Coding guidelines and code review checklist

This document is for anyone who want to contribute code to the khmer project, and describes our coding standards and code review checklist.

Coding standards

All plain-text files should have line widths of 80 characters or less unless that is not supported for the particular file format.

For C++, we use Todd Hoff's coding standard, and astyle -A10 / "One True Brace Style" indentation and bracing. Note: @CTB needs Emacs settings that work for this.

Vim users may want to set the ARTISTIC_STYLE_OPTIONS shell variable to "-A10 --max-code-length=80" and run `:%!astyle` to reformat. The four space indentation can be set with:

set expandtab
set shiftwidth=4
set softtabstop=4

For Python, PEP 8 is our standard. The `pep8` and `autopep8` Makefile targets are helpful.

Code, scripts, and documentation must have its spelling checked. Vim users can run:

:setlocal spell spelllang=en_us

Use ]s and [s to navigate between misspellings and z= to suggest a correctly spelled word. zg will add a word as a good word.

GNU aspell can also be used to check the spelling in a single file:

aspell check --mode ccpp $filename


Copy and paste the following into a pull request comment when it is ready for review:

- [ ] Is it mergeable?
- [ ] Did it pass the tests?
- [ ] If it introduces new functionality in scripts/ is it tested?
  Check for code coverage with `make clean diff-cover`
- [ ] Is it well formatted? Look at `make pep8`, `make diff_pylint_report`,
  `make cppcheck`, and `make doc` output. Use `make format` and manual
  fixing as needed.
- [ ] Did it change the command-line interface? Only additions are allowed
  without a major version increment. Changing file formats also requires a
  major version number increment.
- [ ] Is it documented in the ChangeLog?
- [ ] Was a spellchecker run on the source code and documentation after
  changes were made?
- [ ] Is the Copyright year up to date?

Note that after you submit the comment you can check and uncheck the individual boxes on the formatted comment; no need to put x or y in the middle.

CPython Checklist

Here's a checklist for new CPython types with future-proofing for Python 3:

- [ ] the CPython object name is of the form `khmer_${OBJECTNAME}_Object`
- [ ] Named struct with `PyObject_HEAD` macro
- [ ] `static PyTypeObject khmer_${OBJECTNAME}_Type` with the following
   - [ ] `PyVarObject_HEAD_INIT(NULL, 0)` as the object init (this includes
     the `ob_size` field).
   - [ ] all fields should have their name in a comment for readability
   - [ ] The `tp_name` filed is a dotted name with both the module name and
     the name of the type within the module. Example: `khmer.ReadAligner`
   - [ ] Deallocator defined and cast to `(destructor)` in tp_dealloc
     - [ ] The object's deallocator must be
   - [ ] Do _not_ define a `tp_getattr`
   - [ ] BONUS: write methods to present the state of the object via
     `tp_str` & `tp_repr`
   - [ ] _Do_ pass in the array of methods in `tp_methods`
   - [ ] _Do_ define a new method in `tp_new`
- [ ] PyMethodDef arrays contain doc strings
   - [ ] Methods are cast to `PyCFunctions`s
- [ ] Type methods use their type Object in the method signature.
- [ ] Type creation method decrements the reference to self
  (`Py_DECREF(self);`) before each error-path exit (`return NULL;`)
- [ ] No factory methods. Example: `khmer_new_readaligner`
- [ ] Type object is passed to `PyType_Ready` and its return code is checked
  in `init_khmer()`
- [ ] The reference count for the type object is incremented before adding
  it to the module: `Py_INCREF(&khmer_${OBJECTNAME}_Type);`.
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