linux with all c++ compiler warnings, and fail job if the
+# number of warnings has increased using the warnings_ss_ref.txt file under 
+# workflows > reference_files.
+# Only runs on a pull request and a push to main if the tpl files have changed
 name: build-ss3-warnings
 
 # Controls when the action will run.
@@ -32,7 +34,7 @@ jobs:
       - name: Update Ubuntu packages
         run: sudo apt-get update
 
-      - name: setup R
+      - name: Setup R
         uses: r-lib/actions/setup-r@v2
 
       # - name: Get admb and put in path, linux
@@ -42,15 +44,15 @@ jobs:
         #   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 using admb docker image
+      - name: Build stock synthesis with warnings using admb docker image and display in console
         run: |
           rm -rf SS330
           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
+      - name: Build stock synthesis with warnings using admb docker image again to save to file
         run: |
           rm -rf SS330
           rm -rf ss3_osx.tar
@@ -77,10 +79,10 @@ jobs:
         # txt <- txt[(warn_line+1):length(txt)]
         shell: Rscript {0}
 
-      - name:  Print warnings
+      - name: Print warnings
         run: cat warnings_ss.txt
 
-      - name: determine if fails/passes
+      - name: Determine if fails/passes based on the number of warnings
         run: |
           ref <- readLines(".github/workflows/reference_files/warnings_ss_ref.txt")
           n_warn <- read.table("n_warn.txt")