Development miscellany
======================

Build framework
---------------

'make' should build everything, including tests and "development" code.

Coding standards
----------------

For C++, let's use `Todd Hoff's coding standard
<http://www.possibility.com/Cpp/CppCodingStandard.html>`__, and
`astyle -A10 / "One True Brace Style"
<http://astyle.sourceforge.net/astyle.html>`__ indentation and
bracing.  Note: we need to find vi and emacs settings that work for this!

For Python, `PEP 8 <http://www.python.org/dev/peps/pep-0008/>`__ seems
like a good standard to default to, and there are tools to check it,
too.

git and github strategies
-------------------------

Still in the works, but read `this
<http://scottchacon.com/2011/08/31/github-flow.html>`__.

Testing
-------

'nosetests' is the canonical way to run the tests.  This is what 'make test'
does.

Pipelines
---------

All khmer scripts used by a published recommended analysis pipeline must be
included in scripts/ and meet the standards therein implied.

Command line scripts
--------------------

Python command-line scripts should use '-' instead of '_' in the name.
(Only filenames containing code for import imported should use _.)

Please follow the command-line conventions used under scripts/.  This
includes most especially standardization of '-x' to be hash table size,
'-N' to be number of hash tables, and '-k' to always refer to the
k-mer size.

Command line thoughts:

   If a filename is required, typically UNIX commands don't use a flag to
   specify it.

   Also, positional arguments typically aren't used with multiple files.

   CTB's overall philosophy is that new files, with new names, should
   be created as the result of filtering etc.; this allows easy
   chaining of commands.  We're thinking about how best to allow
   override of this, e.g. ::

      filter-abund.py <kh file> <filename> [ -o <filename.keep> ]

----

All code in scripts/ must have automated tests; see tests/test_scripts.py.
Otherwise it belongs in sandbox/.

When files are overwritten, they should only be opened to be overwritten
after the input files have been shown to exist.  That prevents stupid
command like mistakes from trashing important files.

It would be nice to allow piping from one command to another where possible.
But this seems complicated.

CTB: should we squash output files (overwrite them if they exist), or not?
So far, leaning towards 'not', as that way no one is surprised and loses
their data.

----

CLI reading:

   http://stackoverflow.com/questions/1183876/what-are-the-best-practices-for-implementing-a-cli-tool-in-perl

   http://catb.org/esr/writings/taoup/html/ch11s06.html

   http://figshare.com/articles/tutorial_pdf/643388

Python / C integration
----------------------

The Python extension that wraps the C++ core of khmer lives in
khmer/_khmermodule.CC

This wrapper code is tedious and annoying so we use a static analysis tool to
check for correctness.

https://gcc-python-plugin.readthedocs.org/en/latest/cpychecker.html

Developers using Ubuntu Precise will want to install the gcc-4.6-plugin-dev package

Example usage:

  CC="/home/mcrusoe/src/gcc-plugin-python/gcc-python-plugin/gcc-with-cpychecker
--maxtrans=512" python setup.py build_ext 2>&1 | less

False positives abound: ignore errors about the C++ standard library. This tool
is primarily useful for reference count checking, error-handling checking, and
format string checking.

Errors to ignore: "Unhandled Python exception raised calling 'execute' method",
"AttributeError: 'NoneType' object has no attribute 'file'"

Warnings to address: 

"khmer/_khmermodule.cc:3109:1: note: this function is too complicated for the
reference-count checker to fully analyze: not all paths were analyze"

Adjust --maxtrans and re-run.

khmer/_khmermodule.cc:2191:61: warning: Mismatching type in call to
Py_BuildValue with format code "i" [enabled by default]
  argument 2 ("D.68937") had type
    "long long unsigned int"
  but was expecting
    "int"
  for format code "i"

See below for a format string cheatsheet One also benefits by matching C type
with the function signature used later. 

"I" for unsinged int
"K" for unsigned long long a.k.a khmer::HashIntoType.

Upstream sources
----------------

ez_setup.py is from https://bitbucket.org/pypa/setuptools/raw/bootstrap/

Before major releases it should be examined to see if there is a new version