Release v0.7.2 - SampleTab format support

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 is a minor update to 0.7.0 to fix containerisation issue reported in phnmnl/container-mtblisa#1

Release v0.7.0 - SampleTab format support

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

Release v0.6.2 - Enhanced ISA-Tab r/w performance and more

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.

Release v0.6.0 - Enhanced ISA-Tab r/w performance and more

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

Release v0.5.0 - Performance enhancements

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 theisatab.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

Release v0.4.0 - Creation of ISA content and enhancements

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

Release v0.3.6 - New SRA exporter, DB importers

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.

Release v0.3.5 - New SRA exporter, DB importers

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 third minor update that fixes ISA-Tab validator issues reported in #162 and #163.

Release v0.3.4 - New SRA exporter, DB importers

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 second minor update that fixes the SRA XML submission issues to ENA reported in #158.

Release v0.3.3 - New SRA exporter, DB importers

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 the SRA XML submission issues to ENA reported in #158.