From a2b1ba20a9fcbedfb47adf7ea9c2a111376cd4d9 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 10:56:23 -0400
Subject: [PATCH 01/30] try fix to static build; add new workflow to test ss3
 exe artifacts

---
 Make_SS_330_new.sh                 |  20 ++--
 test-simple-with-ss3-artifacts.yml | 150 +++++++++++++++++++++++++++++
 2 files changed, 162 insertions(+), 8 deletions(-)
 create mode 100644 test-simple-with-ss3-artifacts.yml

diff --git a/Make_SS_330_new.sh b/Make_SS_330_new.sh
index ae2743b7..d4d0b358 100755
--- a/Make_SS_330_new.sh
+++ b/Make_SS_330_new.sh
@@ -19,8 +19,9 @@ function usage()
   echo ""
   echo "Call this script as follows:"
   echo "  ./Make_SS_330_new.sh [(-s | --source) source_dir] [(-b | --build) build_dir]" 
-  echo "   [(-a | --admb) admb_dir] [[-o | --opt] | [-f | --safe] [-p] "
+  echo "   [(-a | --admb) admb_dir] [[-o | --opt] | [-f | --safe] [-p]"
   echo "   [-w | --warn] [-d | --debug] [-h | --help]"
+  # build statically (full static)
   echo "Notes:"
   echo "   -p is an ADMB flag to build statically and will be passed. "
   echo "   -w re-compiles with common warnings enabled. "
@@ -175,28 +176,31 @@ if [[ "$ADMB_HOME" == "docker" ]] ; then
     fi
     if [[ "$WARNINGS" == "on" ]] ; then
       if [[ "$WINDOWS10" == "true" ]] ; then
-        docker run --env CXXFLAGS="-Wall -Wextra" --rm --mount source=`cygpath -w $PWD`\\$BUILD_DIR,destination=C:\\$BUILD_TYPE,mount=bind --workdir C:\\$BUILD_TYPE johnoel/admb-13.2:windows10 $BUILD_TYPE.tpl
+        docker run --env CXXFLAGS="-Wall -Wextra" --rm --mount source=`cygpath -w $PWD`\\$BUILD_DIR,destination=C:\\$BUILD_TYPE,mount=bind --workdir C:\\$BUILD_TYPE johnoel/admb-13.2:windows10 $OPTFLAG $STATICFLAG $BUILD_TYPE.tpl
       else
-        docker run --env CXXFLAGS="-Wall -Wextra" --rm --mount source=`cygpath -w $PWD`\\$BUILD_DIR,destination=C:\\$BUILD_TYPE,mount=bind --workdir C:\\$BUILD_TYPE johnoel/admb-13.2:windows $BUILD_TYPE.tpl
+        docker run --env CXXFLAGS="-Wall -Wextra" --rm --mount source=`cygpath -w $PWD`\\$BUILD_DIR,destination=C:\\$BUILD_TYPE,mount=bind --workdir C:\\$BUILD_TYPE johnoel/admb-13.2:windows $OPTFLAG $STATICFLAG $BUILD_TYPE.tpl
       fi 
     else
       if [[ "$WINDOWS10" == "true" ]] ; then
-        docker run --rm --mount source=`cygpath -w $PWD`\\$BUILD_DIR,destination=C:\\$BUILD_TYPE,mount=bind --workdir C:\\$BUILD_TYPE johnoel/admb-13.2:windows10 $BUILD_TYPE.tpl
+        docker run --rm --mount source=`cygpath -w $PWD`\\$BUILD_DIR,destination=C:\\$BUILD_TYPE,mount=bind --workdir C:\\$BUILD_TYPE johnoel/admb-13.2:windows10 $OPTFLAG $STATICFLAG $BUILD_TYPE.tpl
       else
-        docker run --rm --mount source=`cygpath -w $PWD`\\$BUILD_DIR,destination=C:\\$BUILD_TYPE,mount=bind --workdir C:\\$BUILD_TYPE johnoel/admb-13.2:windows $BUILD_TYPE.tpl
+        docker run --rm --mount source=`cygpath -w $PWD`\\$BUILD_DIR,destination=C:\\$BUILD_TYPE,mount=bind --workdir C:\\$BUILD_TYPE johnoel/admb-13.2:windows $OPTFLAG $STATICFLAG $BUILD_TYPE.tpl
       fi 
     fi
   else
     if [[ "$WARNINGS" == "on" ]] ; then
-      docker run --env CXXFLAGS="-Wall -Wextra" --rm --mount source=$PWD/$BUILD_DIR,destination=/$BUILD_TYPE,type=bind --workdir /$BUILD_TYPE johnoel/admb-13.2:linux $BUILD_TYPE.tpl
+      export CXXFLAGS="-Wall -Wextra -static-libstdc++ -static-libgcc"
     else
-      docker run --rm --mount source=$PWD/$BUILD_DIR,destination=/$BUILD_TYPE,type=bind --workdir /$BUILD_TYPE johnoel/admb-13.2:linux $BUILD_TYPE.tpl
+      export CXXFLAGS="-static-libstdc++ -static-libgcc"
     fi
+    docker run --env CXXFLAGS="$CXXFLAGS" --rm --mount source=$PWD/$BUILD_DIR,destination=/$BUILD_TYPE,type=bind --workdir /$BUILD_TYPE johnoel/admb-13.2:linux $OPTFLAG $STATICFLAG $BUILD_TYPE.tpl
   fi
 else
   command pushd $BUILD_DIR > /dev/null
   if [[ "$WARNINGS" == "on" ]] ; then
-    export CXXFLAGS="-Wall -Wextra"
+    export CXXFLAGS="-Wall -Wextra -static-libstdc++ -static-libgcc"
+  else
+    export CXXFLAGS="-static-libstdc++ -static-libgcc"
   fi
   if [[ "$OS" == "Windows_NT" ]] ; then
     admb.sh $OPTFLAG $STATICFLAG $BUILD_TYPE
diff --git a/test-simple-with-ss3-artifacts.yml b/test-simple-with-ss3-artifacts.yml
new file mode 100644
index 00000000..70bc4f2b
--- /dev/null
+++ b/test-simple-with-ss3-artifacts.yml
@@ -0,0 +1,150 @@
+on:
+  push:
+      paths:
+      - '**.tpl'
+      - '**.sh'
+  workflow_dispatch:
+
+jobs:
+  test-simple-model:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-13, macos-latest]
+        include:
+          - os: ubuntu-latest
+            artifact_name: ss3-ubuntu-latest
+            exe_name: ss3_linux
+          - os: windows-latest
+            artifact_name: ss3-windows-latest
+            exe_name: ss3_win.exe
+          - os: macos-13
+            artifact_name: ss3-macos-13
+            exe_name: ss3_osx
+          - os: macos-latest
+            artifact_name: ss3-macos-latest
+            exe_name: ss3_osx
+
+    steps:
+      - name: Checkout test repo (this repo)
+        uses: actions/checkout@v4
+
+      - name: Set up jq and unzip (Linux/macOS)
+        if: runner.os != 'Windows'
+        run: |
+          sudo apt-get update || true
+          sudo apt-get install -y jq unzip || brew install jq unzip
+
+      - name: Set up jq (Windows)
+        if: runner.os == 'Windows'
+        run: choco install jq
+
+      - name: Find latest successful ss3-build workflow run in nmfs-ost/ss3-source-code
+        id: get_run
+        uses: actions/github-script@v7
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            const { data: workflows } = await github.rest.actions.listRepoWorkflows({
+              owner: "nmfs-ost",
+              repo: "ss3-source-code"
+            });
+            const workflow = workflows.workflows.find(wf => wf.name === "ss3-build");
+            if (!workflow) throw "Workflow 'ss3-build' not found.";
+            const { data: runs } = await github.rest.actions.listWorkflowRuns({
+              owner: "nmfs-ost",
+              repo: "ss3-source-code",
+              workflow_id: workflow.id,
+              status: "success",
+              per_page: 1
+            });
+            if (!runs.workflow_runs.length) throw "No successful runs found for 'ss3-build'.";
+            core.setOutput("run_id", runs.workflow_runs[0].id);
+
+      - name: List artifacts from ss3-build run
+        id: list_artifacts
+        uses: actions/github-script@v7
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            const run_id = ${{ steps.get_run.outputs.run_id }};
+            const { data: artifacts } = await github.rest.actions.listWorkflowRunArtifacts({
+              owner: "nmfs-ost",
+              repo: "ss3-source-code",
+              run_id
+            });
+            core.setOutput("artifacts", JSON.stringify(artifacts.artifacts));
+
+      - name: Download artifact for this OS
+        id: download_artifact
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          set -e
+          mkdir -p ss3_artifacts
+          os_artifact="${{ matrix.artifact_name }}"
+          artifacts=$(echo '${{ steps.list_artifacts.outputs.artifacts }}' | jq -r '.[] | @base64')
+          found_id=""
+          for artifact in $artifacts; do
+            _jq() {
+              echo ${artifact} | base64 --decode | jq -r ${1}
+            }
+            name=$(_jq '.name')
+            id=$(_jq '.id')
+            if [[ "$name" == "$os_artifact" ]]; then
+              found_id="$id"
+              break
+            fi
+          done
+          if [ -z "$found_id" ]; then
+            echo "Artifact $os_artifact not found!"
+            exit 1
+          fi
+          # Download the artifact
+          echo "Downloading artifact: $os_artifact"
+          gh api \
+            -H "Accept: application/vnd.github+json" \
+            -H "Authorization: Bearer $GH_TOKEN" \
+            "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/$os_artifact.zip"
+
+      - name: Unzip SS3 executable
+        run: |
+          cd ss3_artifacts
+          if [ "${{ runner.os }}" = "Windows" ]; then
+            powershell -Command "Expand-Archive -Path '${{ matrix.artifact_name }}.zip' -DestinationPath ."
+          else
+            unzip -o "${{ matrix.artifact_name }}.zip"
+          fi
+
+      - name: Checkout test models repository
+        uses: actions/checkout@v4
+        with:
+          repository: nmfs-ost/ss3-test-models
+          path: ss3-test-models
+
+      - name: Copy SS3 executable to simple model directory
+        run: |
+          exe="${{ matrix.exe_name }}"
+          src="ss3_artifacts/$exe"
+          dest="ss3-test-models/models/simple/$exe"
+          if [ "${{ runner.os }}" = "Windows" ]; then
+            cp "$src" "$dest"
+          else
+            cp "$src" "$dest"
+            chmod +x "$dest"
+          fi
+
+      - name: Run SS3 on simple model
+        run: |
+          cd ss3-test-models/models/simple
+          if [ "${{ runner.os }}" = "Windows" ]; then
+            .\${{ matrix.exe_name }}
+          else
+            ./${{ matrix.exe_name }}
+          fi
+
+      - name: Archive simple model output
+        uses: actions/upload-artifact@v4
+        with:
+          name: simple-model-output-${{ matrix.os }}
+          path: ss3-test-models/models/simple/
\ No newline at end of file

From 65377daaabc5b55d27f18a475d15ad04b747ff11 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 11:08:57 -0400
Subject: [PATCH 02/30] move workflow of test to right place

---
 .../workflows/test-simple-with-ss3-artifacts.yml                  | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename test-simple-with-ss3-artifacts.yml => .github/workflows/test-simple-with-ss3-artifacts.yml (100%)

diff --git a/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
similarity index 100%
rename from test-simple-with-ss3-artifacts.yml
rename to .github/workflows/test-simple-with-ss3-artifacts.yml

From b64992be1e592fe4b8d436484eeabf45ffc337ed Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 11:36:12 -0400
Subject: [PATCH 03/30] comment out push paths to test workflow on push

---
 .github/workflows/test-simple-with-ss3-artifacts.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index 70bc4f2b..4fd6af48 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -1,8 +1,8 @@
 on:
   push:
-      paths:
-      - '**.tpl'
-      - '**.sh'
+      # paths:
+      # - '**.tpl'
+      # - '**.sh'
   workflow_dispatch:
 
 jobs:

From acea26a38bf99f8ffb7b7119ab6e402e5c5d07f8 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 11:40:27 -0400
Subject: [PATCH 04/30] fix build-ss3 name

---
 .github/workflows/test-simple-with-ss3-artifacts.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index 4fd6af48..7aa3d26d 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -39,7 +39,7 @@ jobs:
         if: runner.os == 'Windows'
         run: choco install jq
 
-      - name: Find latest successful ss3-build workflow run in nmfs-ost/ss3-source-code
+      - name: Find latest successful build-ss3 workflow run in nmfs-ost/ss3-source-code
         id: get_run
         uses: actions/github-script@v7
         with:
@@ -49,8 +49,8 @@ jobs:
               owner: "nmfs-ost",
               repo: "ss3-source-code"
             });
-            const workflow = workflows.workflows.find(wf => wf.name === "ss3-build");
-            if (!workflow) throw "Workflow 'ss3-build' not found.";
+            const workflow = workflows.workflows.find(wf => wf.name === "build-ss3");
+            if (!workflow) throw "Workflow 'build-ss3' not found.";
             const { data: runs } = await github.rest.actions.listWorkflowRuns({
               owner: "nmfs-ost",
               repo: "ss3-source-code",
@@ -58,10 +58,10 @@ jobs:
               status: "success",
               per_page: 1
             });
-            if (!runs.workflow_runs.length) throw "No successful runs found for 'ss3-build'.";
+            if (!runs.workflow_runs.length) throw "No successful runs found for 'build-ss3'.";
             core.setOutput("run_id", runs.workflow_runs[0].id);
 
-      - name: List artifacts from ss3-build run
+      - name: List artifacts from build-ss3 run
         id: list_artifacts
         uses: actions/github-script@v7
         with:

From 81e512924e963a5ee4e38fd345643bab921fe030 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 12:02:15 -0400
Subject: [PATCH 05/30] fix capitalization of simple model

---
 .github/workflows/test-simple-with-ss3-artifacts.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index 7aa3d26d..89279d85 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -122,11 +122,11 @@ jobs:
           repository: nmfs-ost/ss3-test-models
           path: ss3-test-models
 
-      - name: Copy SS3 executable to simple model directory
+      - name: Copy SS3 executable to Simple model directory
         run: |
           exe="${{ matrix.exe_name }}"
           src="ss3_artifacts/$exe"
-          dest="ss3-test-models/models/simple/$exe"
+          dest="ss3-test-models/models/Simple/$exe"
           if [ "${{ runner.os }}" = "Windows" ]; then
             cp "$src" "$dest"
           else
@@ -134,17 +134,17 @@ jobs:
             chmod +x "$dest"
           fi
 
-      - name: Run SS3 on simple model
+      - name: Run SS3 on Simple model
         run: |
-          cd ss3-test-models/models/simple
+          cd ss3-test-models/models/Simple
           if [ "${{ runner.os }}" = "Windows" ]; then
             .\${{ matrix.exe_name }}
           else
             ./${{ matrix.exe_name }}
           fi
 
-      - name: Archive simple model output
+      - name: Archive Simple model output
         uses: actions/upload-artifact@v4
         with:
           name: simple-model-output-${{ matrix.os }}
-          path: ss3-test-models/models/simple/
\ No newline at end of file
+          path: ss3-test-models/models/Simple/
\ No newline at end of file

From 119587ede01de595d5d32a1bd1de7d5f5be0ba58 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 12:14:22 -0400
Subject: [PATCH 06/30] add shell command

---
 .github/workflows/test-simple-with-ss3-artifacts.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index 89279d85..c1f856ad 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -77,6 +77,7 @@ jobs:
 
       - name: Download artifact for this OS
         id: download_artifact
+        shell: bash
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |

From 5dfc9d8dfd627f1d6e2f6ac203b750e46373708f Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 12:27:19 -0400
Subject: [PATCH 07/30] try fix for windows using bash

---
 .../test-simple-with-ss3-artifacts.yml        | 23 ++++++++++++-------
 1 file changed, 15 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index c1f856ad..eea3b01d 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -85,10 +85,14 @@ jobs:
           mkdir -p ss3_artifacts
           os_artifact="${{ matrix.artifact_name }}"
           artifacts=$(echo '${{ steps.list_artifacts.outputs.artifacts }}' | jq -r '.[] | @base64')
+          if [[ ${#artifacts[@]} -eq 0 ]]; then
+            echo "No artifacts found."
+            exit 1
+          fi
           found_id=""
-          for artifact in $artifacts; do
+          for artifact in "${artifacts[@]}"; do
             _jq() {
-              echo ${artifact} | base64 --decode | jq -r ${1}
+              echo "${artifact}" | base64 --decode | jq -r "${1}"
             }
             name=$(_jq '.name')
             id=$(_jq '.id')
@@ -109,6 +113,7 @@ jobs:
             "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/$os_artifact.zip"
 
       - name: Unzip SS3 executable
+        shell: bash
         run: |
           cd ss3_artifacts
           if [ "${{ runner.os }}" = "Windows" ]; then
@@ -123,19 +128,21 @@ jobs:
           repository: nmfs-ost/ss3-test-models
           path: ss3-test-models
 
+      - name: Ensure Simple model directory exists
+        shell: bash
+        run: mkdir -p ss3-test-models/models/Simple
+
       - name: Copy SS3 executable to Simple model directory
+        shell: bash
         run: |
           exe="${{ matrix.exe_name }}"
           src="ss3_artifacts/$exe"
           dest="ss3-test-models/models/Simple/$exe"
-          if [ "${{ runner.os }}" = "Windows" ]; then
-            cp "$src" "$dest"
-          else
-            cp "$src" "$dest"
-            chmod +x "$dest"
-          fi
+          cp "$src" "$dest"
+          chmod +x "$dest" || true
 
       - name: Run SS3 on Simple model
+        shell: bash
         run: |
           cd ss3-test-models/models/Simple
           if [ "${{ runner.os }}" = "Windows" ]; then

From e57a3523a2bfbbdb1dc819cc7f02400a04c9b199 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 12:34:22 -0400
Subject: [PATCH 08/30] readarray fix

---
 .github/workflows/test-simple-with-ss3-artifacts.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index eea3b01d..9fbb8d28 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -84,11 +84,15 @@ jobs:
           set -e
           mkdir -p ss3_artifacts
           os_artifact="${{ matrix.artifact_name }}"
-          artifacts=$(echo '${{ steps.list_artifacts.outputs.artifacts }}' | jq -r '.[] | @base64')
+          readarray -t artifacts < <(echo '${{ steps.list_artifacts.outputs.artifacts }}' | jq -r '.[] | @base64')
           if [[ ${#artifacts[@]} -eq 0 ]]; then
             echo "No artifacts found."
             exit 1
           fi
+          echo "Available artifacts:"
+          for artifact in "${artifacts[@]}"; do
+            echo "${artifact}" | base64 --decode | jq -r '.name'
+          done
           found_id=""
           for artifact in "${artifacts[@]}"; do
             _jq() {

From 24930e7f15b4334552e2bea134ac4237ddc9043c Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 12:52:38 -0400
Subject: [PATCH 09/30] fix bash for macos

---
 .../test-simple-with-ss3-artifacts.yml         | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index 9fbb8d28..73a2d377 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -39,6 +39,14 @@ jobs:
         if: runner.os == 'Windows'
         run: choco install jq
 
+      - name: Use Bash 5 on macOS
+        if: runner.os == 'macOS'
+        run: brew install bash
+
+      - name: Set SHELL to bash 5 on macOS
+        if: runner.os == 'macOS'
+        run: echo "/opt/homebrew/bin/bash" >> $GITHUB_PATH
+
       - name: Find latest successful build-ss3 workflow run in nmfs-ost/ss3-source-code
         id: get_run
         uses: actions/github-script@v7
@@ -77,7 +85,7 @@ jobs:
 
       - name: Download artifact for this OS
         id: download_artifact
-        shell: bash
+        shell: shell: ${{ runner.os == 'macOS' && '/opt/homebrew/bin/bash {0}' || 'bash' }}
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
@@ -117,7 +125,7 @@ jobs:
             "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/$os_artifact.zip"
 
       - name: Unzip SS3 executable
-        shell: bash
+        shell: shell: ${{ runner.os == 'macOS' && '/opt/homebrew/bin/bash {0}' || 'bash' }}
         run: |
           cd ss3_artifacts
           if [ "${{ runner.os }}" = "Windows" ]; then
@@ -133,11 +141,11 @@ jobs:
           path: ss3-test-models
 
       - name: Ensure Simple model directory exists
-        shell: bash
+        shell: shell: ${{ runner.os == 'macOS' && '/opt/homebrew/bin/bash {0}' || 'bash' }}
         run: mkdir -p ss3-test-models/models/Simple
 
       - name: Copy SS3 executable to Simple model directory
-        shell: bash
+        shell: shell: ${{ runner.os == 'macOS' && '/opt/homebrew/bin/bash {0}' || 'bash' }}
         run: |
           exe="${{ matrix.exe_name }}"
           src="ss3_artifacts/$exe"
@@ -146,7 +154,7 @@ jobs:
           chmod +x "$dest" || true
 
       - name: Run SS3 on Simple model
-        shell: bash
+        shell: shell: ${{ runner.os == 'macOS' && '/opt/homebrew/bin/bash {0}' || 'bash' }}
         run: |
           cd ss3-test-models/models/Simple
           if [ "${{ runner.os }}" = "Windows" ]; then

From ef6b28242fa0122adc5c69d5959f300fe8757773 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 12:59:44 -0400
Subject: [PATCH 10/30] fix shell command

---
 .github/workflows/test-simple-with-ss3-artifacts.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index 73a2d377..408049dc 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -85,7 +85,7 @@ jobs:
 
       - name: Download artifact for this OS
         id: download_artifact
-        shell: shell: ${{ runner.os == 'macOS' && '/opt/homebrew/bin/bash {0}' || 'bash' }}
+        shell: ${{ runner.os == 'macOS' && '/opt/homebrew/bin/bash {0}' || 'bash' }}
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
@@ -125,7 +125,7 @@ jobs:
             "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/$os_artifact.zip"
 
       - name: Unzip SS3 executable
-        shell: shell: ${{ runner.os == 'macOS' && '/opt/homebrew/bin/bash {0}' || 'bash' }}
+        shell: ${{ runner.os == 'macOS' && '/opt/homebrew/bin/bash {0}' || 'bash' }}
         run: |
           cd ss3_artifacts
           if [ "${{ runner.os }}" = "Windows" ]; then
@@ -145,7 +145,7 @@ jobs:
         run: mkdir -p ss3-test-models/models/Simple
 
       - name: Copy SS3 executable to Simple model directory
-        shell: shell: ${{ runner.os == 'macOS' && '/opt/homebrew/bin/bash {0}' || 'bash' }}
+        shell: ${{ runner.os == 'macOS' && '/opt/homebrew/bin/bash {0}' || 'bash' }}
         run: |
           exe="${{ matrix.exe_name }}"
           src="ss3_artifacts/$exe"
@@ -154,7 +154,7 @@ jobs:
           chmod +x "$dest" || true
 
       - name: Run SS3 on Simple model
-        shell: shell: ${{ runner.os == 'macOS' && '/opt/homebrew/bin/bash {0}' || 'bash' }}
+        shell: ${{ runner.os == 'macOS' && '/opt/homebrew/bin/bash {0}' || 'bash' }}
         run: |
           cd ss3-test-models/models/Simple
           if [ "${{ runner.os }}" = "Windows" ]; then

From 49ec8bd4a4d3a28536066c74a930ab08120ea014 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 13:00:46 -0400
Subject: [PATCH 11/30] fix shell command again

---
 .github/workflows/test-simple-with-ss3-artifacts.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index 408049dc..5c2445fb 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -141,7 +141,7 @@ jobs:
           path: ss3-test-models
 
       - name: Ensure Simple model directory exists
-        shell: shell: ${{ runner.os == 'macOS' && '/opt/homebrew/bin/bash {0}' || 'bash' }}
+        shell: ${{ runner.os == 'macOS' && '/opt/homebrew/bin/bash {0}' || 'bash' }}
         run: mkdir -p ss3-test-models/models/Simple
 
       - name: Copy SS3 executable to Simple model directory

From 1a9c31601ffdb595c737e97ba8c08a0aad41a834 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 13:05:55 -0400
Subject: [PATCH 12/30] fix shell macos

---
 .../workflows/test-simple-with-ss3-artifacts.yml   | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index 5c2445fb..6219cf8a 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -40,11 +40,11 @@ jobs:
         run: choco install jq
 
       - name: Use Bash 5 on macOS
-        if: runner.os == 'macOS'
+        if: startsWith(matrix.os, 'macos-')
         run: brew install bash
 
       - name: Set SHELL to bash 5 on macOS
-        if: runner.os == 'macOS'
+        if: startsWith(matrix.os, 'macos-')
         run: echo "/opt/homebrew/bin/bash" >> $GITHUB_PATH
 
       - name: Find latest successful build-ss3 workflow run in nmfs-ost/ss3-source-code
@@ -85,7 +85,7 @@ jobs:
 
       - name: Download artifact for this OS
         id: download_artifact
-        shell: ${{ runner.os == 'macOS' && '/opt/homebrew/bin/bash {0}' || 'bash' }}
+        shell: ${{ startsWith(matrix.os, 'macos-') && '/opt/homebrew/bin/bash {0}' || 'bash' }}
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
@@ -125,7 +125,7 @@ jobs:
             "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/$os_artifact.zip"
 
       - name: Unzip SS3 executable
-        shell: ${{ runner.os == 'macOS' && '/opt/homebrew/bin/bash {0}' || 'bash' }}
+        shell: ${{ startsWith(matrix.os, 'macos-') && '/opt/homebrew/bin/bash {0}' || 'bash' }}
         run: |
           cd ss3_artifacts
           if [ "${{ runner.os }}" = "Windows" ]; then
@@ -141,11 +141,11 @@ jobs:
           path: ss3-test-models
 
       - name: Ensure Simple model directory exists
-        shell: ${{ runner.os == 'macOS' && '/opt/homebrew/bin/bash {0}' || 'bash' }}
+        shell: ${{ startsWith(matrix.os, 'macos-') && '/opt/homebrew/bin/bash {0}' || 'bash' }}
         run: mkdir -p ss3-test-models/models/Simple
 
       - name: Copy SS3 executable to Simple model directory
-        shell: ${{ runner.os == 'macOS' && '/opt/homebrew/bin/bash {0}' || 'bash' }}
+        shell: ${{ startsWith(matrix.os, 'macos-') && '/opt/homebrew/bin/bash {0}' || 'bash' }}
         run: |
           exe="${{ matrix.exe_name }}"
           src="ss3_artifacts/$exe"
@@ -154,7 +154,7 @@ jobs:
           chmod +x "$dest" || true
 
       - name: Run SS3 on Simple model
-        shell: ${{ runner.os == 'macOS' && '/opt/homebrew/bin/bash {0}' || 'bash' }}
+        shell: ${{ startsWith(matrix.os, 'macos-') && '/opt/homebrew/bin/bash {0}' || 'bash' }}
         run: |
           cd ss3-test-models/models/Simple
           if [ "${{ runner.os }}" = "Windows" ]; then

From c42f46798fdcb992b5c0c299c7bf1f6720461702 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 13:14:53 -0400
Subject: [PATCH 13/30] try fix again for mac

---
 .../test-simple-with-ss3-artifacts.yml        | 54 +++++++++++++++++--
 1 file changed, 49 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index 6219cf8a..9d8e2009 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -85,7 +85,8 @@ jobs:
 
       - name: Download artifact for this OS
         id: download_artifact
-        shell: ${{ startsWith(matrix.os, 'macos-') && '/opt/homebrew/bin/bash {0}' || 'bash' }}
+        if: "!startsWith(matrix.os, 'macos-')"
+        shell: bash
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
@@ -124,8 +125,51 @@ jobs:
             -H "Authorization: Bearer $GH_TOKEN" \
             "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/$os_artifact.zip"
 
+      - name: Download artifact for this OS mac
+        id: download_artifact
+        if: startsWith(matrix.os, 'macos-')
+        shell: /opt/homebrew/bin/bash {0}
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          set -e
+          mkdir -p ss3_artifacts
+          os_artifact="${{ matrix.artifact_name }}"
+          readarray -t artifacts < <(echo '${{ steps.list_artifacts.outputs.artifacts }}' | jq -r '.[] | @base64')
+          if [[ ${#artifacts[@]} -eq 0 ]]; then
+            echo "No artifacts found."
+            exit 1
+          fi
+          echo "Available artifacts:"
+          for artifact in "${artifacts[@]}"; do
+            echo "${artifact}" | base64 --decode | jq -r '.name'
+          done
+          found_id=""
+          for artifact in "${artifacts[@]}"; do
+            _jq() {
+              echo "${artifact}" | base64 --decode | jq -r "${1}"
+            }
+            name=$(_jq '.name')
+            id=$(_jq '.id')
+            if [[ "$name" == "$os_artifact" ]]; then
+              found_id="$id"
+              break
+            fi
+          done
+          if [ -z "$found_id" ]; then
+            echo "Artifact $os_artifact not found!"
+            exit 1
+          fi
+          # Download the artifact
+          echo "Downloading artifact: $os_artifact"
+          gh api \
+            -H "Accept: application/vnd.github+json" \
+            -H "Authorization: Bearer $GH_TOKEN" \
+            "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/$os_artifact.zip"
+
+
       - name: Unzip SS3 executable
-        shell: ${{ startsWith(matrix.os, 'macos-') && '/opt/homebrew/bin/bash {0}' || 'bash' }}
+        shell: bash
         run: |
           cd ss3_artifacts
           if [ "${{ runner.os }}" = "Windows" ]; then
@@ -141,11 +185,11 @@ jobs:
           path: ss3-test-models
 
       - name: Ensure Simple model directory exists
-        shell: ${{ startsWith(matrix.os, 'macos-') && '/opt/homebrew/bin/bash {0}' || 'bash' }}
+        shell: bash
         run: mkdir -p ss3-test-models/models/Simple
 
       - name: Copy SS3 executable to Simple model directory
-        shell: ${{ startsWith(matrix.os, 'macos-') && '/opt/homebrew/bin/bash {0}' || 'bash' }}
+        shell: bash
         run: |
           exe="${{ matrix.exe_name }}"
           src="ss3_artifacts/$exe"
@@ -154,7 +198,7 @@ jobs:
           chmod +x "$dest" || true
 
       - name: Run SS3 on Simple model
-        shell: ${{ startsWith(matrix.os, 'macos-') && '/opt/homebrew/bin/bash {0}' || 'bash' }}
+        shell: bash
         run: |
           cd ss3-test-models/models/Simple
           if [ "${{ runner.os }}" = "Windows" ]; then

From 7ef583eafba9d0a9164ef351d2b49e849a307291 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 13:16:55 -0400
Subject: [PATCH 14/30] unique id

---
 .github/workflows/test-simple-with-ss3-artifacts.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index 9d8e2009..c35cd4ac 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -126,7 +126,7 @@ jobs:
             "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/$os_artifact.zip"
 
       - name: Download artifact for this OS mac
-        id: download_artifact
+        id: download_artifact-mac
         if: startsWith(matrix.os, 'macos-')
         shell: /opt/homebrew/bin/bash {0}
         env:

From 00141363a8056d2862032d4b8d8eb2ba26ddc83a Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 13:26:54 -0400
Subject: [PATCH 15/30] try different mac ones

---
 .../test-simple-with-ss3-artifacts.yml        | 52 ++++++++++++++++---
 1 file changed, 46 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index c35cd4ac..26b58204 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -43,9 +43,9 @@ jobs:
         if: startsWith(matrix.os, 'macos-')
         run: brew install bash
 
-      - name: Set SHELL to bash 5 on macOS
-        if: startsWith(matrix.os, 'macos-')
-        run: echo "/opt/homebrew/bin/bash" >> $GITHUB_PATH
+      # - name: Set SHELL to bash 5 on macOS
+      #   if: startsWith(matrix.os, 'macos-')
+      #   run: echo "/opt/homebrew/bin/bash" >> $GITHUB_PATH
 
       - name: Find latest successful build-ss3 workflow run in nmfs-ost/ss3-source-code
         id: get_run
@@ -126,8 +126,8 @@ jobs:
             "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/$os_artifact.zip"
 
       - name: Download artifact for this OS mac
-        id: download_artifact-mac
-        if: startsWith(matrix.os, 'macos-')
+        id: download_artifact-mac-silicon
+        if: runner.os == 'macos-latest'
         shell: /opt/homebrew/bin/bash {0}
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -167,7 +167,47 @@ jobs:
             -H "Authorization: Bearer $GH_TOKEN" \
             "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/$os_artifact.zip"
 
-
+      - name: Download artifact for this OS mac
+        id: download_artifact-mac-intel
+        if: runner.os == 'macos-13'
+        shell: /opt/homebrew/bin/bash {0}
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          set -e
+          mkdir -p ss3_artifacts
+          os_artifact="${{ matrix.artifact_name }}"
+          readarray -t artifacts < <(echo '${{ steps.list_artifacts.outputs.artifacts }}' | jq -r '.[] | @base64')
+          if [[ ${#artifacts[@]} -eq 0 ]]; then
+            echo "No artifacts found."
+            exit 1
+          fi
+          echo "Available artifacts:"
+          for artifact in "${artifacts[@]}"; do
+            echo "${artifact}" | base64 --decode | jq -r '.name'
+          done
+          found_id=""
+          for artifact in "${artifacts[@]}"; do
+            _jq() {
+              echo "${artifact}" | base64 --decode | jq -r "${1}"
+            }
+            name=$(_jq '.name')
+            id=$(_jq '.id')
+            if [[ "$name" == "$os_artifact" ]]; then
+              found_id="$id"
+              break
+            fi
+          done
+          if [ -z "$found_id" ]; then
+            echo "Artifact $os_artifact not found!"
+            exit 1
+          fi
+          # Download the artifact
+          echo "Downloading artifact: $os_artifact"
+          gh api \
+            -H "Accept: application/vnd.github+json" \
+            -H "Authorization: Bearer $GH_TOKEN" \
+            "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/$os_artifact.zip"
       - name: Unzip SS3 executable
         shell: bash
         run: |

From 1da0fb909cfe2bc03931fcc35c709cac9119d400 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 13:27:27 -0400
Subject: [PATCH 16/30] different shell for macos 13

---
 .github/workflows/test-simple-with-ss3-artifacts.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index 26b58204..d1a4675b 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -170,7 +170,7 @@ jobs:
       - name: Download artifact for this OS mac
         id: download_artifact-mac-intel
         if: runner.os == 'macos-13'
-        shell: /opt/homebrew/bin/bash {0}
+        shell: /usr/local/bin/bash {0}
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |

From 0c4287e41cb613d004aceba4f50e461b6dd51f88 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 13:32:47 -0400
Subject: [PATCH 17/30] try again

---
 .../test-simple-with-ss3-artifacts.yml        | 252 +++++++++---------
 1 file changed, 130 insertions(+), 122 deletions(-)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index d1a4675b..09069e36 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -85,7 +85,7 @@ jobs:
 
       - name: Download artifact for this OS
         id: download_artifact
-        if: "!startsWith(matrix.os, 'macos-')"
+        # if: "!startsWith(matrix.os, 'macos-')"
         shell: bash
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -93,130 +93,138 @@ jobs:
           set -e
           mkdir -p ss3_artifacts
           os_artifact="${{ matrix.artifact_name }}"
-          readarray -t artifacts < <(echo '${{ steps.list_artifacts.outputs.artifacts }}' | jq -r '.[] | @base64')
-          if [[ ${#artifacts[@]} -eq 0 ]]; then
-            echo "No artifacts found."
-            exit 1
-          fi
-          echo "Available artifacts:"
-          for artifact in "${artifacts[@]}"; do
-            echo "${artifact}" | base64 --decode | jq -r '.name'
-          done
-          found_id=""
-          for artifact in "${artifacts[@]}"; do
-            _jq() {
-              echo "${artifact}" | base64 --decode | jq -r "${1}"
-            }
-            name=$(_jq '.name')
-            id=$(_jq '.id')
-            if [[ "$name" == "$os_artifact" ]]; then
-              found_id="$id"
-              break
-            fi
-          done
-          if [ -z "$found_id" ]; then
-            echo "Artifact $os_artifact not found!"
-            exit 1
-          fi
-          # Download the artifact
-          echo "Downloading artifact: $os_artifact"
-          gh api \
-            -H "Accept: application/vnd.github+json" \
-            -H "Authorization: Bearer $GH_TOKEN" \
-            "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/$os_artifact.zip"
-
-      - name: Download artifact for this OS mac
-        id: download_artifact-mac-silicon
-        if: runner.os == 'macos-latest'
-        shell: /opt/homebrew/bin/bash {0}
-        env:
-          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          set -e
-          mkdir -p ss3_artifacts
-          os_artifact="${{ matrix.artifact_name }}"
-          readarray -t artifacts < <(echo '${{ steps.list_artifacts.outputs.artifacts }}' | jq -r '.[] | @base64')
-          if [[ ${#artifacts[@]} -eq 0 ]]; then
-            echo "No artifacts found."
-            exit 1
+          if [[ "${{ matrix.os }}" == "macos-13" ]]; then
+            BASH_PATH="/usr/local/bin/bash"
+          elif [[ "${{ matrix.os }}" == "macos-latest" ]]; then
+            BASH_PATH="/opt/homebrew/bin/bash"
+          else
+            BASH_PATH="bash"
           fi
-          echo "Available artifacts:"
-          for artifact in "${artifacts[@]}"; do
-            echo "${artifact}" | base64 --decode | jq -r '.name'
-          done
-          found_id=""
-          for artifact in "${artifacts[@]}"; do
-            _jq() {
-              echo "${artifact}" | base64 --decode | jq -r "${1}"
-            }
-            name=$(_jq '.name')
-            id=$(_jq '.id')
-            if [[ "$name" == "$os_artifact" ]]; then
-              found_id="$id"
-              break
+          $BASH_PATH -c '
+            readarray -t artifacts < <(echo "${{ steps.list_artifacts.outputs.artifacts }}" | jq -r ".[] | @base64")
+            if [[ ${#artifacts[@]} -eq 0 ]]; then
+              echo "No artifacts found."
+              exit 1
             fi
-          done
-          if [ -z "$found_id" ]; then
-            echo "Artifact $os_artifact not found!"
-            exit 1
-          fi
-          # Download the artifact
-          echo "Downloading artifact: $os_artifact"
-          gh api \
-            -H "Accept: application/vnd.github+json" \
-            -H "Authorization: Bearer $GH_TOKEN" \
-            "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/$os_artifact.zip"
-
-      - name: Download artifact for this OS mac
-        id: download_artifact-mac-intel
-        if: runner.os == 'macos-13'
-        shell: /usr/local/bin/bash {0}
-        env:
-          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          set -e
-          mkdir -p ss3_artifacts
-          os_artifact="${{ matrix.artifact_name }}"
-          readarray -t artifacts < <(echo '${{ steps.list_artifacts.outputs.artifacts }}' | jq -r '.[] | @base64')
-          if [[ ${#artifacts[@]} -eq 0 ]]; then
-            echo "No artifacts found."
-            exit 1
-          fi
-          echo "Available artifacts:"
-          for artifact in "${artifacts[@]}"; do
-            echo "${artifact}" | base64 --decode | jq -r '.name'
-          done
-          found_id=""
-          for artifact in "${artifacts[@]}"; do
-            _jq() {
-              echo "${artifact}" | base64 --decode | jq -r "${1}"
-            }
-            name=$(_jq '.name')
-            id=$(_jq '.id')
-            if [[ "$name" == "$os_artifact" ]]; then
-              found_id="$id"
-              break
+            echo "Available artifacts:"
+            for artifact in "${artifacts[@]}"; do
+              echo "${artifact}" | base64 --decode | jq -r ".name"
+            done
+            found_id=""
+            for artifact in "${artifacts[@]}"; do
+              _jq() {
+                echo "${artifact}" | base64 --decode | jq -r "${1}"
+              }
+              name=$(_jq ".name")
+              id=$(_jq ".id")
+              if [[ "$name" == "${os_artifact}" ]]; then
+                found_id="$id"
+                break
+              fi
+            done
+            if [ -z "$found_id" ]; then
+              echo "Artifact ${os_artifact} not found!"
+              exit 1
             fi
-          done
-          if [ -z "$found_id" ]; then
-            echo "Artifact $os_artifact not found!"
-            exit 1
-          fi
-          # Download the artifact
-          echo "Downloading artifact: $os_artifact"
-          gh api \
-            -H "Accept: application/vnd.github+json" \
-            -H "Authorization: Bearer $GH_TOKEN" \
-            "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/$os_artifact.zip"
-      - name: Unzip SS3 executable
-        shell: bash
-        run: |
-          cd ss3_artifacts
-          if [ "${{ runner.os }}" = "Windows" ]; then
-            powershell -Command "Expand-Archive -Path '${{ matrix.artifact_name }}.zip' -DestinationPath ."
-          else
-            unzip -o "${{ matrix.artifact_name }}.zip"
-          fi
+            echo "Downloading artifact: ${os_artifact}"
+            gh api \
+              -H "Accept: application/vnd.github+json" \
+              -H "Authorization: Bearer $GH_TOKEN" \
+              "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/${os_artifact}.zip"
+          '
+
+      # - name: Download artifact for this OS mac
+      #   id: download_artifact-mac-silicon
+      #   if: runner.os == 'macos-latest'
+      #   shell: /opt/homebrew/bin/bash {0}
+      #   env:
+      #     GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      #   run: |
+      #     set -e
+      #     mkdir -p ss3_artifacts
+      #     os_artifact="${{ matrix.artifact_name }}"
+      #     readarray -t artifacts < <(echo '${{ steps.list_artifacts.outputs.artifacts }}' | jq -r '.[] | @base64')
+      #     if [[ ${#artifacts[@]} -eq 0 ]]; then
+      #       echo "No artifacts found."
+      #       exit 1
+      #     fi
+      #     echo "Available artifacts:"
+      #     for artifact in "${artifacts[@]}"; do
+      #       echo "${artifact}" | base64 --decode | jq -r '.name'
+      #     done
+      #     found_id=""
+      #     for artifact in "${artifacts[@]}"; do
+      #       _jq() {
+      #         echo "${artifact}" | base64 --decode | jq -r "${1}"
+      #       }
+      #       name=$(_jq '.name')
+      #       id=$(_jq '.id')
+      #       if [[ "$name" == "$os_artifact" ]]; then
+      #         found_id="$id"
+      #         break
+      #       fi
+      #     done
+      #     if [ -z "$found_id" ]; then
+      #       echo "Artifact $os_artifact not found!"
+      #       exit 1
+      #     fi
+      #     # Download the artifact
+      #     echo "Downloading artifact: $os_artifact"
+      #     gh api \
+      #       -H "Accept: application/vnd.github+json" \
+      #       -H "Authorization: Bearer $GH_TOKEN" \
+      #       "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/$os_artifact.zip"
+
+      # - name: Download artifact for this OS mac
+      #   id: download_artifact-mac-intel
+      #   if: runner.os == 'macos-13'
+      #   shell: /usr/local/bin/bash {0}
+      #   env:
+      #     GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      #   run: |
+      #     set -e
+      #     mkdir -p ss3_artifacts
+      #     os_artifact="${{ matrix.artifact_name }}"
+      #     readarray -t artifacts < <(echo '${{ steps.list_artifacts.outputs.artifacts }}' | jq -r '.[] | @base64')
+      #     if [[ ${#artifacts[@]} -eq 0 ]]; then
+      #       echo "No artifacts found."
+      #       exit 1
+      #     fi
+      #     echo "Available artifacts:"
+      #     for artifact in "${artifacts[@]}"; do
+      #       echo "${artifact}" | base64 --decode | jq -r '.name'
+      #     done
+      #     found_id=""
+      #     for artifact in "${artifacts[@]}"; do
+      #       _jq() {
+      #         echo "${artifact}" | base64 --decode | jq -r "${1}"
+      #       }
+      #       name=$(_jq '.name')
+      #       id=$(_jq '.id')
+      #       if [[ "$name" == "$os_artifact" ]]; then
+      #         found_id="$id"
+      #         break
+      #       fi
+      #     done
+      #     if [ -z "$found_id" ]; then
+      #       echo "Artifact $os_artifact not found!"
+      #       exit 1
+      #     fi
+      #     # Download the artifact
+      #     echo "Downloading artifact: $os_artifact"
+      #     gh api \
+      #       -H "Accept: application/vnd.github+json" \
+      #       -H "Authorization: Bearer $GH_TOKEN" \
+      #       "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/$os_artifact.zip"
+      # - name: Unzip SS3 executable
+      #   shell: bash
+      #   run: |
+      #     cd ss3_artifacts
+      #     if [ "${{ runner.os }}" = "Windows" ]; then
+      #       powershell -Command "Expand-Archive -Path '${{ matrix.artifact_name }}.zip' -DestinationPath ."
+      #     else
+      #       unzip -o "${{ matrix.artifact_name }}.zip"
+      #     fi
 
       - name: Checkout test models repository
         uses: actions/checkout@v4

From 241a87d1a28942acf190a2cd81e8eef6e3d49262 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 13:38:09 -0400
Subject: [PATCH 18/30] try again

---
 .../test-simple-with-ss3-artifacts.yml        | 168 ++++--------------
 1 file changed, 38 insertions(+), 130 deletions(-)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index 09069e36..ce04232d 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -85,7 +85,6 @@ jobs:
 
       - name: Download artifact for this OS
         id: download_artifact
-        # if: "!startsWith(matrix.os, 'macos-')"
         shell: bash
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -93,138 +92,47 @@ jobs:
           set -e
           mkdir -p ss3_artifacts
           os_artifact="${{ matrix.artifact_name }}"
-          if [[ "${{ matrix.os }}" == "macos-13" ]]; then
-            BASH_PATH="/usr/local/bin/bash"
-          elif [[ "${{ matrix.os }}" == "macos-latest" ]]; then
-            BASH_PATH="/opt/homebrew/bin/bash"
-          else
-            BASH_PATH="bash"
+          ARTIFACTS_JSON='${{ steps.list_artifacts.outputs.artifacts }}'
+          echo "RAW ARTIFACTS OUTPUT:"
+          echo "$ARTIFACTS_JSON"
+
+          if [ -z "$ARTIFACTS_JSON" ]; then
+            echo "No artifacts JSON found -- previous step may have failed."
+            exit 1
           fi
-          $BASH_PATH -c '
-            readarray -t artifacts < <(echo "${{ steps.list_artifacts.outputs.artifacts }}" | jq -r ".[] | @base64")
-            if [[ ${#artifacts[@]} -eq 0 ]]; then
-              echo "No artifacts found."
-              exit 1
-            fi
-            echo "Available artifacts:"
-            for artifact in "${artifacts[@]}"; do
-              echo "${artifact}" | base64 --decode | jq -r ".name"
-            done
-            found_id=""
-            for artifact in "${artifacts[@]}"; do
-              _jq() {
-                echo "${artifact}" | base64 --decode | jq -r "${1}"
-              }
-              name=$(_jq ".name")
-              id=$(_jq ".id")
-              if [[ "$name" == "${os_artifact}" ]]; then
-                found_id="$id"
-                break
-              fi
-            done
-            if [ -z "$found_id" ]; then
-              echo "Artifact ${os_artifact} not found!"
-              exit 1
-            fi
-            echo "Downloading artifact: ${os_artifact}"
-            gh api \
-              -H "Accept: application/vnd.github+json" \
-              -H "Authorization: Bearer $GH_TOKEN" \
-              "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/${os_artifact}.zip"
-          '
 
-      # - name: Download artifact for this OS mac
-      #   id: download_artifact-mac-silicon
-      #   if: runner.os == 'macos-latest'
-      #   shell: /opt/homebrew/bin/bash {0}
-      #   env:
-      #     GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      #   run: |
-      #     set -e
-      #     mkdir -p ss3_artifacts
-      #     os_artifact="${{ matrix.artifact_name }}"
-      #     readarray -t artifacts < <(echo '${{ steps.list_artifacts.outputs.artifacts }}' | jq -r '.[] | @base64')
-      #     if [[ ${#artifacts[@]} -eq 0 ]]; then
-      #       echo "No artifacts found."
-      #       exit 1
-      #     fi
-      #     echo "Available artifacts:"
-      #     for artifact in "${artifacts[@]}"; do
-      #       echo "${artifact}" | base64 --decode | jq -r '.name'
-      #     done
-      #     found_id=""
-      #     for artifact in "${artifacts[@]}"; do
-      #       _jq() {
-      #         echo "${artifact}" | base64 --decode | jq -r "${1}"
-      #       }
-      #       name=$(_jq '.name')
-      #       id=$(_jq '.id')
-      #       if [[ "$name" == "$os_artifact" ]]; then
-      #         found_id="$id"
-      #         break
-      #       fi
-      #     done
-      #     if [ -z "$found_id" ]; then
-      #       echo "Artifact $os_artifact not found!"
-      #       exit 1
-      #     fi
-      #     # Download the artifact
-      #     echo "Downloading artifact: $os_artifact"
-      #     gh api \
-      #       -H "Accept: application/vnd.github+json" \
-      #       -H "Authorization: Bearer $GH_TOKEN" \
-      #       "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/$os_artifact.zip"
+          IFS=$'\n' artifacts=($(echo "$ARTIFACTS_JSON" | jq -r '.[] | @base64'))
+          if [[ ${#artifacts[@]} -eq 0 ]]; then
+            echo "No artifacts found."
+            exit 1
+          fi
 
-      # - name: Download artifact for this OS mac
-      #   id: download_artifact-mac-intel
-      #   if: runner.os == 'macos-13'
-      #   shell: /usr/local/bin/bash {0}
-      #   env:
-      #     GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      #   run: |
-      #     set -e
-      #     mkdir -p ss3_artifacts
-      #     os_artifact="${{ matrix.artifact_name }}"
-      #     readarray -t artifacts < <(echo '${{ steps.list_artifacts.outputs.artifacts }}' | jq -r '.[] | @base64')
-      #     if [[ ${#artifacts[@]} -eq 0 ]]; then
-      #       echo "No artifacts found."
-      #       exit 1
-      #     fi
-      #     echo "Available artifacts:"
-      #     for artifact in "${artifacts[@]}"; do
-      #       echo "${artifact}" | base64 --decode | jq -r '.name'
-      #     done
-      #     found_id=""
-      #     for artifact in "${artifacts[@]}"; do
-      #       _jq() {
-      #         echo "${artifact}" | base64 --decode | jq -r "${1}"
-      #       }
-      #       name=$(_jq '.name')
-      #       id=$(_jq '.id')
-      #       if [[ "$name" == "$os_artifact" ]]; then
-      #         found_id="$id"
-      #         break
-      #       fi
-      #     done
-      #     if [ -z "$found_id" ]; then
-      #       echo "Artifact $os_artifact not found!"
-      #       exit 1
-      #     fi
-      #     # Download the artifact
-      #     echo "Downloading artifact: $os_artifact"
-      #     gh api \
-      #       -H "Accept: application/vnd.github+json" \
-      #       -H "Authorization: Bearer $GH_TOKEN" \
-      #       "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/$os_artifact.zip"
-      # - name: Unzip SS3 executable
-      #   shell: bash
-      #   run: |
-      #     cd ss3_artifacts
-      #     if [ "${{ runner.os }}" = "Windows" ]; then
-      #       powershell -Command "Expand-Archive -Path '${{ matrix.artifact_name }}.zip' -DestinationPath ."
-      #     else
-      #       unzip -o "${{ matrix.artifact_name }}.zip"
-      #     fi
+          echo "Available artifacts:"
+          for artifact in "${artifacts[@]}"; do
+            echo "${artifact}" | base64 --decode | jq -r '.name'
+          done
+
+          found_id=""
+          for artifact in "${artifacts[@]}"; do
+            _jq() {
+              echo "${artifact}" | base64 --decode | jq -r "${1}"
+            }
+            name=$(_jq '.name')
+            id=$(_jq '.id')
+            if [[ "$name" == "$os_artifact" ]]; then
+              found_id="$id"
+              break
+            fi
+          done
+          if [ -z "$found_id" ]; then
+            echo "Artifact $os_artifact not found!"
+            exit 1
+          fi
+          echo "Downloading artifact: $os_artifact"
+          gh api \
+            -H "Accept: application/vnd.github+json" \
+            -H "Authorization: Bearer $GH_TOKEN" \
+            "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/$os_artifact.zip"
 
       - name: Checkout test models repository
         uses: actions/checkout@v4

From 3edcc2a482a7d05e9920d88a17c22ef4dba1691e Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 14:02:27 -0400
Subject: [PATCH 19/30] add subdir name

---
 .github/workflows/test-simple-with-ss3-artifacts.yml | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index ce04232d..e6571951 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -43,10 +43,6 @@ jobs:
         if: startsWith(matrix.os, 'macos-')
         run: brew install bash
 
-      # - name: Set SHELL to bash 5 on macOS
-      #   if: startsWith(matrix.os, 'macos-')
-      #   run: echo "/opt/homebrew/bin/bash" >> $GITHUB_PATH
-
       - name: Find latest successful build-ss3 workflow run in nmfs-ost/ss3-source-code
         id: get_run
         uses: actions/github-script@v7
@@ -147,8 +143,9 @@ jobs:
       - name: Copy SS3 executable to Simple model directory
         shell: bash
         run: |
+          subdir="${{ matrix.artifact_name}}"
           exe="${{ matrix.exe_name }}"
-          src="ss3_artifacts/$exe"
+          src="ss3_artifacts/$subdir/$exe"
           dest="ss3-test-models/models/Simple/$exe"
           cp "$src" "$dest"
           chmod +x "$dest" || true
@@ -158,9 +155,9 @@ jobs:
         run: |
           cd ss3-test-models/models/Simple
           if [ "${{ runner.os }}" = "Windows" ]; then
-            .\${{ matrix.exe_name }}
+            .\${{ matrix.exe_name }} - nohess -stopph 0
           else
-            ./${{ matrix.exe_name }}
+            ./${{ matrix.exe_name }} -nohess -stopph 0
           fi
 
       - name: Archive Simple model output

From 631b07d41e116765d404c7d5a0014208b13c79a6 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 14:26:54 -0400
Subject: [PATCH 20/30] look at all files from ss3_artifacts

---
 .github/workflows/test-simple-with-ss3-artifacts.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index e6571951..bd8b1805 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -140,6 +140,12 @@ jobs:
         shell: bash
         run: mkdir -p ss3-test-models/models/Simple
 
+      - name: see what files exist
+        shell: bash
+        run: |
+          echo "Files in ss3_artifacts:"
+          find ss3_artifacts
+
       - name: Copy SS3 executable to Simple model directory
         shell: bash
         run: |

From 93cae22693f070c8a0b02e5d62228c48935f5c4b Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 15:26:17 -0400
Subject: [PATCH 21/30] add back step to unzip files

---
 .github/workflows/test-simple-with-ss3-artifacts.yml | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index bd8b1805..97ee3e90 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -130,6 +130,16 @@ jobs:
             -H "Authorization: Bearer $GH_TOKEN" \
             "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/$os_artifact.zip"
 
+      - name: Unzip SS3 executable
+        shell: bash
+        run: |
+          cd ss3_artifacts
+          if [ "${{ runner.os }}" = "Windows" ]; then
+            powershell -Command "Expand-Archive -Path '${{ matrix.artifact_name }}.zip' -DestinationPath ."
+          else
+            unzip -o "${{ matrix.artifact_name }}.zip"
+          fi
+          
       - name: Checkout test models repository
         uses: actions/checkout@v4
         with:

From dc63fd2435278fbee32e3ee732d101af7e27fd2b Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 15:32:02 -0400
Subject: [PATCH 22/30] remove subdir

---
 .github/workflows/test-simple-with-ss3-artifacts.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index 97ee3e90..4bd9c158 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -139,7 +139,7 @@ jobs:
           else
             unzip -o "${{ matrix.artifact_name }}.zip"
           fi
-          
+
       - name: Checkout test models repository
         uses: actions/checkout@v4
         with:
@@ -159,9 +159,8 @@ jobs:
       - name: Copy SS3 executable to Simple model directory
         shell: bash
         run: |
-          subdir="${{ matrix.artifact_name}}"
           exe="${{ matrix.exe_name }}"
-          src="ss3_artifacts/$subdir/$exe"
+          src="ss3_artifacts/$exe"
           dest="ss3-test-models/models/Simple/$exe"
           cp "$src" "$dest"
           chmod +x "$dest" || true

From 1b5508657d4e4f8944537705d6b00952413edbaf Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 15:51:58 -0400
Subject: [PATCH 23/30] add debugging lines

---
 .github/workflows/test-simple-with-ss3-artifacts.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index 4bd9c158..2df92670 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -92,6 +92,13 @@ jobs:
           echo "RAW ARTIFACTS OUTPUT:"
           echo "$ARTIFACTS_JSON"
 
+
+          echo "RAW ARTIFACTS OUTPUT:"
+          echo "$ARTIFACTS_JSON" | cat -v
+          echo "jq output is:"
+          echo "$ARTIFACTS_JSON" | jq -cr '.[] | select(. != null) | @base64' | cat -v
+
+
           if [ -z "$ARTIFACTS_JSON" ]; then
             echo "No artifacts JSON found -- previous step may have failed."
             exit 1

From 9a8fa422f421531d56b7ff8b36d85be4a9366666 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 16:00:18 -0400
Subject: [PATCH 24/30] add portion to remove extra carriage returns

---
 .../workflows/test-simple-with-ss3-artifacts.yml  | 15 ++-------------
 1 file changed, 2 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index 2df92670..6e0047bf 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -89,22 +89,11 @@ jobs:
           mkdir -p ss3_artifacts
           os_artifact="${{ matrix.artifact_name }}"
           ARTIFACTS_JSON='${{ steps.list_artifacts.outputs.artifacts }}'
-          echo "RAW ARTIFACTS OUTPUT:"
-          echo "$ARTIFACTS_JSON"
-
-
+          ARTIFACTS_JSON=$(echo "$ARTIFACTS_JSON" | tr -d '\r')
           echo "RAW ARTIFACTS OUTPUT:"
           echo "$ARTIFACTS_JSON" | cat -v
-          echo "jq output is:"
-          echo "$ARTIFACTS_JSON" | jq -cr '.[] | select(. != null) | @base64' | cat -v
-
-
-          if [ -z "$ARTIFACTS_JSON" ]; then
-            echo "No artifacts JSON found -- previous step may have failed."
-            exit 1
-          fi
 
-          IFS=$'\n' artifacts=($(echo "$ARTIFACTS_JSON" | jq -r '.[] | @base64'))
+          IFS=$'\n' artifacts=($(echo "$ARTIFACTS_JSON" | jq -cr '.[] | select(. != null) | @base64' | tr -d '\r' | grep -v '^$'))
           if [[ ${#artifacts[@]} -eq 0 ]]; then
             echo "No artifacts found."
             exit 1

From 07de98149d4659ff197ab116be249016dfc1366a Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 16:10:01 -0400
Subject: [PATCH 25/30] fix api call

---
 .github/workflows/test-simple-with-ss3-artifacts.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index 6e0047bf..1c16a31b 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -124,7 +124,7 @@ jobs:
           gh api \
             -H "Accept: application/vnd.github+json" \
             -H "Authorization: Bearer $GH_TOKEN" \
-            "/repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/$os_artifact.zip"
+            "./repos/nmfs-ost/ss3-source-code/actions/artifacts/$found_id/zip" > "ss3_artifacts/$os_artifact.zip"
 
       - name: Unzip SS3 executable
         shell: bash

From 2511cce38c2a20b795fe5c109aba4c0919ab54f2 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 16:14:07 -0400
Subject: [PATCH 26/30] fix run command

---
 .github/workflows/test-simple-with-ss3-artifacts.yml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index 1c16a31b..391d8026 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -165,11 +165,7 @@ jobs:
         shell: bash
         run: |
           cd ss3-test-models/models/Simple
-          if [ "${{ runner.os }}" = "Windows" ]; then
-            .\${{ matrix.exe_name }} - nohess -stopph 0
-          else
-            ./${{ matrix.exe_name }} -nohess -stopph 0
-          fi
+          ./${{ matrix.exe_name }} -nohess -stopph 0
 
       - name: Archive Simple model output
         uses: actions/upload-artifact@v4

From 6c455dcbd81f5d758d807182ed99c0f704f5864c Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 16:22:43 -0400
Subject: [PATCH 27/30] add fail if control new file isn't found

---
 .github/workflows/test-simple-with-ss3-artifacts.yml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index 391d8026..0be92aa8 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -167,6 +167,14 @@ jobs:
           cd ss3-test-models/models/Simple
           ./${{ matrix.exe_name }} -nohess -stopph 0
 
+      - name: Check if model ran successfully
+        shell: bash
+        run: |
+          if [ ! -f "ss3-test-models/models/Simple/control.ss_new" ]; then
+            echo "ERROR: control.ss_new not found in ss3-test-models/models/Simple
+            exit 1
+          fi
+
       - name: Archive Simple model output
         uses: actions/upload-artifact@v4
         with:

From 5629962acea36c0de64ebd97dc8a5e94fe31e505 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 7 Jul 2025 16:28:07 -0400
Subject: [PATCH 28/30] fix

---
 .github/workflows/test-simple-with-ss3-artifacts.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index 0be92aa8..4e99336d 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -171,7 +171,7 @@ jobs:
         shell: bash
         run: |
           if [ ! -f "ss3-test-models/models/Simple/control.ss_new" ]; then
-            echo "ERROR: control.ss_new not found in ss3-test-models/models/Simple
+            echo "ERROR: control.ss_new not found!"
             exit 1
           fi
 

From 73a6ce72fcfc19c2caf2f413bd1120d1e44d3bf6 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Mon, 14 Jul 2025 14:24:41 +0000
Subject: [PATCH 29/30] only have test simple with artifacts run with success
 of build; add cancel concurrent actions

---
 .github/workflows/build-ss3-warnings.yml            |  4 ++++
 .github/workflows/build-ss3.yml                     |  5 ++++-
 .github/workflows/run-ss3-bootstrap.yml             |  4 ++++
 .github/workflows/run-ss3-mcmc.yml                  |  6 +++++-
 .github/workflows/run-ss3-no-est.yml                |  4 ++++
 .github/workflows/run-ss3-with-est.yml              |  4 ++++
 .github/workflows/test-r4ss-with-ss3.yml            |  4 ++++
 .../workflows/test-simple-with-ss3-artifacts.yml    | 13 +++++++++----
 8 files changed, 38 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/build-ss3-warnings.yml b/.github/workflows/build-ss3-warnings.yml
index 7bd21116..945ef67c 100644
--- a/.github/workflows/build-ss3-warnings.yml
+++ b/.github/workflows/build-ss3-warnings.yml
@@ -19,6 +19,10 @@ on:
     branches:
       - main
 
+concurrency:
+    group: ${{ github.workflow}}-${{ github.ref }}
+    cancel-in-progress: true
+    
 jobs:
   build-warnings:
     if: github.event.pull_request.draft == false
diff --git a/.github/workflows/build-ss3.yml b/.github/workflows/build-ss3.yml
index 7418bae5..655a9a46 100644
--- a/.github/workflows/build-ss3.yml
+++ b/.github/workflows/build-ss3.yml
@@ -10,7 +10,10 @@ on:
       - '**.sh'
     workflow_dispatch:
 
-
+concurrency:
+    group: ${{ github.workflow}}-${{ github.ref }}
+    cancel-in-progress: true
+    
 jobs:
   build-ss3:
     runs-on: ${{ matrix.config.os }}
diff --git a/.github/workflows/run-ss3-bootstrap.yml b/.github/workflows/run-ss3-bootstrap.yml
index af3fd92d..aa1e8910 100644
--- a/.github/workflows/run-ss3-bootstrap.yml
+++ b/.github/workflows/run-ss3-bootstrap.yml
@@ -17,6 +17,10 @@ on:
     branches:
       - main
 
+concurrency:
+    group: ${{ github.workflow}}-${{ github.ref }}
+    cancel-in-progress: true
+    
 jobs:
   run-ss3-bootstrap-files:
     if: github.event.pull_request.draft == false
diff --git a/.github/workflows/run-ss3-mcmc.yml b/.github/workflows/run-ss3-mcmc.yml
index 29b29df5..8ec627bf 100644
--- a/.github/workflows/run-ss3-mcmc.yml
+++ b/.github/workflows/run-ss3-mcmc.yml
@@ -15,7 +15,11 @@ on:
       - '**.tpl'
     branches:
       - main
-      
+
+concurrency:
+    group: ${{ github.workflow}}-${{ github.ref }}
+    cancel-in-progress: true
+    
 # Check MCMC works
 jobs:
   run-ss3-no-est:
diff --git a/.github/workflows/run-ss3-no-est.yml b/.github/workflows/run-ss3-no-est.yml
index ccd0e537..b8d18e54 100644
--- a/.github/workflows/run-ss3-no-est.yml
+++ b/.github/workflows/run-ss3-no-est.yml
@@ -14,6 +14,10 @@ on:
     branches: 
       - main
 
+concurrency:
+    group: ${{ github.workflow}}-${{ github.ref }}
+    cancel-in-progress: true
+
 # Run models without estimation, then try to run again with .ss_new
 jobs:
   run-ss3-no-est:
diff --git a/.github/workflows/run-ss3-with-est.yml b/.github/workflows/run-ss3-with-est.yml
index 2225df50..f3611431 100644
--- a/.github/workflows/run-ss3-with-est.yml
+++ b/.github/workflows/run-ss3-with-est.yml
@@ -17,6 +17,10 @@ on:
     branches:
       - main
 
+concurrency:
+    group: ${{ github.workflow}}-${{ github.ref }}
+    cancel-in-progress: true
+    
 # Run fast running SS3 test models with estimation
 jobs:
   run-ss3-with-est:
diff --git a/.github/workflows/test-r4ss-with-ss3.yml b/.github/workflows/test-r4ss-with-ss3.yml
index e1d9e618..e24f4475 100644
--- a/.github/workflows/test-r4ss-with-ss3.yml
+++ b/.github/workflows/test-r4ss-with-ss3.yml
@@ -16,6 +16,10 @@ on:
     branches:
       - main
 
+concurrency:
+    group: ${{ github.workflow}}-${{ github.ref }}
+    cancel-in-progress: true
+
 # Run models without estimation, then run r4ss SS_plots() and SS_output()
 jobs:
   test-r4ss-with-ss3:
diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index 4e99336d..5fadf56f 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -1,12 +1,17 @@
 on:
-  push:
-      # paths:
-      # - '**.tpl'
-      # - '**.sh'
+  workflow_run:
+    workflows: ["build-ss3"]
+    types:
+      - completed
   workflow_dispatch:
 
+concurrency:
+    group: ${{ github.workflow}}-${{ github.ref }}
+    cancel-in-progress: true
+
 jobs:
   test-simple-model:
+    if: ${{ github.event.workflow_run.conclusion == 'success' }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:

From 96e3c8282fc44038b3363b6da6bbfc3abbef0261 Mon Sep 17 00:00:00 2001
From: Elizabeth Perl <elizabeth.gugliotti@noaa.gov>
Date: Tue, 15 Jul 2025 15:02:11 -0400
Subject: [PATCH 30/30] Potential fix for code scanning alert no. 26: Workflow
 does not contain permissions

Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>
---
 .github/workflows/test-simple-with-ss3-artifacts.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/test-simple-with-ss3-artifacts.yml b/.github/workflows/test-simple-with-ss3-artifacts.yml
index 5fadf56f..4399d23f 100644
--- a/.github/workflows/test-simple-with-ss3-artifacts.yml
+++ b/.github/workflows/test-simple-with-ss3-artifacts.yml
@@ -5,6 +5,10 @@ on:
       - completed
   workflow_dispatch:
 
+permissions:
+  contents: read
+  actions: read
+
 concurrency:
     group: ${{ github.workflow}}-${{ github.ref }}
     cancel-in-progress: true