From d61e590b76da2f698a7a1f67eebf40eceb9ad07b Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Thu, 23 May 2024 16:43:45 -0400
Subject: [PATCH 01/19] action testing

---
 .github/run_jcb_basic_testing.yaml | 62 ++++++++++++++++++++++++++++++
 1 file changed, 62 insertions(+)
 create mode 100644 .github/run_jcb_basic_testing.yaml

diff --git a/.github/run_jcb_basic_testing.yaml b/.github/run_jcb_basic_testing.yaml
new file mode 100644
index 0000000..8e9b500
--- /dev/null
+++ b/.github/run_jcb_basic_testing.yaml
@@ -0,0 +1,62 @@
+name: Run JCB basic testing with jcb-gdas changes
+
+on:
+  push:
+    branches:
+      - develop
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    env:
+      JCB_REPO: https://github.com/NOAA-EMC/jcb.git
+      JCB_DEVELOP_BRANCH: develop
+
+    steps:
+    - name: Checkout submodule repository
+      uses: actions/checkout@v3
+      with:
+        submodules: true
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.x'  # specify your python version
+
+    - name: Determine branch to use
+      id: determine-branch
+      run: |
+        # Determine if the branch exists in the jcb repo
+        BRANCH_NAME=${{ github.ref_name }}
+        git ls-remote --exit-code --heads $JCB_REPO $BRANCH_NAME
+        if [ $? -eq 0 ]; then
+          echo "Branch $BRANCH_NAME exists in jcb repo."
+          echo "BRANCH_NAME=$BRANCH_NAME" >> $GITHUB_ENV
+        else
+          echo "Branch $BRANCH_NAME does not exist in jcb repo. Using develop branch."
+          echo "BRANCH_NAME=$JCB_DEVELOP_BRANCH" >> $GITHUB_ENV
+        fi
+
+    - name: Clone jcb repository
+      run: |
+        echo "BRANCH_NAME=${{ env.BRANCH_NAME }}"
+        git clone --branch ${{ env.BRANCH_NAME }} $JCB_REPO jcb_repo
+        cd jcb_repo/src/jcb/configuration/apps/gdas
+        git checkout ${{ env.BRANCH_NAME }}
+        cd -
+
+    - name: Install dependencies
+      run: |
+        cd jcb_repo
+        pip install .[testing]
+
+    - name: Run unit tests
+      run: |
+        cd $GITHUB_WORKSPACE
+        pytest -v

From ddaad0e25e072de9453ccb0e246c4c423b6470f1 Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Fri, 24 May 2024 09:04:23 -0400
Subject: [PATCH 02/19] action debugging

---
 .github/workflows/run_jcb_basic_testing.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
index de73834..5253e2a 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -34,6 +34,7 @@ jobs:
       run: |
         # Determine if the branch exists in the jcb repo
         BRANCH_NAME=${{ github.ref_name }}
+        echo "BRANCH NAME IS $BRANCH_NAME"
         git ls-remote --exit-code --heads $JCB_REPO $BRANCH_NAME
         if [ $? -eq 0 ]; then
           echo "Branch $BRANCH_NAME exists in jcb repo."

From 68fcc34d07fb130918cfabb78d200f16c47cb4f6 Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Fri, 24 May 2024 09:18:05 -0400
Subject: [PATCH 03/19] action debugging

---
 .github/run_jcb_basic_testing.yaml           | 62 --------------------
 .github/workflows/run_jcb_basic_testing.yaml |  3 +-
 2 files changed, 2 insertions(+), 63 deletions(-)
 delete mode 100644 .github/run_jcb_basic_testing.yaml

diff --git a/.github/run_jcb_basic_testing.yaml b/.github/run_jcb_basic_testing.yaml
deleted file mode 100644
index 8e9b500..0000000
--- a/.github/run_jcb_basic_testing.yaml
+++ /dev/null
@@ -1,62 +0,0 @@
-name: Run JCB basic testing with jcb-gdas changes
-
-on:
-  push:
-    branches:
-      - develop
-  pull_request:
-    types:
-      - opened
-      - synchronize
-      - reopened
-
-jobs:
-  test:
-    runs-on: ubuntu-latest
-
-    env:
-      JCB_REPO: https://github.com/NOAA-EMC/jcb.git
-      JCB_DEVELOP_BRANCH: develop
-
-    steps:
-    - name: Checkout submodule repository
-      uses: actions/checkout@v3
-      with:
-        submodules: true
-
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: '3.x'  # specify your python version
-
-    - name: Determine branch to use
-      id: determine-branch
-      run: |
-        # Determine if the branch exists in the jcb repo
-        BRANCH_NAME=${{ github.ref_name }}
-        git ls-remote --exit-code --heads $JCB_REPO $BRANCH_NAME
-        if [ $? -eq 0 ]; then
-          echo "Branch $BRANCH_NAME exists in jcb repo."
-          echo "BRANCH_NAME=$BRANCH_NAME" >> $GITHUB_ENV
-        else
-          echo "Branch $BRANCH_NAME does not exist in jcb repo. Using develop branch."
-          echo "BRANCH_NAME=$JCB_DEVELOP_BRANCH" >> $GITHUB_ENV
-        fi
-
-    - name: Clone jcb repository
-      run: |
-        echo "BRANCH_NAME=${{ env.BRANCH_NAME }}"
-        git clone --branch ${{ env.BRANCH_NAME }} $JCB_REPO jcb_repo
-        cd jcb_repo/src/jcb/configuration/apps/gdas
-        git checkout ${{ env.BRANCH_NAME }}
-        cd -
-
-    - name: Install dependencies
-      run: |
-        cd jcb_repo
-        pip install .[testing]
-
-    - name: Run unit tests
-      run: |
-        cd $GITHUB_WORKSPACE
-        pytest -v
diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
index 5253e2a..1948236 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -16,6 +16,7 @@ jobs:
 
     env:
       JCB_REPO: https://github.com/NOAA-EMC/jcb.git
+      JCB_APP_REPO: https://github.com/NOAA-EMC/jcb-gdas.git
       JCB_DEVELOP_BRANCH: develop
 
     steps:
@@ -33,7 +34,7 @@ jobs:
       id: determine-branch
       run: |
         # Determine if the branch exists in the jcb repo
-        BRANCH_NAME=${{ github.ref_name }}
+        BRANCH_NAME=${{ github.ref }}
         echo "BRANCH NAME IS $BRANCH_NAME"
         git ls-remote --exit-code --heads $JCB_REPO $BRANCH_NAME
         if [ $? -eq 0 ]; then

From b04477d40f7392c2ebde6dfb545559e35c11ce1e Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Fri, 24 May 2024 09:20:49 -0400
Subject: [PATCH 04/19] action debugging

---
 .github/workflows/run_jcb_basic_testing.yaml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
index 1948236..c6765d9 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -33,6 +33,14 @@ jobs:
     - name: Determine branch to use
       id: determine-branch
       run: |
+        if [ "${{ github.event_name }}" == "pull_request" ]; then
+          BRANCH_NAME=${{ github.head_ref }}
+        else
+          BRANCH_REF=${{ github.ref }}
+          BRANCH_NAME=${BRANCH_REF#refs/heads/}
+        fi
+        echo "Branch name: $BRANCH_NAME"
+
         # Determine if the branch exists in the jcb repo
         BRANCH_NAME=${{ github.ref }}
         echo "BRANCH NAME IS $BRANCH_NAME"

From 33f40de08c9f69e26ceba25825075efb900ae791 Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Fri, 24 May 2024 09:22:30 -0400
Subject: [PATCH 05/19] action debugging

---
 .github/workflows/run_jcb_basic_testing.yaml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
index c6765d9..200ad11 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -40,9 +40,6 @@ jobs:
           BRANCH_NAME=${BRANCH_REF#refs/heads/}
         fi
         echo "Branch name: $BRANCH_NAME"
-
-        # Determine if the branch exists in the jcb repo
-        BRANCH_NAME=${{ github.ref }}
         echo "BRANCH NAME IS $BRANCH_NAME"
         git ls-remote --exit-code --heads $JCB_REPO $BRANCH_NAME
         if [ $? -eq 0 ]; then

From ec4daddb26de43b4a32d11ff467c3ae61882f3b9 Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Fri, 24 May 2024 09:28:00 -0400
Subject: [PATCH 06/19] action debugging

---
 .github/workflows/run_jcb_basic_testing.yaml | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
index 200ad11..baa7665 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -39,20 +39,18 @@ jobs:
           BRANCH_REF=${{ github.ref }}
           BRANCH_NAME=${BRANCH_REF#refs/heads/}
         fi
-        echo "Branch name: $BRANCH_NAME"
-        echo "BRANCH NAME IS $BRANCH_NAME"
-        git ls-remote --exit-code --heads $JCB_REPO $BRANCH_NAME
-        if [ $? -eq 0 ]; then
+
+        if git ls-remote --heads $REPO_URL $BRANCH_NAME | grep -q "refs/heads/$BRANCH_NAME"; then
           echo "Branch $BRANCH_NAME exists in jcb repo."
-          echo "BRANCH_NAME=$BRANCH_NAME" >> $GITHUB_ENV
+          echo "JCB_BRANCH_NAME=$BRANCH_NAME" >> $GITHUB_ENV
         else
           echo "Branch $BRANCH_NAME does not exist in jcb repo. Using develop branch."
-          echo "BRANCH_NAME=$JCB_DEVELOP_BRANCH" >> $GITHUB_ENV
+          echo "JCB_BRANCH_NAME=develop" >> $GITHUB_ENV
         fi
 
     - name: Clone jcb repository
       run: |
-        git clone --branch ${{ env.BRANCH_NAME }} $JCB_REPO jcb_repo
+        git clone --branch ${{ env.JCB_BRANCH_NAME }} --recursive $JCB_REPO jcb_repo
         cd jcb_repo/src/jcb/configuration/apps/gdas
         git checkout ${{ env.BRANCH_NAME }}
         cd -

From e1d3dac484f948853e646a0ceafff6df4bd6512e Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Fri, 24 May 2024 09:29:29 -0400
Subject: [PATCH 07/19] action debugging

---
 .github/workflows/run_jcb_basic_testing.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
index baa7665..1cebd20 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -40,7 +40,7 @@ jobs:
           BRANCH_NAME=${BRANCH_REF#refs/heads/}
         fi
 
-        if git ls-remote --heads $REPO_URL $BRANCH_NAME | grep -q "refs/heads/$BRANCH_NAME"; then
+        if git ls-remote --heads $JCB_REPO $BRANCH_NAME | grep -q "refs/heads/$BRANCH_NAME"; then
           echo "Branch $BRANCH_NAME exists in jcb repo."
           echo "JCB_BRANCH_NAME=$BRANCH_NAME" >> $GITHUB_ENV
         else

From f99052767fd400a6d7659598526ece9038e82599 Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Fri, 24 May 2024 09:31:56 -0400
Subject: [PATCH 08/19] action debugging

---
 .github/workflows/run_jcb_basic_testing.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
index 1cebd20..206d3ff 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -50,6 +50,7 @@ jobs:
 
     - name: Clone jcb repository
       run: |
+        GIT_CLONE_PROTECTION_ACTIVE=false
         git clone --branch ${{ env.JCB_BRANCH_NAME }} --recursive $JCB_REPO jcb_repo
         cd jcb_repo/src/jcb/configuration/apps/gdas
         git checkout ${{ env.BRANCH_NAME }}

From 454c4c0825965949e2ff742a6526929dd0d3b098 Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Fri, 24 May 2024 09:33:03 -0400
Subject: [PATCH 09/19] action debugging

---
 .github/workflows/run_jcb_basic_testing.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
index 206d3ff..f82b452 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -50,7 +50,8 @@ jobs:
 
     - name: Clone jcb repository
       run: |
-        GIT_CLONE_PROTECTION_ACTIVE=false
+        mkdir -p empty_hooks
+        git config --global core.hooksPath empty_hooks
         git clone --branch ${{ env.JCB_BRANCH_NAME }} --recursive $JCB_REPO jcb_repo
         cd jcb_repo/src/jcb/configuration/apps/gdas
         git checkout ${{ env.BRANCH_NAME }}

From ffb7c2d4ee065a9a52ea9d67abc0ab63d986b311 Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Fri, 24 May 2024 09:35:43 -0400
Subject: [PATCH 10/19] action debugging

---
 .github/workflows/run_jcb_basic_testing.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
index f82b452..aa6d53e 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -55,6 +55,9 @@ jobs:
         git clone --branch ${{ env.JCB_BRANCH_NAME }} --recursive $JCB_REPO jcb_repo
         cd jcb_repo/src/jcb/configuration/apps/gdas
         git checkout ${{ env.BRANCH_NAME }}
+        echo `git rev-parse HEAD`
+        git branch
+        ls -l
         cd -
 
     - name: Install dependencies

From 5d3ab7b10bf9ffdb5e9cdd4207982b97087727a9 Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Fri, 24 May 2024 09:44:04 -0400
Subject: [PATCH 11/19] action debugging

---
 .github/workflows/run_jcb_basic_testing.yaml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
index aa6d53e..7bdaf3b 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -16,8 +16,6 @@ jobs:
 
     env:
       JCB_REPO: https://github.com/NOAA-EMC/jcb.git
-      JCB_APP_REPO: https://github.com/NOAA-EMC/jcb-gdas.git
-      JCB_DEVELOP_BRANCH: develop
 
     steps:
     - name: Checkout submodule repository
@@ -40,6 +38,8 @@ jobs:
           BRANCH_NAME=${BRANCH_REF#refs/heads/}
         fi
 
+        echo "JCB_APP_BRANCH_NAME=$BRANCH_NAME" >> $GITHUB_ENV
+
         if git ls-remote --heads $JCB_REPO $BRANCH_NAME | grep -q "refs/heads/$BRANCH_NAME"; then
           echo "Branch $BRANCH_NAME exists in jcb repo."
           echo "JCB_BRANCH_NAME=$BRANCH_NAME" >> $GITHUB_ENV
@@ -54,7 +54,7 @@ jobs:
         git config --global core.hooksPath empty_hooks
         git clone --branch ${{ env.JCB_BRANCH_NAME }} --recursive $JCB_REPO jcb_repo
         cd jcb_repo/src/jcb/configuration/apps/gdas
-        git checkout ${{ env.BRANCH_NAME }}
+        git checkout ${{ env.JCB_APP_BRANCH_NAME }}
         echo `git rev-parse HEAD`
         git branch
         ls -l
@@ -65,7 +65,8 @@ jobs:
         cd jcb_repo
         pip install .[testing]
 
-    - name: Run unit tests
+    - name: Run the JCB client integration tests
       run: |
         cd $GITHUB_WORKSPACE
+        cd test/client_integration
         pytest -v

From 0f9b01131a6dd8bf93dc75d32b396c9d98d95284 Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Fri, 24 May 2024 09:47:15 -0400
Subject: [PATCH 12/19] action debugging

---
 .github/workflows/run_jcb_basic_testing.yaml | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
index 7bdaf3b..99a703c 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -55,10 +55,6 @@ jobs:
         git clone --branch ${{ env.JCB_BRANCH_NAME }} --recursive $JCB_REPO jcb_repo
         cd jcb_repo/src/jcb/configuration/apps/gdas
         git checkout ${{ env.JCB_APP_BRANCH_NAME }}
-        echo `git rev-parse HEAD`
-        git branch
-        ls -l
-        cd -
 
     - name: Install dependencies
       run: |
@@ -67,6 +63,5 @@ jobs:
 
     - name: Run the JCB client integration tests
       run: |
-        cd $GITHUB_WORKSPACE
-        cd test/client_integration
+        cd jcb_repo/test/client_integration
         pytest -v

From b19a6aee0111cf73e5e9c5c919e1e93b052d0e2b Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Fri, 24 May 2024 10:30:29 -0400
Subject: [PATCH 13/19] action debugging

---
 .github/workflows/run_jcb_basic_testing.yaml | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
index 99a703c..ddaf929 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -1,4 +1,4 @@
-name: Run JCB basic testing with jcb-gdas changes
+name: Run JCB basic testing with client changes
 
 on:
   push:
@@ -16,6 +16,7 @@ jobs:
 
     env:
       JCB_REPO: https://github.com/NOAA-EMC/jcb.git
+      JCB_APP_REPO: "https://github.com/${GITHUB_REPOSITORY}"
 
     steps:
     - name: Checkout submodule repository
@@ -53,7 +54,11 @@ jobs:
         mkdir -p empty_hooks
         git config --global core.hooksPath empty_hooks
         git clone --branch ${{ env.JCB_BRANCH_NAME }} --recursive $JCB_REPO jcb_repo
-        cd jcb_repo/src/jcb/configuration/apps/gdas
+
+        cd jcb_repo
+        python get_submod_path.py $JCB_APP_REPO > SUBMODPATH
+        SUBMODPATH=$(cat SUBMODPATH)
+        cd $SUBMODPATH
         git checkout ${{ env.JCB_APP_BRANCH_NAME }}
 
     - name: Install dependencies

From 46c791c04fb2dc35c769ca7cd23c36fd2c5d230c Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Fri, 24 May 2024 10:34:01 -0400
Subject: [PATCH 14/19] action debugging

---
 .github/workflows/run_jcb_basic_testing.yaml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
index ddaf929..c6e2da8 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -16,7 +16,6 @@ jobs:
 
     env:
       JCB_REPO: https://github.com/NOAA-EMC/jcb.git
-      JCB_APP_REPO: "https://github.com/${GITHUB_REPOSITORY}"
 
     steps:
     - name: Checkout submodule repository
@@ -29,6 +28,11 @@ jobs:
       with:
         python-version: '3.x'  # specify your python version
 
+    - name: Add repo url to the environment
+      run: |
+        echo ${{ github.repository }}
+        echo "JCB_APP_REPO=${{ github.repository }}" >> $GITHUB_ENV
+
     - name: Determine branch to use
       id: determine-branch
       run: |

From 7e2d65ebe8a53c80566743e2a9a84442d92d158b Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Fri, 24 May 2024 10:35:15 -0400
Subject: [PATCH 15/19] action debugging

---
 .github/workflows/run_jcb_basic_testing.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
index c6e2da8..81169d6 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -30,8 +30,8 @@ jobs:
 
     - name: Add repo url to the environment
       run: |
-        echo ${{ github.repository }}
-        echo "JCB_APP_REPO=${{ github.repository }}" >> $GITHUB_ENV
+        echo "https://github.com/${{ github.repository }}"
+        echo "JCB_APP_REPO="https://github.com/${{ github.repository }}" >> $GITHUB_ENV
 
     - name: Determine branch to use
       id: determine-branch

From a91b81fc135872631215140a2c5495e22bbc675d Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Fri, 24 May 2024 10:37:04 -0400
Subject: [PATCH 16/19] action debugging

---
 .github/workflows/run_jcb_basic_testing.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
index 81169d6..646224c 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -30,8 +30,8 @@ jobs:
 
     - name: Add repo url to the environment
       run: |
-        echo "https://github.com/${{ github.repository }}"
-        echo "JCB_APP_REPO="https://github.com/${{ github.repository }}" >> $GITHUB_ENV
+        JCB_APP_REPO="https://github.com/${{ github.repository }}"
+        echo "JCB_APP_REPO=${JCB_APP_REPO}" >> $GITHUB_ENV
 
     - name: Determine branch to use
       id: determine-branch

From b66c34cdc0eaf80eaf4c40b1d82fae6bf97db6be Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Fri, 24 May 2024 10:39:27 -0400
Subject: [PATCH 17/19] action debugging

---
 .github/workflows/run_jcb_basic_testing.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
index 646224c..68c96ba 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -62,6 +62,7 @@ jobs:
         cd jcb_repo
         python get_submod_path.py $JCB_APP_REPO > SUBMODPATH
         SUBMODPATH=$(cat SUBMODPATH)
+        echo $SUBMODPATH
         cd $SUBMODPATH
         git checkout ${{ env.JCB_APP_BRANCH_NAME }}
 

From 6906a1faefaa15bb140a1148a9fc216e7d5fbdda Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Fri, 24 May 2024 10:47:27 -0400
Subject: [PATCH 18/19] action debugging

---
 .github/workflows/run_jcb_basic_testing.yaml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
index 68c96ba..8bb388b 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -60,10 +60,7 @@ jobs:
         git clone --branch ${{ env.JCB_BRANCH_NAME }} --recursive $JCB_REPO jcb_repo
 
         cd jcb_repo
-        python get_submod_path.py $JCB_APP_REPO > SUBMODPATH
-        SUBMODPATH=$(cat SUBMODPATH)
-        echo $SUBMODPATH
-        cd $SUBMODPATH
+        cd $(python get_submod_path.py $JCB_APP_REPO)
         git checkout ${{ env.JCB_APP_BRANCH_NAME }}
 
     - name: Install dependencies

From ade6f8b3cfc73a1646ea7fa293a2aeaa152fbebe Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Fri, 24 May 2024 10:56:24 -0400
Subject: [PATCH 19/19] action debugging

---
 .github/workflows/run_jcb_basic_testing.yaml | 29 +++++++++++---------
 1 file changed, 16 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
index 8bb388b..283ba9a 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -1,4 +1,4 @@
-name: Run JCB basic testing with client changes
+name: Run JCB client testing with client changes
 
 on:
   push:
@@ -18,7 +18,7 @@ jobs:
       JCB_REPO: https://github.com/NOAA-EMC/jcb.git
 
     steps:
-    - name: Checkout submodule repository
+    - name: Checkout application client repository
       uses: actions/checkout@v3
       with:
         submodules: true
@@ -26,42 +26,45 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.x'  # specify your python version
+        python-version: '3.x'
 
     - name: Add repo url to the environment
       run: |
         JCB_APP_REPO="https://github.com/${{ github.repository }}"
         echo "JCB_APP_REPO=${JCB_APP_REPO}" >> $GITHUB_ENV
 
-    - name: Determine branch to use
-      id: determine-branch
+    - name: Determine the name of the client branch
       run: |
         if [ "${{ github.event_name }}" == "pull_request" ]; then
-          BRANCH_NAME=${{ github.head_ref }}
+        JCB_APP_BRANCH=${{ github.head_ref }}
         else
           BRANCH_REF=${{ github.ref }}
-          BRANCH_NAME=${BRANCH_REF#refs/heads/}
+          JCB_APP_BRANCH=${BRANCH_REF#refs/heads/}
         fi
+        echo "JCB_APP_BRANCH=$JCB_APP_BRANCH" >> $GITHUB_ENV
 
-        echo "JCB_APP_BRANCH_NAME=$BRANCH_NAME" >> $GITHUB_ENV
-
+    - name: Determine branch to use for main jcb repo
+      run: |
+        BRANCH_NAME=${{ env.JCB_APP_BRANCH }}
         if git ls-remote --heads $JCB_REPO $BRANCH_NAME | grep -q "refs/heads/$BRANCH_NAME"; then
           echo "Branch $BRANCH_NAME exists in jcb repo."
-          echo "JCB_BRANCH_NAME=$BRANCH_NAME" >> $GITHUB_ENV
+          echo "JCB_BRANCH=$BRANCH_NAME" >> $GITHUB_ENV
         else
           echo "Branch $BRANCH_NAME does not exist in jcb repo. Using develop branch."
-          echo "JCB_BRANCH_NAME=develop" >> $GITHUB_ENV
+          echo "JCB_BRANCH=develop" >> $GITHUB_ENV
         fi
 
     - name: Clone jcb repository
       run: |
         mkdir -p empty_hooks
         git config --global core.hooksPath empty_hooks
-        git clone --branch ${{ env.JCB_BRANCH_NAME }} --recursive $JCB_REPO jcb_repo
+        git clone --branch ${{ env.JCB_BRANCH }} --recursive $JCB_REPO jcb_repo
 
+    - name: Switch the application branch to match the action
+      run: |
         cd jcb_repo
         cd $(python get_submod_path.py $JCB_APP_REPO)
-        git checkout ${{ env.JCB_APP_BRANCH_NAME }}
+        git checkout ${{ env.JCB_APP_BRANCH }}
 
     - name: Install dependencies
       run: |