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Release v0.12.0 - Release Candidate 2

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@Zigur Zigur released this 02 Feb 12:48
· 544 commits to master since this release
v0.12.0-rc.2
b8f2f55

Release v0.12.0 - Release Candidate

Features:

  • Added the isatools.create.connectors module. This module contains the generate_study_design_from_config function to generate an isatools.create.StudyDesign from a JSON configuration document containing metadata about the study design, including sampling and assay plan. These JSON documents can be generated by the Datascriptor application.(issues #355, #356, #377)
  • Added support for observational variables to isatools.create.model.StudyArm (with the parameter source_characteristics) (PR #367)
  • StudyDesign.generate_isa_study()now generates one Assay per assay type (via StudyDesign._generate_samples()). (issue #369, #373)
  • The names of the assay nodes (extract, labelled, extract, protocol node, and data file) (issue #370, #373)
  • isatools.create.model.ProductNode now has an attribute extension (e.g. a file extension fo a DataFile node) (issue #378)

Enhancements and Cleanup:

  • Introduced support for (built-in, non-configurable) synonyms in protocol types. Protocol types have also been made case insensitive. (issue #382)
  • Refactored constants and error messages for the create mode, introducing the modules isatools.create.constants and isatools.create.errors (issue #342, #368)
  • Removed asterisk imports (*) from all the core modules (issue #368)
  • Removed leftover print() statements (issue #374)
  • overall test coverage increased from 67% to 75%. The increase is due both to an increase in the number of tests and the removal of some deprecated, experimental or spurious modules.

Breaking changes:

  • isatools.create.models has been renamed to isatools.create.model (issue #368)
  • IsaModelAttributeError has been replaced with AttributeError. We will favour standard Exceptions whenever applicable.

Bug Fixes:

  • Fixed typo in NAME_PROPERTY_ASSIGNMENT_ERROR (issue #328)
  • Silent expansion of Characteristic categories from str to OntologyAnnotation now supported. You can assign a string to a characteristic category and it will be automatically wrapped into an ontology annotation. (issue #332)
  • Fixed duplicated in OntologyAnnotation ids (issue #381)
  • Fixed raising of an error when correctly setting a comment value (issue #360)
  • Assigned correct header "Data Transformation Name" for protocol type "sequence analysis data transformation"
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