v0.7.0

json2args

The json2args package can be used in docker container following the Tool specification.
Following these specifications, docker-based and reproducible scientifc tools or workflows can be implemented
upon a set of additional files inside the container. Minimal metadata is added via a tool.yml and the
parameterization and data specification is done via a input.json, mounted along with the data files into the container.

This package is a utility for Python based docker tools, that loads, parses and validates the input parameters.
Optionally, you can use the package to pre-load standard input files into the appropriate Python data strurctures.

from json2args import get_parameter, get_data

params = get_parameter()
iris_dataset = get_data('iris')  # optional

# usage
params['foo']   # can be a string 'bar'
iris_dataset    # This is a pandas.Dataframe, loaded from a standard CSV

What's Changed

• add the common logger by @mmaelicke in #17
• Update pypi-publish.yml by @mmaelicke in #20
• Typed by @mmaelicke in #19

Full Changelog: v0.6.2...v0.7.0

v0.6.0

json2args

The json2args package can be used in docker container following the Tool specification.
Following these specifications, docker-based and reproducible scientifc tools or workflows can be implemented
upon a set of additional files inside the container. Minimal metadata is added via a tool.yml and the
parameterization and data specification is done via a input.json, mounted along with the data files into the container.

This package is a utility for Python based docker tools, that loads, parses and validates the input parameters.
Optionally, you can use the package to pre-load standard input files into the appropriate Python data strurctures.

from json2args import get_parameter, get_data

params = get_parameter()
iris_dataset = get_data('iris')  # optional

# usage
params['foo']   # can be a string 'bar'
iris_dataset    # This is a pandas.Dataframe, loaded from a standard CSV

What's Changed

• Json tests by @mmaelicke in #12

Full Changelog: v0.5.3...v0.6.0

Version 0.5

Intermediate version as a starting point to implement the current state of the tool specifications.

Separates data from parameters, with two distinct functions to be used to load either the data from json config files, or pre-load the data from standard file formats.

Version 0.4

Renamed in/tool.json to in/parameters.json as this filename is more accurate.

Version 0.3

Now updated to .dat files

Version 0.2

Minor release with import bugfixes and deprecation warnings.
Now the package should actually work.

Full Changelog: v0.1.0...v0.2.0

Initial release

This is the initial release. It just contains the parameter.py imported from toolbox_runner as a standalone package.
The parse_parameter function has been deprecated in favor of get_parameter, which is as of this writing exactly the same function.