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CHANGELOG.rst

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Release History

1.2.5.post1 (2022-05-11)

Improvements

  • Add citation information to GitHub repository.

    • Adds CITATION.cff file with citation info.

1.2.5 (2022-03-18)

Improvements

  • Updates mwschema.py and validator.py modules to match Metabolomics Workbench's mwTab File Format

Specification Version 1.5 (March 2022).

  • Adds optional NMR_RESULTS_FILE field to NMR block.
  • Adds optional MS_COMMENTS field to MS block.
  • Removes requirement for there to be data results for every sample listed in the Study Design

(SUBJECT_SAMPLE_FACTORS). Allows for instances where samples have technical issues preventing data from being provided.

1.2.4 (2022-01-07)

Improvements

  • Adds check for blank source files when parsing to create mwtab objects.

1.2.3 (2021-11-02)

Bugfixes

  • Removes hard coding of version number in validator.validate_file() method.
  • Removes mention of Python 3.4 support in README.

1.2.2 (2021-10-22)

Improvements

  • Migrates Continuous Integration (CI) from Travis CI to GitHub Actions.

    • Adds .github/workflows/ folder which contains .yml files for workflows.

    • Changes build and codecov badges to match new sources.

1.2.1 (2021-09-03)

Improvements

  • Updates format of ~mwtab.mwtab.validate_file() validation log generated during validation.

    • Includes metadata header in validation logs containing; datetime, mwtab version, file source, study id, analysis id, and file format.
    • Minor changes to error messages for MS(NMR)_METABOLITE_DATA, NMR_BINNED_DATA, and SUBJECT_SAMPLE_FACTORS sections.

Bugfixes

  • Fixes error where pytests for ~mwtab.mwtab.validate_file() method were repeatedly using the same text files for

validation rather than both the test text and JSON files.

  • Verbose file validation enabled in commandline.
  • Default value given to base_url parameter in ~mwtab.mwatb._pull_study_analysis() methods.

1.0.1 (2021-03-06)

Improvements

  • Updated ~mwtab.mwtab.MWTabFile to match Metabolomics Workbench JSON format.

    • Internal dictionary representation now matches Metabolomics Workbench JSON format.
    • ~mwtab.mwtab.MWTabFile.write() and ~mwtab.mwtab.MWTabFile.write_str() methods now produce files consistent with Metabolomics Workbench's JSON format.

  • Updated mwschema.py to be consistent with Metabolomics Workbench's updated mwTab format specification.

  • Added mwrest.py module for working with Metabolomics Workbench's REST API.

    • Allows for additional data file to be requested through Metabolomics Workbench's REST API.

  • Added mwextract.py module for extracting metadata and metabolites from mwTab formatted files.

  • Updated validator.py.

    • Validator now collects all present errors.
    • Performs detection of common field names in #METABOLITES blocks.

  • Updated docs/tutorial.ipynb to document improved and updated package functionality.

  • Updated mwtab package to include Python 3.8 support.

0.1.10 (2019-02-18)

Bugfixes

  • Metabolomics Workbench started using HTTPS, update reading from ANALYSIS_ID to address the change.

0.1.9 (2018-04-21)

Improvements

  • Added citation link to mwtab package.

0.1.8 (2018-04-05)

Improvements

  • Added mwtab package logo.
  • Minor update: Simplified section validation function.

0.1.7 (2017-12-07)

Improvements

  • Minor update: Included test for additional header line within mwTab files that may or may not be present.

0.1.4, 0.1.5, 0.1.6 (2017-11-13)

Improvements

  • Minor update: package README file examples.
  • Minor update: update README to properly render on PyPI.

0.1.3 (2017-09-14)

Bugfixes

  • Fixed bug in the command-line interface.
  • Fixed bug in mwschema.py module definition causing validation to fail.
  • Fixed validation optional argument (to read_files() generator) in order to validate mwTab formatted files before returning them.
  • Fixed Python2/3 compatibility bug that uses bz2 Python module.
  • Fixed Python2/3 unicode/str compatibility bug in mwschema.py module.

Improvements

0.1.2 (2017-09-14)

Bugfixes

  • Fixed issue with mwTab formatted file printable representation.

0.1.1 (2017-09-12)

Improvements

  • Improved README display on PyPI.

0.1.0 (2017-09-12)

  • Initial public release.