Scientific software engineering with a simple ODE model as example

Contents:

• Scientific software engineering with a simple ODE model as example
• Sample problem and code
  • Mathematical problem
  • Implementation (1)
• User interfaces
  • Creating command-line interfaces
    • Reading a sequence of command-line arguments
    • Working with an argument parser
  • Creating a graphical web user interface
    • Making a compute function
    • Generating the user interface
    • Running the web application
• Verification
  • Comparison with hand calculations
  • Test function
  • Comparison with an exact discrete solution
  • Computing convergence rates
    • Estimating \(r\)
    • Implementation (2)
    • Debugging via convergence rates
• Software engineering
  • Making a module
  • Prefixing imported functions by the module name
  • Doctests
  • Unit testing with nose
    • Basic use of nose
    • Alternative assert statements
    • Applying nose
    • Installation of nose
    • Using nose to test modules with doctests
  • Classical class-based unit testing
    • Basic use of unittest
    • Demonstration of unittest
  • Implementing simple problem and solver classes
    • The problem class (1)
    • The solver class (1)
    • The visualizer class (1)
    • Combining the objects
  • Improving the problem and solver classes
    • A generic class for parameters
    • The problem class (2)
    • The solver class (2)
    • The visualizer class (2)
• Performing scientific experiments
  • Software
  • Combining plot files
  • Interpreting output from other programs
  • Making a report
    • Plain HTML
    • HTML with MathJax
    • LaTeX
    • Sphinx
    • Markdown
    • Wiki formats
    • DocOnce
    • Worked example
  • Publishing a complete project
• Exercises
  • Exercise 1: Refactor a flat program in terms of a function
    • Remarks
  • Exercise 2: Compare methods for a given time mesh
  • Problem 3: Write a doctest
  • Problem 4: Write a nose test
  • Problem 5: Make a module
  • Exercise 6: Make use of a class implementation
  • Exercise 7: Generalize a class implementation
  • Exercise 8: Generalize an advanced class implementation
• Bibliography

Indices and tables

• Index
• Module Index
• Search Page