From ca63feed045ef8ddccc1e20d30f05791aced0cf3 Mon Sep 17 00:00:00 2001
From: "Ian L." <6273252+ilaflott@users.noreply.github.com>
Date: Wed, 15 Jul 2026 12:01:31 -0400
Subject: [PATCH 01/10] Create ai_pytest_workflow.yaml

---
 .github/workflows/ai_pytest_workflow.yaml | 71 +++++++++++++++++++++++
 1 file changed, 71 insertions(+)
 create mode 100644 .github/workflows/ai_pytest_workflow.yaml

diff --git a/.github/workflows/ai_pytest_workflow.yaml b/.github/workflows/ai_pytest_workflow.yaml
new file mode 100644
index 000000000..74922e288
--- /dev/null
+++ b/.github/workflows/ai_pytest_workflow.yaml
@@ -0,0 +1,71 @@
+name: AI Pytest Workflow
+
+on:
+  pull_request:
+    branches: [ main ]
+  # schedule:
+  #   - cron: '0 0 * * *' # Runs once a day at midnight
+
+jobs:
+  ai-pytest-check:
+    runs-on: ubuntu-latest
+    
+    # Required for conda-incubator to work correctly in the runner
+    defaults:
+      run:
+        shell: bash -el {0} 
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Conda environment
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: '3.10' # Adjust based on fre-cli's requirements
+          activate-environment: fre-cli-dev
+
+      - name: Install fre-cli (Developer Style)
+        run: |
+          # Upgrade pip and install standard test requirements
+          python -m pip install --upgrade pip
+          pip install pytest
+          
+          # Editable pip install as requested
+          pip install -e .
+
+      - name: Run Pytest and capture output
+        run: |
+          # Run pytest and pipe output to a file. 
+          # Using `|| true` ensures the workflow continues even if tests fail/warn.
+          pytest > pytest_output.log 2>&1 || true
+          
+          echo "Captured Pytest Output:"
+          cat pytest_output.log
+
+      - name: Setup GitHub Copilot CLI
+        env:
+          # A token is required to authenticate the GitHub CLI extension
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          # The GitHub CLI (gh) is pre-installed on standard Ubuntu runners.
+          # We install the official Copilot extension here.
+          gh extension install github/gh-copilot
+          
+          echo "Testing Copilot Help Command:"
+          gh copilot --help
+
+      - name: Query Copilot for Fixes
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          # Read the pytest output into a variable
+          # You might want to filter this with grep if the log is too long for the prompt limit
+          TEST_OUTPUT=$(cat pytest_output.log)
+          
+          echo "Feeding pytest output to Copilot..."
+          
+          # Pass the prompt and the context to Copilot
+          # Note: `gh copilot suggest` is usually interactive, but we feed it as a single string here
+          gh copilot suggest -t shell "Fix these warnings/errors from pytest: $TEST_OUTPUT"

From 748e202c00863697879bb51ab681075ab7f962a1 Mon Sep 17 00:00:00 2001
From: "Ian L." <6273252+ilaflott@users.noreply.github.com>
Date: Wed, 15 Jul 2026 12:07:30 -0400
Subject: [PATCH 02/10] Update ai_pytest_workflow.yaml

---
 .github/workflows/ai_pytest_workflow.yaml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ai_pytest_workflow.yaml b/.github/workflows/ai_pytest_workflow.yaml
index 74922e288..c34f375f6 100644
--- a/.github/workflows/ai_pytest_workflow.yaml
+++ b/.github/workflows/ai_pytest_workflow.yaml
@@ -22,8 +22,11 @@ jobs:
       - name: Set up Conda environment
         uses: conda-incubator/setup-miniconda@v3
         with:
-          auto-update-conda: true
-          python-version: '3.10' # Adjust based on fre-cli's requirements
+          miniforge-version: latest
+          channels: conda-forge,noaa-gfdl
+          python-version: 3.14
+          conda-remove-defaults: true
+          environment-file: environment.yaml
           activate-environment: fre-cli-dev
 
       - name: Install fre-cli (Developer Style)

From a6cef1133b5c2a02700af5d98c7e1ccc60741785 Mon Sep 17 00:00:00 2001
From: "Ian L." <6273252+ilaflott@users.noreply.github.com>
Date: Wed, 15 Jul 2026 12:15:07 -0400
Subject: [PATCH 03/10] Update ai_pytest_workflow.yaml

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

diff --git a/.github/workflows/ai_pytest_workflow.yaml b/.github/workflows/ai_pytest_workflow.yaml
index c34f375f6..2b5ed6c36 100644
--- a/.github/workflows/ai_pytest_workflow.yaml
+++ b/.github/workflows/ai_pytest_workflow.yaml
@@ -18,6 +18,8 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
+        with:
+          submodules: recursive
 
       - name: Set up Conda environment
         uses: conda-incubator/setup-miniconda@v3
@@ -26,8 +28,8 @@ jobs:
           channels: conda-forge,noaa-gfdl
           python-version: 3.14
           conda-remove-defaults: true
-          environment-file: environment.yaml
-          activate-environment: fre-cli-dev
+          environment-file: environment.yml
+          activate-environment: fre-cli
 
       - name: Install fre-cli (Developer Style)
         run: |

From 2cf0f8354c9a54631f358dfa961ff809a2c68edb Mon Sep 17 00:00:00 2001
From: "Ian L." <6273252+ilaflott@users.noreply.github.com>
Date: Wed, 15 Jul 2026 12:26:25 -0400
Subject: [PATCH 04/10] Update ai_pytest_workflow.yaml

---
 .github/workflows/ai_pytest_workflow.yaml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ai_pytest_workflow.yaml b/.github/workflows/ai_pytest_workflow.yaml
index 2b5ed6c36..1d5802566 100644
--- a/.github/workflows/ai_pytest_workflow.yaml
+++ b/.github/workflows/ai_pytest_workflow.yaml
@@ -59,7 +59,7 @@ jobs:
           gh extension install github/gh-copilot
           
           echo "Testing Copilot Help Command:"
-          gh copilot --help
+          gh copilot -- --help
 
       - name: Query Copilot for Fixes
         env:
@@ -67,10 +67,11 @@ jobs:
         run: |
           # Read the pytest output into a variable
           # You might want to filter this with grep if the log is too long for the prompt limit
-          TEST_OUTPUT=$(cat pytest_output.log)
+          TEST_OUTPUT=$(cat pytest_output.log | grep -B 5 -A 5 'warn')
           
           echo "Feeding pytest output to Copilot..."
           
           # Pass the prompt and the context to Copilot
           # Note: `gh copilot suggest` is usually interactive, but we feed it as a single string here
-          gh copilot suggest -t shell "Fix these warnings/errors from pytest: $TEST_OUTPUT"
+          gh copilot --prompt "Fix these warnings/errors from pytest: \n\n ${TEST_OUTPUT}" --add-dir "${PWD}" --allow-all --attachment pytest_output.log --attachment .github/copilot-instructions.md --model 'Claude Sonnet 4.6' --mode 'autopilot'
+          

From 62372c34e34d7a1d42658c96c6aa9faded399dad Mon Sep 17 00:00:00 2001
From: "Ian L." <6273252+ilaflott@users.noreply.github.com>
Date: Wed, 15 Jul 2026 12:39:31 -0400
Subject: [PATCH 05/10] Update ai_pytest_workflow.yaml

---
 .github/workflows/ai_pytest_workflow.yaml | 56 +++++++++--------------
 1 file changed, 22 insertions(+), 34 deletions(-)

diff --git a/.github/workflows/ai_pytest_workflow.yaml b/.github/workflows/ai_pytest_workflow.yaml
index 1d5802566..41d444034 100644
--- a/.github/workflows/ai_pytest_workflow.yaml
+++ b/.github/workflows/ai_pytest_workflow.yaml
@@ -9,11 +9,6 @@ on:
 jobs:
   ai-pytest-check:
     runs-on: ubuntu-latest
-    
-    # Required for conda-incubator to work correctly in the runner
-    defaults:
-      run:
-        shell: bash -el {0} 
 
     steps:
       - name: Checkout repository
@@ -21,33 +16,27 @@ jobs:
         with:
           submodules: recursive
 
-      - name: Set up Conda environment
-        uses: conda-incubator/setup-miniconda@v3
-        with:
-          miniforge-version: latest
-          channels: conda-forge,noaa-gfdl
-          python-version: 3.14
-          conda-remove-defaults: true
-          environment-file: environment.yml
-          activate-environment: fre-cli
-
-      - name: Install fre-cli (Developer Style)
+      - name: Fetch recent workflow logs from main
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          # Upgrade pip and install standard test requirements
-          python -m pip install --upgrade pip
-          pip install pytest
+          # Get the ID of the most recent workflow run on the main branch.
+          # Note: If you want logs from a *specific* workflow, add `--workflow "Your Workflow Name"` to this command.
+          RUN_ID=$(gh run list --branch main --limit 1 --json databaseId --jq '.[0].databaseId')
           
-          # Editable pip install as requested
-          pip install -e .
-
-      - name: Run Pytest and capture output
-        run: |
-          # Run pytest and pipe output to a file. 
-          # Using `|| true` ensures the workflow continues even if tests fail/warn.
-          pytest > pytest_output.log 2>&1 || true
+          if [ -z "$RUN_ID" ]; then
+            echo "No recent runs found on the main branch."
+            exit 1
+          fi
+          
+          echo "Fetching logs for Run ID: $RUN_ID"
           
-          echo "Captured Pytest Output:"
-          cat pytest_output.log
+          # Download the logs and pipe output to a file. 
+          # Using `|| true` ensures the workflow continues even if the command has a hiccup.
+          gh run view $RUN_ID --log > pytest_output.log || true
+          
+          echo "Captured Logs Preview:"
+          head -n 20 pytest_output.log
 
       - name: Setup GitHub Copilot CLI
         env:
@@ -66,12 +55,11 @@ jobs:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
           # Read the pytest output into a variable
-          # You might want to filter this with grep if the log is too long for the prompt limit
-          TEST_OUTPUT=$(cat pytest_output.log | grep -B 5 -A 5 'warn')
+          # Filtering with grep for warnings/errors (case-insensitive) to stay within the prompt limit
+          TEST_OUTPUT=$(cat pytest_output.log | grep -i -E -B 5 -A 5 'warn|error|fail')
           
-          echo "Feeding pytest output to Copilot..."
+          echo "Feeding workflow logs to Copilot..."
           
           # Pass the prompt and the context to Copilot
           # Note: `gh copilot suggest` is usually interactive, but we feed it as a single string here
-          gh copilot --prompt "Fix these warnings/errors from pytest: \n\n ${TEST_OUTPUT}" --add-dir "${PWD}" --allow-all --attachment pytest_output.log --attachment .github/copilot-instructions.md --model 'Claude Sonnet 4.6' --mode 'autopilot'
-          
+          gh copilot --prompt "Fix these warnings/errors from the recent test run: \n\n ${TEST_OUTPUT}" --add-dir "${PWD}" --allow-all --attachment pytest_output.log --attachment .github/copilot-instructions.md --model 'Claude Sonnet 4.6' --mode 'autopilot'

From 01e59ff858c89f8eacc4529868334435c659d642 Mon Sep 17 00:00:00 2001
From: "Ian L." <6273252+ilaflott@users.noreply.github.com>
Date: Wed, 15 Jul 2026 12:41:36 -0400
Subject: [PATCH 06/10] Update ai_pytest_workflow.yaml

---
 .github/workflows/ai_pytest_workflow.yaml | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ai_pytest_workflow.yaml b/.github/workflows/ai_pytest_workflow.yaml
index 41d444034..679ccb2e7 100644
--- a/.github/workflows/ai_pytest_workflow.yaml
+++ b/.github/workflows/ai_pytest_workflow.yaml
@@ -43,12 +43,9 @@ jobs:
           # A token is required to authenticate the GitHub CLI extension
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          # The GitHub CLI (gh) is pre-installed on standard Ubuntu runners.
-          # We install the official Copilot extension here.
-          gh extension install github/gh-copilot
           
-          echo "Testing Copilot Help Command:"
-          gh copilot -- --help
+          echo "Testing Copilot command"
+          gh copilot
 
       - name: Query Copilot for Fixes
         env:

From 0318f8e2396aa5ec3746c19a223e9d7194ee26b7 Mon Sep 17 00:00:00 2001
From: "Ian L." <6273252+ilaflott@users.noreply.github.com>
Date: Wed, 15 Jul 2026 12:42:50 -0400
Subject: [PATCH 07/10] Update ai_pytest_workflow.yaml

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

diff --git a/.github/workflows/ai_pytest_workflow.yaml b/.github/workflows/ai_pytest_workflow.yaml
index 679ccb2e7..14cc54ae2 100644
--- a/.github/workflows/ai_pytest_workflow.yaml
+++ b/.github/workflows/ai_pytest_workflow.yaml
@@ -45,7 +45,7 @@ jobs:
         run: |
           
           echo "Testing Copilot command"
-          gh copilot
+          gh copilot || echo "returning 1 is OK for this line"
 
       - name: Query Copilot for Fixes
         env:

From 678af2b692477caf16d82ba11298866c2da8779b Mon Sep 17 00:00:00 2001
From: "Ian L." <6273252+ilaflott@users.noreply.github.com>
Date: Wed, 15 Jul 2026 12:44:35 -0400
Subject: [PATCH 08/10] Update ai_pytest_workflow.yaml

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

diff --git a/.github/workflows/ai_pytest_workflow.yaml b/.github/workflows/ai_pytest_workflow.yaml
index 14cc54ae2..728fa2e9e 100644
--- a/.github/workflows/ai_pytest_workflow.yaml
+++ b/.github/workflows/ai_pytest_workflow.yaml
@@ -59,4 +59,4 @@ jobs:
           
           # Pass the prompt and the context to Copilot
           # Note: `gh copilot suggest` is usually interactive, but we feed it as a single string here
-          gh copilot --prompt "Fix these warnings/errors from the recent test run: \n\n ${TEST_OUTPUT}" --add-dir "${PWD}" --allow-all --attachment pytest_output.log --attachment .github/copilot-instructions.md --model 'Claude Sonnet 4.6' --mode 'autopilot'
+          gh copilot --prompt "The following warnings and errors come from pytest_output.log. Fix these warnings/errors from the recent test run: \n\n ${TEST_OUTPUT}" --add-dir "${PWD}" --allow-all --model 'Claude Sonnet 4.6' --mode 'autopilot'

From 1e0f573d286a34dc0981967b2d304b84d0958542 Mon Sep 17 00:00:00 2001
From: "Ian L." <6273252+ilaflott@users.noreply.github.com>
Date: Wed, 15 Jul 2026 12:48:05 -0400
Subject: [PATCH 09/10] Create codeql.yml

---
 .github/workflows/codeql.yml | 101 +++++++++++++++++++++++++++++++++++
 1 file changed, 101 insertions(+)
 create mode 100644 .github/workflows/codeql.yml

diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
new file mode 100644
index 000000000..6ea8e53ea
--- /dev/null
+++ b/.github/workflows/codeql.yml
@@ -0,0 +1,101 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL Advanced"
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+  schedule:
+    - cron: '41 3 * * 3'
+
+jobs:
+  analyze:
+    name: Analyze (${{ matrix.language }})
+    # Runner size impacts CodeQL analysis time. To learn more, please see:
+    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+    #   - https://gh.io/supported-runners-and-hardware-resources
+    #   - https://gh.io/using-larger-runners (GitHub.com only)
+    # Consider using larger runners or machines with greater resources for possible analysis time improvements.
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    permissions:
+      # required for all workflows
+      security-events: write
+
+      # required to fetch internal or private CodeQL packs
+      packages: read
+
+      # only required for workflows in private repositories
+      actions: read
+      contents: read
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - language: actions
+          build-mode: none
+        - language: python
+          build-mode: none
+        # CodeQL supports the following values keywords for 'language': 'actions', 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'rust', 'swift'
+        # Use `c-cpp` to analyze code written in C, C++ or both
+        # Use 'java-kotlin' to analyze code written in Java, Kotlin or both
+        # Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
+        # To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
+        # see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
+        # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
+        # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    # Add any setup steps before running the `github/codeql-action/init` action.
+    # This includes steps like installing compilers or runtimes (`actions/setup-node`
+    # or others). This is typically only required for manual builds.
+    # - name: Setup runtime (example)
+    #   uses: actions/setup-example@v1
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v4
+      with:
+        languages: ${{ matrix.language }}
+        build-mode: ${{ matrix.build-mode }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+    # If the analyze step fails for one of the languages you are analyzing with
+    # "We were unable to automatically build your code", modify the matrix above
+    # to set the build mode to "manual" for that language. Then modify this step
+    # to build your code.
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+    - name: Run manual build steps
+      if: matrix.build-mode == 'manual'
+      shell: bash
+      run: |
+        echo 'If you are using a "manual" build mode for one or more of the' \
+          'languages you are analyzing, replace this with the commands to build' \
+          'your code, for example:'
+        echo '  make bootstrap'
+        echo '  make release'
+        exit 1
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v4
+      with:
+        category: "/language:${{matrix.language}}"

From d78bd44eb65c2a40b0c60f9987ba2a41f90ae3be Mon Sep 17 00:00:00 2001
From: "Ian L." <6273252+ilaflott@users.noreply.github.com>
Date: Wed, 15 Jul 2026 12:56:21 -0400
Subject: [PATCH 10/10] Delete .github/workflows/ai_pytest_workflow.yaml

---
 .github/workflows/ai_pytest_workflow.yaml | 62 -----------------------
 1 file changed, 62 deletions(-)
 delete mode 100644 .github/workflows/ai_pytest_workflow.yaml

diff --git a/.github/workflows/ai_pytest_workflow.yaml b/.github/workflows/ai_pytest_workflow.yaml
deleted file mode 100644
index 728fa2e9e..000000000
--- a/.github/workflows/ai_pytest_workflow.yaml
+++ /dev/null
@@ -1,62 +0,0 @@
-name: AI Pytest Workflow
-
-on:
-  pull_request:
-    branches: [ main ]
-  # schedule:
-  #   - cron: '0 0 * * *' # Runs once a day at midnight
-
-jobs:
-  ai-pytest-check:
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-        with:
-          submodules: recursive
-
-      - name: Fetch recent workflow logs from main
-        env:
-          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          # Get the ID of the most recent workflow run on the main branch.
-          # Note: If you want logs from a *specific* workflow, add `--workflow "Your Workflow Name"` to this command.
-          RUN_ID=$(gh run list --branch main --limit 1 --json databaseId --jq '.[0].databaseId')
-          
-          if [ -z "$RUN_ID" ]; then
-            echo "No recent runs found on the main branch."
-            exit 1
-          fi
-          
-          echo "Fetching logs for Run ID: $RUN_ID"
-          
-          # Download the logs and pipe output to a file. 
-          # Using `|| true` ensures the workflow continues even if the command has a hiccup.
-          gh run view $RUN_ID --log > pytest_output.log || true
-          
-          echo "Captured Logs Preview:"
-          head -n 20 pytest_output.log
-
-      - name: Setup GitHub Copilot CLI
-        env:
-          # A token is required to authenticate the GitHub CLI extension
-          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          
-          echo "Testing Copilot command"
-          gh copilot || echo "returning 1 is OK for this line"
-
-      - name: Query Copilot for Fixes
-        env:
-          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          # Read the pytest output into a variable
-          # Filtering with grep for warnings/errors (case-insensitive) to stay within the prompt limit
-          TEST_OUTPUT=$(cat pytest_output.log | grep -i -E -B 5 -A 5 'warn|error|fail')
-          
-          echo "Feeding workflow logs to Copilot..."
-          
-          # Pass the prompt and the context to Copilot
-          # Note: `gh copilot suggest` is usually interactive, but we feed it as a single string here
-          gh copilot --prompt "The following warnings and errors come from pytest_output.log. Fix these warnings/errors from the recent test run: \n\n ${TEST_OUTPUT}" --add-dir "${PWD}" --allow-all --model 'Claude Sonnet 4.6' --mode 'autopilot'