Using YAML tags and Python types with PyYAML.

[grabear]

(Note: This is mostly just a forum for discussing different ways of using these YAML tags to do work with various python modules. It makes it convenient to store Path-Like objects as well as with using the pkg_resources module.)

PyYaml Documentation

YAML tag	Python type
Standard YAML tags
!!null	None
!!bool	bool
!!int	int or long (int in Python 3)
!!float	float
!!binary	str (bytes in Python 3)
!!timestamp	datetime.datetime
!!omap, !!pairs	list of pairs
!!set	set
!!str	str or unicode (str in Python 3)
!!seq	list
!!map	dict
Python-specific tags
!!python/none	None
!!python/bool	bool
!!python/bytes	(bytes in Python 3)
!!python/str	str (str in Python 3)
!!python/unicode	unicode (str in Python 3)
!!python/int	int
!!python/long	long (int in Python 3)
!!python/float	float
!!python/complex	complex
!!python/list	list
!!python/tuple	tuple
!!python/dict	dict
Complex Python tags
!!python/name:module.name	module.name
!!python/module:package.module	package.module
!!python/object:module.cls	module.cls instance
!!python/object/new:module.cls	module.cls instance
!!python/object/apply:module.f	value of f(...)

Use Case Examples

Importing Data files

Python implementation

from pkg_resources import resource_filename
from Datasnakes.Manager.config import references
path = resource_filename(references.__name__, "Local_Reliability_Measures_from_Sets_of_Co-optimal_Multiple_Sequence_Alignments.pdf")

YAML implementation

path: '!!python/object/apply:pkg_resources.resource_filename [Datasnakes.Manager.config.references, "Local_Reliability_Measures_from_Sets_of_Co-optimal_Multiple_Sequence_Alignments.pdf"]'

Importing path-like objects

Python implementation

from pathlib import Path
NCBI_refseq_release = Path('NCBI/refseq/release') 

YAML implementation

NCBI_refseq_release: "!!python/object/apply:pathlib.Path ['NCBI/refseq/release']"

[grabear]

Currently doing this with #95.

[grabear]

This has been perfected in our workflows. Especially with the most recent PR #145