1. Developer Documentation

• 1.1. HORTON Development with Git
  • 1.1.1. Additional steps required to build the development version of HORTON
    • 1.1.1.1. Reference atoms
    • 1.1.1.2. Other development tools
    • 1.1.1.3. Building the documentation
  • 1.1.2. Git
    • 1.1.2.1. Git configuration
    • 1.1.2.2. Some terminology
    • 1.1.2.3. Cloning the HORTON git repository
  • 1.1.3. Work flow for adding a new feature
    • 1.1.3.1. Develop the feature in a topic branch
    • 1.1.3.2. Make your branch available for review with a pull request (PR)
    • 1.1.3.3. Merging your pull request with the master branch
  • 1.1.4. Common issues
• 1.2. Branch review checklist
  • 1.2.1. Reviewing protocol
    • 1.2.1.1. Step 1. Automatic QA testing
    • 1.2.1.2. Step 2. Human review
    • 1.2.1.3. Step 3. Merging
  • 1.2.2. Mindful criteria
    • 1.2.2.1. Atomic commits
    • 1.2.2.2. Unit tests (other than coverage, see below)
    • 1.2.2.3. Code structure
    • 1.2.2.4. Modularity
    • 1.2.2.5. Cython is evil
  • 1.2.3. General mindless criteria
    • 1.2.3.1. Miscellaneous (MG01##)
    • 1.2.3.2. Whitespace errors
    • 1.2.3.3. Comments (MG02##)
    • 1.2.3.4. Author name and e-mail (MG03##)
    • 1.2.3.5. Git commit message format (MG04##)
    • 1.2.3.6. Units and unit conversion
  • 1.2.4. Mindless Python criteria
    • 1.2.4.1. pycodestyle
    • 1.2.4.2. Pydocstyle
    • 1.2.4.3. PyLint
    • 1.2.4.4. Code coverage by (fast) unit tests
    • 1.2.4.5. Mindless Python criteria to be checked manually
  • 1.2.5. Mindless C++ criteria
    • 1.2.5.1. CPPCheck
    • 1.2.5.2. CPPLint
    • 1.2.5.3. Manual checks
    • 1.2.5.4. API documentation
    • 1.2.5.5. Code coverage
  • 1.2.6. Mindless Cython criteria
• 1.3. Writing documentation
  • 1.3.1. Introduction
  • 1.3.2. Building documentation
  • 1.3.3. Common issues
• 1.4. Writing unit tests
  • 1.4.1. Running the tests
  • 1.4.2. Writing new tests
  • 1.4.3. Writing tests that need a temporary directory
  • 1.4.4. Writing tests that use random numbers
• 1.5. Writing examples scripts
• 1.6. Citing scientific work
• 1.7. Accelerating HORTON code with Cython
  • 1.7.1. Before you begin
  • 1.7.2. Basic example
    • 1.7.2.1. Background
    • 1.7.2.2. Cythonizing your code
  • 1.7.3. Additional notes
  • 1.7.4. Further reading