Parametric scientific computing package

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Project description

FZ - Parametric Scientific Computing Framework

A powerful Python package for parametric simulations and computational experiments. FZ wraps your simulation codes to automatically run parametric studies, manage input/output files, handle parallel execution, and collect results in structured DataFrames.

Features
Installation
Quick Start
CLI Usage
Core Functions
Model Definition
Calculator Types
Advanced Features
Complete Examples
- Interactive Jupyter Notebooks
Writing Custom Algorithms for fzd
Configuration
Interrupt Handling
Breaking Changes
Development
Troubleshooting
Performance Tips
Documentation
Support

Features

Core Capabilities

🔄 Parametric Studies: Factorial designs (dict with Cartesian product) or non-factorial designs (DataFrame with specific cases)
⚡ Parallel Execution: Run multiple cases concurrently across multiple calculators with automatic load balancing
💾 Smart Caching: Reuse previous calculation results based on input file hashes to avoid redundant computations
🔁 Retry Mechanism: Automatically retry failed calculations with alternative calculators
🌐 Remote Execution: Execute calculations on remote servers via SSH with automatic file transfer
📊 DataFrame I/O: Input and output using pandas DataFrames with automatic type casting and variable extraction
🛑 Interrupt Handling: Gracefully stop long-running calculations with Ctrl+C while preserving partial results
🔍 Formula Evaluation: Support for calculated parameters using Python or R expressions
📁 Directory Management: Automatic organization of inputs, outputs, and logs for each case
🎯 Adaptive Algorithms: Iterative design of experiments with intelligent sampling strategies (fzd)
⚠️ Error Reporting: Protocol-specific error classification with descriptive messages recorded in results
🖥️ Cross-Platform: Works on Linux, macOS, and Windows (MSYS2/Git Bash) with configurable shell paths

Six Core Functions

fzi - Parse Input files to identify variables
fzc - Compile input files by substituting variable values
fzo - Parse Output files from calculations
fzr - Run complete parametric calculations end-to-end
fzd - Run iterative Design of experiments with adaptive algorithms
fzl - List and validate installed models and calculators

Installation

Using pip

pip install funz-fz

Using pipx (recommended for CLI tools)

pipx install funz-fz

pipx installs the package in an isolated environment while making the CLI commands (fz, fzi, fzc, fzo, fzr, fzl, fzd) available globally.

From Source

git clone https://github.com/Funz/fz.git
cd fz
pip install -e .

Or straight from GitHub via pip:

pip install -e git+https://github.com/Funz/fz.git

Dependencies

# Optional dependencies:

# for SSH support
pip install paramiko

# for DataFrame support (recommended)
pip install pandas

# for fzd (design of experiments) - REQUIRED
pip install pandas

# for R interpreter support
pip install funz-fz[r]
# OR
pip install rpy2
# Note: Requires R installed with system libraries - see examples/r_interpreter_example.md

# for optimization algorithms (scipy-based algorithms in examples/)
pip install scipy numpy

Quick Start

Here's a complete example for a simple parametric study:

1. Create an Input Template

Create input.txt:

# input file for Perfect Gaz Pressure, with variables n_mol, T_celsius, V_L
n_mol=$n_mol
T_kelvin=@{$T_celsius + 273.15}
#@ def L_to_m3(L):
#@     return(L / 1000)
V_m3=@{L_to_m3($V_L)}

Or using R for formulas (assuming R interpreter is set up: fz.set_interpreter("R")):

# input file for Perfect Gaz Pressure, with variables n_mol, T_celsius, V_L
n_mol=$n_mol
T_kelvin=@{$T_celsius + 273.15}
#@ L_to_m3 <- function(L) {
#@     return (L / 1000)
#@ }
V_m3=@{L_to_m3($V_L)}

2. Create a Calculation Script

Create PerfectGazPressure.sh:

#!/bin/bash

# read input file
source $1

sleep 5 # simulate a calculation time

echo 'pressure = '`echo "scale=4;$n_mol*8.314*$T_kelvin/$V_m3" | bc` > output.txt

echo 'Done'

Make it executable:

chmod +x PerfectGazPressure.sh

3. Run Parametric Study

Create run_study.py:

import fz

# Define the model
model = {
    "varprefix": "$",
    "formulaprefix": "@",
    "delim": "{}",
    "commentline": "#",
    "output": {
        "pressure": "grep 'pressure = ' output.txt | awk '{print $3}'"
    }
}

# Define parameter values
input_variables = {
    "T_celsius": [10, 20, 30, 40],  # 4 temperatures
    "V_L": [1, 2, 5],                # 3 volumes
    "n_mol": 1.0                     # fixed amount
}

# Run all combinations (4 × 3 = 12 cases)
results = fz.fzr(
    "input.txt",
    input_variables,
    model,
    calculators="sh://bash PerfectGazPressure.sh",
    results_dir="results"
)

# Display results
print(results)
print(f"\nCompleted {len(results)} calculations")

Run it:

python run_study.py

Expected output:

   T_celsius  V_L  n_mol     pressure status calculator       error command
0         10  1.0    1.0  235358.1200   done     sh://        None    bash...
1         10  2.0    1.0  117679.0600   done     sh://        None    bash...
2         10  5.0    1.0   47071.6240   done     sh://        None    bash...
3         20  1.0    1.0  243730.2200   done     sh://        None    bash...
...

Completed 12 calculations

CLI Usage

FZ provides command-line tools for quick operations without writing Python scripts. All four core functions are available as CLI commands.

Installation of CLI Tools

The CLI commands are automatically installed when you install the fz package:

pip install -e .

Available commands:

fz - Main entry point (general configuration, plugins management, logging, ...)
fzi - Parse input variables
fzc - Compile input files
fzo - Read output files
fzr - Run parametric calculations
fzl - List and validate installed models and calculators
fzd - Run design of experiments with adaptive algorithms

fzi - Parse Input Variables

Identify variables in input files:

# Parse a single file
fzi input.txt --model perfectgas

# Parse a directory
fzi input_dir/ --model mymodel

# Output formats
fzi input.txt --model perfectgas --format json
fzi input.txt --model perfectgas --format table
fzi input.txt --model perfectgas --format csv

Example:

$ fzi input.txt --model perfectgas --format table
┌──────────────┬───────┐
│ Variable     │ Value │
├──────────────┼───────┤
│ T_celsius    │ None  │
│ V_L          │ None  │
│ n_mol        │ None  │
└──────────────┴───────┘

With inline model definition:

fzi input.txt \
  --varprefix '$' \
  --delim '{}' \
  --format json

Output (JSON):

{
  "T_celsius": null,
  "V_L": null,
  "n_mol": null
}

fzc - Compile Input Files

Substitute variables and create compiled input files:

# Basic usage
fzc input.txt \
  --model perfectgas \
  --variables '{"T_celsius": 25, "V_L": 10, "n_mol": 1}' \
  --output compiled/

# Grid of values (creates subdirectories)
fzc input.txt \
  --model perfectgas \
  --variables '{"T_celsius": [10, 20, 30], "V_L": [1, 2], "n_mol": 1}' \
  --output compiled_grid/

Directory structure created:

compiled_grid/
├── T_celsius=10,V_L=1/
│   └── input.txt
├── T_celsius=10,V_L=2/
│   └── input.txt
├── T_celsius=20,V_L=1/
│   └── input.txt
...

Using formula evaluation:

# Input file with formulas
cat > input.txt << 'EOF'
Temperature: $T_celsius C
#@ T_kelvin = $T_celsius + 273.15
Calculated T: @{T_kelvin} K
EOF

# Compile with formula evaluation
fzc input.txt \
  --varprefix '$' \
  --formulaprefix '@' \
  --delim '{}' \
  --commentline '#' \
  --variables '{"T_celsius": 25}' \
  --output compiled/

fzo - Read Output Files

Parse calculation results:

# Read single directory
fzo results/case1/ --model perfectgas --format table

# Read directory with subdirectories
fzo results/ --model perfectgas --format json

# Different output formats
fzo results/ --model perfectgas --format csv > results.csv
fzo results/ --model perfectgas --format html > results.html
fzo results/ --model perfectgas --format markdown

Example output:

$ fzo results/ --model perfectgas --format table
┌─────────────────────────┬──────────┬────────────┬──────┬───────┐
│ path                    │ pressure │ T_celsius  │ V_L  │ n_mol │
├─────────────────────────┼──────────┼────────────┼──────┼───────┤
│ T_celsius=10,V_L=1      │ 235358.1 │ 10         │ 1.0  │ 1.0   │
│ T_celsius=10,V_L=2      │ 117679.1 │ 10         │ 2.0  │ 1.0   │
│ T_celsius=20,V_L=1      │ 243730.2 │ 20         │ 1.0  │ 1.0   │
└─────────────────────────┴──────────┴────────────┴──────┴───────┘

With inline model definition:

fzo results/ \
  --output-cmd pressure="grep 'pressure = ' output.txt | awk '{print \$3}'" \
  --output-cmd temperature="cat temp.txt" \
  --format json

fzl - List and Validate Models/Calculators

List installed models and calculators with optional validation:

# List all models and calculators
fzl

# List with validation checks
fzl --check

# Filter by pattern
fzl --models "perfect*" --calculators "ssh*"

# Different output formats
fzl --format json
fzl --format table
fzl --format markdown  # default

Example output:

$ fzl --check --format table

=== MODELS ===

Model: perfectgas ✓
  Path: /home/user/project/.fz/models/perfectgas.json
  Supported Calculators: 2
    - local
    - ssh_cluster

Model: navier-stokes ✗
  Path: /home/user/.fz/models/navier-stokes.json
  Error: Missing required field 'output'
  Supported Calculators: 0

=== CALCULATORS ===

Calculator: local ✓
  Path: /home/user/project/.fz/calculators/local.json
  URI: sh://
  Models: 1
    - perfectgas

Calculator: ssh_cluster ✓
  Path: /home/user/.fz/calculators/ssh_cluster.json
  URI: ssh://user@cluster.edu
  Models: 2
    - perfectgas
    - navier-stokes

fzr - Run Parametric Calculations

Execute complete parametric studies from the command line:

# Basic usage
fzr input.txt \
  --model perfectgas \
  --variables '{"T_celsius": [10, 20, 30], "V_L": [1, 2], "n_mol": 1}' \
  --calculator "sh://bash PerfectGazPressure.sh" \
  --results results/

# Multiple calculators for parallel execution
fzr input.txt \
  --model perfectgas \
  --variables '{"param": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]}' \
  --calculator "sh://bash calc.sh" \
  --calculator "sh://bash calc.sh" \
  --calculator "sh://bash calc.sh" \
  --results results/ \
  --format table

Using cache:

# First run
fzr input.txt \
  --model perfectgas \
  --variables '{"T_celsius": [10, 20, 30], "V_L": [1, 2]}' \
  --calculator "sh://bash PerfectGazPressure.sh" \
  --results run1/

# Resume with cache (only runs missing cases)
fzr input.txt \
  --model perfectgas \
  --variables '{"T_celsius": [10, 20, 30, 40], "V_L": [1, 2, 3]}' \
  --calculator "cache://run1" \
  --calculator "sh://bash PerfectGazPressure.sh" \
  --results run2/ \
  --format table

Remote SSH execution:

fzr input.txt \
  --model mymodel \
  --variables '{"mesh_size": [100, 200, 400]}' \
  --calculator "ssh://user@cluster.edu/bash /path/to/submit.sh" \
  --results hpc_results/ \
  --format json

Output formats:

# Table (default)
fzr input.txt --model perfectgas --variables '{"x": [1, 2, 3]}' --calculator "sh://calc.sh"

# JSON
fzr ... --format json

# CSV
fzr ... --format csv > results.csv

# Markdown
fzr ... --format markdown

# HTML
fzr ... --format html > results.html

fzd - Design of Experiments

Run iterative design of experiments with adaptive algorithms:

# Basic usage with random sampling
fzd --input_dir input/ \
  --model perfectgas \
  --input_vars '{"x": "[-2;2]", "y": "[-2;2]"}' \
  --output_expression "result" \
  --algorithm examples/algorithms/randomsampling.py \
  --options '{"nvalues": 20, "seed": 42}'

# With multiple calculators for parallel evaluation
fzd --input_dir input/ \
  --model perfectgas \
  --input_vars '{"x": "[-2;2]", "y": "[-2;2]"}' \
  --output_expression "result" \
  --algorithm examples/algorithms/bfgs.py \
  --calculators '["sh://bash calc.sh", "sh://bash calc.sh"]' \
  --options '{"max_iter": 20, "tol": 1e-4}' \
  --results_dir optimization_results/

Algorithm options from file:

# Store options in a JSON file
cat > algo_config.json << 'EOF'
{"nvalues": 50, "seed": 42}
EOF

fzd -i input/ -m perfectgas \
  -v '{"x": "[-2;2]", "y": "[-2;2]"}' \
  -e "result" \
  -a examples/algorithms/randomsampling.py \
  -o algo_config.json

Also available as subcommand: fz design ...

fz install / uninstall

Install models or algorithms from GitHub or local zip files:

# Install a model (to .fz/models/ in current project)
fz install model perfectgas
fz install model https://github.com/user/model-repo.git

# Install globally (to ~/.fz/models/)
fz install model perfectgas --global

# Install an algorithm
fz install algorithm https://github.com/user/algo-repo.git

# Uninstall
fz uninstall model perfectgas
fz uninstall algorithm myalgo

CLI Options Reference

Common Options (all commands)

--help, -h                Show help message
--version                 Show version
--model MODEL             Model alias or inline definition
--varprefix PREFIX        Variable prefix (default: $)
--delim DELIMITERS        Formula delimiters (default: {})
--formulaprefix PREFIX    Formula prefix (default: @)
--commentline CHAR        Comment character (default: #)
--format FORMAT           Output format: json, table, csv, markdown, html

Exit Codes and Output Streams

CLI commands are script-friendly: results are printed to stdout, while log messages (FZ_LOG_LEVEL), the progress bar, and error messages go to stderr. The progress bar is automatically disabled when stderr is not a terminal (piped/redirected output or CI).

# stdout contains only the JSON results; logs and progress stay on stderr
fzr input.txt --model perfectgas --variables '{"x": [1, 2]}' \
    --calculator "sh://bash calc.sh" --format json > results.json 2> run.log

Exit codes: 0 on success, non-zero on errors (invalid arguments, missing files, ...). fzr also exits with 1 when no case succeeded; partial success exits 0 with per-case details in the status column.

Argument Formats

FZ CLI commands support three flexible formats for specifying models, calculators, and variables:

1. Inline JSON - Direct JSON string:

fzr input.txt \
  --model '{"varprefix": "$", "output": {"result": "cat output.txt"}}' \
  --variables '{"temp": [10, 20, 30], "pressure": 1}' \
  --calculator "sh://bash calc.sh"

2. JSON File - Path to JSON file:

# Create model file
cat > mymodel.json << 'EOF'
{
  "varprefix": "$",
  "formulaprefix": "@",
  "delim": "{}",
  "output": {
    "result": "cat output.txt"
  }
}
EOF

# Use file path
fzr input.txt --model mymodel.json --variables vars.json --calculator "sh://calc.sh"

3. Alias - Named configuration from .fz/ directory:

# Uses .fz/models/perfectgas.json
fzr input.txt --model perfectgas --calculator local

Automatic Detection:

FZ automatically detects which format you're using
Tries formats in order: Alias → JSON File → Inline JSON
Provides helpful error messages if parsing fails
Works for --model, --calculator, and --variables arguments

Format Detection Logic:

# Examples of automatic detection
"perfectgas"                          # → Alias (no .json, no braces)
"model.json"                          # → File (ends with .json)
'{"varprefix": "$"}'                  # → Inline JSON (starts with {)

Mixing Formats:

# Mix different formats in the same command
fzr input.txt \
  --model perfectgas \                              # Alias
  --variables '{"temp": [10, 20, 30]}' \           # Inline JSON
  --calculator cluster                              # Alias

Model Definition Options

Instead of using --model alias, you can define the model inline:

fzr input.txt \
  --varprefix '$' \
  --formulaprefix '@' \
  --delim '{}' \
  --commentline '#' \
  --output-cmd pressure="grep 'pressure' output.txt | awk '{print \$2}'" \
  --output-cmd temp="cat temperature.txt" \
  --variables '{"x": 10}' \
  --calculator "sh://bash calc.sh"

fzr-Specific Options

--calculator URI          Calculator URI (can be specified multiple times)
--results DIR             Results directory (default: results)

Complete CLI Examples

Example 1: Quick Variable Discovery

# Check what variables are in your input files
$ fzi simulation_template.txt --varprefix '$' --format table
┌──────────────┬───────┐
│ Variable     │ Value │
├──────────────┼───────┤
│ mesh_size    │ None  │
│ timestep     │ None  │
│ iterations   │ None  │
└──────────────┴───────┘

Example 2: Quick Compilation Test

# Test variable substitution
$ fzc simulation_template.txt \
  --varprefix '$' \
  --variables '{"mesh_size": 100, "timestep": 0.01, "iterations": 1000}' \
  --output test_compiled/

$ cat test_compiled/simulation_template.txt
# Compiled with mesh_size=100
mesh_size=100
timestep=0.01
iterations=1000

Example 3: Parse Existing Results

# Extract results from previous calculations
$ fzo old_results/ \
  --output-cmd energy="grep 'Total Energy' log.txt | awk '{print \$3}'" \
  --output-cmd time="grep 'CPU Time' log.txt | awk '{print \$3}'" \
  --format csv > analysis.csv

Example 4: End-to-End Parametric Study

#!/bin/bash
# run_study.sh - Complete parametric study from CLI

# 1. Parse input to verify variables
echo "Step 1: Parsing input variables..."
fzi input.txt --model perfectgas --format table

# 2. Run parametric study
echo -e "\nStep 2: Running calculations..."
fzr input.txt \
  --model perfectgas \
  --variables '{
    "T_celsius": [10, 20, 30, 40, 50],
    "V_L": [1, 2, 5, 10],
    "n_mol": 1
  }' \
  --calculator "sh://bash PerfectGazPressure.sh" \
  --calculator "sh://bash PerfectGazPressure.sh" \
  --results results/ \
  --format table

# 3. Export results to CSV
echo -e "\nStep 3: Exporting results..."
fzo results/ --model perfectgas --format csv > results.csv
echo "Results saved to results.csv"

Example 5: Using Model and Calculator Aliases

First, create model and calculator configurations:

# Create model alias
mkdir -p .fz/models
cat > .fz/models/perfectgas.json << 'EOF'
{
  "varprefix": "$",
  "formulaprefix": "@",
  "delim": "{}",
  "commentline": "#",
  "output": {
    "pressure": "grep 'pressure = ' output.txt | awk '{print $3}'"
  },
  "id": "perfectgas"
}
EOF

# Create calculator alias
mkdir -p .fz/calculators
cat > .fz/calculators/local.json << 'EOF'
{
  "uri": "sh://",
  "models": {
    "perfectgas": "bash PerfectGazPressure.sh"
  }
}
EOF

# Now run with short aliases
fzr input.txt \
  --model perfectgas \
  --variables '{"T_celsius": [10, 20, 30], "V_L": [1, 2]}' \
  --calculator local \
  --results results/ \
  --format table

Example 6: Interrupt and Resume

# Start long-running calculation
fzr input.txt \
  --model mymodel \
  --variables '{"param": [1..100]}' \
  --calculator "sh://bash slow_calc.sh" \
  --results run1/
# Press Ctrl+C after some cases complete...
# ⚠️  Interrupt received (Ctrl+C). Gracefully shutting down...
# ⚠️  Execution was interrupted. Partial results may be available.

# Resume from cache
fzr input.txt \
  --model mymodel \
  --variables '{"param": [1..100]}' \
  --calculator "cache://run1" \
  --calculator "sh://bash slow_calc.sh" \
  --results run1_resumed/ \
  --format table
# Only runs the remaining cases

fzd - Run Design of Experiments

Run iterative design of experiments with adaptive algorithms:

# Basic usage with Monte Carlo algorithm
fzd --input_dir input/ \
  --model perfectgas \
  --input_vars '{"T_celsius": "[10;50]", "V_L": "[1;10]", "n_mol": "1"}' \
  --calculators "sh://bash PerfectGazPressure.sh" \
  --output_expression "pressure" \
  --algorithm examples/algorithms/montecarlo_uniform.py \
  --options '{"batch_sample_size": 20, "max_iterations": 10}' \
  --results_dir fzd_results/

# With optimization algorithm (BFGS)
fzd --input_dir input/ \
  --model perfectgas \
  --input_vars '{"T_celsius": "[10;50]", "V_L": "[1;10]", "n_mol": "1"}' \
  --calculators "sh://bash calc.sh" \
  --output_expression "pressure" \
  --algorithm examples/algorithms/bfgs.py \
  --options '{"minimize": true, "max_iterations": 50}' \
  --results_dir optimization_results/

# Fixed and variable inputs (V_L fixed at 5.0, T_celsius explored by algorithm)
fzd --input_dir input/ \
  --model perfectgas \
  --input_vars '{"T_celsius": "[10;50]", "V_L": "5.0", "n_mol": "1"}' \
  --calculators "sh://bash calc.sh" \
  --output_expression "pressure" \
  --algorithm examples/algorithms/brent.py \
  --results_dir brent_results/

Short form: fzd -i input/ -m perfectgas -v '...' -e "pressure" -a algo.py

Also available as subcommand: fz design --input_dir input/ ...

Key Differences from fzr:

--input_vars uses "[min;max]" for ranges (algorithm decides values) or "value" (string) for fixed
Requires --algorithm with algorithm name (randomsampling, brent, bfgs, ...) or path to .py file
Algorithm options via --options (JSON dict or file)
Results directory via --results_dir (default: results_fzd); if it already exists it is renamed with a timestamp and its cached results are still reused
Duplicate design points within a batch are automatically deduplicated and results reused

Environment Variables for CLI

# Set logging level
export FZ_LOG_LEVEL=DEBUG
fzr input.txt --model perfectgas ...

# Set maximum parallel workers
export FZ_MAX_WORKERS=4
fzr input.txt --model perfectgas --calculator "sh://calc.sh" ...

# Set retry attempts
export FZ_MAX_RETRIES=3
fzr input.txt --model perfectgas ...

# SSH configuration
export FZ_SSH_AUTO_ACCEPT_HOSTKEYS=1  # Use with caution
export FZ_SSH_KEEPALIVE=300
fzr input.txt --calculator "ssh://user@host/bash calc.sh" ...

# Shell path for binary resolution (Windows)
export FZ_SHELL_PATH="C:\msys64\usr\bin;C:\msys64\mingw64\bin"
fzr input.txt --model perfectgas ...

Core Functions

fzi - Parse Input Variables

Identify all variables in an input file or directory:

import fz

model = {
    "varprefix": "$",
    "delim": "{}"
}

# Parse single file
variables = fz.fzi("input.txt", model)
# Returns: {'T_celsius': None, 'V_L': None, 'n_mol': None}

# Parse directory (scans all files)
variables = fz.fzi("input_dir/", model)

Returns: Dictionary with variable names as keys (values are None)

fzc - Compile Input Files

Substitute variable values and evaluate formulas:

import fz

model = {
    "varprefix": "$",
    "formulaprefix": "@",
    "delim": "{}",
    "commentline": "#"
}

input_variables = {
    "T_celsius": 25,
    "V_L": 10,
    "n_mol": 2
}

# Compile single file
fz.fzc(
    "input.txt",
    input_variables,
    model,
    output_dir="compiled"
)

# Compile with multiple value sets (creates subdirectories)
fz.fzc(
    "input.txt",
    {
        "T_celsius": [20, 30],  # 2 values
        "V_L": [5, 10],         # 2 values
        "n_mol": 1              # fixed
    },
    model,
    output_dir="compiled_grid"
)
# Creates: compiled_grid/T_celsius=20,V_L=5/, T_celsius=20,V_L=10/, etc.

Parameters:

input_path: Path to input file or directory
input_variables: Dictionary of variable values (scalar or list)
model: Model definition (dict or alias name)
output_dir: Output directory path

fzo - Read Output Files

Parse calculation results from output directory:

import fz

model = {
    "output": {
        "pressure": "grep 'Pressure:' output.txt | awk '{print $2}'",
        "temperature": "grep 'Temperature:' output.txt | awk '{print $2}'"
    }
}

# Read from single directory
output = fz.fzo("results/case1", model)
# Returns: DataFrame with 1 row

# Read from directory with subdirectories
output = fz.fzo("results/*", model)
# Returns: DataFrame with 1 row per subdirectory

Automatic Path Parsing: If subdirectory names follow the pattern key1=val1,key2=val2,..., variables are automatically extracted as columns:

# Directory structure:
# results/
#   ├── T_celsius=20,V_L=1/output.txt
#   ├── T_celsius=20,V_L=2/output.txt
#   └── T_celsius=30,V_L=1/output.txt

output = fz.fzo("results/*", model)
print(output)
#                          path  pressure  T_celsius  V_L
# 0  T_celsius=20,V_L=1  2437.30       20.0  1.0
# 1  T_celsius=20,V_L=2  1218.65       20.0  2.0
# 2  T_celsius=30,V_L=1  2520.74       30.0  1.0

fzr - Run Parametric Calculations

Execute complete parametric study with automatic parallelization:

import fz

model = {
    "varprefix": "$",
    "output": {
        "result": "cat output.txt"
    }
}

results = fz.fzr(
    input_path="input.txt",
    input_variables={
        "temperature": [100, 200, 300],
        "pressure": [1, 10, 100],
        "concentration": 0.5
    },
    model=model,
    calculators=["sh://bash calculate.sh"],
    results_dir="results"
)

# Results DataFrame includes:
# - All variable columns
# - All output columns
# - Metadata: status, calculator, error, command
print(results)

Parameters:

input_path: Input file or directory path
input_variables: Variable values - dict (factorial) or DataFrame (non-factorial)
model: Model definition (dict or alias)
calculators: Calculator URI(s) - string or list
results_dir: Results directory path

Returns: pandas DataFrame with all results

fzd - Run Design of Experiments

Execute iterative design of experiments with adaptive algorithms:

import fz

model = {
    "varprefix": "$",
    "output": {
        "result": "grep 'Result:' output.txt | awk '{print $2}'"
    }
}

# Run Monte Carlo sampling
results = fz.fzd(
    input_path="input.txt",
    input_variables={
        "x": "[0;10]",      # Range: algorithm decides values
        "y": "[-5;5]",      # Range: algorithm decides values
        "z": "2.5"          # Fixed value
    },
    model=model,
    output_expression="result",
    algorithm="examples/algorithms/montecarlo_uniform.py",
    calculators=["sh://bash calculate.sh"],
    algorithm_options={"batch_sample_size": 10, "max_iterations": 20},
    analysis_dir="results_fzd"
)

# Results include:
# - results['XY']: DataFrame with all input/output values
# - results['analysis']: Processed analysis (HTML, plots, metrics, etc.)
# - results['iterations']: Number of iterations completed
# - results['total_evaluations']: Total function evaluations
# - results['summary']: Summary text
print(results['XY'])  # All sampled points and outputs
print(results['summary'])  # Algorithm completion summary

Algorithm Examples:

examples/algorithms/montecarlo_uniform.py - Uniform random sampling
examples/algorithms/randomsampling.py - Simple random sampling
examples/algorithms/bfgs.py - BFGS optimization (requires scipy)
examples/algorithms/brent.py - Brent's 1D optimization (requires scipy)

Parameters:

input_path: Input file or directory path
input_variables: Dict where "[min;max]" entries are varied by the algorithm and plain "value" entries are fixed at that value for every evaluation
model: Model definition (dict or alias)
output_expression: Expression to evaluate from outputs (e.g., "pressure" or "out1 + out2 * 2")
algorithm: Algorithm name (randomsampling, brent, bfgs, ...) or path to .py file
calculators: Calculator URI(s) - string or list
algorithm_options: Dict, JSON string, or JSON file path with algorithm-specific options
analysis_dir: Analysis results directory (default: "analysis"); if it already exists it is renamed with a timestamp and its cached results are still reused automatically

Returns: Dict with:

XY: pandas DataFrame with all input and output values
analysis: Processed analysis results (HTML files, plots, metrics)
algorithm: Algorithm path
iterations: Number of iterations completed
total_evaluations: Total number of function evaluations
summary: Human-readable summary text

Automatic behaviors:

Batch deduplication: duplicate points proposed by the algorithm in the same iteration are evaluated only once; results are re-mapped to all occurrences
Cross-iteration caching: results from previous iterations are automatically reused — a point evaluated in iteration 2 is never re-run in iteration 5
Re-run resume: if analysis_dir already exists it is renamed with a timestamp; all its iteration subdirectories are still consulted as cache, so a re-run with different options benefits from all prior computations

Input Variables: Factorial vs Non-Factorial Designs

FZ supports two types of parametric study designs through different input_variables formats:

Factorial Design (Dict)

Use a dict to create a full factorial design (Cartesian product of all variable values):

# Dict with lists creates ALL combinations (factorial)
input_variables = {
    "temp": [100, 200, 300],      # 3 values
    "pressure": [1.0, 2.0]         # 2 values
}
# Creates 6 cases: 3 × 2 = 6
# (100,1.0), (100,2.0), (200,1.0), (200,2.0), (300,1.0), (300,2.0)

results = fz.fzr(input_file, input_variables, model, calculators)

Use factorial design when:

You want to explore all possible combinations
Variables are independent
You need a complete design space exploration

Non-Factorial Design (DataFrame)

Use a pandas DataFrame to specify exactly which cases to run (non-factorial):

import pandas as pd

# DataFrame: each row is ONE case (non-factorial)
input_variables = pd.DataFrame({
    "temp":     [100, 200, 100, 300],
    "pressure": [1.0, 1.0, 2.0, 1.5]
})
# Creates 4 cases ONLY:
# (100,1.0), (200,1.0), (100,2.0), (300,1.5)
# Note: (100,2.0) is included but (200,2.0) is not

results = fz.fzr(input_file, input_variables, model, calculators)

Use non-factorial design when:

You have specific combinations to test
Variables are coupled or have constraints
You want to import a design from another tool
You need an irregular or optimized sampling pattern

Examples of non-factorial patterns:

# Latin Hypercube Sampling
import pandas as pd
from scipy.stats import qmc

sampler = qmc.LatinHypercube(d=2)
sample = sampler.random(n=10)
input_variables = pd.DataFrame({
    "x": sample[:, 0] * 100,  # Scale to [0, 100]
    "y": sample[:, 1] * 10    # Scale to [0, 10]
})

# Constraint-based design (only valid combinations)
input_variables = pd.DataFrame({
    "rpm": [1000, 1500, 2000, 2500],
    "load": [10, 20, 40, 50]  # load increases with rpm
})

# Imported from design of experiments tool
input_variables = pd.read_csv("doe_design.csv")

Model Definition

A model defines how to parse inputs and extract outputs:

model = {
    # Input parsing
    "varprefix": "$",           # Variable marker (e.g., $temp)
    "formulaprefix": "@",       # Formula marker (e.g., @pressure)
    "delim": "{}",              # Formula delimiters
    "commentline": "#",         # Comment character

    # Optional: formula interpreter
    "interpreter": "python",    # "python" (default) or "R"

    # Output extraction (shell commands)
    "output": {
        "pressure": "grep 'P =' out.txt | awk '{print $3}'",
        "temperature": "cat temp.txt",
        "energy": "python extract.py"
    },

    # Optional: model identifier
    "id": "perfectgas"
}

Model Aliases

Store reusable models in .fz/models/:

.fz/models/perfectgas.json:

{
    "varprefix": "$",
    "formulaprefix": "@",
    "delim": "{}",
    "commentline": "#",
    "output": {
        "pressure": "grep 'pressure = ' output.txt | awk '{print $3}'"
    },
    "id": "perfectgas"
}

Use by name:

results = fz.fzr("input.txt", input_variables, "perfectgas")

Formula Evaluation

Formulas in input files are evaluated during compilation using Python or R interpreters.

Python Interpreter (Default)

# Input template with formulas
Temperature: $T_celsius C
Volume: $V_L L

# Context (available in all formulas)
#@import math
#@R = 8.314
#@def celsius_to_kelvin(t):
#@    return t + 273.15

# Calculated value
#@T_kelvin = celsius_to_kelvin($T_celsius)
#@pressure = $n_mol * R * T_kelvin / ($V_L / 1000)

Result: @{pressure} Pa
Circumference: @{2 * math.pi * $radius}

R Interpreter

For statistical computing, you can use R for formula evaluation:

from fz import fzi
from fz.config import set_interpreter

# Set interpreter to R
set_interpreter("R")

# Or specify in model
model = {"interpreter": "R", "formulaprefix": "@", "delim": "{}", "commentline": "#"}

R template example:

# Input template with R formulas
Sample size: $n
Mean: $mu
SD: $sigma

# R context (available in all formulas)
#@samples <- rnorm($n, mean=$mu, sd=$sigma)

Mean (sample): @{mean(samples)}
SD (sample): @{sd(samples)}
Median: @{median(samples)}

Installation requirements: R must be installed along with system libraries. See examples/r_interpreter_example.md for detailed installation instructions.

# Install with R support
pip install funz-fz[r]

Key differences:

Python requires import math for math.pi, R has pi built-in
R excels at statistical functions: mean(), sd(), median(), rnorm(), etc.
R uses <- for assignment in context lines
R is vectorized by default

Variable Default Values

Variables can specify default values using the ${var~default} syntax:

# Configuration template
Host: ${host~localhost}
Port: ${port~8080}
Debug: ${debug~false}
Workers: ${workers~4}

Behavior:

If variable is provided in input_variables, its value is used
If variable is NOT provided but has default, default is used (with warning)
If variable is NOT provided and has NO default, it remains unchanged

Example:

from fz.interpreter import replace_variables_in_content

content = "Server: ${host~localhost}:${port~8080}"
input_variables = {"host": "example.com"}  # port not provided

result = replace_variables_in_content(content, input_variables)
# Result: "Server: example.com:8080"
# Warning: Variable 'port' not found in input_variables, using default value: '8080'

Use cases:

Configuration templates with sensible defaults
Environment-specific deployments
Optional parameters in parametric studies

See examples/variable_substitution.md for comprehensive documentation.

Old Funz Syntax Compatibility

For backward compatibility with legacy Java Funz users, FZ supports the old ?var variable syntax:

# Legacy Funz syntax (still supported)
Temperature: ?T_celsius
Pressure: ?P_bar

# Equivalent modern FZ syntax
Temperature: $T_celsius
Pressure: $P_bar

Behavior:

?variable is automatically converted to $variable
No configuration needed - works transparently
Useful for migrating existing Funz projects to Python
Can mix both syntaxes in the same file

Example:

import fz

# Input file with old Funz syntax
content = """
n_mol=?n_mol
T_celsius=?T_celsius
"""

model = {"varprefix": "$"}  # Standard FZ configuration

# Works automatically - ?n_mol treated as $n_mol
variables = fz.fzi("input.txt", model)
# Returns: {'n_mol': None, 'T_celsius': None}

See examples/java_funz_syntax_example.py for more examples.

Features:

Python or R expression evaluation
Multi-line function definitions
Variable substitution in formulas
Default values for variables
Nested formula evaluation

Calculator Types

Local Shell Execution

Execute calculations locally:

# Basic shell command
calculators = "sh://bash script.sh"

# With multiple arguments
calculators = "sh://python calculate.py --verbose"

# Multiple calculators (tries in order, parallel execution)
calculators = [
    "sh://bash method1.sh",
    "sh://bash method2.sh",
    "sh://python method3.py"
]

How it works:

Input files copied to temporary directory
Command executed in that directory with input files as arguments
Outputs parsed from result directory
Temporary files cleaned up (preserved in DEBUG mode)

SSH Remote Execution

Execute calculations on remote servers:

# SSH with password
calculators = "ssh://user:password@server.com:22/bash /absolutepath/to/calc.sh"

# SSH with key-based auth (recommended)
calculators = "ssh://user@server.com/bash /absolutepath/to/calc.sh"

# SSH with custom port
calculators = "ssh://user@server.com:2222/bash /absolutepath/to/calc.sh"

Features:

Automatic file transfer (SFTP)
Remote execution with timeout
Result retrieval
SSH key-based or password authentication
Host key verification

Security:

Interactive host key acceptance
Warning for password-based auth
Environment variable for auto-accepting host keys: FZ_SSH_AUTO_ACCEPT_HOSTKEYS=1

SLURM Workload Manager

Execute calculations on SLURM clusters (local or remote):

# Local SLURM execution
calculators = "slurm://:compute/bash script.sh"

# Remote SLURM execution via SSH
calculators = "slurm://user@cluster.edu:gpu/bash script.sh"

# With custom SSH port
calculators = "slurm://user@cluster.edu:2222:gpu/bash script.sh"

# Multiple partitions for parallel execution
calculators = [
    "slurm://user@hpc.edu:compute/bash calc.sh",
    "slurm://user@hpc.edu:gpu/bash calc.sh"
]

URI Format: slurm://[user@host[:port]]:partition/script

Note: For local execution, the partition must be prefixed with a colon (:partition), e.g., slurm://:compute/script.sh

How it works:

Local execution: Uses srun --partition=<partition> <script> directly
Remote execution: Connects via SSH, transfers files, runs srun on remote cluster
Automatically handles SLURM partition scheduling
Supports interrupt handling (Ctrl+C terminates SLURM jobs)

Features:

Local or remote SLURM execution
Automatic file transfer for remote execution (via SFTP)
SLURM partition specification
Timeout and interrupt handling
Compatible with all SLURM schedulers

Requirements:

Local: SLURM installed (srun command available)
Remote: SSH access to SLURM cluster + paramiko library

Funz Server Execution

Execute calculations using the Funz server protocol (compatible with legacy Java Funz servers):

# Connect to local Funz server
calculators = "funz://:5555/R"

# Connect to remote Funz server
calculators = "funz://server.example.com:5555/Python"

# Multiple Funz servers for parallel execution
calculators = [
    "funz://:5555/R",
    "funz://:5556/R",
    "funz://:5557/R"
]

Features:

Compatible with legacy Java Funz calculator servers
Automatic file upload to server
Remote execution with the Funz protocol
Result download and extraction
Support for interrupt handling
UDP discovery for automatic server detection

UDP Discovery:

FZ supports automatic Funz server discovery via UDP broadcast:

from fz.runners import discover_funz_servers

# Discover all available Funz servers on the network
servers = discover_funz_servers(timeout=5)

# Returns list of discovered servers:
# [
#   {'host': '192.168.1.100', 'port': 5555, 'code': 'R'},
#   {'host': '192.168.1.101', 'port': 5555, 'code': 'Python'},
#   ...
# ]

# Use discovered servers
calculators = [f"funz://{s['host']}:{s['port']}/{s['code']}" for s in servers]
results = fz.fzr("input.txt", input_variables, model, calculators=calculators)

Discovery Protocol:

Broadcasts UDP message on port 19001
Servers respond with their host, port, and supported codes
Useful for dynamic calculator allocation in cluster environments
See doc/funz-protocol.md for detailed protocol documentation

Protocol:

Text-based TCP socket communication
Calculator reservation with authentication
Automatic cleanup and unreservation

URI Format: funz://[host]:<port>/<code>

host: Server hostname (default: localhost)
port: Server port (required)
code: Calculator code/model name (e.g., "R", "Python", "Modelica")

Example:

import fz

model = {
    "output": {
        "pressure": "grep 'pressure = ' output.txt | awk '{print $3}'"
    }
}

results = fz.fzr(
    "input.txt",
    {"temp": [100, 200, 300]},
    model,
    calculators="funz://:5555/R"
)

Cache Calculator

Reuse previous calculation results:

# Check single cache directory
calculators = "cache://previous_results"

# Check multiple cache locations
calculators = [
    "cache://run1",
    "cache://run2/results",
    "sh://bash calculate.sh"  # Fallback to actual calculation
]

# Use glob patterns
calculators = "cache://archive/*/results"

Cache Matching:

Based on MD5 hash of input files (.fz_hash)
Validates outputs are not None
Falls through to next calculator on miss
No recalculation if cache hit

Calculator Aliases

Store calculator configurations in .fz/calculators/:

.fz/calculators/cluster.json:

{
    "uri": "ssh://user@cluster.university.edu",
    "models": {
        "perfectgas": "bash /home/user/codes/perfectgas/run.sh",
        "navier-stokes": "bash /home/user/codes/cfd/run.sh"
    }
}

Use by name:

results = fz.fzr("input.txt", input_variables, "perfectgas", calculators="cluster")

Calculator-Model Compatibility

FZ automatically validates that calculators support the specified model to prevent incompatible combinations:

# .fz/calculators/cluster.json
{
    "uri": "ssh://user@cluster.edu",
    "models": {
        "perfectgas": "bash /path/to/perfectgas.sh",
        "cfd": "bash /path/to/cfd.sh"
    }
}

Validation:

# This works - perfectgas is supported
results = fz.fzr("input.txt", input_variables, "perfectgas", calculators="cluster")

# This fails with clear error - unsupported_model not in calculator's models
results = fz.fzr("input.txt", input_variables, "unsupported_model", calculators="cluster")
# Error: Calculator 'cluster' does not support model 'unsupported_model'
#        Supported models: perfectgas, cfd

Automatic Resolution:

Model and calculator aliases are resolved from .fz/ directories
Compatibility check happens before execution
Clear error messages indicate which models are supported
Prevents wasted computation on incompatible setups

Direct URIs (No Validation):

When using direct calculator URIs (not aliases), no validation occurs:

# No validation - you're responsible for compatibility
results = fz.fzr(
    "input.txt",
    input_variables,
    "anymodel",
    calculators="sh://bash any_script.sh"
)

Best Practice:

Use calculator aliases for complex setups
Document model compatibility in calculator JSON files
Use fzl --check to validate configurations

Advanced Features

Parallel Execution

FZ automatically parallelizes when you have multiple cases and calculators:

# Sequential: 1 calculator, 10 cases → runs one at a time
results = fz.fzr(
    "input.txt",
    {"temp": list(range(10))},
    model,
    calculators="sh://bash calc.sh"
)

# Parallel: 3 calculators, 10 cases → 3 concurrent
results = fz.fzr(
    "input.txt",
    {"temp": list(range(10))},
    model,
    calculators=[
        "sh://bash calc.sh",
        "sh://bash calc.sh",
        "sh://bash calc.sh"
    ]
)

# Control parallelism with environment variable
import os
os.environ['FZ_MAX_WORKERS'] = '4'

# Or use duplicate calculator URIs
calculators = ["sh://bash calc.sh"] * 4  # 4 parallel workers

Load Balancing:

Round-robin distribution of cases to calculators
Thread-safe calculator locking
Automatic retry on failures
Progress tracking with ETA

Retry Mechanism

Automatic retry on calculation failures:

import os
os.environ['FZ_MAX_RETRIES'] = '3'  # Try each case up to 3 times

results = fz.fzr(
    "input.txt",
    input_variables,
    model,
    calculators=[
        "sh://unreliable_calc.sh",  # Might fail
        "sh://backup_calc.sh"        # Backup method
    ]
)

Retry Strategy:

Try first available calculator
On failure, try next calculator
Repeat up to FZ_MAX_RETRIES times
Report all attempts in logs

Caching Strategy

Intelligent result reuse:

# First run
results1 = fz.fzr(
    "input.txt",
    {"temp": [10, 20, 30]},
    model,
    calculators="sh://expensive_calc.sh",
    results_dir="run1"
)

# Add more cases - reuse previous results
results2 = fz.fzr(
    "input.txt",
    {"temp": [10, 20, 30, 40, 50]},  # 2 new cases
    model,
    calculators=[
        "cache://run1",              # Check cache first
        "sh://expensive_calc.sh"     # Only run new cases
    ],
    results_dir="run2"
)
# Only runs calculations for temp=40 and temp=50

Output Type Casting

Automatic type conversion:

model = {
    "output": {
        "scalar_int": "echo 42",
        "scalar_float": "echo 3.14159",
        "array": "echo '[1, 2, 3, 4, 5]'",
        "single_array": "echo '[42]'",  # → 42 (simplified)
        "json_object": "echo '{\"key\": \"value\"}'",
        "string": "echo 'hello world'"
    }
}

results = fz.fzo("output_dir", model)
# Values automatically cast to int, float, list, dict, or str

Casting Rules:

Try JSON parsing
Try Python literal evaluation
Try numeric conversion (int/float)
Keep as string
Single-element arrays → scalar

Progress Callbacks

Monitor execution progress in real-time with custom callback functions:

import fz

model = {
    "varprefix": "$",
    "output": {"result": "cat output.txt"}
}

# Define callback function
def progress_callback(event_type, case_info):
    """
    Called during execution for each case event.

    Args:
        event_type: One of "case_start", "case_complete", "case_failed"
        case_info: Dict with case details (case_name, calculator, etc.)
    """
    if event_type == "case_start":
        print(f"⏳ Starting: {case_info['case_name']}")
    elif event_type == "case_complete":
        print(f"✅ Completed: {case_info['case_name']}")
    elif event_type == "case_failed":
        print(f"❌ Failed: {case_info['case_name']} - {case_info.get('error', 'Unknown error')}")

# Run with callback
results = fz.fzr(
    "input.txt",
    {"param": [1, 2, 3, 4, 5]},
    model,
    calculators="sh://bash calc.sh",
    results_dir="results",
    callbacks=[progress_callback]
)

Use Cases:

Custom progress bars
Real-time logging and monitoring
Integration with external monitoring systems
UI updates for long-running calculations
Performance profiling

Multiple Callbacks:

def logger_callback(event_type, case_info):
    # Log to file
    with open("execution.log", "a") as f:
        f.write(f"{event_type}: {case_info}\n")

def metrics_callback(event_type, case_info):
    # Send to monitoring system
    send_to_prometheus(event_type, case_info)

results = fz.fzr(..., callbacks=[logger_callback, metrics_callback])

Complete Examples

Interactive Jupyter Notebooks

Explore fz features hands-on with these notebooks — open directly in Google Colab, no local install needed:

Notebook	Topic	Colab
01 Getting Started	fzl, fzi, fzc, fzo, fzr — Perfect Gas PV=nRT
02 Variable Syntax & Formulas	All syntax styles, `@{}` formulas, `#@` context
03 Parametric Studies (fzr)	Grid inputs, DataFrame inputs, callbacks, parallel calculators
04 Design of Experiments (fzd)	Random sampling, Brent 1D minimization, BFGS 2D, Monte Carlo
05 Caching & Advanced	Cache reuse, multi-output, logging, coarse-to-fine DOE

Example 1: Perfect Gas Pressure Study

Input file (input.txt):

# input file for Perfect Gaz Pressure, with variables n_mol, T_celsius, V_L
n_mol=$n_mol
T_kelvin=@{$T_celsius + 273.15}
#@ def L_to_m3(L):
#@     return(L / 1000)
V_m3=@{L_to_m3($V_L)}

Calculation script (PerfectGazPressure.sh):

#!/bin/bash

# read input file
source $1

sleep 5 # simulate a calculation time

echo 'pressure = '`echo "scale=4;$n_mol*8.314*$T_kelvin/$V_m3" | bc` > output.txt

echo 'Done'

Python script (run_perfectgas.py):

import fz
import matplotlib.pyplot as plt

# Define model
model = {
    "varprefix": "$",
    "formulaprefix": "@",
    "delim": "{}",
    "commentline": "#",
    "output": {
        "pressure": "grep 'pressure = ' output.txt | awk '{print $3}'"
    }
}

# Parametric study
results = fz.fzr(
    "input.txt",
    {
        "n_mol": [1, 2, 3],
        "T_celsius": [10, 20, 30],
        "V_L": [5, 10]
    },
    model,
    calculators="sh://bash PerfectGazPressure.sh",
    results_dir="perfectgas_results"
)

print(results)

# Plot results: pressure vs temperature for different volumes
for volume in results['V_L'].unique():
    for n in results['n_mol'].unique():
        data = results[(results['V_L'] == volume) & (results['n_mol'] == n)]
        plt.plot(data['T_celsius'], data['pressure'],
                 marker='o', label=f'n={n} mol, V={volume} L')

plt.xlabel('Temperature (°C)')
plt.ylabel('Pressure (Pa)')
plt.title('Ideal Gas: Pressure vs Temperature')
plt.legend()
plt.grid(True)
plt.savefig('perfectgas_results.png')
print("Plot saved to perfectgas_results.png")

Example 2: Remote HPC Calculation

import fz

model = {
    "varprefix": "$",
    "output": {
        "energy": "grep 'Total Energy' output.log | awk '{print $4}'",
        "time": "grep 'CPU time' output.log | awk '{print $4}'"
    }
}

# Run on HPC cluster
results = fz.fzr(
    "simulation_input/",
    {
        "mesh_size": [100, 200, 400, 800],
        "timestep": [0.001, 0.01, 0.1],
        "iterations": 1000
    },
    model,
    calculators=[
        "cache://previous_runs/*",  # Check cache first
        "ssh://user@hpc.university.edu/sbatch /path/to/submit.sh"
    ],
    results_dir="hpc_results"
)

# Analyze convergence
import pandas as pd
summary = results.groupby('mesh_size').agg({
    'energy': ['mean', 'std'],
    'time': 'sum'
})
print(summary)

Example 3: Multi-Calculator with Failover

import fz

model = {
    "varprefix": "$",
    "output": {"result": "cat result.txt"}
}

results = fz.fzr(
    "input.txt",
    {"param": list(range(100))},
    model,
    calculators=[
        "cache://previous_results",           # 1. Check cache
        "sh://bash fast_but_unstable.sh",    # 2. Try fast method
        "sh://bash robust_method.sh",        # 3. Fallback to robust
        "ssh://user@server/bash remote.sh"   # 4. Last resort: remote
    ],
    results_dir="results"
)

# Check which calculator was used for each case
print(results[['param', 'calculator', 'status']].head(10))

Example 4: Design of Experiments with Adaptive Sampling

import fz
import matplotlib.pyplot as plt

# Input template with perfect gas law
# (same as Example 1, but using fzd for adaptive design)

model = {
    "varprefix": "$",
    "formulaprefix": "@",
    "delim": "{}",
    "commentline": "#",
    "output": {
        "pressure": "grep 'pressure = ' output.txt | awk '{print $3}'"
    }
}

# Run Monte Carlo sampling to explore pressure distribution
results = fz.fzd(
    input_path="input.txt",
    input_variables={
        "T_celsius": "[10;50]",  # Range: 10 to 50°C
        "V_L": "[1;10]",         # Range: 1 to 10 L
        "n_mol": "1.0"           # Fixed: 1 mole
    },
    model=model,
    output_expression="pressure",
    algorithm="examples/algorithms/montecarlo_uniform.py",
    calculators=["sh://bash PerfectGazPressure.sh"],
    algorithm_options={
        "batch_sample_size": 20,  # 20 samples per iteration
        "max_iterations": 10       # 10 iterations
    },
    analysis_dir="monte_carlo_results"
)

# Results DataFrame has all sampled points
print(f"Total evaluations: {results['total_evaluations']}")
print(f"Iterations: {results['iterations']}")
print(results['summary'])

# Access the data
df = results['XY']
print(df.head())

# Plot the sampled points
fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(12, 5))

# Scatter plot: Temperature vs Volume colored by Pressure
scatter = ax1.scatter(df['T_celsius'], df['V_L'], c=df['pressure'],
                      cmap='viridis', s=50, alpha=0.6)
ax1.set_xlabel('Temperature (°C)')
ax1.set_ylabel('Volume (L)')
ax1.set_title('Sampled Design Space')
plt.colorbar(scatter, ax=ax1, label='Pressure (Pa)')

# Histogram of pressure values
ax2.hist(df['pressure'], bins=20, edgecolor='black')
ax2.set_xlabel('Pressure (Pa)')
ax2.set_ylabel('Frequency')
ax2.set_title('Pressure Distribution')

plt.tight_layout()
plt.savefig('monte_carlo_analysis.png')
print("Analysis plot saved to monte_carlo_analysis.png")

Example 5: Optimization with BFGS

import fz

# Find temperature and volume that minimize pressure

model = {
    "varprefix": "$",
    "formulaprefix": "@",
    "delim": "{}",
    "commentline": "#",
    "output": {
        "pressure": "grep 'pressure = ' output.txt | awk '{print $3}'"
    }
}

results = fz.fzd(
    input_path="input.txt",
    input_variables={
        "T_celsius": "[10;50]",  # Search range
        "V_L": "[1;10]",         # Search range
        "n_mol": "1.0"           # Fixed
    },
    model=model,
    output_expression="pressure",
    algorithm="examples/algorithms/bfgs.py",
    calculators=["sh://bash PerfectGazPressure.sh"],
    algorithm_options={
        "minimize": True,        # Minimize pressure
        "max_iterations": 50
    },
    analysis_dir="optimization_results"
)

# Get optimal point
df = results['XY']
optimal_idx = df['pressure'].idxmin()
optimal = df.loc[optimal_idx]

print(f"Optimal temperature: {optimal['T_celsius']:.2f}°C")
print(f"Optimal volume: {optimal['V_L']:.2f} L")
print(f"Minimum pressure: {optimal['pressure']:.2f} Pa")
print(f"Total evaluations: {results['total_evaluations']}")

# Plot optimization path
import matplotlib.pyplot as plt
plt.figure(figsize=(10, 6))
plt.scatter(df['T_celsius'], df['V_L'], c=df['pressure'],
            cmap='coolwarm', s=100, edgecolor='black')
plt.plot(df['T_celsius'], df['V_L'], 'k--', alpha=0.3, label='Optimization path')
plt.scatter(optimal['T_celsius'], optimal['V_L'],
            color='red', s=300, marker='*',
            edgecolor='black', label='Optimum')
plt.xlabel('Temperature (°C)')
plt.ylabel('Volume (L)')
plt.title('BFGS Optimization Path')
plt.colorbar(label='Pressure (Pa)')
plt.legend()
plt.savefig('optimization_path.png')
print("Optimization path saved to optimization_path.png")

Writing Custom Algorithms for fzd

FZ provides an extensible framework for implementing adaptive algorithms. Each algorithm is a Python class with specific methods.

Algorithm Interface

Create a Python file with a class implementing these methods:

class MyAlgorithm:
    """Custom algorithm for design of experiments"""

    def __init__(self, **options):
        """
        Initialize algorithm with options passed from algorithm_options.

        Args:
            **options: Algorithm-specific parameters (e.g., batch_size, max_iter)
        """
        self.batch_size = options.get('batch_size', 10)
        self.max_iterations = options.get('max_iterations', 100)
        self.iteration = 0

    def get_initial_design(self, input_vars, output_vars):
        """
        Return initial design points to evaluate.

        Args:
            input_vars: Dict[str, tuple] - {var_name: (min, max)}
                       e.g., {"x": (0.0, 10.0), "y": (-5.0, 5.0)}
            output_vars: List[str] - Output variable names

        Returns:
            List[Dict[str, float]] - Initial points to evaluate
                                    e.g., [{"x": 0.5, "y": 0.0}, {"x": 7.5, "y": 2.3}]
        """
        # Generate initial sample points
        import random
        points = []
        for _ in range(self.batch_size):
            point = {
                var: random.uniform(bounds[0], bounds[1])
                for var, bounds in input_vars.items()
            }
            points.append(point)
        return points

    def get_next_design(self, previous_input_vars, previous_output_values):
        """
        Return next design points based on previous results.

        Args:
            previous_input_vars: List[Dict[str, float]] - All previous input combinations
            previous_output_values: List[float] - Corresponding outputs (may contain None)

        Returns:
            List[Dict[str, float]] - Next points to evaluate
                                    Empty list [] signals algorithm is finished
        """
        self.iteration += 1

        # Stop if max iterations reached
        if self.iteration >= self.max_iterations:
            return []  # Empty list = finished

        # Generate next batch based on results
        # ... your adaptive logic here ...

        return next_points

    def get_analysis(self, input_vars, output_values):
        """
        Return final analysis results.

        Args:
            input_vars: List[Dict[str, float]] - All evaluated inputs
            output_values: List[float] - All outputs (may contain None)

        Returns:
            Dict with analysis information (can include 'text', 'data', etc.)
        """
        # Filter out failed evaluations (None values)
        valid_results = [(x, y) for x, y in zip(input_vars, output_values) if y is not None]

        return {
            'text': f"Algorithm completed: {len(valid_results)} successful evaluations",
            'data': {'mean': sum(y for _, y in valid_results) / len(valid_results)}
        }

    def get_analysis_tmp(self, input_vars, output_values):
        """
        [OPTIONAL] Return intermediate results at each iteration.

        Args:
            input_vars: List[Dict[str, float]] - All inputs so far
            output_values: List[float] - All outputs so far

        Returns:
            Dict with intermediate analysis information
        """
        valid_count = sum(1 for y in output_values if y is not None)
        return {
            'text': f"Iteration {self.iteration}: {valid_count} valid samples"
        }

Algorithm Examples

1. Monte Carlo Sampling

See examples/algorithms/montecarlo_uniform.py:

import fz

results = fz.fzd(
    input_path="input.txt",
    input_variables={"x": "[0;10]", "y": "[0;5]"},
    model="mymodel",
    output_expression="result",
    algorithm="examples/algorithms/montecarlo_uniform.py",
    calculators=["sh://bash calc.sh"],
    algorithm_options={"batch_sample_size": 20, "max_iterations": 10}
)

2. BFGS Optimization

See examples/algorithms/bfgs.py (requires scipy):

results = fz.fzd(
    input_path="input.txt",
    input_variables={"x": "[0;10]", "y": "[0;5]"},
    model="mymodel",
    output_expression="energy",
    algorithm="examples/algorithms/bfgs.py",
    calculators=["sh://bash calc.sh"],
    algorithm_options={"minimize": True, "max_iterations": 50}
)

3. Brent's Method (1D Optimization)

See examples/algorithms/brent.py (requires scipy):

results = fz.fzd(
    input_path="input.txt",
    input_variables={"temperature": "[0;100]"},  # Single variable
    model="mymodel",
    output_expression="efficiency",
    algorithm="examples/algorithms/brent.py",
    calculators=["sh://bash calc.sh"],
    algorithm_options={"minimize": False}  # Maximize efficiency
)

Algorithm Features

Content Format Detection

Algorithms can return analysis results in multiple formats:

def get_analysis(self, input_vars, output_values):
    # Return HTML
    return {
        'text': '<html><body><h1>Results</h1><p>Mean: 42.5</p></body></html>',
        'data': {'mean': 42.5}
    }
    # Saved to: analysis_<iteration>.html

    # Return JSON
    return {
        'text': '{"mean": 42.5, "std": 3.2}',
        'data': {}
    }
    # Saved to: analysis_<iteration>.json

    # Return Markdown
    return {
        'text': '# Results\n\n**Mean**: 42.5\n**Std**: 3.2',
        'data': {}
    }
    # Saved to: analysis_<iteration>.md

    # Return key-value format
    return {
        'text': 'mean=42.5\nstd=3.2\nsamples=100',
        'data': {}
    }
    # Saved to: analysis_<iteration>.txt

See docs/FZD_CONTENT_FORMATS.md for detailed format documentation.

Dependency Management

Specify required packages using __require__:

__require__ = ["numpy", "scipy", "matplotlib"]

class MyAlgorithm:
    def __init__(self, **options):
        import numpy as np
        import scipy.optimize
        # ...

FZ will check dependencies at load time and warn if packages are missing.

Configuration

Environment Variables

# Logging level (DEBUG, INFO, WARNING, ERROR)
export FZ_LOG_LEVEL=INFO

# Maximum retry attempts per case
export FZ_MAX_RETRIES=5

# Thread pool size for parallel execution
export FZ_MAX_WORKERS=8

# SSH keepalive interval (seconds)
export FZ_SSH_KEEPALIVE=300

# Auto-accept SSH host keys (use with caution!)
export FZ_SSH_AUTO_ACCEPT_HOSTKEYS=0

# Default formula interpreter (python or R)
export FZ_INTERPRETER=python

# Custom shell binary search path (overrides system PATH)
# Windows example: SET FZ_SHELL_PATH=C:\msys64\usr\bin;C:\Program Files\Git\usr\bin
# Linux/macOS example: export FZ_SHELL_PATH=/opt/custom/bin:/usr/local/bin
export FZ_SHELL_PATH=/usr/local/bin:/usr/bin

# Run timeout in seconds (default: 600 = 10 minutes)
export FZ_RUN_TIMEOUT=3600

Shell Path Configuration (FZ_SHELL_PATH)

The FZ_SHELL_PATH environment variable allows you to specify custom locations for shell binaries (grep, awk, sed, etc.) used in model output expressions and calculator commands. This is particularly important on Windows where Unix-like tools may be installed in non-standard locations.

Why use FZ_SHELL_PATH?

Windows compatibility: Locate tools in MSYS2, Git Bash, Cygwin, or WSL
Custom installations: Use specific versions of tools from custom directories
Priority control: Override system PATH to ensure correct tool versions
Performance: Cached binary paths for faster resolution

Usage examples:

# Windows with MSYS2 (use semicolon separator)
SET FZ_SHELL_PATH=C:\msys64\usr\bin;C:\msys64\mingw64\bin

# Windows with Git Bash
SET FZ_SHELL_PATH=C:\Program Files\Git\usr\bin;C:\Program Files\Git\bin

# Linux/macOS (use colon separator)
export FZ_SHELL_PATH=/opt/homebrew/bin:/usr/local/bin

# Priority: FZ_SHELL_PATH paths are checked BEFORE system PATH

How it works:

Commands in model output dictionaries are parsed for binary names (grep, awk, etc.)
Binary names are resolved to absolute paths using FZ_SHELL_PATH
Commands in sh:// calculators are similarly resolved
Windows: Automatically tries both command and command.exe
Resolved paths are cached for performance

Example in model:

model = {
    "output": {
        "pressure": "grep 'pressure' output.txt | awk '{print $2}'"
    }
}
# With FZ_SHELL_PATH=C:\msys64\usr\bin, executes:
# C:\msys64\usr\bin\grep.exe 'pressure' output.txt | C:\msys64\usr\bin\awk.exe '{print $2}'

See doc/shell-path.md and examples/shell_path_example.md for detailed documentation.

Timeout Configuration

FZ provides flexible timeout settings at multiple levels for controlling calculation execution time:

1. Environment Variable (Global Default)

# Set default timeout for all calculations (in seconds)
export FZ_RUN_TIMEOUT=3600  # 1 hour (default: 600 seconds = 10 minutes)

2. Model Configuration (Per-Model)

model = {
    "varprefix": "$",
    "output": {"result": "cat output.txt"},
    "timeout": 1800  # 30 minutes for this model
}

results = fz.fzr("input.txt", input_variables, model, calculators="sh://calc.sh")

3. Calculator URI Parameter (Per-Calculator)

# Set timeout directly in calculator URI
calculators = [
    "sh://bash quick_calc.sh?timeout=300",      # 5 minutes
    "sh://bash slow_calc.sh?timeout=7200",       # 2 hours
    "ssh://user@hpc.edu/sbatch job.sh?timeout=86400"  # 24 hours
]

results = fz.fzr("input.txt", input_variables, model, calculators=calculators)

Priority Order (highest to lowest)

Calculator URI parameter (?timeout=300)
Model configuration (model["timeout"])
Environment variable (FZ_RUN_TIMEOUT)
Default (600 seconds = 10 minutes)

Example combining multiple levels:

import os

# Global default: 1 hour
os.environ['FZ_RUN_TIMEOUT'] = '3600'

# Model-specific: 30 minutes
model = {
    "timeout": 1800,
    "output": {"result": "cat output.txt"}
}

# Override for specific calculator: 2 hours
calculators = [
    "cache://previous_results",
    "sh://bash calc.sh?timeout=7200",  # Uses 2 hours (URI overrides)
    "sh://bash calc.sh"                 # Uses 30 minutes (model timeout)
]

results = fz.fzr("input.txt", input_variables, model, calculators=calculators)

Timeout Behavior:

Calculation terminates after timeout expires
Marked as "failed" with timeout error
Retry mechanism may attempt with next calculator
Partial results preserved for debugging

Python Configuration

from fz import get_config

# Get current config
config = get_config()
print(f"Max retries: {config.max_retries}")
print(f"Max workers: {config.max_workers}")

# Modify configuration
config.max_retries = 10
config.max_workers = 4

Directory Structure

FZ uses the following directory structure:

your_project/
├── input.txt                 # Your input template
├── calculate.sh              # Your calculation script
├── run_study.py             # Your Python script
├── .fz/                     # FZ configuration (optional)
│   ├── models/              # Model aliases
│   │   └── mymodel.json
│   ├── calculators/         # Calculator aliases
│   │   └── mycluster.json
│   ├── algorithms/          # Algorithm plugins
│   │   ├── myalgo.py
│   │   └── myalgo.R
│   └── tmp/                 # Temporary files (auto-created)
│       └── fz_temp_*/       # Per-run temp directories
└── results/                 # Results directory
    ├── case1/               # One directory per case
    │   ├── input.txt        # Compiled input
    │   ├── output.txt       # Calculation output
    │   ├── log.txt          # Execution metadata
    │   ├── out.txt          # Standard output
    │   ├── err.txt          # Standard error
    │   └── .fz_hash         # File checksums (for caching)
    └── case2/
        └── ...

Installing Plugins

FZ supports installing models and algorithms as plugins from GitHub repositories, local zip files, or URLs.

Installing Algorithm Plugins

Algorithm plugins enable design of experiments and optimization workflows. Install algorithms from GitHub repositories in the fz-<algorithm> format:

From GitHub Repository Name

# Install from Funz organization (convention: fz-<algorithm>)
fz install algorithm montecarlo

# This installs from: https://github.com/Funz/fz-montecarlo

# Python API
import fz

# Install locally (.fz/algorithms/)
fz.install_algorithm("montecarlo")

# Install globally (~/.fz/algorithms/)
fz.install_algorithm("montecarlo", global_install=True)

From GitHub URL

# Install from full URL
fz install algorithm https://github.com/YourOrg/fz-custom-algo

fz.install_algorithm("https://github.com/YourOrg/fz-custom-algo")

From Local Zip File

# Install from downloaded zip
fz install algorithm ./fz-myalgo.zip

fz.install_algorithm("./fz-myalgo.zip")

Using Installed Algorithms

Once installed, algorithms can be referenced by name:

import fz

# Use installed algorithm plugin
results = fz.fzd(
    input_path="input.txt",
    input_variables={"x": "[0;10]", "y": "[-5;5]"},
    model="mymodel",
    output_expression="result",
    algorithm="montecarlo",  # Plugin name (no path or extension)
    calculators=["sh://bash calc.sh"],
    algorithm_options={"batch_sample_size": 20}
)

Installing Model Plugins

Model plugins define input parsing and output extraction patterns. Install models from GitHub:

From GitHub Repository Name

# Install from Funz organization (convention: fz-<model>)
fz install model moret

# This installs from: https://github.com/Funz/fz-moret

# Python API
import fz

# Install locally (.fz/models/)
fz.install("moret")

# Install globally (~/.fz/models/)
fz.install("moret", global_install=True)

From GitHub URL or Local Zip

fz install model https://github.com/Funz/fz-moret
fz install model ./fz-moret.zip

Listing Installed Plugins

# List installed algorithms
fz list algorithms

# List only global algorithms
fz list algorithms --global

# List installed models
fz list models

# List only global models
fz list models --global

# Python API
import fz

# List algorithms
algorithms = fz.list_algorithms()
for name, info in algorithms.items():
    print(f"{name} ({info['type']}) - {info['file']}")

# List models
models = fz.list_models()
for name, model in models.items():
    print(f"{name}: {model.get('id', 'N/A')}")

Uninstalling Plugins

# Uninstall algorithm
fz uninstall algorithm montecarlo

# Uninstall from global location
fz uninstall algorithm montecarlo --global

# Uninstall model
fz uninstall model moret

# Python API
import fz

# Uninstall algorithm
fz.uninstall_algorithm("montecarlo")

# Uninstall model
fz.uninstall("moret")

Plugin Priority

When the same plugin exists in multiple locations, FZ uses the following priority:

Project-level (.fz/algorithms/ or .fz/models/) - Highest priority
Global (~/.fz/algorithms/ or ~/.fz/models/) - Fallback

This allows project-specific customization while maintaining a personal library of reusable plugins.

Creating Algorithm Plugins

To create your own algorithm plugin repository (for sharing or distribution):

Create repository named fz-<algorithm> (e.g., fz-montecarlo)
Add algorithm file as <algorithm>.py or <algorithm>.R in repository root or .fz/algorithms/:

# montecarlo.py
class MonteCarlo:
    def __init__(self, **options):
        self.n_samples = options.get("n_samples", 100)

    def get_initial_design(self, input_vars, output_vars):
        import random
        samples = []
        for _ in range(self.n_samples):
            sample = {}
            for var, (min_val, max_val) in input_vars.items():
                sample[var] = random.uniform(min_val, max_val)
            samples.append(sample)
        return samples

    def get_next_design(self, X, Y):
        return []  # One-shot sampling

    def get_analysis(self, X, Y):
        valid_Y = [y for y in Y if y is not None]
        mean = sum(valid_Y) / len(valid_Y) if valid_Y else 0
        return {"text": f"Mean: {mean:.2f}", "data": {"mean": mean}}

Push to GitHub and share repository URL
Install using fz install algorithm <name> or fz install algorithm <url>

See examples/algorithms/PLUGIN_SYSTEM.md for complete documentation on the algorithm plugin system.

Interrupt Handling

FZ supports graceful interrupt handling for long-running calculations:

How to Interrupt

Press Ctrl+C during execution:

python run_study.py
# ... calculations running ...
# Press Ctrl+C
⚠️  Interrupt received (Ctrl+C). Gracefully shutting down...
⚠️  Press Ctrl+C again to force quit (not recommended)

What Happens

First Ctrl+C:
- Currently running calculations complete
- No new calculations start
- Partial results are saved
- Resources are cleaned up
- Signal handlers restored
Second Ctrl+C (not recommended):
- Immediate termination
- May leave resources in inconsistent state

Resuming After Interrupt

Use caching to resume from where you left off:

# First run (interrupted after 50/100 cases)
results1 = fz.fzr(
    "input.txt",
    {"param": list(range(100))},
    model,
    calculators="sh://bash calc.sh",
    results_dir="results"
)
print(f"Completed {len(results1)} cases before interrupt")

# Resume using cache
results2 = fz.fzr(
    "input.txt",
    {"param": list(range(100))},
    model,
    calculators=[
        "cache://results",      # Reuse completed cases
        "sh://bash calc.sh"     # Run remaining cases
    ],
    results_dir="results_resumed"
)
print(f"Total completed: {len(results2)} cases")

Example with Interrupt Handling

import fz
import signal
import sys

model = {
    "varprefix": "$",
    "output": {"result": "cat output.txt"}
}

def main():
    try:
        results = fz.fzr(
            "input.txt",
            {"param": list(range(1000))},  # Many cases
            model,
            calculators="sh://bash slow_calculation.sh",
            results_dir="results"
        )

        print(f"\n✅ Completed {len(results)} calculations")
        return results

    except KeyboardInterrupt:
        # This should rarely happen (graceful shutdown handles it)
        print("\n❌ Forcefully terminated")
        sys.exit(1)

if __name__ == "__main__":
    main()

Output File Structure

Each case creates a directory with complete execution metadata:

`log.txt` - Execution Metadata

Command: bash calculate.sh input.txt
Exit code: 0
Time start: 2024-03-15T10:30:45.123456
Time end: 2024-03-15T10:32:12.654321
Execution time: 87.531 seconds
User: john_doe
Hostname: compute-01
Operating system: Linux
Platform: Linux-5.15.0-x86_64
Working directory: /tmp/fz_temp_abc123/case1
Original directory: /home/john/project

`.fz_hash` - Input File Checksums

a1b2c3d4e5f6...  input.txt
f6e5d4c3b2a1...  config.dat

Used for cache matching.

Breaking Changes

Version 0.9.1

fzr Directory Structure Change

Previous behavior (< 0.9.1):

fzr created subdirectories only when multiple values were provided for variables
Single values resulted in flat directory structure

New behavior (>= 0.9.1):

fzr creates subdirectories in results_dir as long as any input_variable is provided
No subdirectories only when input_variables={} (empty dict)
More consistent and predictable behavior

Example:

import fz

model = {"output": {"result": "cat output.txt"}}

# Single value - OLD: flat directory, NEW: subdirectory
results = fz.fzr(
    "input.txt",
    {"temp": 25},  # Single value
    model,
    calculators="sh://bash calc.sh",
    results_dir="results"
)

# OLD (< 0.9.1):
#   results/input.txt, results/output.txt, ...
#
# NEW (>= 0.9.1):
#   results/temp=25/input.txt, results/temp=25/output.txt, ...

# Only flat when explicitly empty
results = fz.fzr(
    "input.txt",
    {},  # Empty - no variables
    model,
    calculators="sh://bash calc.sh",
    results_dir="results"
)
# Both versions: results/input.txt, results/output.txt, ... (flat)

Migration:

Update scripts expecting flat directory structure for single-value cases
Use path parsing from fzo to handle subdirectory names
Benefits: Better organization, consistent with parametric study expectations

Development

Running Tests

# Install development dependencies
pip install -e .[dev]

# Run all tests
python -m pytest tests/ -v

# Run specific test file
python -m pytest tests/test_examples_perfectgaz.py -v

# Run with debug output
FZ_LOG_LEVEL=DEBUG python -m pytest tests/test_parallel.py -v

# Run tests matching pattern
python -m pytest tests/ -k "parallel" -v

# Test interrupt handling
python -m pytest tests/test_interrupt_handling.py -v

# Run examples
python example_usage.py
python example_interrupt.py  # Interactive interrupt demo

Project Structure

fz/
├── fz/                          # Main package
│   ├── __init__.py              # Public API exports
│   ├── core.py                  # Core functions (fzi, fzc, fzo, fzr, fzd)
│   ├── interpreter.py           # Variable parsing, formula evaluation
│   ├── runners.py               # Calculation execution (sh, ssh, cache)
│   ├── helpers.py               # Parallel execution, retry logic
│   ├── io.py                    # File I/O, caching, hashing
│   ├── algorithms.py            # Algorithm framework for fzd
│   ├── shell.py                 # Shell utilities, binary path resolution
│   ├── logging.py               # Logging configuration
│   ├── cli.py                   # Command-line interface
│   └── config.py                # Configuration management
├── examples/                    # Example files
│   └── algorithms/              # Example algorithms for fzd
│       ├── montecarlo_uniform.py  # Monte Carlo sampling
│       ├── randomsampling.py      # Simple random sampling
│       ├── bfgs.py                # BFGS optimization
│       └── brent.py               # Brent's 1D optimization
├── tests/                       # Test suite
│   ├── test_parallel.py         # Parallel execution tests
│   ├── test_interrupt_handling.py  # Interrupt handling tests
│   ├── test_fzd.py              # Design of experiments tests
│   ├── test_examples_*.py       # Example-based tests
│   └── ...
├── docs/                        # Documentation
│   └── FZD_CONTENT_FORMATS.md  # fzd content format documentation
├── README.md                    # This file
└── setup.py                     # Package configuration

Testing Your Own Models

Create a test following this pattern:

import fz
import tempfile
from pathlib import Path

def test_my_model():
    # Create input
    with tempfile.TemporaryDirectory() as tmpdir:
        input_file = Path(tmpdir) / "input.txt"
        input_file.write_text("Parameter: $param\n")

        # Create calculator script
        calc_script = Path(tmpdir) / "calc.sh"
        calc_script.write_text("""#!/bin/bash
source $1
echo "result=$param" > output.txt
""")
        calc_script.chmod(0o755)

        # Define model
        model = {
            "varprefix": "$",
            "output": {
                "result": "grep 'result=' output.txt | cut -d= -f2"
            }
        }

        # Run test
        results = fz.fzr(
            str(input_file),
            {"param": [1, 2, 3]},
            model,
            calculators=f"sh://bash {calc_script}",
            results_dir=str(Path(tmpdir) / "results")
        )

        # Verify
        assert len(results) == 3
        assert list(results['result']) == [1, 2, 3]
        assert all(results['status'] == 'done')

        print("✅ Test passed!")

if __name__ == "__main__":
    test_my_model()

Troubleshooting

Common Issues

Problem: Calculations fail with "command not found"

# Solution: Use absolute paths in calculator URIs
calculators = "sh://bash /full/path/to/script.sh"

Problem: SSH calculations hang

# Solution: Increase timeout or check SSH connectivity
calculators = "ssh://user@host/bash script.sh"
# Test manually: ssh user@host "bash script.sh"

Problem: Cache not working

# Solution: Check .fz_hash files exist in cache directories
# Enable debug logging to see cache matching process
import os
os.environ['FZ_LOG_LEVEL'] = 'DEBUG'

Problem: Out of memory with many parallel cases

# Solution: Limit parallel workers
export FZ_MAX_WORKERS=2

Windows / Cross-Platform

Problem: Shell commands fail on Windows

# Solution: Install MSYS2 and set FZ_SHELL_PATH to point to its binaries
SET FZ_SHELL_PATH=C:\msys64\usr\bin;C:\msys64\mingw64\bin
# See examples/shell_path_example.md for details

Problem: Line ending issues on Windows

# Solution: Write input files with Unix line endings (newline='\n')
# FZ templates and shell scripts expect LF, not CRLF
with open("input.txt", "w", newline='\n') as f:
    f.write(content)

Problem: chmod has no effect on Windows

# This is expected — Windows does not support Unix file permissions.
# Shell scripts run via sh:// do not need chmod on Windows.

Debug Mode

Enable detailed logging:

import os
os.environ['FZ_LOG_LEVEL'] = 'DEBUG'

results = fz.fzr(...)  # Will show detailed execution logs

Debug output includes:

Calculator selection and locking
File operations
Command execution
Cache matching
Thread pool management
Temporary directory preservation

Performance Tips

Use caching: Reuse previous results when possible
Limit parallelism: Don't exceed your CPU/memory limits
Optimize calculators: Fast calculators first in the list
Batch similar cases: Group cases that use the same calculator
Use SSH keepalive: For long-running remote calculations
Clean old results: Remove old result directories to save disk space

License

BSD 3-Clause License. See LICENSE file for details.

Contributing

Contributions welcome! Please:

Fork the repository
Create a feature branch
Add tests for new features
Ensure all tests pass
Submit a pull request

Citation

If you use FZ in your research, please cite:

@software{fz,
  title = {FZ: Parametric Scientific Computing Framework},
  designers = {[Yann Richet]},
  authors = {[Claude Sonnet, Yann Richet]},
  year = {2025},
  url = {https://github.com/Funz/fz}
}

Using fz with AI Coding Agents

An Agent Skill is bundled in skills/fz/ to teach AI coding agents (Claude Code, and other agents supporting the skills format) the fz workflow: parameterizing input files, defining models, choosing calculators, and running parametric studies.

Easiest (Claude Code plugin) — install straight from Claude Code, no shell needed:

/plugin marketplace add Funz/fz
/plugin install fz@funz

The skill then loads automatically in every project, and updates with the marketplace.

Manual install — copy (or symlink) the skill into your project or user skills directory:

# Project-level (recommended): available to anyone working in the project
mkdir -p .claude/skills
cp -r /path/to/fz/skills/fz .claude/skills/

# Or user-level: available in all your projects
mkdir -p ~/.claude/skills
cp -r /path/to/fz/skills/fz ~/.claude/skills/

Then just ask the agent things like "wrap my simulation code with fz and run a parameter study over mesh_size and timestep" — the skill is loaded automatically when relevant.

The skill contains:

skills/fz/SKILL.md - Step-by-step workflow for wrapping a simulation code
skills/fz/reference.md - Condensed API/CLI reference, JSON schemas, environment variables
skills/fz/algorithm-wrapper.md - Interface for writing custom fzd algorithms

See skills/howto.md for a complete walkthrough with example prompts (parametric studies, SSH execution, cache reuse, optimization, headless usage).

Documentation

Main Documentation

README.md (this file) - Complete user guide with examples
NEWS.md - Release notes and changelog (version 0.9.1 and later)
doc/funz-protocol.md - Funz protocol and UDP discovery documentation
doc/shell-path.md - FZ_SHELL_PATH configuration details

Context Documentation

Modular documentation in the doc/ directory:

doc/INDEX.md - Documentation overview and navigation
doc/overview.md - High-level FZ concepts and design
doc/core-functions.md - API reference for fzi, fzc, fzo, fzr, fzl, fzd
doc/installing-models.md - Installing models and algorithms (fz install)
doc/calculators.md - Calculator types, URIs, and configuration
doc/model-definition.md - Model structure, aliases, and output parsing
doc/formulas-and-interpreters.md - Formula evaluation (Python/R)
doc/syntax-guide.md - Input template syntax reference
doc/parallel-and-caching.md - Performance optimization strategies
doc/quick-examples.md - Common usage patterns and snippets

Examples

Practical examples in the examples/ directory:

examples/examples.md - Overview of all examples
examples/fzd_example.md - Iterative design of experiments (fzd) examples
examples/dataframe_input.md - DataFrame input for non-factorial designs
examples/algorithm_options_example.md - Algorithm options format guide
examples/r_interpreter_example.md - R interpreter setup and usage
examples/shell_path_example.md - FZ_SHELL_PATH configuration examples
examples/java_funz_syntax_example.py - Legacy Funz syntax compatibility
examples/fzi_formulas_example.py - Formula evaluation examples
examples/fzi_static_objects_example.py - Static object handling

Test Examples

Working examples in test files:

tests/test_examples_*.py - Comprehensive integration tests
tests/test_parallel.py - Parallel execution examples
tests/test_interrupt_handling.py - Interrupt handling demonstrations
tests/test_funz_protocol.py - Funz server protocol examples
tests/test_slurm_runner.py - SLURM workload manager examples

Support

Issues: https://github.com/Funz/fz/issues
Documentation: https://fz.github.io
Repository: https://github.com/Funz/fz

Project details

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Jun 15, 2026

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Apr 29, 2026

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funz-fz 1.1

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Project description

FZ - Parametric Scientific Computing Framework

Table of Contents

Features

Core Capabilities

Six Core Functions

Installation

Using pip

Using pipx (recommended for CLI tools)

From Source

Dependencies

Quick Start

1. Create an Input Template

2. Create a Calculation Script

3. Run Parametric Study

CLI Usage

Installation of CLI Tools

fzi - Parse Input Variables

fzc - Compile Input Files

fzo - Read Output Files

fzl - List and Validate Models/Calculators

fzr - Run Parametric Calculations

fzd - Design of Experiments

fz install / uninstall

CLI Options Reference

Common Options (all commands)

Exit Codes and Output Streams

Argument Formats

Model Definition Options

fzr-Specific Options

Complete CLI Examples

Example 1: Quick Variable Discovery

Example 2: Quick Compilation Test

Example 3: Parse Existing Results

Example 4: End-to-End Parametric Study

Example 5: Using Model and Calculator Aliases

Example 6: Interrupt and Resume

fzd - Run Design of Experiments

Environment Variables for CLI

Core Functions

fzi - Parse Input Variables

fzc - Compile Input Files

fzo - Read Output Files

fzr - Run Parametric Calculations

fzd - Run Design of Experiments

Input Variables: Factorial vs Non-Factorial Designs

Factorial Design (Dict)

Non-Factorial Design (DataFrame)

Model Definition

Model Aliases

Formula Evaluation

Python Interpreter (Default)

R Interpreter

Variable Default Values

Old Funz Syntax Compatibility

Calculator Types

Local Shell Execution

SSH Remote Execution

SLURM Workload Manager

Funz Server Execution

Cache Calculator

Calculator Aliases

Calculator-Model Compatibility

Advanced Features

Parallel Execution

Retry Mechanism

Caching Strategy

Output Type Casting

Progress Callbacks

Complete Examples

Interactive Jupyter Notebooks

`log.txt` - Execution Metadata

`.fz_hash` - Input File Checksums