diff --git a/.codecov.yml b/.codecov.yaml
similarity index 100%
rename from .codecov.yml
rename to .codecov.yaml
diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
deleted file mode 100644
index 5155aa3..0000000
--- a/.github/CODEOWNERS
+++ /dev/null
@@ -1 +0,0 @@
-* @mdolab/infrastructure-maintainers
diff --git a/.github/dependabot.yml b/.github/dependabot.yaml
similarity index 100%
rename from .github/dependabot.yml
rename to .github/dependabot.yaml
diff --git a/.github/stale.yml b/.github/stale.yaml
similarity index 100%
rename from .github/stale.yml
rename to .github/stale.yaml
diff --git a/.github/workflows/README.md b/.github/workflows/README.md
new file mode 100644
index 0000000..8b65332
--- /dev/null
+++ b/.github/workflows/README.md
@@ -0,0 +1,234 @@
+# GitHub Actions Workflows
+
+Reusable GitHub Actions workflows for Supercritical repositories. These workflows are called from individual repositories using the `workflow_call` trigger.
+
+## Available Workflows
+
+| Workflow | Description |
+| :------- | :---------- |
+| `build.yaml` | Build and test code in Docker container |
+| `tapenade.yaml` | Tapenade automatic differentiation checks |
+| `clang_format.yaml` | C/C++ formatting checks |
+| `fprettify.yaml` | Fortran 90 formatting checks |
+| `ruff.yaml` | Python formatting and linting with Ruff |
+| `mypy.yaml` | Python type checking with MyPy |
+| `branch-name-check.yaml` | Enforce branch naming conventions |
+
+---
+
+## Workflow Options
+
+Configuration inheritance/overrides are documented in each workflow section below.
+
+### build.yaml
+
+Docker-based build and test workflow using the `scritical/private-dev` image.
+Runs GCC and/or Intel jobs based on `GCC` and `INTEL` input flags.
+
+| Name | Type | Default | Description |
+| :--- | :--- | :------ | :---------- |
+| `TIMEOUT` | number | `120` | Runtime allowed for the job, in minutes |
+| `GCC_CONFIG` | string | `""` | Path to GCC configuration file (from repository root) |
+| `INTEL_CONFIG` | string | `""` | Path to Intel configuration file (from repository root) |
+| `INTEL` | boolean | `false` | Whether to run Intel-specific build and test steps |
+| `GCC` | boolean | `true` | Whether to run GCC-specific build and test steps |
+| `BUILD_SCRIPT` | string | `.github/build_real.sh` | Path to build script. Empty string skips this step |
+| `TEST_SCRIPT` | string | `.github/test_real.sh` | Path to test script. Empty string skips this step |
+| `TEST` | boolean | `true` | Whether to run the test step |
+
+**Required Secrets:**
+| Name | Description |
+| :--- | :---------- |
+| `DOCKER_USER` | Docker registry username |
+| `DOCKER_OAT` | Docker registry Organization Access Token |
+
+If these secrets are configured at the organization level, callers can use `secrets: inherit` instead of listing each secret.
+
+---
+
+### ruff.yaml
+
+Python formatting and linting using Ruff.
+The workflow checks out the org-wide Ruff configuration from `scritical/.github` and uses it for format, lint, and isort checks.
+
+| Name | Type | Default | Description |
+| :--- | :--- | :------ | :---------- |
+| `MCCABE` | boolean | `false` | Enable McCabe complexity check (pass/fail, max complexity = 10) |
+| `ISORT` | boolean | `false` | Enable import sorting check (pass/fail) |
+
+**Configuration Override:** Create a `ruff.toml` in your repo with:
+```toml
+extend = "~/.config/ruff/ruff.toml"
+
+# Local overrides here
+[lint]
+ignore = ["N802"]
+```
+
+---
+
+### mypy.yaml
+
+Runs MyPy type checking in the GCC OpenMPI Docker image.
+
+| Name | Type | Default | Description |
+| :--- | :--- | :------ | :---------- |
+| `TIMEOUT` | number | `30` | Runtime allowed for the job, in minutes |
+
+**Required Secrets:**
+| Name | Description |
+| :--- | :---------- |
+| `DOCKER_USER` | Docker registry username |
+| `DOCKER_OAT` | Docker registry Organization Access Token |
+
+If these secrets are configured at the organization level, callers can use `secrets: inherit` instead of listing each secret.
+
+---
+
+### tapenade.yaml
+
+Run Tapenade automatic differentiation and check for uncommitted changes.
+
+| Name | Type | Default | Description |
+| :--- | :--- | :------ | :---------- |
+| `TIMEOUT` | number | `10` | Runtime allowed for the job, in minutes |
+| `TAPENADE_SCRIPT` | string | `.github/build_tapenade.sh` | Path to Tapenade build script |
+
+Uses Tapenade version 3.16 from tapenade_3.16-v2-723-ge8da61555.tar. Using a different version will create a diff.
+
+Here is the link to our tapenade version: https://gitlab.inria.fr/tapenade/tapenade/-/package_files/112870/download
+
+---
+
+### clang_format.yaml
+
+C/C++ code formatting checks using clang-format.
+
+| Name | Type | Default | Description |
+| :--- | :--- | :------ | :---------- |
+| `TIMEOUT` | number | `10` | Runtime allowed for the job, in minutes |
+
+**Configuration Override:** Create a `.clang-format` file in your repo root.
+
+---
+
+### fprettify.yaml
+
+Fortran 90 code formatting checks using fprettify.
+
+| Name | Type | Default | Description |
+| :--- | :--- | :------ | :---------- |
+| `TIMEOUT` | number | `10` | Runtime allowed for the job, in minutes |
+
+**Configuration Override:** Create a `.fprettify.rc` file in your repo root.
+
+---
+
+### branch-name-check.yaml
+
+Enforces branch naming conventions for pull requests:
+
+- For PRs targeting `main`, source branches must start with `feature-`, `bugfix-`, or `hotfix-`.
+- For PRs targeting `client-*`, source branches must start with `feature-`, `bugfix-`, or `hotfix-`.
+
+## Setting Up Workflows
+
+### Step 1: Create Workflow File
+
+Create `.github/workflows/ci.yaml` in your repository:
+
+```yaml
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  build:
+    uses: scritical/.github/.github/workflows/build.yaml@main
+    with:
+      GCC_CONFIG: config/defaults/config.LINUX_GFORTRAN.mk # If necessary
+    secrets:
+      DOCKER_USER: ${{ secrets.DOCKER_USER }}
+      DOCKER_OAT: ${{ secrets.DOCKER_OAT }}
+
+  ruff:
+    uses: scritical/.github/.github/workflows/ruff.yaml@main
+
+  clang-format:
+    uses: scritical/.github/.github/workflows/clang_format.yaml@main
+
+  fprettify:
+    uses: scritical/.github/.github/workflows/fprettify.yaml@main
+```
+
+### Step 2: Write Build Script
+
+Create `.github/build_real.sh` in your repository:
+
+```bash
+#!/bin/bash
+set -e
+cp $CONFIG_FILE config/config.mk
+make
+pip install .
+```
+
+### Step 3: Write Test Script
+
+Create `.github/test_real.sh` in your repository:
+
+```bash
+#!/bin/bash
+set -e
+./input_files/get-input-files.sh
+testflo -v . -n 1
+```
+
+### Step 4: Add Secrets
+
+In your orginaization settings, add the required secrets:
+- `DOCKER_USER` - Docker organization name
+- `DOCKER_OAT` - Docker Organization Access Token for pulling private images
+
+---
+
+## Complex Builds
+
+For repositories requiring both real and complex builds:
+
+```yaml
+jobs:
+  build-real:
+    uses: scritical/.github/.github/workflows/build.yaml@main
+    with:
+      GCC_CONFIG: config/defaults/config.LINUX_GFORTRAN.mk
+      BUILD_SCRIPT: .github/build_real.sh
+      TEST_SCRIPT: .github/test_real.sh
+    secrets:
+      DOCKER_USER: ${{ secrets.DOCKER_USER }}
+      DOCKER_OAT: ${{ secrets.DOCKER_OAT }}
+
+  build-complex:
+    uses: scritical/.github/.github/workflows/build.yaml@main
+    with:
+      GCC_CONFIG: config/defaults/config.LINUX_GFORTRAN.mk
+      BUILD_SCRIPT: .github/build_complex.sh
+      TEST_SCRIPT: .github/test_complex.sh
+    secrets:
+      DOCKER_USER: ${{ secrets.DOCKER_USER }}
+      DOCKER_OAT: ${{ secrets.DOCKER_OAT }}
+```
+
+---
+
+## Adding Status Badge
+
+Add a status badge to your README:
+
+```markdown
+![CI](https://github.com/scritical/REPO_NAME/actions/workflows/ci.yaml/badge.svg)
+```
diff --git a/.github/workflows/branch-name-check.yml b/.github/workflows/branch-name-check.yaml
similarity index 88%
rename from .github/workflows/branch-name-check.yml
rename to .github/workflows/branch-name-check.yaml
index f02ea69..cd70185 100644
--- a/.github/workflows/branch-name-check.yml
+++ b/.github/workflows/branch-name-check.yaml
@@ -1,15 +1,9 @@
-name: Branch Name Check
-
 on:
-  pull_request:
-    types: [opened, synchronize, reopened, edited]
-    branches:
-      - main
-      - 'client-*'
+  workflow_call:
 
 jobs:
   check-branch-name:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     steps:
       - name: Check branch name for main
         if: github.base_ref == 'main'
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
new file mode 100644
index 0000000..49497d1
--- /dev/null
+++ b/.github/workflows/build.yaml
@@ -0,0 +1,113 @@
+on:
+  workflow_call:
+    inputs:
+      TIMEOUT:
+        type: number
+        default: 120
+        description: "Timeout for the job in minutes"
+      GCC_CONFIG:
+        type: string
+        default: ""
+        description: "Path to GCC configuration file"
+      INTEL_CONFIG:
+        type: string
+        default: ""
+        description: "Path to Intel configuration file"
+      INTEL:
+        type: boolean
+        default: false
+        description: "Whether to run Intel-specific build and test steps (if false, runs GCC steps)"
+      GCC:
+        type: boolean
+        default: true
+        description: "Whether to run GCC-specific build and test steps (if false, runs Intel steps)"
+      BUILD_SCRIPT:
+        type: string
+        default: ".github/build_real.sh"
+        description: "Path to build script"
+      TEST_SCRIPT:
+        type: string
+        default: ".github/test_real.sh"
+        description: "Path to test script"
+      TEST:
+        type: boolean
+        default: true
+        description: "Whether to run the test step"
+    secrets:
+      DOCKER_USER:
+        required: true
+        description: "Docker registry username"
+      DOCKER_OAT:
+        required: true
+        description: "Docker registry Organization Access Token"
+
+env:
+  SCRITICAL_HOMEDIR: /home/scriticaluser
+  BASHRC: /home/scriticaluser/.bashrc_scritical
+
+jobs:
+  build-gcc:
+    if: inputs.GCC
+    runs-on: ubuntu-24.04
+    timeout-minutes: ${{ inputs.TIMEOUT }}
+    env:
+      DOCKER_TAG: u24-gcc-ompi-latest
+      CONFIG_FILE: ${{ inputs.GCC_CONFIG }}
+    steps: &build_steps
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      - name: Set repo environment variables
+        run: |
+          repo_name="${{ github.event.repository.name }}"
+          echo "REPO_NAME=$repo_name" >> "$GITHUB_ENV"
+          echo "DOCKER_WORKING_DIR=${{ env.SCRITICAL_HOMEDIR }}/repos/$repo_name" >> "$GITHUB_ENV"
+          echo "DOCKER_MOUNT_DIR=${{ env.SCRITICAL_HOMEDIR }}/mount/$repo_name" >> "$GITHUB_ENV"
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKER_USER }}
+          password: ${{ secrets.DOCKER_OAT }}
+
+      - name: Start Docker container
+        run: |
+          docker run -t -d --name app \
+            --mount "type=bind,src=${{ github.workspace }},target=${{ env.DOCKER_MOUNT_DIR }}" \
+            scritical/private-dev:${{ env.DOCKER_TAG }} /bin/bash
+
+          # Copy repo to working directory
+          docker exec app /bin/bash -c "rm -rf $DOCKER_WORKING_DIR && mkdir -p $DOCKER_WORKING_DIR && cp -a $DOCKER_MOUNT_DIR/. $DOCKER_WORKING_DIR/"
+
+      - name: Build
+        if: inputs.BUILD_SCRIPT != ''
+        run: |
+          docker exec \
+            -e CONFIG_FILE="${{ env.CONFIG_FILE }}" \
+            app /bin/bash -c ". $BASHRC && cd $DOCKER_WORKING_DIR && /bin/bash ${{ inputs.BUILD_SCRIPT }}"
+
+      - name: Test
+        if: inputs.TEST_SCRIPT != '' && inputs.TEST
+        run: |
+          docker exec \
+            -e AGENT_NAME="${{ runner.name }}" \
+            -e BUILD_REASON="${{ github.event_name }}" \
+            app /bin/bash -c ". $BASHRC && cd $DOCKER_WORKING_DIR && source ~/MPIOversubscribe.sh && /bin/bash ${{ inputs.TEST_SCRIPT }}"
+
+      - name: Cleanup
+        if: always()
+        run: |
+          # Stop and remove the container only if it exists to avoid noisy errors.
+          if docker ps -a --format '{{.Names}}' | grep -qx app; then
+            docker stop app && docker rm app || true
+          fi
+
+  build-intel:
+    if: inputs.INTEL
+    runs-on: ubuntu-24.04
+    timeout-minutes: ${{ inputs.TIMEOUT }}
+    env:
+      DOCKER_TAG: u24-intel-impi-latest
+      CONFIG_FILE: ${{ inputs.INTEL_CONFIG }}
+    steps: *build_steps
+          
diff --git a/.github/workflows/clang_format.yaml b/.github/workflows/clang_format.yaml
index 03aeea9..b76cdd8 100644
--- a/.github/workflows/clang_format.yaml
+++ b/.github/workflows/clang_format.yaml
@@ -1,13 +1,32 @@
 on:
   workflow_call:
+    inputs:
+      TIMEOUT:
+        type: number
+        default: 10
+        description: "Timeout for the job in minutes"
 
 jobs:
   clang_format:
     runs-on: ubuntu-24.04
+    timeout-minutes: ${{ inputs.TIMEOUT }}
     steps:
-      - name: Install dependencies
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      - name: Install clang-format
+        run: sudo apt-get install clang-format-20 -y
+
+      - name: Get clang-format config
         run: |
-          sudo apt-get install clang-format-10 -y
-      - name: Run clang_format
+          LOCAL_CONFIG_FILE=".clang-format"
+          GLOBAL_CONFIG_URL="https://raw.githubusercontent.com/scritical/.github/main/.clang-format"
+
+          if [[ ! -f "$LOCAL_CONFIG_FILE" ]]; then
+            echo "Downloading global clang-format config..."
+            wget "$GLOBAL_CONFIG_URL" -O "$LOCAL_CONFIG_FILE" || echo "No global clang-format config found; proceeding without a config file. The subsequent clang-format step may fail because -style=file requires a .clang-format configuration."
+          fi
+
+      - name: Run clang-format
         run: |
-          bash ./.github/clang_format.sh
+          find . -iname '*.h' -o -iname '*.hpp' -o -iname '*.c' -o -iname '*.cpp' | xargs clang-format -style=file --dry-run --Werror
diff --git a/.github/workflows/format-and-lint.yaml b/.github/workflows/format-and-lint.yaml
deleted file mode 100644
index 4ff965c..0000000
--- a/.github/workflows/format-and-lint.yaml
+++ /dev/null
@@ -1,31 +0,0 @@
-on:
-  workflow_call:
-
-jobs:
-  format-and-lint:
-    runs-on: ubuntu-24.04
-    steps:
-      - uses: actions/checkout@v5
-      - name: Set up Python
-        uses: actions/setup-python@v6
-        with:
-          python-version: 3.12
-      - name: Install dependencies
-        run: |
-          wget https://raw.githubusercontent.com/mdolab/.github/main/.pre-commit-config.yaml
-          pip install pre-commit
-
-          # Set the ruff config in the .github repo as the global config, then the local config should extend it by including the line `extend = "~/.config/ruff/ruff.toml"`
-          mkdir -p ~/.config/ruff
-          url=https://raw.githubusercontent.com/mdolab/.github/main/ruff.toml
-          wget $url -O ~/.config/ruff/ruff.toml
-
-          echo "Ruff config:"
-          cat ~/.config/ruff/ruff.toml
-          if [[ -f "ruff.toml" ]]; then
-              cat ruff.toml
-          fi
-
-      - name: Run pre-commit checks
-        run: |
-          pre-commit run --all-files --show-diff-on-failure
diff --git a/.github/workflows/fprettify.yaml b/.github/workflows/fprettify.yaml
new file mode 100644
index 0000000..9f65560
--- /dev/null
+++ b/.github/workflows/fprettify.yaml
@@ -0,0 +1,52 @@
+on:
+  workflow_call:
+    inputs:
+      TIMEOUT:
+        type: number
+        default: 10
+        description: "Timeout for the job in minutes"
+
+jobs:
+  fprettify:
+    runs-on: ubuntu-24.04
+    timeout-minutes: ${{ inputs.TIMEOUT }}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+
+      - name: Install fprettify
+        run: pip install fprettify==0.3.7
+
+      - name: Get fprettify config
+        run: |
+          LOCAL_CONFIG_FILE=".fprettify.rc"
+          GLOBAL_CONFIG_URL="https://raw.githubusercontent.com/scritical/.github/main/.fprettify.rc"
+
+          if [[ ! -f "$LOCAL_CONFIG_FILE" ]]; then
+            echo "Downloading global fprettify config..."
+            wget "$GLOBAL_CONFIG_URL" -O "$LOCAL_CONFIG_FILE" || echo "No global config found; fprettify will use its built-in defaults"
+          fi
+
+      - name: Run fprettify
+        run: |
+          CONFIG_FILE=".fprettify.rc"
+          CONFIG_ARG=""
+          if [[ -f "$CONFIG_FILE" ]]; then
+            CONFIG_ARG="--config-file $CONFIG_FILE"
+          fi
+
+          # Run fprettify on non-differentiated Fortran 90 source files
+          find . -type f -iname '*.f90' ! -iname '*_b.f90' ! -iname '*_d.f90' -print0 | while read -d $'\0' fileName
+          do
+            echo "Checking $fileName"
+            fprettify $CONFIG_ARG "$fileName"
+          done
+
+      - name: Check for changes
+        run: |
+          git diff --summary --exit-code || (echo "fprettify produced changes. Please format and commit." && exit 1)
diff --git a/.github/workflows/isort.yaml b/.github/workflows/isort.yaml
deleted file mode 100644
index 37c8e44..0000000
--- a/.github/workflows/isort.yaml
+++ /dev/null
@@ -1,19 +0,0 @@
-on:
-  workflow_call:
-
-jobs:
-  isort:
-    runs-on: ubuntu-24.04
-    steps:
-      - uses: actions/checkout@v5
-      - name: Set up Python
-        uses: actions/setup-python@v6
-        with:
-          python-version: 3.9
-      - name: Get isort config file
-        run: |
-          # copy over the isort config file
-          if [[ ! -f ".isort.cfg" ]]; then
-            wget https://raw.githubusercontent.com/mdolab/.github/main/.isort.cfg
-          fi
-      - uses: isort/isort-action@master
diff --git a/.github/workflows/mypy.yaml b/.github/workflows/mypy.yaml
index 97c4221..eb31ad0 100644
--- a/.github/workflows/mypy.yaml
+++ b/.github/workflows/mypy.yaml
@@ -1,23 +1,65 @@
 on:
   workflow_call:
+    inputs:
+      TIMEOUT:
+        type: number
+        default: 30
+        description: "Timeout for the job in minutes"
+    secrets:
+      DOCKER_USER:
+        required: true
+        description: "Docker registry username"
+      DOCKER_OAT:
+        required: true
+        description: "Docker registry Organization Access Token"
+
+env:
+  SCRITICAL_HOMEDIR: /home/scriticaluser
+  BASHRC: /home/scriticaluser/.bashrc_scritical
 
 jobs:
   mypy:
     runs-on: ubuntu-24.04
-    strategy:
-      matrix:
-        python-version: [3.9, 3.11]
+    timeout-minutes: ${{ inputs.TIMEOUT }}
+    env:
+      DOCKER_TAG: u24-gcc-ompi-latest
     steps:
-      - uses: actions/checkout@v5
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v6
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      - name: Set repo environment variables
+        run: |
+          repo_name="${{ github.event.repository.name }}"
+          echo "REPO_NAME=$repo_name" >> "$GITHUB_ENV"
+          echo "DOCKER_WORKING_DIR=${{ env.SCRITICAL_HOMEDIR }}/repos/$repo_name" >> "$GITHUB_ENV"
+          echo "DOCKER_MOUNT_DIR=${{ env.SCRITICAL_HOMEDIR }}/mount/$repo_name" >> "$GITHUB_ENV"
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v3
         with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
+          username: ${{ secrets.DOCKER_USER }}
+          password: ${{ secrets.DOCKER_OAT }}
+
+      - name: Start Docker container
         run: |
-          pip install wheel
-          pip install mypy
-      - name: Mypy check
+          docker run -t -d --name app \
+            --mount "type=bind,src=${{ github.workspace }},target=${{ env.DOCKER_MOUNT_DIR }}" \
+            scritical/private-dev:${{ env.DOCKER_TAG }} /bin/bash
+
+          # Copy repo to working directory
+          docker exec app /bin/bash -c "rm -rf $DOCKER_WORKING_DIR && mkdir -p $DOCKER_WORKING_DIR && cp -a $DOCKER_MOUNT_DIR/. $DOCKER_WORKING_DIR/"
+
+      - name: MyPy type checking
+        run: |
+          docker exec \
+            -e AGENT_NAME="${{ runner.name }}" \
+            -e BUILD_REASON="${{ github.event_name }}" \
+            app /bin/bash -c ". $BASHRC && cd $DOCKER_WORKING_DIR && mypy ."
+
+      - name: Cleanup
+        if: always()
         run: |
-          mypy --any-exprs-report mypy-output .
-          cat mypy-output/any-exprs.txt
+          # Stop and remove the container only if it exists to avoid noisy errors.
+          if docker ps -a --format '{{.Names}}' | grep -qx app; then
+            docker stop app && docker rm app || true
+          fi
diff --git a/.github/workflows/pylint.yaml b/.github/workflows/pylint.yaml
deleted file mode 100644
index 01921c6..0000000
--- a/.github/workflows/pylint.yaml
+++ /dev/null
@@ -1,21 +0,0 @@
-on:
-  workflow_call:
-
-jobs:
-  pylint:
-    runs-on: ubuntu-24.04
-    steps:
-      - uses: actions/checkout@v5
-      - name: Set up Python
-        uses: actions/setup-python@v6
-        with:
-          python-version: 3.9
-      - name: Install dependencies
-        run: |
-          pip install wheel
-          pip install pylint
-      - name: Run pylint
-        run: |
-          # copy over the pylint config file
-          wget https://raw.githubusercontent.com/mdolab/.github/main/.pylintrc
-          find . -type f -name "*.py" -not -path "*/doc/*" | xargs pylint
diff --git a/.github/workflows/pypi.yaml b/.github/workflows/pypi.yaml
deleted file mode 100644
index 1ecfb57..0000000
--- a/.github/workflows/pypi.yaml
+++ /dev/null
@@ -1,26 +0,0 @@
-on:
-  workflow_call:
-    secrets:
-      PYPI_API_TOKEN:
-        required: true
-
-jobs:
-  pypi:
-    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
-    runs-on: ubuntu-24.04
-    steps:
-      - uses: actions/checkout@v5
-      - uses: actions/setup-python@v6
-        with:
-          python-version: 3.9
-      - name: Build package
-        run: |
-          python --version
-          python -m pip install -U pip
-          pip install setuptools wheel
-          python setup.py bdist_wheel
-      - name: Publish package
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/.github/workflows/ruff.yaml b/.github/workflows/ruff.yaml
new file mode 100644
index 0000000..d697baf
--- /dev/null
+++ b/.github/workflows/ruff.yaml
@@ -0,0 +1,78 @@
+on:
+  workflow_call:
+    inputs:
+      MCCABE:
+        type: boolean
+        default: false
+        description: "Enable McCabe complexity check (pass/fail)"
+      ISORT:
+        type: boolean
+        default: false
+        description: "Enable isort import sorting check (pass/fail)"
+
+jobs:
+  ruff:
+    runs-on: ubuntu-24.04
+    defaults:
+      run:
+        working-directory: project
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+        with:
+          path: project
+      
+      - name: Checkout org-wide configs
+        uses: actions/checkout@v6
+        with:
+          repository: scritical/.github
+          path: .org-dotgithub
+          fetch-depth: 1
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+
+      - name: Setup Ruff Configuration
+        run: |
+          # Get the org-wide ruff config and copy it to ~/.config/ruff/ruff.toml
+          mkdir -p ~/.config/ruff
+          cp ../.org-dotgithub/ruff.toml ~/.config/ruff/ruff.toml
+
+          if [[ -f ruff.toml ]]; then
+            echo "Found repo-specific ruff.toml"
+            echo "RUFF_CONFIG=ruff.toml" >> "$GITHUB_ENV"
+            cat ruff.toml
+          else
+            echo "No repo-specific ruff.toml found, using org-wide config"
+            echo "RUFF_CONFIG=~/.config/ruff/ruff.toml" >> "$GITHUB_ENV"
+          fi
+      
+      - name: Install Ruff
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+      
+      - name: Ruff formatting
+        run: |
+          echo "=== Ruff Formatting Check ==="
+          ruff format --check --exit-non-zero-on-fix --config $RUFF_CONFIG .
+      
+      - name: Ruff linting
+        run: |
+          echo "=== Ruff Linting Check ==="
+          ruff check --exit-non-zero-on-fix --config $RUFF_CONFIG .
+      
+      - name: isort check
+        if: inputs.ISORT
+        run: |
+          echo "=== isort Import Sorting Check ==="
+          ruff check --exit-non-zero-on-fix --select=I --config $RUFF_CONFIG .
+
+      - name: McCabe complexity check
+        if: inputs.MCCABE
+        run: |
+          echo "=== McCabe Complexity Report ==="
+          echo "Checking for functions with complexity > 10..."
+          ruff check --select=C90 --config $RUFF_CONFIG .
\ No newline at end of file
diff --git a/.github/workflows/tapenade.yaml b/.github/workflows/tapenade.yaml
new file mode 100644
index 0000000..3bc90f7
--- /dev/null
+++ b/.github/workflows/tapenade.yaml
@@ -0,0 +1,41 @@
+on:
+  workflow_call:
+    inputs:
+      TIMEOUT:
+        type: number
+        default: 10
+        description: "Timeout for the job in minutes"
+      TAPENADE_SCRIPT:
+        type: string
+        default: ".github/build_tapenade.sh"
+        description: "Path to Tapenade build script"
+
+jobs:
+  tapenade:
+    runs-on: ubuntu-24.04
+    timeout-minutes: ${{ inputs.TIMEOUT }}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      - name: Set up Java
+        uses: actions/setup-java@v4
+        with:
+          distribution: temurin
+          java-version: 8
+
+      - name: Install and run Tapenade
+        run: |
+          # Download Tapenade 3.16 (tapenade_3.16-v2-723-ge8da61555.tar)
+          TAPENADE_URL="https://gitlab.inria.fr/tapenade/tapenade/-/package_files/112870/download"
+          wget "$TAPENADE_URL" -O tapenade_3.16.tar
+          tar -xzf tapenade_3.16.tar
+          export PATH=$(pwd)/tapenade_3.16/bin:$PATH
+
+          # Run Tapenade
+          touch config.mk  # empty config file to make "make" happy
+          bash ${{ inputs.TAPENADE_SCRIPT }}
+
+      - name: Check for changes
+        run: |
+          git diff --exit-code || (echo "Tapenade produced changes. Please regenerate and commit." && exit 1)
diff --git a/.isort.cfg b/.isort.cfg
deleted file mode 100644
index d6b8b9d..0000000
--- a/.isort.cfg
+++ /dev/null
@@ -1,9 +0,0 @@
-[isort]
-profile=black
-line_length=120
-force_sort_within_sections=true
-import_heading_stdlib=Standard Python modules
-import_heading_thirdparty=External modules
-import_heading_firstparty=First party modules
-import_heading_localfolder=Local modules
-skip_glob=**__init__.py,**setup.py
diff --git a/README.md b/README.md
index 6b306c3..1672029 100644
--- a/README.md
+++ b/README.md
@@ -1,14 +1,18 @@
 # .github
 This repo stores the following shared repository settings/configurations/templates:
 - Issue and pull request templates on GitHub
-- Shared configurations for
-  - `pre-commit`
-  - `ruff`
-  - `isort`
-  - `pylint`
-  - `codecov`
-  - `mypy`
-- Shared configurations for Azure Pipelines
 - Shared configurations for GitHub Actions
+  - `ruff`
+    - formatting
+    - linting
+    - isort
+    - McCabe Complexity
+  - `clang_format`
+  - `build`
+    - Docker build
+    - Integration testing
+    - `mypy`
+  - `fprettify`
+  - `tapenade`
+  - `branch-name-check`
 - Issue/PR labels shared across the organization
-- Configuration script for the build bot
diff --git a/azure/README.md b/azure/README.md
deleted file mode 100644
index 32c5aed..0000000
--- a/azure/README.md
+++ /dev/null
@@ -1,170 +0,0 @@
-# Azure
-The Supercritical Azure Pipelines page is found on the [Azure Website](https://dev.azure.com/scritical/).
-The process outlined here is split into Public and Private projects, used accordingly for public and private repositories.
-However, at the moment we only support Private projects, but the processes support public repositories.
-The pipelines for each repository can be found by selecting its parent project and then the pipelines button.
-Each pipeline is set up using the templates located in this `.github` repository so only configuration files are needed in each repository.
-
-The templates are organized into the following files:
-- `azure_build.yaml` which handles the build and test jobs for the code
-- `azure_pypi.yaml` which handles the PyPI deployment if applicable
-- `azure_style.yaml` which handles style checks on the code
-- `azure_template.yaml` which handles the job itself, calling the necessary sub-templates.
-
-## Template Options
-| Name                   | Type    | Default                     | Description.                                                                                                                                |
-| :--------------------- | :------ | :-------------------------- | :------------------------------------------------------------------------------------------------------------------------------------------ |
-| `REPO_NAME`            | string  |                             | Name of repository                                                                                                                          |
-| `COMPLEX`              | boolean | `false`                     | Flag for triggering complex build and tests                                                                                                 |
-| `TIMEOUT_BUILD`        | number  | `120`                       | Runtime allowed for each build and test job, in minutes                                                                                     |
-| `GCC_CONFIG`           | string  | `None`                      | Path to GCC configuration file (from repository root)                                                                                       |
-| `INTEL_CONFIG`         | string  | `None`                      | Path to Intel configuration file (from repository root)                                                                                     |
-| `BUILD_REAL`           | string  | `.github/build_real.sh`     | Path to Bash script with commands to build real code. Using `None` will skip this step.                                                     |
-| `TEST_REAL`            | string  | `.github/text_real.sh`      | Path to Bash script to run real tests. Using `None` will skip this step.                                                                    |
-| `BUILD_COMPLEX`        | string  | `.github/build_complex.sh`  | Path to Bash script with commands to build complex code. Using `None` will skip this step.                                                  |
-| `TEST_COMPLEX`         | string  | `.github/text_complex.sh`   | Path to Bash script with commands to run complex tests. Using `None` will skip this step.                                                   |
-| `IMAGE`                | string  | `public`                    | Select Docker image. Can be `public`, `private`, or `auto`. `auto` uses the private image on trusted builds and the public image otherwise. |
-| `COVERAGE`             | boolean | `false`                     | Flag to report test coverage to `codecov`                                                                                                   |
-| `TIMEOUT_STYLE`        | number  | `10`                        | Runtime allowed for each style check, in minutes                                                                                            |
-| `IGNORE_STYLE`         | boolean | `false`                     | Flag to allow `formatting and linting` checks to fail without failing the pipeline                                                          |
-| `BASE_FORMAT_AND_LINT` | boolean | `true`                      | Flag to trigger the `base_format_and_lint` check                                                                                            |
-| `ISORT`                | boolean | `false`                     | Flag to trigger the `isort` check                                                                                                           |
-| `PYLINT`               | boolean | `false`                     | Flag to trigger the `pylint` check                                                                                                          |
-| `CLANG_FORMAT`         | boolean | `false`                     | Flag to trigger the `clang-format` check                                                                                                    |
-| `FPRETTIFY`            | boolean | `false`                     | Flag to trigger the `fprettify` check                                                                                                       |
-| `MYPY`                 | boolean | `false`                     | Flag to trigger the `mypy` check                                                                                                            |
-| `TAPENADE`             | boolean | `false`                     | Flag to trigger the Tapenade check                                                                                                          |
-| `TIMEOUT_TAPENADE`     | number  | `10`                        | Runtime allowed for the Tapenade check, in minutes                                                                                          |
-| `TAPENADE_SCRIPT`      | string  | `.github/build_tapenade.sh` | Path to Bash script with commands to run Tapenade                                                                                           |
-| `TAPENADE_VERSION`     | string  | `3.10`                      | Version of Tapenade to use                                                                                                                  |
-
-## Setting up a pipeline
-### Step 1: Setup Azure Pipelines YAML File:
-
-1. Create `azure_template.yaml` in the `.github/` directory of your repository
-2. Add triggers (see example below)
- 	- Only set triggers for the `main` branch and pull requests to `main`
-3. Add resources (see example below)
-	- This resource pulls the `azure_template` from the `scritical/.github` repository
-4. Add parameters (see example below and the options table above)
-
-```
-trigger:
-- main
-
-pr:
-- main
-
-resources:
-  repositories:
-  - repository: azure_template
-    type: github
-    name: scritical/.github
-    endpoint: scritical
-
-extends:
-  template: azure/azure_template.yaml@azure_template
-  parameters:
-    REPO_NAME: adflow
-    IGNORE_STYLE: true
-    COMPLEX: true
-    GCC_CONFIG: config/defaults/config.LINUX_GFORTRAN.mk
-    INTEL_CONFIG: config/defaults/config.LINUX_INTEL.mk
-```
-
-### Step 2: Write Build Bash Script:
-
-1. Create `build_real.sh` in the `.github/` directory of your repository
-2. Add `#!/bin/bash` followed by `set -e` as the first two lines
-3. Add configuration file copy if needed (see example below). Note that the environment variable `$CONFIG_FILE` is provided by the Azure template and is automatically set depending on the compiler used for each build.
-4. Add make command if needed (see example below)
-5. Add python install command (see example below)
-6. Repeat with `build_complex.sh` if needed
-
-```
-#!/bin/bash
-set -e
-cp $CONFIG_FILE config/config.mk
-make
-pip install .
-```
-
-### Step 3: Write Test Bash Script:
-
-1. Create `test_real.sh` in `.github/` directory of your repository
-2. Add `#!/bin/bash` followed by `set -e` as the first two lines
-3. Add input file download if needed (see example below)
-4. Add `testflo` command
-5. Repeat with `test_complex.sh` if needed
-
-```
-#!/bin/bash
-set -e
-./input_files/get-input-files.sh
-testflo -v . -n 1
-```
-
-### Step 4: Push branch to `scritical/` repository and create pull request
-
-1. Push branch directly to `scritical` repository, not your personal fork
-
-### Step 5: Create new Pipeline on Microsoft Azure
-
-1. Go to [Azure Pipelines](https://dev.azure.com/scritical/) and select public / private as needed by current repository
-2. Select "Pipelines" and "New pipeline"
-3. Select "Github" and authorize the Azure Pipeline app if you have not already
-4. Select correct scritical repository (again, not personal fork)
-5. Select "Existing Azure Pipelines YAML file"
-6. In pop-up menu, set "Branch" to your new Azure-transition branch and "Path" to `.github/azure-pipelines.yaml`
-7. Click "continue"
-
-### Step 6: Add Badge to README
-
-1. Go to the pipeline on Azure
-2. Click on the three dots next to "Run pipeline"
-3. Click on "status badge"
-4. Set "Branch" to "main"
-5. Copy the text for "Sample markdown" and paste it into README
-
-### Step 7: Create PR
-
-1. Create pull request to `main`
-2. Ensure the Azure jobs start and appear in the pull request
-
-## PyPI with Azure
-If using PyPI for a repository, the yaml file does not follow this same structure, but imports components as stages instead of as an extend.
-An example yaml file using PyPI is:
-
-```
-trigger:
-  branches:
-    include:
-    - main
-  tags:
-    include:
-    - v*.*.*
-
-pr:
-- main
-
-resources:
-  repositories:
-  - repository: azure_template
-    type: github
-    name: scritical/.github
-    endpoint: scritical
-
-stages:
-- template: azure/azure_template.yaml@azure_template
-  parameters:
-    REPO_NAME: REPOSITORY NAME
-
-- stage:
-  dependsOn:
-  - Test_Real
-  - Style
-  displayName: PyPI
-  condition: and(succeeded(), contains(variables['build.sourceBranch'], 'tags'))
-  jobs:
-  - template: azure/azure_pypi.yaml@azure_template
-```
diff --git a/azure/azure_build.yaml b/azure/azure_build.yaml
deleted file mode 100644
index effbc18..0000000
--- a/azure/azure_build.yaml
+++ /dev/null
@@ -1,157 +0,0 @@
-parameters:
-  - name: REPO_NAME
-    type: string
-  - name: TIMEOUT
-    type: number
-  - name: GCC_CONFIG
-    type: string
-  - name: INTEL_CONFIG
-    type: string
-  - name: BUILD
-    type: string
-  - name: TEST
-    type: string
-  - name: IMAGE
-    type: string
-  - name: COVERAGE
-    type: boolean
-  - name: C_COVERAGE
-    type: boolean
-
-jobs:
-  - job:
-    pool:
-      vmImage: "ubuntu-24.04"
-    timeoutInMinutes: ${{ parameters.TIMEOUT }}
-    strategy:
-      matrix:
-        "u24-gcc-ompi-latest":
-          DOCKER_TAG: u24-gcc-ompi-latest
-          CONFIG_FILE: ${{ parameters.GCC_CONFIG }}
-        # "u22-gcc-ompi-stable":
-        #   DOCKER_TAG: u22-gcc-ompi-stable
-        #   CONFIG_FILE: ${{ parameters.GCC_CONFIG }}
-    variables:
-      - group: Docker
-      - group: Codecov
-      - name: SCRITICAL_HOMEDIR
-        value: /home/scriticaluser
-      - name: DOCKER_WORKING_DIR
-        value: ${{ variables.SCRITICAL_HOMEDIR }}/repos/${{ parameters.REPO_NAME }}
-      - name: DOCKER_MOUNT_DIR
-        value: ${{ variables.SCRITICAL_HOMEDIR }}/azure/${{ parameters.REPO_NAME }}
-      - name: BASHRC
-        value: ${{ variables.SCRITICAL_HOMEDIR }}/.bashrc_scritical
-    steps:
-      - checkout: self
-      - checkout: azure_template
-      - script: |
-          # This is a trusted build if DOCKER_USERNAME is defined
-          if [[ ! -z $(DOCKER_USERNAME) ]] ; then
-            echo $(DOCKER_PASSWORD) | docker login -u $(DOCKER_USERNAME) --password-stdin;
-          fi
-          # "auto" pulls the private image for trusted builds
-          if [[ "${{ parameters.IMAGE }}" == "private" ]] || [[ "${{ parameters.IMAGE }}" == "auto" && ! -z $(DOCKER_USERNAME) ]] ; then
-            export DOCKER_IMAGE=private-dev;
-          else
-            export DOCKER_IMAGE=public-dev;
-          fi
-          docker pull scritical/$DOCKER_IMAGE:$(DOCKER_TAG);
-          docker run -t -d --name app --mount "type=bind,src=$(pwd)/${{ parameters.REPO_NAME }},target=${{ variables.DOCKER_MOUNT_DIR }}" scritical/$DOCKER_IMAGE:$(DOCKER_TAG) /bin/bash;
-          docker exec app /bin/bash -c "rm -rf ${{ variables.DOCKER_WORKING_DIR }} && cp -r ${{ variables.DOCKER_MOUNT_DIR }} ${{ variables.DOCKER_WORKING_DIR }}";
-        displayName: Prepare Repository
-      - script: docker exec -e CONFIG_FILE=$(CONFIG_FILE) app /bin/bash -c ". ${{ variables.BASHRC }} && cd ${{ variables.DOCKER_WORKING_DIR }} && /bin/bash ${{ parameters.BUILD }}"
-        displayName: Build
-        condition: and(succeeded(), ne('${{ parameters.BUILD }}', 'None'))
-      - script: |
-          set -e
-          docker exec -e AGENT_NAME="$AGENT_NAME" -e BUILD_REASON=$(Build.Reason) app /bin/bash -c ". ${{ variables.BASHRC }} && cd ${{ variables.DOCKER_WORKING_DIR }} && source ~/MPIOversubscribe.sh && /bin/bash ${{ parameters.TEST }}"
-        displayName: Run Tests
-        condition: and(succeeded(), ne('${{ parameters.TEST }}', 'None'))
-      - script: |
-          cd ${{ parameters.REPO_NAME }}
-
-          # validate the uploader
-          curl https://keybase.io/codecovsecurity/pgp_keys.asc | gpg --no-default-keyring --keyring trustedkeys.gpg --import
-          curl -Os https://uploader.codecov.io/latest/linux/codecov
-          curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM
-          curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM.sig
-          gpgv codecov.SHA256SUM.sig codecov.SHA256SUM
-          shasum -a 256 -c codecov.SHA256SUM
-
-          # exit if checksum fails
-          if [[ $? -ne 0 ]] ; then
-            echo "checksum failed"
-            exit 1
-          fi
-
-          # clean validation files
-          rm codecov.SHA256SUM*
-
-          # grab the token
-          if [[ ! -z $(${{ parameters.REPO_NAME }}_CODECOV_TOKEN) ]] ; then
-            echo "codecov token found!"
-            export CODECOV_TOKEN=$(${{ parameters.REPO_NAME }}_CODECOV_TOKEN)
-            export CODECOV_ARGS="-t $CODECOV_TOKEN"
-          else
-            export CODECOV_ARGS=""
-          fi
-
-          # convert coverage file to xml inside Docker
-          sudo docker exec app /bin/bash -c ". ${{ variables.BASHRC }} && cd ${{ variables.DOCKER_WORKING_DIR }} && \
-          mv \$(find . -name ".coverage" -type f) . && coverage xml"
-
-          # copy coverage file out of Docker
-          docker cp app:${{ variables.DOCKER_WORKING_DIR }}/coverage.xml $(pwd)
-
-          # run codecov
-          chmod +x codecov
-          ./codecov $CODECOV_ARGS
-        condition: and(succeeded(), ${{ parameters.COVERAGE }})
-        displayName: Coverage
-      - script: |
-          cd ${{ parameters.REPO_NAME }}
-
-          # validate the uploader
-          curl https://keybase.io/codecovsecurity/pgp_keys.asc | gpg --no-default-keyring --keyring trustedkeys.gpg --import
-          curl -Os https://uploader.codecov.io/latest/linux/codecov
-          curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM
-          curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM.sig
-          gpgv codecov.SHA256SUM.sig codecov.SHA256SUM
-          shasum -a 256 -c codecov.SHA256SUM
-
-          # exit if checksum fails
-          if [[ $? -ne 0 ]] ; then
-            echo "checksum failed"
-            exit 1
-          fi
-
-          # clean validation files
-          rm codecov.SHA256SUM*
-
-          # grab the token
-          if [[ ! -z $(${{ parameters.REPO_NAME }}_CODECOV_TOKEN) ]] ; then
-            echo "codecov token found!"
-            export CODECOV_TOKEN=$(${{ parameters.REPO_NAME }}_CODECOV_TOKEN)
-            export CODECOV_ARGS="-t $CODECOV_TOKEN"
-          else
-            export CODECOV_ARGS=""
-          fi
-
-          # convert coverage file to xml inside Docker
-          sudo docker exec app /bin/bash -c ". ${{ variables.BASHRC }} && cd ${{ variables.DOCKER_WORKING_DIR }} && \
-          lcov --capture --directory . --output-file coverage.info && \
-          lcov --remove coverage.info '/usr/*' --output-file coverage.info && \
-          lcov --remove coverage.info '*/numpy/*' --output-file coverage.info && \
-          lcov --remove coverage.info '*/.pyenv/versions/*' --output-file coverage.info && \
-          lcov --remove coverage.info '*mpi4py*' --output-file coverage.info" && \
-          lcov --list coverage.info
-
-          # copy coverage file out of Docker
-          docker cp app:${{ variables.DOCKER_WORKING_DIR }}/coverage.info $(pwd)
-
-          # run codecov
-          chmod +x codecov
-          ./codecov $CODECOV_ARGS
-        condition: ${{ parameters.C_COVERAGE }}
-        displayName: C Coverage
diff --git a/azure/azure_pypi.yaml b/azure/azure_pypi.yaml
deleted file mode 100644
index 7ed4c46..0000000
--- a/azure/azure_pypi.yaml
+++ /dev/null
@@ -1,29 +0,0 @@
-parameters:
-  - name: SERVICE_CONNECTION
-    type: string
-    default: pypi
-  - name: TIMEOUT
-    type: number
-    default: 10
-
-jobs:
-  - job: PyPI_Deploy
-    pool:
-      vmImage: "ubuntu-22.04"
-    timeoutInMinutes: ${{ parameters.TIMEOUT }}
-    steps:
-      - task: UsePythonVersion@0
-        inputs:
-          versionSpec: "3.8"
-      - script: |
-          python3 --version
-          python3 -m pip install -U pip
-          pip3 install setuptools wheel twine
-          python3 setup.py bdist_wheel
-        displayName: "Install Packages"
-      - task: TwineAuthenticate@1
-        displayName: "Twine Authenticate"
-        inputs:
-          pythonUploadServiceConnection: ${{ parameters.SERVICE_CONNECTION }}
-      - script: python3 -m twine upload --config-file $(PYPIRC_PATH) dist/*.whl
-        displayName: "Twine Upload"
diff --git a/azure/azure_style.yaml b/azure/azure_style.yaml
deleted file mode 100644
index 7bbd391..0000000
--- a/azure/azure_style.yaml
+++ /dev/null
@@ -1,208 +0,0 @@
-parameters:
-  - name: REPO_NAME
-    type: string
-  - name: IMAGE
-    type: string
-  # The following parameters have defaults because this template could be used by repos directly
-  - name: TIMEOUT
-    type: number
-    default: 10
-  - name: IGNORE_STYLE
-    type: boolean
-    default: false
-  - name: BASE_FORMAT_AND_LINT
-    type: boolean
-    default: true
-  - name: ISORT
-    type: boolean
-    default: false
-  - name: PYLINT
-    type: boolean
-    default: false
-  - name: CLANG_FORMAT
-    type: boolean
-    default: false
-  - name: FPRETTIFY
-    type: boolean
-    default: false
-  - name: MYPY
-    type: boolean
-    default: false
-jobs:
-  - job: base_format_and_lint
-    pool:
-      vmImage: "ubuntu-22.04"
-    timeoutInMinutes: ${{ parameters.TIMEOUT }}
-    continueOnError: ${{ parameters.IGNORE_STYLE }}
-    condition: ${{ parameters.BASE_FORMAT_AND_LINT }}
-    steps:
-      - checkout: self
-      - checkout: azure_template
-      - task: UsePythonVersion@0
-        inputs:
-          versionSpec: "3.11"
-      - script: |
-          cd ${{ parameters.REPO_NAME }}
-          cp ../.github/.pre-commit-config.yaml .
-          pip install pre-commit
-
-          # Set the ruff config in the .github repo as the global config, then the local config should extend it by including the line `extend = "~/.config/ruff/ruff.toml"`
-          mkdir -p ~/.config/ruff
-          cp ../.github/ruff.toml ~/.config/ruff/ruff.toml
-
-          echo "Ruff config:"
-          cat ~/.config/ruff/ruff.toml
-          if [[ -f "ruff.toml" ]]; then
-              cat ruff.toml
-          fi
-
-          # Run the pre-commit checks
-          pre-commit run --all-files --show-diff-on-failure
-
-  - job: isort
-    pool:
-      vmImage: "ubuntu-22.04"
-    timeoutInMinutes: ${{ parameters.TIMEOUT }}
-    continueOnError: ${{ parameters.IGNORE_STYLE }}
-    condition: ${{ parameters.ISORT }}
-    steps:
-      - checkout: self
-      - checkout: azure_template
-      - task: UsePythonVersion@0
-        inputs:
-          versionSpec: "3.11"
-      - script: |
-          cd ${{ parameters.REPO_NAME }}
-
-          # copy over the isort config file
-          if [[ ! -f ".isort.cfg" ]]; then
-            cp ../.github/.isort.cfg .
-          fi
-
-          pip install wheel
-          pip install isort
-          isort . -c
-
-  - job: pylint
-    pool:
-      vmImage: "ubuntu-22.04"
-    timeoutInMinutes: ${{ parameters.TIMEOUT }}
-    continueOnError: ${{ parameters.IGNORE_STYLE }}
-    condition: ${{ parameters.PYLINT }}
-    steps:
-      - checkout: self
-      - checkout: azure_template
-      - task: UsePythonVersion@0
-        inputs:
-          versionSpec: "3.11"
-      - script: |
-          cd ${{ parameters.REPO_NAME }}
-
-          # copy over the pylint config file
-          cp ../.github/.pylintrc .
-
-          pip install pylint
-          find . -type f -name "*.py" -not -path "*/doc/*" | xargs pylint
-
-  - job: clang_format
-    pool:
-      vmImage: "ubuntu-22.04"
-    timeoutInMinutes: ${{ parameters.TIMEOUT }}
-    continueOnError: ${{ parameters.IGNORE_STYLE }}
-    condition: ${{ parameters.CLANG_FORMAT }}
-    steps:
-      - checkout: self
-      - checkout: azure_template
-      - script: |
-          # Install prerequisites
-          sudo apt-get install clang-format-10 -y
-
-          cd ${{ parameters.REPO_NAME }}
-
-          # Check if we can access script, if not exit
-          if [[ ! -f ../.github/azure/clang-format.sh ]]; then
-            echo "clang-format.sh not found. Exiting."
-            exit 1
-          fi
-
-          # Run the formatting
-          bash ../.github/azure/clang-format.sh --dry-run || exit $?
-
-  - job: fprettify
-    pool:
-      vmImage: "ubuntu-22.04"
-    timeoutInMinutes: ${{ parameters.TIMEOUT }}
-    continueOnError: ${{ parameters.IGNORE_STYLE }}
-    condition: ${{ parameters.FPRETTIFY }}
-    steps:
-      - checkout: self
-      - checkout: azure_template
-      - task: UsePythonVersion@0
-        inputs:
-          versionSpec: "3.11"
-      - script: |
-          cd ${{ parameters.REPO_NAME }}
-
-          # Check if we can access script, if not exit
-          if [[ ! -f ../.github/azure/fprettify.sh ]]; then
-            echo "fprettify.sh not found. Exiting."
-            exit 1
-          fi
-
-          # Install fprettify
-          pip install fprettify==0.3.7
-
-          # Run the formatting
-          bash ../.github/azure/fprettify.sh || exit $?
-
-          # Exit with an error if any of the tracked files changed
-          git diff --summary --exit-code
-
-  - job: mypy
-    pool:
-      vmImage: "ubuntu-22.04"
-    timeoutInMinutes: ${{ parameters.TIMEOUT }}
-    continueOnError: ${{ parameters.IGNORE_STYLE }}
-    condition: ${{ parameters.MYPY }}
-    strategy:
-      matrix:
-        "u24-gcc-ompi-latest":
-          DOCKER_TAG: u24-gcc-ompi-latest
-    variables:
-      - group: Docker
-      - name: SCRITICAL_HOMEDIR
-        value: /home/scriticaluser
-      - name: DOCKER_WORKING_DIR
-        value: ${{ variables.SCRITICAL_HOMEDIR }}/repos/${{ parameters.REPO_NAME }}
-      - name: DOCKER_MOUNT_DIR
-        value: ${{ variables.SCRITICAL_HOMEDIR }}/azure/${{ parameters.REPO_NAME }}
-      - name: BASHRC
-        value: ${{ variables.SCRITICAL_HOMEDIR }}/.bashrc_scritical
-    steps:
-      - checkout: self
-      - checkout: azure_template
-      - task: UsePythonVersion@0
-        inputs:
-          versionSpec: "3.11"
-      - script: |
-          # This is a trusted build if DOCKER_USERNAME is defined
-          if [[ ! -z $(DOCKER_USERNAME) ]] ; then
-            echo $(DOCKER_PASSWORD) | docker login -u $(DOCKER_USERNAME) --password-stdin;
-          fi
-          # "auto" pulls the private image for trusted builds
-          if [[ "${{ parameters.IMAGE }}" == "private" ]] || [[ "${{ parameters.IMAGE }}" == "auto" && ! -z $(DOCKER_USERNAME) ]] ; then
-            export DOCKER_IMAGE=private-dev;
-          else
-            export DOCKER_IMAGE=public-dev;
-          fi
-          docker pull scritical/$DOCKER_IMAGE:$(DOCKER_TAG);
-          docker run -t -d --name app --mount "type=bind,src=$(pwd)/${{ parameters.REPO_NAME }},target=${{ variables.DOCKER_MOUNT_DIR }}" scritical/$DOCKER_IMAGE:$(DOCKER_TAG) /bin/bash;
-          docker exec app /bin/bash -c "rm -rf ${{ variables.DOCKER_WORKING_DIR }} && cp -r ${{ variables.DOCKER_MOUNT_DIR }} ${{ variables.DOCKER_WORKING_DIR }}";
-        displayName: Prepare Repository
-      - script: |
-          set -e
-          docker exec app /bin/bash -c ". ${{ variables.BASHRC }} && cd ${{ variables.DOCKER_WORKING_DIR }} && mypy"
-        displayName: Run mypy
-        condition: succeeded()
-
-
diff --git a/azure/azure_tapenade.yaml b/azure/azure_tapenade.yaml
deleted file mode 100644
index a6209e4..0000000
--- a/azure/azure_tapenade.yaml
+++ /dev/null
@@ -1,45 +0,0 @@
-parameters:
-  - name: REPO_NAME
-    type: string
-  - name: TIMEOUT
-    type: number
-  - name: TAPENADE_SCRIPT
-    type: string
-  - name: TAPENADE_VERSION
-    type: string
-
-jobs:
-  - job: tapenade
-    pool:
-      vmImage: "ubuntu-22.04"
-    timeoutInMinutes: ${{ parameters.TIMEOUT }}
-    steps:
-      - task: JavaToolInstaller@0
-        inputs:
-          versionSpec: "8"
-          jdkArchitectureOption: "x64"
-          jdkSourceOption: "PreInstalled"
-      - script: |
-          if [[ "${{ parameters.TAPENADE_VERSION }}" == "3.10" ]]; then
-            export TAPENADE_URL=https://websites.umich.edu/~mdolaboratory/misc/tapenade3.10.tar
-            export TAPENADE_HOME=$(pwd)/tapenade${{ parameters.TAPENADE_VERSION }}
-          elif [[ "${{ parameters.TAPENADE_VERSION }}" == "3.16" ]]; then
-            # The following link corresponds to tapenade_3.16-v2-723-ge8da61555.tar
-            export TAPENADE_URL="https://gitlab.inria.fr/tapenade/tapenade/-/package_files/112870/download -O tapenade_3.16.tar"
-            export TAPENADE_HOME=$(pwd)/tapenade_${{ parameters.TAPENADE_VERSION }}
-          fi
-
-          # Install Tapenade
-          wget $TAPENADE_URL
-          tar -xzf $TAPENADE_HOME.tar
-          export PATH=$TAPENADE_HOME/bin:$PATH
-
-          # Run Tapenade
-          touch config.mk # empty config file to make "make" happy
-          bash ${{ parameters.TAPENADE_SCRIPT }}
-          if [ $? -ne 0 ]; then
-            echo "Tapenade runscript failed"
-            exit 1
-          fi
-
-          git diff --exit-code
diff --git a/azure/azure_template.yaml b/azure/azure_template.yaml
deleted file mode 100644
index 783c31e..0000000
--- a/azure/azure_template.yaml
+++ /dev/null
@@ -1,139 +0,0 @@
-parameters:
-  - name: REPO_NAME
-    type: string
-  # Build and test
-  - name: COMPLEX
-    type: boolean
-    default: false
-  - name: TIMEOUT_BUILD
-    type: number
-    default: 120
-  - name: GCC_CONFIG
-    type: string
-    default: None
-  - name: INTEL_CONFIG
-    type: string
-    default: None
-  - name: BUILD_REAL
-    type: string
-    default: .github/build_real.sh
-  - name: TEST_REAL
-    type: string
-    default: .github/test_real.sh
-  - name: BUILD_COMPLEX
-    type: string
-    default: .github/build_complex.sh
-  - name: TEST_COMPLEX
-    type: string
-    default: .github/test_complex.sh
-  - name: IMAGE
-    type: string
-    default: private
-  - name: COVERAGE
-    type: boolean
-    default: false
-  - name: C_COVERAGE
-    type: boolean
-    default: false
-  # Style checks
-  - name: TIMEOUT_STYLE
-    type: number
-    default: 10
-  - name: IGNORE_STYLE
-    type: boolean
-    default: false
-  - name: BASE_FORMAT_AND_LINT
-    type: boolean
-    default: true
-  - name: ISORT
-    type: boolean
-    default: false
-  - name: PYLINT
-    type: boolean
-    default: false
-  - name: CLANG_FORMAT
-    type: boolean
-    default: false
-  - name: FPRETTIFY
-    type: boolean
-    default: false
-  - name: MYPY
-    type: boolean
-    default: false
-  # Tapenade
-  - name: TAPENADE
-    type: boolean
-    default: false
-  - name: TIMEOUT_TAPENADE
-    type: number
-    default: 10
-  - name: TAPENADE_SCRIPT
-    type: string
-    default: .github/build_tapenade.sh
-  - name: TAPENADE_VERSION
-    type: string
-    default: 3.10
-
-
-stages:
-  - stage: Test_Real
-    dependsOn: []
-    displayName: Real Test
-    jobs:
-      - template: azure_build.yaml
-        parameters:
-          REPO_NAME: ${{ parameters.REPO_NAME }}
-          TIMEOUT: ${{ parameters.TIMEOUT_BUILD }}
-          GCC_CONFIG: ${{ parameters.GCC_CONFIG }}
-          INTEL_CONFIG: ${{ parameters.INTEL_CONFIG }}
-          BUILD: ${{ parameters.BUILD_REAL }}
-          TEST: ${{ parameters.TEST_REAL }}
-          IMAGE: ${{ parameters.IMAGE }}
-          COVERAGE: ${{ parameters.COVERAGE }}
-          C_COVERAGE: ${{ parameters.C_COVERAGE }}
-
-  - stage: Test_Complex
-    dependsOn: []
-    displayName: Complex Test
-    condition: ${{ parameters.COMPLEX }}
-    jobs:
-      - template: azure_build.yaml
-        parameters:
-          REPO_NAME: ${{ parameters.REPO_NAME }}
-          TIMEOUT: ${{ parameters.TIMEOUT_BUILD }}
-          GCC_CONFIG: ${{ parameters.GCC_CONFIG }}
-          INTEL_CONFIG: ${{ parameters.INTEL_CONFIG }}
-          BUILD: ${{ parameters.BUILD_COMPLEX }}
-          TEST: ${{ parameters.TEST_COMPLEX }}
-          IMAGE: ${{ parameters.IMAGE }}
-          COVERAGE: ${{ parameters.COVERAGE }}
-          C_COVERAGE: ${{ parameters.C_COVERAGE }}
-
-  - stage: Style
-    dependsOn: []
-    displayName: Style Checks
-    jobs:
-      - template: azure_style.yaml
-        parameters:
-          REPO_NAME: ${{ parameters.REPO_NAME }}
-          IMAGE: ${{ parameters.IMAGE }}
-          TIMEOUT: ${{ parameters.TIMEOUT_STYLE }}
-          IGNORE_STYLE: ${{ parameters.IGNORE_STYLE }}
-          BASE_FORMAT_AND_LINT: ${{ parameters.BASE_FORMAT_AND_LINT }}
-          ISORT: ${{ parameters.ISORT }}
-          PYLINT: ${{ parameters.PYLINT }}
-          CLANG_FORMAT: ${{ parameters.CLANG_FORMAT }}
-          FPRETTIFY: ${{ parameters.FPRETTIFY }}
-          MYPY: ${{ parameters.MYPY }}
-
-  - stage: Tapenade
-    dependsOn: []
-    displayName: Tapenade Checks
-    condition: ${{ parameters.TAPENADE }}
-    jobs:
-      - template: azure_tapenade.yaml
-        parameters:
-          REPO_NAME: ${{ parameters.REPO_NAME }}
-          TIMEOUT: ${{ parameters.TIMEOUT_TAPENADE }}
-          TAPENADE_SCRIPT: ${{ parameters.TAPENADE_SCRIPT }}
-          TAPENADE_VERSION: ${{ parameters.TAPENADE_VERSION }}
diff --git a/azure/clang-format.sh b/azure/clang-format.sh
deleted file mode 100644
index ac6ded6..0000000
--- a/azure/clang-format.sh
+++ /dev/null
@@ -1,70 +0,0 @@
-#!/bin/bash
-
-# clang-format expects a .clang-format file in the root (local dir) where the command
-# is run. Need to check for existing files first. If none copy over the global file
-# and remove once done to make sure its not added to git.
-
-# -------------- Command line input --------------
-USAGE="
-usage: [-d]
-
-Argument description:
-    -d|--dry-run    Do not make changes, only simulate formatting changes
-"
-DRY_RUN=""
-while [[ "$#" -gt 0 ]]; do
-    case $1 in
-        -d|--dry-run) DRY_RUN="--dry-run"; shift ;;
-        -h|--help) echo "$USAGE";  exit 1 ;;
-        *) echo "Unknown parameter passed: $1"; echo "$USAGE"; exit 1 ;;
-    esac
-    shift
-done
-
-# Set some constants
-CLANGFORMAT_CONFIG_FILE=""
-LOCAL_CONFIG_FILE=".clang-format"
-GLOBAL_CONFIG_FILE="../.github/.clang-format"
-
-# Initialize variables
-global=0
-
-if [[ -f "$LOCAL_CONFIG_FILE" ]]; then
-    # Use local config file
-    echo "Using local config file: $LOCAL_CONFIG_FILE"
-    CLANGFORMAT_CONFIG_FILE="$LOCAL_CONFIG_FILE"
-elif [[ -f "$GLOBAL_CONFIG_FILE" ]]; then
-    # Use global config file
-    echo "Using .github shared config file: $GLOBAL_CONFIG_FILE"
-    CLANGFORMAT_CONFIG_FILE="$GLOBAL_CONFIG_FILE"
-    cp "$GLOBAL_CONFIG_FILE" .
-    global=1
-else
-    echo "No clang-format config was found. Exiting"
-    exit 2
-fi
-
-# Setting common values
-clang_format_args="-style=file --verbose --Werror"
-if [[ -z "$DRY_RUN" ]]; then
-    # Apply the formatting inplace
-    clang_format_args="$clang_format_args -i"
-else
-    # Only do a dry run
-    clang_format_args="$clang_format_args --dry-run"
-fi
-
-echo "Running clang-format with args: $clang_format_args"
-
-# Run the formatting
-find . -iname '*.h' -o -iname '*.hpp' -o -iname '*.c' -o -iname '*.cpp' | xargs clang-format $clang_format_args
-
-# Store the exit code in case we are running dry-run and find
-clang_exit_code=$?
-
-if [[ 1 == "$global" ]]; then
-    # Remove only of we copied over
-    rm "$LOCAL_CONFIG_FILE"
-fi
-
-exit $clang_exit_code
\ No newline at end of file
diff --git a/azure/combine-config.py b/azure/combine-config.py
deleted file mode 100644
index 9de9d6a..0000000
--- a/azure/combine-config.py
+++ /dev/null
@@ -1,28 +0,0 @@
-"""
-This script will read in two files via command line arguments
-It will then merge them, and write it out to the appropriate output file name
-"""
-import argparse
-import configparser
-
-parser = argparse.ArgumentParser()
-parser.add_argument("default", type=str, help="file name for the default config file")
-parser.add_argument("repo", type=str, help="file name for the repo-specific config file")
-parser.add_argument("output", type=str, help="output file name")
-args = parser.parse_args()
-
-# default config
-config_def = configparser.ConfigParser()
-config_def.read(args.default)
-# project config
-config_repo = configparser.ConfigParser()
-config_repo.read(args.repo)
-
-# merge them together, with existing keys overwritten by project config
-for config in config_def.keys():
-    for key in config_repo[config].keys():
-        config_def[config][key] = config_repo[config][key]
-
-# write out the file
-with open(args.output, "w") as configfile:
-    config_def.write(configfile)
diff --git a/combine-config.py b/combine-config.py
new file mode 100644
index 0000000..9b8c282
--- /dev/null
+++ b/combine-config.py
@@ -0,0 +1,93 @@
+#!/usr/bin/env python3
+"""Merge two INI-style configuration files.
+
+This script merges a *default* INI config with an optional *repo-specific* INI
+config, writing the merged result to an output path. If the repo-specific
+config file does not exist, the default config is written as-is.
+
+Notes
+-----
+The merge behavior is:
+
+- Sections present only in the default config are preserved.
+- Sections present in the repo config are added if missing.
+- For keys present in both configs, the repo config value overrides the
+    default.
+
+Examples
+--------
+From the command line::
+
+        python combine-config.py default.cfg repo.cfg merged.cfg
+
+"""
+import argparse
+import configparser
+import sys
+from pathlib import Path
+
+
+def merge_configs(default_path: str, repo_path: str, output_path: str) -> None:
+    """Merge a default config with an optional repo config.
+
+    Parameters
+    ----------
+    default_path : str
+        Path to the default INI-style configuration file.
+    repo_path : str
+        Path to the repo-specific INI-style configuration file. If this file
+        does not exist, the default config is used without modification.
+    output_path : str
+        Path to write the merged INI configuration.
+
+    Returns
+    -------
+    None
+        This function writes the merged configuration to ``output_path``.
+    """
+    # Read default config
+    config = configparser.ConfigParser()
+    config.read(default_path)
+
+    # Read and merge repo config if it exists
+    repo_file = Path(repo_path)
+    if repo_file.exists():
+        config_repo = configparser.ConfigParser()
+        config_repo.read(repo_path)
+
+        # Merge: repo config overrides default
+        for section in config_repo.sections():
+            if not config.has_section(section):
+                config.add_section(section)
+            for key, value in config_repo.items(section):
+                config.set(section, key, value)
+
+    # Write merged config
+    with open(output_path, "w") as f:
+        config.write(f)
+
+
+def main() -> int:
+    """CLI entry point.
+
+    Parses command-line arguments and writes a merged configuration file.
+
+    Returns
+    -------
+    int
+        Process exit code. Returns ``0`` on successful completion.
+    """
+    parser = argparse.ArgumentParser(
+        description="Merge two INI-style configuration files"
+    )
+    parser.add_argument("default", type=str, help="Path to default config file")
+    parser.add_argument("repo", type=str, help="Path to repo-specific config file")
+    parser.add_argument("output", type=str, help="Path for merged output file")
+    args = parser.parse_args()
+
+    merge_configs(args.default, args.repo, args.output)
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/azure/fprettify.sh b/fprettify.sh
similarity index 96%
rename from azure/fprettify.sh
rename to fprettify.sh
index 91333e8..ea941b8 100644
--- a/azure/fprettify.sh
+++ b/fprettify.sh
@@ -2,7 +2,7 @@
 
 FPRETTIFY_CONFIG_FILE=""
 LOCAL_CONFIG_FILE=".fprettify.rc"
-GLOBAL_CONFIG_FILE="../.github/.fprettify.rc"
+GLOBAL_CONFIG_FILE="./.fprettify.rc"
 
 if [[ ! -z "$1" ]]; then
     # Offer the option of supplying config file through an argument
diff --git a/ruff.toml b/ruff.toml
index d59433f..c2d4df6 100644
--- a/ruff.toml
+++ b/ruff.toml
@@ -1,5 +1,5 @@
 # Minimum Python syntax support
-target-version = "py39"
+target-version = "py311"
 
 line-length = 120
 
@@ -18,7 +18,7 @@ ignore = [
     "E501", # line length, exceeded by some docstrings
     "W605", # TODO (to be fixed), invalid escape sequence, necessary for sphinx directives in docstrings but should switch to raw string
     "D301", # Same reason as W605
-    "D10", # D100-107, missing docstring in public function, class etc (yes we should have docstrings for all public methods, but that is a pipe dream)
+    "D10",  # D100-107, missing docstring in public function, class etc (yes we should have docstrings for all public methods, but that is a pipe dream)
     "D400", # First line of docstring should end with a period (assumes the summary fits on one line, which is not always the case)
     "D205", # 1 blank line required between summary line and description (Makes same assumption as D400)
     "D200", # One-line docstring should fit on one line, don't like this because it enforces inconsistent formatting between one-line and multi-line docstrings
@@ -27,17 +27,17 @@ ignore = [
     "D404", # First word of the docstring should not be "This" (Probably a good rule to follow going forward but it occurs in so many places in our code and it's not a big enough issue to warrant fixing)
 ]
 
-select = [
-    "B",
-    "D",
-    "E",
-    "F",
-    "W",
-]
+select = ["B", "D", "E", "F", "W"]
 
 [lint.pydocstyle]
 convention = "numpy"
 
+[lint.mccabe]
+max-complexity = 10
+
+[lint.isort]
+force-sort-within-sections = true
+
 [format]
 quote-style = "double"
 indent-style = "space"