Chaining/graphing containers support

0.8

Biggest addition is helper code for chaining containers in a dependency graph, for example using Luigi.

full list:

• Add luigi support for chaining containers (#18)
• create temp files in work folder (#19)
• properly expose param_files path in paramaters file (#21)
• Small bug fixes

small fixes

• Run /kliko, not the default docker CMD
• Add simms example
• dont try to copy empty file field
• remove explicit pyyaml dependency

various improvements, schema increment

• Install docker by default
• Made container, author and email fields optional in specification
• Increased specification number (3)
• Don't put parameter files in /input but in /param_files
• Renamed char field type to str
• Add option to override paths using environment variables (INPUT, OUTPUT, WORK,
  PARAM_FILES, KLIKO_FILE, PARAM_FILE)
• Change behaviour of kliko-run, it now accepts the --input, --output, --work

small bug fix

solves problem if docker is not installed, which is not a forced dependency.

new entrypoint and CLI kliko runner

• Added a command line kliko image runner (kliko-run)
• Kliko entrypoint is now /kliko. This makes it easier to integrate kliko with existing containers
• parameters file is now consistently in /parameters.json.

all changes: 0.5...0.6

Add a CLI from kliko definition generator

and polished the docs.

all changes: 0.4...0.5

added doc and restucture

• Wrote much more doc
• small restructure of API
• Added kliko-validate.py script

small bug fix

fix setup if pykwalify is not installed.

0.3

• renamed /param_spec.yml to /kliko.yml
• added a parameter parser. This parser is generated from your kliko.yml file
• also parse the required field when generating django form
• Increased schema version to number 2
• Added IO type to schema (split or join)

add a extract_params() function, improve testing

• Add an extract_params() functions which will extract content from param_spec.yml from image
• improved testing
• fixing small bugs.