Skip to content

Latest commit

 

History

History
121 lines (94 loc) · 5.2 KB

scripts-and-sandbox.rst

File metadata and controls

121 lines (94 loc) · 5.2 KB
Raw

Command line scripts, scripts/, and sandbox/

Note

This document applies through khmer/oxli 2.0/3.0 (see ../roadmap) - we will revisit when the Python API falls under semantic versioning for oxli 4.0.

khmer has two conflicting goals: first, we want to provide a reliable piece of software to our users; and second, we want to be flexible and enable exploration of new algorithms and programs. To this end, we've split our command line scripts across two directories, scripts/ and sandbox/. The former is the staid, boring, reliable code; the latter is a place for exploration.

As a result, we are committed to high test coverage, stringent code review, and Semantic Versioning for files in scripts/, but explicitly not committed to this for files and functionality implemented in sandbox/. So, putting a file into scripts/ is a big deal, especially since it increases our maintenance burden for the indefinite future.

We've roughed out the following process for moving scripts into scripts/:

  • Command line scripts start in sandbox/;
  • Once their utility is proven (in a paper, for example), we can propose to move them into scripts/;
  • There's a procedure for moving scripts from sandbox/ into scripts/.

Read on!

Sandbox script requirements and suggestions

All scripts in sandbox/ must:

  • be importable (enforced by test_import_all in test_sandbox_scripts.py)
  • be mentioned in sandbox/README.rst
  • have a hash-bang line (#! /usr/bin/env python) at the top
  • be command-line executable (chmod a+x)
  • have a Copyright message (see below)
  • have lowercase names
  • use '-' as a word separator, rather than '_' or CamelCase

All new scripts being added to sandbox/ should:

  • have decent automated tests
  • be used in a protocol (see khmer-protocols) or a recipe (see khmer-recipes)
  • be pep8 clean and pylint clean-ish (see make pep8 and make_diff_pylint).

Command line standard options for scripts/

All scripts in scripts/ should have the following options, if they could apply:

  • --version - should always apply
  • --help - should always apply
  • --force - override any sanity checks that may prevent the script from running
  • --loadtable and --savetable - where appropriate (see khmer_args.py)

Copyright message

Our current Copyright message is:

#
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) Michigan State University, 2009-2015. It is licensed under
# the three-clause BSD license; see doc/LICENSE.txt.
# Contact: khmer-project@idyll.org
#

The beginning year should be the first year that this file existed in the repo; the end year should be the last year a coding change was made in the file.

Upgrading a script from 'sandbox' to 'scripts'

First, everything needed (all library support code) should be already committed to khmer master after the usual review process; the relevant script(s) should be in sandbox/.

Second, an issue should be started explicitly to discuss whether the script(s) should be moved from sandbox/ into scripts/. This issue should discuss the general need for this script, outside of a particular paper pipeline. (Note that there is no imperative to move a script out of sandbox/; if we think it's useful code to have around and want to keep it functioning, we should just add in automated tests and otherwise level it up.)

Third, assuming we reach general agreement about moving the script(s) into scripts/, start a pull request to do so, referencing the issue and containing the following checklist. The PR should start by moving the script from sandbox/ into scripts/, and moving the tests out of the test_sandbox_scripts.py file.

Last but not least, intensive code review may raise more general issues that could apply to the entire code base; if contentious or needing discussion, these issues may be punted to general issues so as to not block a merge.

A checklist for moving a script into the scripts/ directory from sandbox/

Copy or paste this checklist into the PR, in addition to the normal development/PR checklist:

- [ ] most or all lines of code are covered by automated tests (see output of ``make diff-cover``)
- [ ] ``make diff_pylint`` is clean
- [ ] the script has been updated with a ``get_parser()`` and added to doc/user/scripts.txt
- [ ] argparse help text exists, with an epilog docstring, with examples and options
- [ ] standard command line options are implemented
- [ ] version and citation information is output to STDERR (`khmer_args.info(...)`)
- [ ] support '-' (STDIN) as an input file, if appropriate
- [ ] support designation of an output file (including STDOUT), if appropriate
- [ ] script reads and writes sequences in compressed format
- [ ] runtime diagnostic information (progress, etc.) is output to STDERR
- [ ] script has been removed from sandbox/README.rst