Isatools

This release of `isatools` implements new SampleTab format read/write capability, including import and export between SampleTab and ISA formats (ISA-Tab and ISA-JSON).

* SampleTab import to ISA 190
* SampleTab export from ISA 120
* Support for command-line calls to SampleTab converters 182
* Fixes ISA-Tab r/w for NMR 187
* Fixes issues 154, 199, 200, 201, 202

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

This release of isatools focuses on further performance enhancements to the existing API functionality, in particular the ISA-Tab r/w, and a range of new features:

- Performance enhancements to ISA-Tab read and write 184
- New feature to load and dump only Investigation file of ISA-Tab 185
- New feature to export ISArchive zip from ISA content 180
- New feature to search Ontology Lookup Service and return OntologyAnnotation object 1
- New feature to search Entrez for publications and return Publication object 157
- New feature to merge Study and Assay table ISA-Tab files (of same assay type) 186
- Refactoring of example data and tests data to pull from centralised https://github.com/ISA-tools/ISAdatasets repository #78 183
- Bug fixes to ISA-Tab investigation file loading issues 196 197

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

This is a minor update to v0.6.0 that fixes ISA-Tab load issues reported in 199 and 202.

This release of `isatools` focuses on further performance enhancements to the existing API functionality, in particular the ISA-Tab r/w, and a range of new features:
- Performance enhancements to ISA-Tab read and write 184
- New feature to load and dump only Investigation file of ISA-Tab 185
- New feature to export ISArchive zip from ISA content 180
- New feature to search Ontology Lookup Service and return OntologyAnnotation object 1
- New feature to search Entrez for publications and return Publication object 157
- New feature to merge Study and Assay table ISA-Tab files (of same assay type) 186
- Refactoring of example data and tests data to pull from centralised https://github.com/ISA-tools/ISAdatasets repository #78 183
- Bug fixes to ISA-Tab investigation file loading issues 196 197

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

This release of `isatools` focuses on implementing new performance enhancements to the existing API functionality:
- Bug fixes and minor enhancements in issues 147, 174 and 176
- Implementation of a wholesale replacement for the ISA-Tab parser, now found in the`isatab.load()` function, which loads ISA-Tab content into ISA model objects. This represents work towards harmonisation of the loading of ISA-Tab content into the same model as the ISA JSON loader, and a big improvement on loading performance (e.g. loading BII-I-1 test data down from 3.7s to 0.6s in tests using the `timeit` module) 168
- Implementation of a ISA JSON Encoder to write out ISA model objects to the ISA-JSON representation. This is implemented as the `ISAJSONEncoder` class that can be passed to the Python `json` package used to dump JSON.
- Integration of the new ISA-Tab loader and the new ISA JSON Encoder into the `isatab2json` converter 181
- Where the `isatab2json` is used elsewhere in the API, updates have been made to use the enhanced performance converter, where appropriate.

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

This release of `isatools` firms up ISA content creation with example code and added documentation; implemented a range of enhancements and bug fixes, including boosting test coverage from 55% to 73%. New features and enhancements include:
- A more complete user guide to creating ISA content using objects
- Validator reports generated as JSON
- Batch validation scripts
- Integration of the `mzml2isa` tool into the ISA API

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

This release of `isatools` implements new ISA to SRA exporters, and 4 data importers into ISA-Tab:
- ISA JSON to SRA export
- Replacement ISA-Tab to SRA export (legacy exporter still included while new exporter becomes stable)
- Importer for MetaboLights to ISA-Tab and ISA JSON
- Importer for MetabolomicsWorkbench to ISA-Tab
- Importer for Biocrates to ISA-Tab
- Importer for European Nucleotide Archive (SRA) to ISA-Tab

For more information on the known issues with this release, please check the documentation at http://isatools.readthedocs.org

This is a minor update that fixes ISA-Tab writer issue 172.