Scientific software engineering; ODE model

Contents:

• Scientific software engineering; ODE model
• Basic implementations
  • Mathematical problem and solution technique
  • A first, quick implementation
  • A more decent program
    • Comments
    • Refactoring into functions
    • Program file vs IDE vs notebook
  • Implementing the numerical algorithm in a function
  • Do not have several versions of a code
  • Making a module
  • Prefixing imported functions by the module name
  • Example on extending the module code
  • Documenting functions and modules
• User interfaces
  • Command-line arguments
  • Positional command-line arguments
  • Option-value pairs on the command line
  • Creating a graphical web user interface
    • Making a compute function
    • Generating the user interface
    • Running the web application
• Tests for verifying implementations
  • Doctests
  • Unit tests and test functions
    • Two Python test frameworks: nose and pytest
    • Test function requirements
    • Comparison of real numbers
    • Special assert functions from nose
    • Locating test functions
    • Running tests
    • Embedding doctests in a test function
    • Installing nose and pytest
  • Test function for the solver
  • Test function for reading positional command-line arguments
  • Test function for reading option-value pairs
  • Classical class-based unit testing
• Sharing the software with other users
  • Organizing the software directory tree
    • Distributing just a module file
    • Distributing a package
  • Publishing the software at GitHub
  • Downloading and installing the software
    • Installing just a module file
    • Installing a package
• Classes for problem and solution method
  • The problem class
  • The solver class
    • Combining the objects
  • Improving the problem and solver classes
    • A generic class for parameters
• Automating scientific experiments
  • Available software
  • Required new results
  • Combining plot files
  • Running a program from Python
  • The automating script
  • Making a report
    • Word, OpenOffice, GoogleDocs
    • HTML with MathJax
    • LaTeX
    • Sphinx
    • Markdown
    • IPython/Jupyter notebooks
    • Wiki formats
    • DocOnce
  • Publishing a complete project
• Exercises
  • Problem 1: Make a tool for differentiating curves
  • Problem 2: Make solid software for the Trapezoidal rule
  • Problem 3: Implement classes for the Trapezoidal rule
  • Problem 4: Write a doctest and a test function
  • Problem 5: Experiment with tolerances in comparisons
    • Remarks
  • Exercise 6: Make use of a class implementation
  • Exercise 7: Make solid software for a difference equation
• Bibliography

Indices and tables

• Index
• Module Index
• Search Page