From 6a5d253a627c2e06c42a4c90c50641cab1807c38 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 5 Dec 2025 13:29:05 +0000
Subject: [PATCH 1/4] Initial plan


From b7866c4251c81156b66997d710915dec17ef440c Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 5 Dec 2025 13:41:25 +0000
Subject: [PATCH 2/4] Refactor repository structure to match fz-Model template

Co-authored-by: yannrichet-asnr <148193180+yannrichet-asnr@users.noreply.github.com>
---
 ...ocalhost_MCNP.json => localhost_MCNP.json} |   0
 .gitignore                                    |  43 +---
 CONTRIBUTING.md                               |   2 +-
 MIGRATION.md                                  |  14 +-
 QUICKSTART.md                                 |  10 +-
 README.md                                     |  32 +--
 .../MCNP/example_godiva.py                    |   9 +-
 godiva.inp => examples/MCNP/godiva.inp        |   0
 tests/test_plugin.py                          | 202 ++++++++++++++++++
 9 files changed, 247 insertions(+), 65 deletions(-)
 rename .fz/calculators/{Localhost_MCNP.json => localhost_MCNP.json} (100%)
 rename example_godiva.py => examples/MCNP/example_godiva.py (92%)
 rename godiva.inp => examples/MCNP/godiva.inp (100%)
 create mode 100755 tests/test_plugin.py

diff --git a/.fz/calculators/Localhost_MCNP.json b/.fz/calculators/localhost_MCNP.json
similarity index 100%
rename from .fz/calculators/Localhost_MCNP.json
rename to .fz/calculators/localhost_MCNP.json
diff --git a/.gitignore b/.gitignore
index 04d0ed8..f66a2ed 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,9 +7,12 @@ srctp
 *.s
 PID
 
-# Results directories
+# Results and temporary files
 results/
 *_results/
+*.out
+*.msg
+*.html
 
 # Python
 __pycache__/
@@ -17,43 +20,19 @@ __pycache__/
 *$py.class
 *.so
 .Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-
-# Virtual environments
 venv/
 ENV/
-env/
+.venv
 
-# IDE
-.vscode/
-.idea/
-*.swp
-*.swo
-*~
+# fz temporary files
+.fz/tmp/
 
 # OS
 .DS_Store
 Thumbs.db
 
-# Temporary files
-.fz/tmp/
-*.tmp
-*.bak
-*.log
+# Build artifacts
+build/
+dist/
+*.egg-info/
 
-# Test outputs
-test_results/
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index fd5a993..a672a03 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -92,7 +92,7 @@ When requesting a feature:
    
    # Validate JSON files
    python -m json.tool .fz/models/MCNP.json
-   python -m json.tool .fz/calculators/Localhost_MCNP.json
+   python -m json.tool .fz/calculators/localhost_MCNP.json
    
    # Check shell script syntax
    bash -n .fz/calculators/MCNP.sh
diff --git a/MIGRATION.md b/MIGRATION.md
index e5e8d0b..062b93d 100644
--- a/MIGRATION.md
+++ b/MIGRATION.md
@@ -24,7 +24,7 @@ fz-mcnp/
 ├── .fz/
 │   ├── calculators/
 │   │   ├── MCNP.sh                 # Calculator script
-│   │   └── Localhost_MCNP.json     # Calculator configuration
+│   │   └── localhost_MCNP.json     # Calculator configuration
 │   └── models/
 │       └── MCNP.json               # Model definition
 ├── .gitignore
@@ -111,7 +111,7 @@ if [ -f "PID" ]; then rm -f "PID"; fi
 }
 ```
 
-This allows using the calculator by name: `calculators="Localhost_MCNP"`
+This allows using the calculator by name: `calculators="localhost_MCNP"`
 
 ## Feature Mapping
 
@@ -172,7 +172,7 @@ results = fz.fzr(
     "godiva.inp",
     {"r": 8.741},
     "MCNP",
-    calculators="Localhost_MCNP"
+    calculators="localhost_MCNP"
 )
 keff = results['mean_keff'][0]
 ```
@@ -182,7 +182,7 @@ keff = results['mean_keff'][0]
 - [x] Port MCNP.ioplugin to MCNP.json model
 - [x] Convert output parsing to shell commands
 - [x] Enhance MCNP.sh calculator script
-- [x] Create Localhost_MCNP.json calculator config
+- [x] Create localhost_MCNP.json calculator config
 - [x] Migrate godiva sample file
 - [x] Create comprehensive README
 - [x] Add Python example script
@@ -203,9 +203,9 @@ To test the migrated plugin:
 Expected output structure:
 ```
      r  mean_keff  sigma_keff  status     calculator
-0  8.5     0.9850      0.0012    done  Localhost_MCNP
-1  8.741   0.9995      0.0006    done  Localhost_MCNP
-2  9.0     1.0145      0.0008    done  Localhost_MCNP
+0  8.5     0.9850      0.0012    done  localhost_MCNP
+1  8.741   0.9995      0.0006    done  localhost_MCNP
+2  9.0     1.0145      0.0008    done  localhost_MCNP
 ```
 
 ## Future Enhancements
diff --git a/QUICKSTART.md b/QUICKSTART.md
index 9227239..c162bbc 100644
--- a/QUICKSTART.md
+++ b/QUICKSTART.md
@@ -68,9 +68,9 @@ Results:
 ============================================================
 
      r  mean_keff  sigma_keff  status     calculator
-0  8.5     0.9850      0.0012    done  Localhost_MCNP
-1  8.741   0.9995      0.0006    done  Localhost_MCNP
-2  9.0     1.0145      0.0008    done  Localhost_MCNP
+0  8.5     0.9850      0.0012    done  localhost_MCNP
+1  8.741   0.9995      0.0006    done  localhost_MCNP
+2  9.0     1.0145      0.0008    done  localhost_MCNP
 
 ------------------------------------------------------------
 Total calculations: 3
@@ -106,7 +106,7 @@ results = fz.fzr(
         "r": [8.0, 8.5, 9.0, 9.5]  # Parameter values to study
     },
     model="MCNP",                  # Use MCNP model
-    calculators="Localhost_MCNP",  # Use local calculator
+    calculators="localhost_MCNP",  # Use local calculator
     results_dir="my_results"       # Where to store results
 )
 
@@ -169,7 +169,7 @@ results = fz.fzr(
         "cycles": [110, 510, 1010]        # Total cycles
     },
     "MCNP",
-    calculators="Localhost_MCNP",
+    calculators="localhost_MCNP",
     results_dir="multi_param_study"
 )
 
diff --git a/README.md b/README.md
index e25a74e..7bcbcce 100644
--- a/README.md
+++ b/README.md
@@ -40,15 +40,15 @@ This plugin enables parametric studies with MCNP using the [fz framework](https:
 3. The plugin is ready to use! The `.fz` directory contains:
    - `.fz/models/MCNP.json` - Model definition
    - `.fz/calculators/MCNP.sh` - Calculation script
-   - `.fz/calculators/Localhost_MCNP.json` - Calculator configuration
+   - `.fz/calculators/localhost_MCNP.json` - Calculator configuration
 
 ## Usage
 
 ### Example: Godiva Critical Reactor Study
 
-The repository includes a sample input file `godiva.inp` demonstrating a parametric study of a Godiva-type critical reactor.
+The repository includes example files in `examples/MCNP/` demonstrating a parametric study of a Godiva-type critical reactor.
 
-**Input file (`godiva.inp`):**
+**Input file (`examples/MCNP/godiva.inp`):**
 ```
 Godiva-type critical reactor and kcode example
 c skip 10 and run a total of 110 keff cycles with 1000 neutrons per cycle
@@ -62,7 +62,7 @@ c skip 10 and run a total of 110 keff cycles with 1000 neutrons per cycle
  m1    92235 -93.71  92238 -5.27  92234 -1.02  $ define u with weight fractions
 ```
 
-**Python script to run parametric study:**
+**Python script to run parametric study (`examples/MCNP/example_godiva.py`):**
 ```python
 import fz
 import os
@@ -77,10 +77,10 @@ input_variables = {
 
 # Run parametric study
 results = fz.fzr(
-    input_path="godiva.inp",
+    input_path="examples/MCNP/godiva.inp",
     input_variables=input_variables,
     model="MCNP",
-    calculators="Localhost_MCNP",
+    calculators="localhost_MCNP",
     results_dir="results"
 )
 
@@ -92,9 +92,9 @@ print(f"\nCompleted {len(results)} calculations")
 **Expected output:**
 ```
      r  mean_keff  sigma_keff  status     calculator
-0  8.5     0.9850      0.0012    done  Localhost_MCNP
-1  8.741   0.9995      0.0006    done  Localhost_MCNP
-2  9.0     1.0145      0.0008    done  Localhost_MCNP
+0  8.5     0.9850      0.0012    done  localhost_MCNP
+1  8.741   0.9995      0.0006    done  localhost_MCNP
+2  9.0     1.0145      0.0008    done  localhost_MCNP
 
 Completed 3 calculations
 ```
@@ -144,7 +144,7 @@ Run MCNP on a remote server via SSH:
 import fz
 
 results = fz.fzr(
-    "godiva.inp",
+    "examples/MCNP/godiva.inp",
     {"r": [8.5, 8.741, 9.0]},
     "MCNP",
     calculators="ssh://user@hpc.example.com/bash /path/to/fz-mcnp/.fz/calculators/MCNP.sh",
@@ -159,21 +159,21 @@ import fz
 
 # First run
 results1 = fz.fzr(
-    "godiva.inp",
+    "examples/MCNP/godiva.inp",
     {"r": [8.5, 8.741, 9.0]},
     "MCNP",
-    calculators="Localhost_MCNP",
+    calculators="localhost_MCNP",
     results_dir="run1"
 )
 
 # Second run with additional values - reuses previous results
 results2 = fz.fzr(
-    "godiva.inp",
+    "examples/MCNP/godiva.inp",
     {"r": [8.5, 8.741, 9.0, 9.5, 10.0]},  # Added 9.5 and 10.0
     "MCNP",
     calculators=[
         "cache://run1",          # Check cache first
-        "Localhost_MCNP"         # Only run new cases
+        "localhost_MCNP"         # Only run new cases
     ],
     results_dir="run2"
 )
@@ -188,10 +188,10 @@ import fz
 
 # Use multiple calculator instances for parallel execution
 results = fz.fzr(
-    "godiva.inp",
+    "examples/MCNP/godiva.inp",
     {"r": list(range(8, 11, 0.1))},  # Many parameter values
     "MCNP",
-    calculators=["Localhost_MCNP"] * 4,  # 4 parallel workers
+    calculators=["localhost_MCNP"] * 4,  # 4 parallel workers
     results_dir="parallel_results"
 )
 ```
diff --git a/example_godiva.py b/examples/MCNP/example_godiva.py
similarity index 92%
rename from example_godiva.py
rename to examples/MCNP/example_godiva.py
index 20b7ad7..9aad2f8 100755
--- a/example_godiva.py
+++ b/examples/MCNP/example_godiva.py
@@ -30,13 +30,14 @@ def main():
         os.environ['MCNP_PATH'] = '/Applications/MCNP6'
         print("(You will need to update this for actual calculations)\n")
     
-    # Define the input file
-    input_file = "godiva.inp"
+    # Define the input file (in the same directory as this script)
+    script_dir = os.path.dirname(os.path.abspath(__file__))
+    input_file = os.path.join(script_dir, "godiva.inp")
     
     # Check if input file exists
     if not os.path.exists(input_file):
         print(f"Error: Input file '{input_file}' not found.")
-        print("Please run this script from the fz-mcnp directory.")
+        print("Please run this script from the examples/MCNP directory.")
         sys.exit(1)
     
     print("=" * 60)
@@ -64,7 +65,7 @@ def main():
             input_path=input_file,
             input_variables=input_variables,
             model="MCNP",
-            calculators="Localhost_MCNP",
+            calculators="localhost_MCNP",
             results_dir="results"
         )
         
diff --git a/godiva.inp b/examples/MCNP/godiva.inp
similarity index 100%
rename from godiva.inp
rename to examples/MCNP/godiva.inp
diff --git a/tests/test_plugin.py b/tests/test_plugin.py
new file mode 100755
index 0000000..be6a189
--- /dev/null
+++ b/tests/test_plugin.py
@@ -0,0 +1,202 @@
+#!/usr/bin/env python3
+"""
+Basic test suite for fz-MCNP plugin.
+
+These tests verify the plugin structure.
+They test:
+- Model file validity
+- Variable parsing
+- Input file compilation
+- Calculator configuration
+"""
+
+import os
+import json
+import tempfile
+import sys
+
+
+def test_model_files():
+    """Test that all model JSON files are valid and have required fields."""
+    print("Testing model files...")
+    
+    models = [
+        ".fz/models/MCNP.json"
+    ]
+    
+    required_fields = ["id", "varprefix", "delim", "commentline", "output"]
+    
+    for model_file in models:
+        print(f"  Checking {model_file}...", end=" ")
+        
+        # Check file exists
+        assert os.path.exists(model_file), f"File not found: {model_file}"
+        
+        # Load and validate JSON
+        with open(model_file, 'r') as f:
+            model = json.load(f)
+        
+        # Check required fields
+        for field in required_fields:
+            assert field in model, f"Missing field '{field}' in {model_file}"
+        
+        # Check output section has at least one variable
+        assert len(model["output"]) > 0, f"No output variables in {model_file}"
+        
+        print("✓")
+    
+    print("  All model files valid!\n")
+
+
+def test_calculator_files():
+    """Test that calculator JSON files are valid."""
+    print("Testing calculator configuration files...")
+
+    calculators = [
+        ".fz/calculators/localhost_MCNP.json"
+    ]
+    
+    for calc_file in calculators:
+        print(f"  Checking {calc_file}...", end=" ")
+        
+        # Check file exists
+        assert os.path.exists(calc_file), f"File not found: {calc_file}"
+        
+        # Load and validate JSON
+        with open(calc_file, 'r') as f:
+            calc = json.load(f)
+        
+        # Check required fields
+        assert "uri" in calc, f"Missing 'uri' field in {calc_file}"
+        assert "models" in calc, f"Missing 'models' field in {calc_file}"
+        
+        print("✓")
+    
+    print("  All calculator files valid!\n")
+
+
+def test_calculator_scripts():
+    """Test that calculator shell scripts exist and are executable."""
+    print("Testing calculator shell scripts...")
+    
+    scripts = [
+        ".fz/calculators/MCNP.sh"
+    ]
+    
+    for script_file in scripts:
+        print(f"  Checking {script_file}...", end=" ")
+        
+        # Check file exists
+        assert os.path.exists(script_file), f"File not found: {script_file}"
+        
+        # Check if executable
+        assert os.access(script_file, os.X_OK), f"Script not executable: {script_file}"
+        
+        print("✓")
+    
+    print("  All calculator scripts valid!\n")
+
+
+def test_example_files():
+    """Test that example files exist."""
+    print("Testing example files...")
+    
+    examples = [
+        "examples/MCNP/godiva.inp",
+        "examples/MCNP/example_godiva.py"
+    ]
+    
+    for example_file in examples:
+        print(f"  Checking {example_file}...", end=" ")
+        assert os.path.exists(example_file), f"File not found: {example_file}"
+        print("✓")
+    
+    print("  All example files present!\n")
+
+
+def test_with_fz():
+    """Test integration with fz framework (if available)."""
+    print("Testing fz framework integration...")
+    
+    try:
+        import fz
+        print("  fz module found ✓")
+        
+        # Test parsing input file
+        print("  Testing fz.fzi() on godiva.inp...", end=" ")
+        variables = fz.fzi("examples/MCNP/godiva.inp", "MCNP")
+        assert "r" in variables, "Variable 'r' not found in parsed input"
+        print("✓")
+        
+        # Test compiling input file
+        print("  Testing fz.fzc() compilation...", end=" ")
+        with tempfile.TemporaryDirectory() as tmpdir:
+            fz.fzc(
+                "examples/MCNP/godiva.inp",
+                {"r": 8.741},
+                "MCNP",
+                output_dir=tmpdir
+            )
+            
+            # Check compiled file exists (it may be in a subdirectory)
+            compiled_file = None
+            for root, dirs, files in os.walk(tmpdir):
+                if "godiva.inp" in files:
+                    compiled_file = os.path.join(root, "godiva.inp")
+                    break
+            assert compiled_file is not None, "Compiled file not created"
+            
+            # Check variable was substituted
+            with open(compiled_file, 'r') as f:
+                content = f.read()
+                assert "8.741" in content, "Variable r not substituted"
+                assert "%(r)" not in content, "Variable marker %(r) still present"
+        print("✓")
+        
+        print("  fz integration tests passed!\n")
+        
+    except ImportError:
+        print("  fz module not installed - skipping integration tests")
+        print("  (Install with: pip install git+https://github.com/Funz/fz.git)\n")
+
+
+def main():
+    """Run all tests."""
+    print("=" * 70)
+    print("fz-MCNP Plugin Test Suite")
+    print("=" * 70)
+    print()
+    
+    # Change to repository root if needed
+    if not os.path.exists(".fz"):
+        if os.path.exists("../fz-MCNP/.fz"):
+            os.chdir("../fz-MCNP")
+        else:
+            print("Error: Could not find .fz directory")
+            print("Please run this script from the fz-MCNP repository root")
+            return 1
+    
+    try:
+        test_model_files()
+        test_calculator_files()
+        test_calculator_scripts()
+        test_example_files()
+        test_with_fz()
+        
+        print("=" * 70)
+        print("All tests passed! ✓")
+        print("=" * 70)
+        return 0
+        
+    except AssertionError as e:
+        print(f"\n✗ Test failed: {e}")
+        return 1
+    except Exception as e:
+        print(f"\n✗ Unexpected error: {e}")
+        import traceback
+        traceback.print_exc()
+        return 1
+
+
+if __name__ == "__main__":
+    sys.exit(main())

From c4fc844c19eb6afcbdd8e0e29d647091d2106697 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 5 Dec 2025 13:59:33 +0000
Subject: [PATCH 3/4] Align with fz-Model template: remove extra docs, add CI,
 add notebook, flatten examples

Co-authored-by: yannrichet-asnr <148193180+yannrichet-asnr@users.noreply.github.com>
---
 .github/workflows/ci.yml              | 122 +++++++++
 CONTRIBUTING.md                       | 297 ---------------------
 MIGRATION.md                          | 220 ----------------
 QUICKSTART.md                         | 195 --------------
 README.md                             |  16 +-
 example_usage.ipynb                   | 364 ++++++++++++++++++++++++++
 examples/{MCNP => }/example_godiva.py |   2 +-
 examples/{MCNP => }/godiva.inp        |   0
 tests/test_plugin.py                  |   8 +-
 9 files changed, 499 insertions(+), 725 deletions(-)
 create mode 100644 .github/workflows/ci.yml
 delete mode 100644 CONTRIBUTING.md
 delete mode 100644 MIGRATION.md
 delete mode 100644 QUICKSTART.md
 create mode 100644 example_usage.ipynb
 rename examples/{MCNP => }/example_godiva.py (98%)
 rename examples/{MCNP => }/godiva.inp (100%)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 0000000..e38c611
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,122 @@
+name: CI
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    name: Test Plugin Structure
+    runs-on: ubuntu-latest
+    
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+    
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.10'
+    
+    - name: Install fz framework
+      run: |
+        pip install git+https://github.com/Funz/fz.git
+     
+    - name: Validate JSON files
+      run: |
+        echo "Validating model files..."
+        for f in .fz/models/*.json; do
+          echo "  Checking $f"
+          python -m json.tool "$f" > /dev/null
+        done
+        echo "Validating calculator config files..."
+        for f in .fz/calculators/*.json; do
+          echo "  Checking $f"
+          python -m json.tool "$f" > /dev/null
+        done
+    
+    - name: Check shell script syntax
+      run: |
+        echo "Checking shell scripts..."
+        for f in .fz/calculators/*.sh; do
+          echo "  Checking $f"
+          bash -n "$f"
+        done
+    
+    - name: Test fzi (parse variables)
+      run: |
+        python -c "
+        import fz
+        variables = fz.fzi('examples/godiva.inp', 'MCNP')
+        print(f'Variables found: {list(variables.keys())}')
+        assert 'r' in variables, 'Variable r not found'
+        print('✓ fzi test passed')
+        "
+    
+    - name: Test fzc (compile input)
+      run: |
+        python -c "
+        import fz
+        import tempfile
+        import os
+        with tempfile.TemporaryDirectory() as tmpdir:
+            fz.fzc('examples/godiva.inp', {'r': 8.741}, 'MCNP', output_dir=tmpdir)
+            compiled = os.path.join(tmpdir, 'r=8.741', 'godiva.inp')
+            assert os.path.exists(compiled), 'Compiled file not created'
+            with open(compiled) as f:
+                content = f.read()
+                assert '8.741' in content, 'Variable not substituted'
+        print('✓ fzc test passed')
+        "
+
+    - name: Run plugin tests
+      run: |
+        python tests/test_plugin.py
+    
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+    
+    - name: Check shell scripts are executable
+      run: |
+        for f in .fz/calculators/*.sh; do
+          if [ ! -x "$f" ]; then
+            echo "Error: $f is not executable"
+            exit 1
+          fi
+        done
+
+  docs:
+    name: Check Documentation
+    runs-on: ubuntu-latest
+    
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+    
+    - name: Check required documentation files
+      run: |
+        for f in README.md LICENSE; do
+          if [ ! -f "$f" ]; then
+            echo "Error: Missing $f"
+            exit 1
+          fi
+          echo "✓ $f exists"
+        done
+    
+    - name: Check example files
+      run: |
+        if [ ! -f "examples/godiva.inp" ]; then
+          echo "Error: Missing example input file"
+          exit 1
+        fi
+        echo "✓ Example files present"
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
deleted file mode 100644
index a672a03..0000000
--- a/CONTRIBUTING.md
+++ /dev/null
@@ -1,297 +0,0 @@
-# Contributing to fz-mcnp
-
-Thank you for your interest in contributing to fz-mcnp! This document provides guidelines for contributing to this project.
-
-## Getting Started
-
-1. Fork the repository on GitHub
-2. Clone your fork locally
-3. Set up your development environment (see below)
-4. Create a feature branch for your changes
-5. Make your changes and test them
-6. Submit a pull request
-
-## Development Environment Setup
-
-### Prerequisites
-
-- MCNP6 installation (for testing)
-- Python 3.7 or higher
-- Git
-- fz framework
-
-### Setup Steps
-
-```bash
-# Clone your fork
-git clone https://github.com/YOUR_USERNAME/fz-mcnp.git
-cd fz-mcnp
-
-# Install fz framework
-cd ..
-git clone https://github.com/Funz/fz.git
-cd fz
-pip install -e .
-
-# Return to fz-mcnp
-cd ../fz-mcnp
-
-# Set MCNP_PATH
-export MCNP_PATH="/path/to/your/MCNP6"
-```
-
-## Types of Contributions
-
-### Bug Reports
-
-When filing a bug report, please include:
-
-- A clear, descriptive title
-- Steps to reproduce the issue
-- Expected behavior
-- Actual behavior
-- MCNP version
-- Python version
-- Operating system
-- Relevant error messages or logs
-
-### Feature Requests
-
-When requesting a feature:
-
-- Explain the use case
-- Describe the desired behavior
-- Provide examples if possible
-- Explain why this would benefit other users
-
-### Code Contributions
-
-#### Before You Start
-
-- Check existing issues and pull requests
-- Discuss major changes in an issue first
-- Follow the coding style of the project
-- Write clear commit messages
-
-#### Making Changes
-
-1. **Create a feature branch:**
-   ```bash
-   git checkout -b feature/your-feature-name
-   ```
-
-2. **Make your changes:**
-   - Keep changes focused and atomic
-   - Update documentation as needed
-   - Add examples if relevant
-
-3. **Test your changes:**
-   ```bash
-   # Test with example
-   python example_godiva.py
-   
-   # Validate JSON files
-   python -m json.tool .fz/models/MCNP.json
-   python -m json.tool .fz/calculators/localhost_MCNP.json
-   
-   # Check shell script syntax
-   bash -n .fz/calculators/MCNP.sh
-   
-   # Check Python syntax
-   python -m py_compile example_godiva.py
-   ```
-
-4. **Commit your changes:**
-   ```bash
-   git add .
-   git commit -m "Add feature: brief description"
-   ```
-
-5. **Push to your fork:**
-   ```bash
-   git push origin feature/your-feature-name
-   ```
-
-6. **Open a Pull Request:**
-   - Go to the original repository on GitHub
-   - Click "New Pull Request"
-   - Select your feature branch
-   - Fill in the PR template
-   - Submit the PR
-
-## Coding Guidelines
-
-### Shell Scripts
-
-- Use `#!/bin/bash` shebang
-- Add comments for complex logic
-- Validate input parameters
-- Provide clear error messages
-- Use `set -e` for critical scripts
-
-Example:
-```bash
-#!/bin/bash
-
-# Check required environment variable
-if [ -z "$MCNP_PATH" ]; then
-  echo "Error: MCNP_PATH is not set"
-  exit 1
-fi
-```
-
-### Python Scripts
-
-- Follow PEP 8 style guide
-- Use meaningful variable names
-- Add docstrings for functions
-- Handle exceptions appropriately
-- Keep functions focused
-
-Example:
-```python
-def run_mcnp_study(input_file, parameters):
-    """
-    Run MCNP parametric study.
-    
-    Args:
-        input_file: Path to MCNP input file
-        parameters: Dict of parameter values
-        
-    Returns:
-        DataFrame with results
-    """
-    # Implementation here
-```
-
-### JSON Configuration
-
-- Use 4-space indentation
-- Keep structure consistent
-- Validate JSON syntax
-- Add comments in documentation
-
-Example:
-```json
-{
-    "id": "MCNP",
-    "varprefix": "%",
-    "delim": "()",
-    "output": {
-        "mean_keff": "shell command here"
-    }
-}
-```
-
-### Documentation
-
-- Use clear, concise language
-- Provide examples
-- Keep README up to date
-- Document all options and parameters
-
-## Testing
-
-### Manual Testing
-
-Test your changes with:
-
-1. **Basic functionality:**
-   ```bash
-   python example_godiva.py
-   ```
-
-2. **Different parameter values:**
-   ```python
-   import fz
-   results = fz.fzr("godiva.inp", {"r": [8.0, 9.0]}, "MCNP")
-   ```
-
-3. **Edge cases:**
-   - Empty parameter lists
-   - Invalid MCNP paths
-   - Missing input files
-   - Malformed MCNP input
-
-### Test Coverage
-
-If adding new features, consider:
-
-- Normal operation
-- Error conditions
-- Edge cases
-- Performance implications
-
-## Documentation Updates
-
-When making changes, update:
-
-- README.md (if user-facing)
-- QUICKSTART.md (if affecting setup)
-- MIGRATION.md (if changing compatibility)
-- Code comments (always)
-- Example scripts (if relevant)
-
-## Pull Request Process
-
-1. **PR Title:** Clear and descriptive (e.g., "Add support for MCNP5")
-2. **PR Description:** Explain what, why, and how
-3. **Testing:** Describe testing performed
-4. **Breaking Changes:** Clearly mark if any
-5. **Documentation:** Confirm docs are updated
-
-### PR Checklist
-
-- [ ] Code follows project style
-- [ ] Tests pass (manual testing)
-- [ ] Documentation updated
-- [ ] Commit messages are clear
-- [ ] No merge conflicts
-- [ ] JSON files validated
-- [ ] Shell scripts validated
-- [ ] Python scripts validated
-
-## Versioning
-
-We use semantic versioning (MAJOR.MINOR.PATCH):
-
-- **MAJOR:** Breaking changes
-- **MINOR:** New features (backward compatible)
-- **PATCH:** Bug fixes
-
-## Code Review
-
-All submissions require review. We'll:
-
-- Review within a week
-- Provide constructive feedback
-- Request changes if needed
-- Merge when approved
-
-Please be patient and responsive to feedback.
-
-## Community
-
-- Be respectful and professional
-- Welcome newcomers
-- Help others learn
-- Share knowledge
-
-## Questions?
-
-- Open an issue for clarification
-- Check existing documentation
-- Review the fz framework docs
-
-## License
-
-By contributing, you agree that your contributions will be licensed under the BSD 3-Clause License.
-
-## Recognition
-
-Contributors are recognized in:
-- Git history
-- Release notes (for significant contributions)
-- Special thanks section (as appropriate)
-
-Thank you for contributing to fz-mcnp! 🎉
diff --git a/MIGRATION.md b/MIGRATION.md
deleted file mode 100644
index 062b93d..0000000
--- a/MIGRATION.md
+++ /dev/null
@@ -1,220 +0,0 @@
-# Migration from Old Plugin-MCNP to fz-mcnp
-
-This document describes how the old MCNP plugin was ported to the new fz framework.
-
-## Migration Overview
-
-### Old Structure (plugin-MCNP)
-```
-plugin-MCNP/
-├── src/main/
-│   ├── io/
-│   │   └── MCNP.ioplugin          # Old configuration format
-│   ├── samples/
-│   │   └── godiva                  # Sample input file
-│   └── scripts/
-│       ├── MCNP.sh                 # Shell script for Unix/Mac
-│       └── MCNP.bat                # Batch script for Windows
-└── build.xml                       # Ant build file
-```
-
-### New Structure (fz-mcnp)
-```
-fz-mcnp/
-├── .fz/
-│   ├── calculators/
-│   │   ├── MCNP.sh                 # Calculator script
-│   │   └── localhost_MCNP.json     # Calculator configuration
-│   └── models/
-│       └── MCNP.json               # Model definition
-├── .gitignore
-├── README.md
-├── example_godiva.py               # Python example
-└── godiva.inp                      # Sample input file
-```
-
-## Key Changes
-
-### 1. Configuration Format
-
-**Old (.ioplugin format):**
-```
-variableStartSymbol=%
-variableLimit=(...)
-formulaStartSymbol=@
-formulaLimit={...}
-commentLineChar=C 
-output.mean_keff.get=grep("outp"," the final estimated combined") >> get(0) >> cut("keff = ",2) >> substring("ZZZ","with an estimated") >> asNumeric()
-```
-
-**New (JSON format):**
-```json
-{
-    "id": "MCNP",
-    "varprefix": "%",
-    "formulaprefix": "@",
-    "delim": "()",
-    "commentline": "C ",
-    "output": {
-        "mean_keff": "grep 'the final estimated combined' outp | head -n 1 | awk '{match($0, /keff = ([0-9.]+)/, arr); print arr[1]}'"
-    }
-}
-```
-
-### 2. Output Parsing
-
-**Old approach:**
-- Custom parsing DSL with operators like `>>`, `cut()`, `substring()`, `asNumeric()`
-
-**New approach:**
-- Standard shell commands (grep, awk, etc.)
-- More flexible and Unix-standard
-- Example: `grep 'pattern' file | awk '{print $N}'`
-
-### 3. Calculator Script
-
-**Old script:**
-```bash
-#!/bin/bash
-export MCNP_PATH="/Applications/MCNP6"
-export DATAPATH=$MCNP_PATH"/MCNP_DATA"
-ulimit -s unlimited
-echo $$ >> PID
-$MCNP_PATH/MCNP_CODE/bin/mcnp6 inp=$* &
-PID_MCNP=$!
-echo $PID_MCNP >> PID
-wait $PID_MCNP
-if [ -f "PID" ]; then rm -f "PID"; fi
-```
-
-**New script:**
-```bash
-#!/bin/bash
-# Enhanced with:
-# - Environment variable validation
-# - Better error handling
-# - Support for directory and file inputs
-# - Automatic input file detection
-# - Comprehensive error messages
-```
-
-### 4. Calculator Configuration
-
-**New addition:**
-```json
-{
-    "uri": "sh://",
-    "n": 1,
-    "models": {
-        "MCNP": "bash .fz/calculators/MCNP.sh"
-    }
-}
-```
-
-This allows using the calculator by name: `calculators="localhost_MCNP"`
-
-## Feature Mapping
-
-| Old Feature | New Feature | Status |
-|-------------|-------------|--------|
-| Variable syntax `%(...)` | Variable syntax `%(...)` | ✅ Preserved |
-| Formula syntax `@{...}` | Formula syntax `@{...}` | ✅ Preserved |
-| Comment char `C ` | Comment char `C ` | ✅ Preserved |
-| Output: mean_keff | Output: mean_keff | ✅ Implemented |
-| Output: sigma_keff | Output: sigma_keff | ✅ Implemented |
-| Dataset filtering | Not applicable | ➖ Simplified |
-| Output functions | Native shell commands | ✅ Enhanced |
-| Shell script | Enhanced shell script | ✅ Improved |
-
-## Improvements in New Version
-
-1. **Better Error Handling**
-   - Validates MCNP_PATH before execution
-   - Checks for MCNP executable existence
-   - Clear error messages
-
-2. **Flexible Input Handling**
-   - Accepts directory or file as input
-   - Auto-detects MCNP input files
-   - Supports multiple input patterns
-
-3. **Standard Tools**
-   - Uses standard Unix tools (grep, awk)
-   - No custom DSL to learn
-   - More maintainable and debuggable
-
-4. **Python Integration**
-   - Example Python script provided
-   - Easy integration with fz framework
-   - Pandas DataFrame output
-
-5. **Documentation**
-   - Comprehensive README
-   - Example usage
-   - Troubleshooting guide
-
-## Usage Comparison
-
-### Old Usage (Funz)
-```java
-// Java/Groovy code
-Run r = new Run("MCNP", "godiva");
-r.setInputVariable("r", 8.741);
-r.execute();
-Double keff = r.getOutputValue("mean_keff");
-```
-
-### New Usage (fz)
-```python
-import fz
-
-results = fz.fzr(
-    "godiva.inp",
-    {"r": 8.741},
-    "MCNP",
-    calculators="localhost_MCNP"
-)
-keff = results['mean_keff'][0]
-```
-
-## Migration Checklist
-
-- [x] Port MCNP.ioplugin to MCNP.json model
-- [x] Convert output parsing to shell commands
-- [x] Enhance MCNP.sh calculator script
-- [x] Create localhost_MCNP.json calculator config
-- [x] Migrate godiva sample file
-- [x] Create comprehensive README
-- [x] Add Python example script
-- [x] Add .gitignore for MCNP outputs
-- [x] Document migration process
-
-## Testing Notes
-
-To test the migrated plugin:
-
-1. Install MCNP and set MCNP_PATH
-2. Install fz framework
-3. Run the example:
-   ```bash
-   python example_godiva.py
-   ```
-
-Expected output structure:
-```
-     r  mean_keff  sigma_keff  status     calculator
-0  8.5     0.9850      0.0012    done  localhost_MCNP
-1  8.741   0.9995      0.0006    done  localhost_MCNP
-2  9.0     1.0145      0.0008    done  localhost_MCNP
-```
-
-## Future Enhancements
-
-Potential improvements for future versions:
-
-- [ ] Support for additional MCNP output parameters
-- [ ] Windows batch script calculator (MCNP.bat equivalent)
-- [ ] Pre-configured remote HPC calculators
-- [ ] Visualization examples for results
-- [ ] Integration tests with mock MCNP outputs
-- [ ] Support for MCNP5 in addition to MCNP6
diff --git a/QUICKSTART.md b/QUICKSTART.md
deleted file mode 100644
index c162bbc..0000000
--- a/QUICKSTART.md
+++ /dev/null
@@ -1,195 +0,0 @@
-# Quick Start Guide
-
-Get started with fz-mcnp in 5 minutes!
-
-## Prerequisites
-
-1. **MCNP6** installed on your system
-2. **Python 3.7+** installed
-3. **fz framework** installed
-
-## Step 1: Install fz Framework
-
-```bash
-git clone https://github.com/Funz/fz.git
-cd fz
-pip install -e .
-```
-
-## Step 2: Clone fz-mcnp
-
-```bash
-cd ..
-git clone https://github.com/Funz/fz-mcnp.git
-cd fz-mcnp
-```
-
-## Step 3: Set MCNP Path
-
-```bash
-# Linux/Mac:
-export MCNP_PATH="/path/to/your/MCNP6"
-
-# Windows (PowerShell):
-$env:MCNP_PATH="C:\path\to\your\MCNP6"
-
-# Windows (Command Prompt):
-set MCNP_PATH=C:\path\to\your\MCNP6
-```
-
-**Common MCNP paths:**
-- Mac: `/Applications/MCNP6`
-- Linux: `/opt/MCNP6` or `/usr/local/MCNP6`
-- Windows: `C:\MCNP\MCNP6`
-
-## Step 4: Test the Installation
-
-Run the example script:
-
-```bash
-python example_godiva.py
-```
-
-You should see output similar to:
-```
-============================================================
-MCNP Parametric Study: Godiva Critical Reactor
-============================================================
-
-Parameters:
-  r: [8.5, 8.741, 9.0]
-
-Running calculations...
-------------------------------------------------------------
-[... calculation progress ...]
-
-============================================================
-Results:
-============================================================
-
-     r  mean_keff  sigma_keff  status     calculator
-0  8.5     0.9850      0.0012    done  localhost_MCNP
-1  8.741   0.9995      0.0006    done  localhost_MCNP
-2  9.0     1.0145      0.0008    done  localhost_MCNP
-
-------------------------------------------------------------
-Total calculations: 3
-Successful: 3
-Failed: 0
-
-Critical Analysis:
-------------------------------------------------------------
-  r=8.500 cm: k_eff = 0.9850 ± 0.0012 (subcritical)
-  r=8.741 cm: k_eff = 0.9995 ± 0.0006 (critical)
-  r=9.000 cm: k_eff = 1.0145 ± 0.0008 (supercritical)
-
-============================================================
-Study completed successfully!
-============================================================
-```
-
-## Step 5: Create Your Own Study
-
-Create a new Python file `my_study.py`:
-
-```python
-import fz
-import os
-
-# Set MCNP path
-os.environ['MCNP_PATH'] = '/path/to/your/MCNP6'
-
-# Run your parametric study
-results = fz.fzr(
-    input_path="godiva.inp",      # Your MCNP input file
-    input_variables={
-        "r": [8.0, 8.5, 9.0, 9.5]  # Parameter values to study
-    },
-    model="MCNP",                  # Use MCNP model
-    calculators="localhost_MCNP",  # Use local calculator
-    results_dir="my_results"       # Where to store results
-)
-
-# Analyze results
-print(results)
-
-# Access specific values
-for idx, row in results.iterrows():
-    print(f"r={row['r']}: k_eff = {row['mean_keff']:.4f} ± {row['sigma_keff']:.4f}")
-```
-
-Run it:
-```bash
-python my_study.py
-```
-
-## Common Issues
-
-### Issue: "MCNP executable not found"
-
-**Solution:** Check your MCNP_PATH is correct:
-```bash
-echo $MCNP_PATH  # Should show your MCNP directory
-ls $MCNP_PATH/MCNP_CODE/bin/mcnp6  # Should exist
-```
-
-### Issue: "ModuleNotFoundError: No module named 'fz'"
-
-**Solution:** Install the fz framework:
-```bash
-pip install -e /path/to/fz
-```
-
-### Issue: "Permission denied" when running MCNP
-
-**Solution:** Make sure the script is executable:
-```bash
-chmod +x .fz/calculators/MCNP.sh
-```
-
-## Next Steps
-
-1. **Modify the input file**: Edit `godiva.inp` to change the MCNP model
-2. **Add more parameters**: Use `%(param)` syntax in your input file
-3. **Run in parallel**: Use multiple calculators for faster execution
-4. **Use remote HPC**: Set up SSH calculator for cluster execution
-5. **Explore caching**: Reuse previous results to save computation time
-
-## Example: Multi-Parameter Study
-
-```python
-import fz
-
-# Study multiple parameters
-results = fz.fzr(
-    "godiva.inp",
-    {
-        "r": [8.5, 8.741, 9.0],           # Sphere radius
-        "neutrons": [1000, 5000, 10000],  # Neutrons per cycle
-        "cycles": [110, 510, 1010]        # Total cycles
-    },
-    "MCNP",
-    calculators="localhost_MCNP",
-    results_dir="multi_param_study"
-)
-
-# This will run 3 × 3 × 3 = 27 calculations
-print(f"Completed {len(results)} calculations")
-```
-
-## Need Help?
-
-- Read the full [README.md](README.md)
-- Check the [MIGRATION.md](MIGRATION.md) for details on porting from old plugin
-- Visit the [fz framework documentation](https://github.com/Funz/fz)
-- Open an issue on [GitHub](https://github.com/Funz/fz-mcnp/issues)
-
-## Tips
-
-- **Start small**: Test with a few parameter values first
-- **Use caching**: Avoid re-running expensive calculations
-- **Monitor resources**: MCNP can be memory-intensive
-- **Check logs**: Look in results directories for detailed execution logs
-- **Validate results**: Always verify MCNP completed successfully
-
-Happy computing! 🚀
diff --git a/README.md b/README.md
index 7bcbcce..cd2fb6d 100644
--- a/README.md
+++ b/README.md
@@ -46,9 +46,9 @@ This plugin enables parametric studies with MCNP using the [fz framework](https:
 
 ### Example: Godiva Critical Reactor Study
 
-The repository includes example files in `examples/MCNP/` demonstrating a parametric study of a Godiva-type critical reactor.
+The repository includes example files in `examples/` demonstrating a parametric study of a Godiva-type critical reactor.
 
-**Input file (`examples/MCNP/godiva.inp`):**
+**Input file (`examples/godiva.inp`):**
 ```
 Godiva-type critical reactor and kcode example
 c skip 10 and run a total of 110 keff cycles with 1000 neutrons per cycle
@@ -62,7 +62,7 @@ c skip 10 and run a total of 110 keff cycles with 1000 neutrons per cycle
  m1    92235 -93.71  92238 -5.27  92234 -1.02  $ define u with weight fractions
 ```
 
-**Python script to run parametric study (`examples/MCNP/example_godiva.py`):**
+**Python script to run parametric study (`examples/example_godiva.py`):**
 ```python
 import fz
 import os
@@ -77,7 +77,7 @@ input_variables = {
 
 # Run parametric study
 results = fz.fzr(
-    input_path="examples/MCNP/godiva.inp",
+    input_path="examples/godiva.inp",
     input_variables=input_variables,
     model="MCNP",
     calculators="localhost_MCNP",
@@ -144,7 +144,7 @@ Run MCNP on a remote server via SSH:
 import fz
 
 results = fz.fzr(
-    "examples/MCNP/godiva.inp",
+    "examples/godiva.inp",
     {"r": [8.5, 8.741, 9.0]},
     "MCNP",
     calculators="ssh://user@hpc.example.com/bash /path/to/fz-mcnp/.fz/calculators/MCNP.sh",
@@ -159,7 +159,7 @@ import fz
 
 # First run
 results1 = fz.fzr(
-    "examples/MCNP/godiva.inp",
+    "examples/godiva.inp",
     {"r": [8.5, 8.741, 9.0]},
     "MCNP",
     calculators="localhost_MCNP",
@@ -168,7 +168,7 @@ results1 = fz.fzr(
 
 # Second run with additional values - reuses previous results
 results2 = fz.fzr(
-    "examples/MCNP/godiva.inp",
+    "examples/godiva.inp",
     {"r": [8.5, 8.741, 9.0, 9.5, 10.0]},  # Added 9.5 and 10.0
     "MCNP",
     calculators=[
@@ -188,7 +188,7 @@ import fz
 
 # Use multiple calculator instances for parallel execution
 results = fz.fzr(
-    "examples/MCNP/godiva.inp",
+    "examples/godiva.inp",
     {"r": list(range(8, 11, 0.1))},  # Many parameter values
     "MCNP",
     calculators=["localhost_MCNP"] * 4,  # 4 parallel workers
diff --git a/example_usage.ipynb b/example_usage.ipynb
new file mode 100644
index 0000000..e627046
--- /dev/null
+++ b/example_usage.ipynb
@@ -0,0 +1,364 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# fz-MCNP Plugin Example Usage\n",
+    "\n",
+    "This notebook demonstrates how to use the fz-MCNP plugin for parametric MCNP calculations.\n",
+    "\n",
+    "The examples cover:\n",
+    "1. Installing dependencies (fz framework and fz-MCNP plugin)\n",
+    "2. Downloading example input files\n",
+    "3. Parsing input files to identify variables\n",
+    "4. Compiling input files with specific parameter values\n",
+    "5. Running calculations with MCNP\n",
+    "6. Performing parametric studies\n",
+    "\n",
+    "**Note:** You must have MCNP installed and the MCNP_PATH environment variable set to use this plugin."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Setup: Install Dependencies\n",
+    "\n",
+    "First, install the Funz framework and the fz-MCNP plugin."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Install fz framework from GitHub\n",
+    "%pip install -q git+https://github.com/Funz/fz.git\n",
+    "\n",
+    "# Install fz-MCNP plugin\n",
+    "import fz\n",
+    "fz.install(\"MCNP\")\n",
+    "\n",
+    "print(\"✓ Dependencies installed successfully!\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Setup: Download Example Files\n",
+    "\n",
+    "Download the example input files from the GitHub repository."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import urllib.request\n",
+    "\n",
+    "# Create directory for examples\n",
+    "os.makedirs(\"MCNP\", exist_ok=True)\n",
+    "\n",
+    "# Base URL for raw GitHub content\n",
+    "base_url = \"https://raw.githubusercontent.com/Funz/fz-MCNP/main/examples\"\n",
+    "\n",
+    "# Download example files\n",
+    "files_to_download = [\n",
+    "    (\"MCNP/godiva.inp\", f\"{base_url}/godiva.inp\"),\n",
+    "]\n",
+    "\n",
+    "print(\"Downloading example files...\")\n",
+    "for local_path, url in files_to_download:\n",
+    "    try:\n",
+    "        urllib.request.urlretrieve(url, local_path)\n",
+    "        print(f\"  ✓ Downloaded: {local_path}\")\n",
+    "    except Exception as e:\n",
+    "        print(f\"  ✗ Failed to download {local_path}: {e}\")\n",
+    "\n",
+    "print(\"\\n✓ Example files ready!\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Setup: Configure MCNP Path\n",
+    "\n",
+    "Set the MCNP_PATH environment variable to point to your MCNP installation."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "\n",
+    "# Set MCNP_PATH - adjust this path for your system\n",
+    "os.environ['MCNP_PATH'] = '/Applications/MCNP6'  # Example path\n",
+    "\n",
+    "print(f\"MCNP_PATH set to: {os.environ['MCNP_PATH']}\")\n",
+    "print(\"Note: Adjust this path to match your MCNP installation\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Import Required Libraries"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import fz\n",
+    "import os\n",
+    "import tempfile\n",
+    "\n",
+    "print(f\"fz version: {fz.__version__ if hasattr(fz, '__version__') else 'unknown'}\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Example 1: Parse Input File for Variables\n",
+    "\n",
+    "Use `fz.fzi()` to identify variables in an MCNP input file."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Parse the input file to find variables\n",
+    "variables = fz.fzi(\n",
+    "    \"MCNP/godiva.inp\",\n",
+    "    \"MCNP\"\n",
+    ")\n",
+    "\n",
+    "print(f\"Variables found in godiva.inp: {list(variables.keys())}\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Example 2: Compile Input Files\n",
+    "\n",
+    "Use `fz.fzc()` to compile input files with specific parameter values. This substitutes variables with actual values."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Create temporary directory for compiled files\n",
+    "with tempfile.TemporaryDirectory() as tmpdir:\n",
+    "    # Compile input with specific value for radius\n",
+    "    fz.fzc(\n",
+    "        \"MCNP/godiva.inp\",\n",
+    "        {\"r\": 8.741},  # Critical radius\n",
+    "        \"MCNP\",\n",
+    "        output_dir=tmpdir\n",
+    "    )\n",
+    "    \n",
+    "    # Show compiled file\n",
+    "    # Find the compiled file (it may be in a subdirectory)\n",
+    "    for root, dirs, files in os.walk(tmpdir):\n",
+    "        for f in files:\n",
+    "            if f == \"godiva.inp\":\n",
+    "                compiled_file = os.path.join(root, f)\n",
+    "                print(f\"Compiled file content (r=8.741):\")\n",
+    "                print(\"=\" * 70)\n",
+    "                with open(compiled_file, 'r') as file:\n",
+    "                    print(file.read())"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Example 3: Run a Basic MCNP Calculation\n",
+    "\n",
+    "Run a simple MCNP calculation with a single parameter value.\n",
+    "\n",
+    "**Note:** This requires MCNP to be installed and properly configured."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Define parameter value\n",
+    "input_variables = {\n",
+    "    \"r\": [8.741]  # Critical radius\n",
+    "}\n",
+    "\n",
+    "try:\n",
+    "    # Run MCNP calculation\n",
+    "    results = fz.fzr(\n",
+    "        input_path=\"MCNP/godiva.inp\",\n",
+    "        input_variables=input_variables,\n",
+    "        model=\"MCNP\",\n",
+    "        calculators=\"localhost_MCNP\",\n",
+    "        results_dir=\"results/basic_study\"\n",
+    "    )\n",
+    "    \n",
+    "    # Display results\n",
+    "    print(\"\\nResults:\")\n",
+    "    print(\"=\" * 70)\n",
+    "    print(results[['r', 'mean_keff', 'sigma_keff', 'status']])\n",
+    "    \n",
+    "except Exception as e:\n",
+    "    print(f\"\\nError running calculation: {e}\")\n",
+    "    print(\"Note: Make sure MCNP is installed and MCNP_PATH is set correctly.\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Example 4: Parametric Study of Godiva Criticality\n",
+    "\n",
+    "Demonstrate a parametric study with multiple sphere radii to study criticality."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "\n",
+    "# Define multiple radius values around the critical radius\n",
+    "input_variables = {\n",
+    "    \"r\": [8.5, 8.741, 9.0]  # Subcritical, critical, supercritical\n",
+    "}\n",
+    "\n",
+    "print(f\"Running parametric study...\")\n",
+    "print(f\"  r values: {input_variables['r']}\")\n",
+    "\n",
+    "try:\n",
+    "    # Run parametric calculation\n",
+    "    results = fz.fzr(\n",
+    "        input_path=\"MCNP/godiva.inp\",\n",
+    "        input_variables=input_variables,\n",
+    "        model=\"MCNP\",\n",
+    "        calculators=\"localhost_MCNP\",\n",
+    "        results_dir=\"results/parametric_study\"\n",
+    "    )\n",
+    "    \n",
+    "    # Display results\n",
+    "    print(\"\\nResults:\")\n",
+    "    print(\"=\" * 70)\n",
+    "    print(results)\n",
+    "    \n",
+    "    # Analyze criticality\n",
+    "    print(\"\\nCriticality Analysis:\")\n",
+    "    print(\"=\" * 70)\n",
+    "    for idx, row in results.iterrows():\n",
+    "        r = row['r']\n",
+    "        keff = row.get('mean_keff', None)\n",
+    "        sigma = row.get('sigma_keff', None)\n",
+    "        if keff is not None and keff != '':\n",
+    "            try:\n",
+    "                keff_val = float(keff)\n",
+    "                sigma_val = float(sigma)\n",
+    "                status = \"supercritical\" if keff_val > 1.0 else \"subcritical\" if keff_val < 1.0 else \"critical\"\n",
+    "                print(f\"  r={r:.3f} cm: k_eff = {keff_val:.4f} ± {sigma_val:.4f} ({status})\")\n",
+    "            except:\n",
+    "                print(f\"  r={r:.3f} cm: Calculation incomplete\")\n",
+    "    \n",
+    "except Exception as e:\n",
+    "    print(f\"\\nError running parametric study: {e}\")\n",
+    "    print(\"Note: Make sure MCNP is installed and MCNP_PATH is set correctly.\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Example 5: Visualization\n",
+    "\n",
+    "If you have results, you can visualize them using matplotlib."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "\n",
+    "# Example visualization (using mock data if real results aren't available)\n",
+    "try:\n",
+    "    # Use actual results if available\n",
+    "    if 'results' in dir() and results is not None:\n",
+    "        r_values = results['r'].values\n",
+    "        keff_values = results['mean_keff'].values.astype(float)\n",
+    "        sigma_values = results['sigma_keff'].values.astype(float)\n",
+    "    else:\n",
+    "        # Use mock data for demonstration\n",
+    "        r_values = [8.5, 8.741, 9.0]\n",
+    "        keff_values = [0.9850, 0.9995, 1.0145]  # Example values\n",
+    "        sigma_values = [0.0012, 0.0006, 0.0008]\n",
+    "    \n",
+    "    plt.figure(figsize=(10, 6))\n",
+    "    plt.errorbar(r_values, keff_values, yerr=sigma_values, \n",
+    "                 fmt='o-', linewidth=2, markersize=8, capsize=5)\n",
+    "    plt.axhline(y=1.0, color='r', linestyle='--', label='Critical (k_eff=1.0)')\n",
+    "    plt.xlabel('Sphere Radius (cm)', fontsize=12)\n",
+    "    plt.ylabel('k_effective', fontsize=12)\n",
+    "    plt.title('Godiva Critical Reactor: k_eff vs Radius', fontsize=14, fontweight='bold')\n",
+    "    plt.grid(True, alpha=0.3)\n",
+    "    plt.legend()\n",
+    "    plt.tight_layout()\n",
+    "    plt.show()\n",
+    "    \n",
+    "except Exception as e:\n",
+    "    print(f\"Visualization error: {e}\")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.0"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
diff --git a/examples/MCNP/example_godiva.py b/examples/example_godiva.py
similarity index 98%
rename from examples/MCNP/example_godiva.py
rename to examples/example_godiva.py
index 9aad2f8..0666940 100755
--- a/examples/MCNP/example_godiva.py
+++ b/examples/example_godiva.py
@@ -37,7 +37,7 @@ def main():
     # Check if input file exists
     if not os.path.exists(input_file):
         print(f"Error: Input file '{input_file}' not found.")
-        print("Please run this script from the examples/MCNP directory.")
+        print("Please run this script from the examples directory.")
         sys.exit(1)
     
     print("=" * 60)
diff --git a/examples/MCNP/godiva.inp b/examples/godiva.inp
similarity index 100%
rename from examples/MCNP/godiva.inp
rename to examples/godiva.inp
diff --git a/tests/test_plugin.py b/tests/test_plugin.py
index be6a189..5adcc8e 100755
--- a/tests/test_plugin.py
+++ b/tests/test_plugin.py
@@ -102,8 +102,8 @@ def test_example_files():
     print("Testing example files...")
     
     examples = [
-        "examples/MCNP/godiva.inp",
-        "examples/MCNP/example_godiva.py"
+        "examples/godiva.inp",
+        "examples/example_godiva.py"
     ]
     
     for example_file in examples:
@@ -124,7 +124,7 @@ def test_with_fz():
         
         # Test parsing input file
         print("  Testing fz.fzi() on godiva.inp...", end=" ")
-        variables = fz.fzi("examples/MCNP/godiva.inp", "MCNP")
+        variables = fz.fzi("examples/godiva.inp", "MCNP")
         assert "r" in variables, "Variable 'r' not found in parsed input"
         print("✓")
         
@@ -132,7 +132,7 @@ def test_with_fz():
         print("  Testing fz.fzc() compilation...", end=" ")
         with tempfile.TemporaryDirectory() as tmpdir:
             fz.fzc(
-                "examples/MCNP/godiva.inp",
+                "examples/godiva.inp",
                 {"r": 8.741},
                 "MCNP",
                 output_dir=tmpdir

From 4d2b5398af97e48576c3215c321d7fbc7d3268d9 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 5 Dec 2025 14:01:16 +0000
Subject: [PATCH 4/4] Fix notebook paths to match flattened structure

Co-authored-by: yannrichet-asnr <148193180+yannrichet-asnr@users.noreply.github.com>
---
 example_usage.ipynb | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/example_usage.ipynb b/example_usage.ipynb
index e627046..79acfb0 100644
--- a/example_usage.ipynb
+++ b/example_usage.ipynb
@@ -70,7 +70,7 @@
     "\n",
     "# Download example files\n",
     "files_to_download = [\n",
-    "    (\"MCNP/godiva.inp\", f\"{base_url}/godiva.inp\"),\n",
+    "    (\"godiva.inp\", f\"{base_url}/godiva.inp\"),\n",
     "]\n",
     "\n",
     "print(\"Downloading example files...\")\n",
@@ -145,7 +145,7 @@
    "source": [
     "# Parse the input file to find variables\n",
     "variables = fz.fzi(\n",
-    "    \"MCNP/godiva.inp\",\n",
+    "    \"godiva.inp\",\n",
     "    \"MCNP\"\n",
     ")\n",
     "\n",
@@ -171,7 +171,7 @@
     "with tempfile.TemporaryDirectory() as tmpdir:\n",
     "    # Compile input with specific value for radius\n",
     "    fz.fzc(\n",
-    "        \"MCNP/godiva.inp\",\n",
+    "        \"godiva.inp\",\n",
     "        {\"r\": 8.741},  # Critical radius\n",
     "        \"MCNP\",\n",
     "        output_dir=tmpdir\n",
@@ -214,7 +214,7 @@
     "try:\n",
     "    # Run MCNP calculation\n",
     "    results = fz.fzr(\n",
-    "        input_path=\"MCNP/godiva.inp\",\n",
+    "        input_path=\"godiva.inp\",\n",
     "        input_variables=input_variables,\n",
     "        model=\"MCNP\",\n",
     "        calculators=\"localhost_MCNP\",\n",
@@ -259,7 +259,7 @@
     "try:\n",
     "    # Run parametric calculation\n",
     "    results = fz.fzr(\n",
-    "        input_path=\"MCNP/godiva.inp\",\n",
+    "        input_path=\"godiva.inp\",\n",
     "        input_variables=input_variables,\n",
     "        model=\"MCNP\",\n",
     "        calculators=\"localhost_MCNP\",\n",