From a836c699a7fe2780f54916004d9bad737b59882e Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Mon, 3 Jun 2024 17:06:36 -0400
Subject: [PATCH 01/14] Adjust testing for new path checker file

---
 .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 523f976..849e42f 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -66,7 +66,7 @@ jobs:
     - name: Switch the application branch to match the action
       run: |
         cd jcb_repo
-        cd $(python get_submod_path.py $JCB_APP_REPO)
+        cd $(python jcb_client_path.py $JCB_APP_REPO)
         git checkout ${{ env.JCB_APP_BRANCH }}
 
     - name: Install dependencies

From 5f2769b9ca5598611bce999f2703e3a6557954ba Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Tue, 4 Jun 2024 11:24:02 -0400
Subject: [PATCH 02/14] pyyaml

---
 .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 849e42f..1e2df84 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -66,6 +66,7 @@ jobs:
     - name: Switch the application branch to match the action
       run: |
         cd jcb_repo
+        pip install pyyaml
         cd $(python jcb_client_path.py $JCB_APP_REPO)
         git checkout ${{ env.JCB_APP_BRANCH }}
 

From fa5f7266a720eaa7eacb415576c57ba684931906 Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Tue, 4 Jun 2024 11:33:40 -0400
Subject: [PATCH 03/14] Make sure to init clients in GH test

---
 .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 1e2df84..c45c400 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -21,11 +21,6 @@ jobs:
       JCB_REPO: https://github.com/NOAA-EMC/jcb.git
 
     steps:
-    - name: Checkout application client repository
-      uses: actions/checkout@v3
-      with:
-        submodules: true
-
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
@@ -63,11 +58,14 @@ jobs:
         git config --global core.hooksPath empty_hooks
         git clone --branch ${{ env.JCB_BRANCH }} --recursive $JCB_REPO jcb_repo
 
-    - name: Switch the application branch to match the action
+    - name: Clone the clients
       run: |
         cd jcb_repo
         pip install pyyaml
-        cd $(python jcb_client_path.py $JCB_APP_REPO)
+        ./jcb_client_init.py
+        app_path=$(python jcb_client_path.py $JCB_APP_REPO)
+        echo "Application path: $app_path"
+        cd $app_path
         git checkout ${{ env.JCB_APP_BRANCH }}
 
     - name: Install dependencies

From 392b96037447266868a35599377fb33b40f6e1ec Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Tue, 4 Jun 2024 11:36:24 -0400
Subject: [PATCH 04/14] 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 c45c400..b59ba86 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -63,6 +63,7 @@ jobs:
         cd jcb_repo
         pip install pyyaml
         ./jcb_client_init.py
+        echo "JCB_APP_REPO: $JCB_APP_REPO"
         app_path=$(python jcb_client_path.py $JCB_APP_REPO)
         echo "Application path: $app_path"
         cd $app_path

From b2eb15c6f88ef2964cc796093e0ea83136ab481f Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Tue, 4 Jun 2024 11:37:39 -0400
Subject: [PATCH 05/14] 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 b59ba86..9c16cd4 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -63,8 +63,8 @@ jobs:
         cd jcb_repo
         pip install pyyaml
         ./jcb_client_init.py
-        echo "JCB_APP_REPO: $JCB_APP_REPO"
-        app_path=$(python jcb_client_path.py $JCB_APP_REPO)
+        echo "JCB_APP_REPO: ${{ github.repository }}"
+        app_path=$(python jcb_client_path.py ${{ github.repository }})
         echo "Application path: $app_path"
         cd $app_path
         git checkout ${{ env.JCB_APP_BRANCH }}

From 858d76d09ea40d08ed69f1f89f83e5edc70ea2dd Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Tue, 4 Jun 2024 11:48:50 -0400
Subject: [PATCH 06/14] 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 9c16cd4..9f0a745 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -64,6 +64,7 @@ jobs:
         pip install pyyaml
         ./jcb_client_init.py
         echo "JCB_APP_REPO: ${{ github.repository }}"
+        echo "Currect directory: $(pwd)"
         app_path=$(python jcb_client_path.py ${{ github.repository }})
         echo "Application path: $app_path"
         cd $app_path

From 5c8a013b90e412251be296dcaba4849535172735 Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Tue, 4 Jun 2024 11:51:59 -0400
Subject: [PATCH 07/14] 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 9f0a745..6787bd7 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -66,7 +66,7 @@ jobs:
         echo "JCB_APP_REPO: ${{ github.repository }}"
         echo "Currect directory: $(pwd)"
         app_path=$(python jcb_client_path.py ${{ github.repository }})
-        echo "Application path: $app_path"
+        echo "Application path : $app_path"
         cd $app_path
         git checkout ${{ env.JCB_APP_BRANCH }}
 

From 27a3f8732761bf5c58b44b3fce649436749f0253 Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Tue, 4 Jun 2024 11:52:51 -0400
Subject: [PATCH 08/14] 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 6787bd7..9210e61 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -65,6 +65,7 @@ jobs:
         ./jcb_client_init.py
         echo "JCB_APP_REPO: ${{ github.repository }}"
         echo "Currect directory: $(pwd)"
+        python jcb_client_path.py ${{ github.repository }}
         app_path=$(python jcb_client_path.py ${{ github.repository }})
         echo "Application path : $app_path"
         cd $app_path

From 130001f6d340c0d345a6dcb01150bdf277ebd984 Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Tue, 4 Jun 2024 11:54:11 -0400
Subject: [PATCH 09/14] 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 9210e61..874c495 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -65,6 +65,7 @@ jobs:
         ./jcb_client_init.py
         echo "JCB_APP_REPO: ${{ github.repository }}"
         echo "Currect directory: $(pwd)"
+        ls -l
         python jcb_client_path.py ${{ github.repository }}
         app_path=$(python jcb_client_path.py ${{ github.repository }})
         echo "Application path : $app_path"

From e012da614e9ee6b47d2a5729ac93868c9c96be40 Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Tue, 4 Jun 2024 11:56:26 -0400
Subject: [PATCH 10/14] action debugging

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

diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
index 874c495..88c7c79 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -66,6 +66,8 @@ jobs:
         echo "JCB_APP_REPO: ${{ github.repository }}"
         echo "Currect directory: $(pwd)"
         ls -l
+        ls -l src/jcb/configuration
+        ls -l src/jcb/configuration/apps
         python jcb_client_path.py ${{ github.repository }}
         app_path=$(python jcb_client_path.py ${{ github.repository }})
         echo "Application path : $app_path"

From 9dbe5dfc1a354c2baca9fb184b2512495b204984 Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Tue, 4 Jun 2024 11:58:29 -0400
Subject: [PATCH 11/14] action debugging

---
 .github/workflows/run_jcb_basic_testing.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
index 88c7c79..74832eb 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -28,7 +28,7 @@ jobs:
 
     - name: Add repo url to the environment
       run: |
-        JCB_APP_REPO="https://github.com/${{ github.repository }}"
+        JCB_APP_REPO="${{ github.repository }}"
         echo "JCB_APP_REPO=${JCB_APP_REPO}" >> $GITHUB_ENV
 
     - name: Determine the name of the client branch
@@ -63,13 +63,13 @@ jobs:
         cd jcb_repo
         pip install pyyaml
         ./jcb_client_init.py
-        echo "JCB_APP_REPO: ${{ github.repository }}"
+        echo "JCB_APP_REPO: $JCB_APP_REPO"
         echo "Currect directory: $(pwd)"
         ls -l
         ls -l src/jcb/configuration
         ls -l src/jcb/configuration/apps
-        python jcb_client_path.py ${{ github.repository }}
-        app_path=$(python jcb_client_path.py ${{ github.repository }})
+        python jcb_client_path.py $JCB_APP_REPO
+        app_path=$(python jcb_client_path.py $JCB_APP_REPO)
         echo "Application path : $app_path"
         cd $app_path
         git checkout ${{ env.JCB_APP_BRANCH }}

From 4d7c1cc73038feff4f5936eeafcbe4d3be2f1e48 Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Tue, 4 Jun 2024 12:01:58 -0400
Subject: [PATCH 12/14] 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 74832eb..a88fb79 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -65,9 +65,6 @@ jobs:
         ./jcb_client_init.py
         echo "JCB_APP_REPO: $JCB_APP_REPO"
         echo "Currect directory: $(pwd)"
-        ls -l
-        ls -l src/jcb/configuration
-        ls -l src/jcb/configuration/apps
         python jcb_client_path.py $JCB_APP_REPO
         app_path=$(python jcb_client_path.py $JCB_APP_REPO)
         echo "Application path : $app_path"

From f821bfe40aff0a43a476bdfd9e9ab0c474820833 Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Tue, 4 Jun 2024 12:05:09 -0400
Subject: [PATCH 13/14] action debugging

---
 .github/workflows/run_jcb_basic_testing.yaml | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
index a88fb79..d8c318f 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -63,13 +63,14 @@ jobs:
         cd jcb_repo
         pip install pyyaml
         ./jcb_client_init.py
-        echo "JCB_APP_REPO: $JCB_APP_REPO"
-        echo "Currect directory: $(pwd)"
-        python jcb_client_path.py $JCB_APP_REPO
-        app_path=$(python jcb_client_path.py $JCB_APP_REPO)
-        echo "Application path : $app_path"
-        cd $app_path
-        git checkout ${{ env.JCB_APP_BRANCH }}
+        # If all the branches are found then at this point everything should be good.
+        # If not then the apps branch needs to be checked out explicitly.
+        if [ "${{ env.JCB_BRANCH }}" != "${{ env.JCB_APP_BRANCH }}" ]; then
+          echo "Checking out branch ${{ env.JCB_APP_BRANCH }} for ${{ env.JCB_APP_REPO }}"
+          app_path=$(python jcb_client_path.py $JCB_APP_REPO)
+          cd $app_path
+          git checkout ${{ env.JCB_APP_BRANCH }}
+        fi
 
     - name: Install dependencies
       run: |

From d04a99bdeae8bfe6926be190e79467a066ff449f Mon Sep 17 00:00:00 2001
From: danholdaway <danholdaway@users.noreply.github.com>
Date: Tue, 4 Jun 2024 12:09:13 -0400
Subject: [PATCH 14/14] add comment

---
 .github/workflows/run_jcb_basic_testing.yaml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/run_jcb_basic_testing.yaml b/.github/workflows/run_jcb_basic_testing.yaml
index d8c318f..97714eb 100644
--- a/.github/workflows/run_jcb_basic_testing.yaml
+++ b/.github/workflows/run_jcb_basic_testing.yaml
@@ -63,8 +63,10 @@ jobs:
         cd jcb_repo
         pip install pyyaml
         ./jcb_client_init.py
-        # If all the branches are found then at this point everything should be good.
-        # If not then the apps branch needs to be checked out explicitly.
+
+        # If all the branches are found then at this point everything should be good since
+        # jcb_client_init will check out the correct branches. If not then the app branch needs to
+        # be checked out explicitly.
         if [ "${{ env.JCB_BRANCH }}" != "${{ env.JCB_APP_BRANCH }}" ]; then
           echo "Checking out branch ${{ env.JCB_APP_BRANCH }} for ${{ env.JCB_APP_REPO }}"
           app_path=$(python jcb_client_path.py $JCB_APP_REPO)