Strip down to core simulation functionality

.github/pull_request_template.md

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+# Pull Request Template
+
+## Description
+Please include a summary of the change and which issue is addressed. Please also include relevant motivation and context.
+
+## Type of Change
+- [ ] Bug fix
+- [ ] New feature
+- [ ] New model
+- [ ] Code improvement
+- [ ] README update
+
+## Code Changes
+### Summary of Changes
+- Describe the changes made in the codebase.
+- Link to any relevant issues or discussions.
+
+### Unit Testing
+- Provide a list of unit tests added or updated.
+- Ensure all tests pass before submitting the PR.
+
+## Supporting Analysis
+- Provide description of analysis and relevant output
+
+## Example Job
+### Subheader Describing any Comparisons / Analysis
+- Provide a description of how to execute the new feature/model.
+- Compare to benchmark results if applicable.
+- Include any relevant logs, graphs, or data files.
+
+## Checklist
+- [ ] Code is commented
+- [ ] I have made corresponding changes to the documentation
+- [ ] Unit tests are present and working
+
+## Additional Notes
+- Add any other context about the pull request here.

.github/workflows/FormatCheck.yml

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+name: format-check
+
+on:
+  push:
+    branches:
+      - 'main'
+  pull_request:
+    branches:
+      - dev*
+      - staging
+      - main
+
+jobs:
+  format_check:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.12'
+
+      - name: Create and activate virtual environment
+        run: |
+          python -m venv venv
+          source venv/bin/activate
+
+      - name: Install black in virtual environment
+        run: |
+          venv/bin/pip install black
+
+      - name: Check Python Code Formatting
+        run: |
+          venv/bin/black --check --diff ./cellmodeller/
+          venv/bin/black --check --diff ./scripts/

.github/workflows/SpellCheck.yml

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+name: Spell Check
+
+on: [pull_request]
+
+jobs:
+  typos-check:
+    name: Spell Check with Typos
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Actions Repository
+        uses: actions/checkout@v4
+      - name: Check spelling
+        uses: crate-ci/typos@v1.18.0

.github/workflows/validate-branch-targets.yml

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+name: Validate PR Branch Targets
+
+on:
+  pull_request:
+    branches:
+      - dev*
+      - staging
+      - main
+
+jobs:
+  validate:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Check branch naming and targets
+      run: |
+        HEAD="${{ github.head_ref }}"
+        BASE="${{ github.base_ref }}"
+
+        echo "Head branch: $HEAD"
+        echo "Base branch: $BASE"
+
+        #
+        # === ALLOWED HEAD BRANCH PATTERNS ===
+        #
+        if [[ ! "$HEAD" =~ ^(feature|bug|hotfix)/ && ! "$HEAD" =~ ^dev.*$ && "$HEAD" != "staging" ]]; then
+          echo "❌ Branch name must start with 'feature/', 'bug/', 'hotfix/', 'dev*', or be 'staging'."
+          exit 1
+        fi
+
+        #
+        # === MERGE RULES ===
+        #
+
+        # 1. feature/bug/hotfix/dev* may NOT merge directly into main
+        if [[ ( "$HEAD" =~ ^(feature|bug|hotfix)/ || "$HEAD" =~ ^dev.*$ ) && "$BASE" == "main" ]]; then
+          echo "❌ '$HEAD' cannot merge into 'main'. Merge into 'staging' instead."
+          exit 1
+        fi
+
+        # 2. feature/bug/hotfix branches may only merge into dev* or staging
+        if [[ "$HEAD" =~ ^(feature|bug|hotfix)/ && ! "$BASE" =~ ^(dev.*|staging)$ ]]; then
+          echo "❌ Feature/bug/hotfix branches may only merge into 'dev*' or 'staging'."
+          exit 1
+        fi
+
+        # 3. dev* branches may only merge into staging or other dev* branches
+        if [[ "$HEAD" =~ ^dev.*$ && ! "$BASE" =~ ^(staging|dev.*)$ ]]; then
+          echo "❌ Dev* branches may only merge into 'staging' or another dev* branch."
+          exit 1
+        fi
+
+        # 4. staging may only merge into main
+        if [[ "$HEAD" == "staging" && "$BASE" != "main" ]]; then
+          echo "❌ 'staging' may only merge into 'main'."
+          exit 1
+        fi
+
+        echo "✅ PR branch name and target are valid."

.gitignore

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+__pycache__/
+*.py[cod]
+*.egg-info/
+build/
+dist/
+.eggs/
+.ipynb_checkpoints/
+.vscode/
+.idea/
+.DS_Store
+data/