Mwtab

~~~~~~~~~~~~~~~~~~

**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.

~~~~~~~~~~~~~~~~~~

**Improvements**

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

~~~~~~~~~~~~~~~~~~

**Bugfixes**

- Removes hard coding of version number in ``validator.validate_file()`` method.

- Removes mention of Python 3.4 support in README.

~~~~~~~~~~~~~~~~~~

**Improvements**

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

- Adds ``.github/workflows/`` folder which contains .yml files for workflows.

- Adds ``build.yml`` to folder for testing build with pytest.

- Adds ``codecov.yml`` to folder for generating/uploading code coverage info to codecov.io
(https://app.codecov.io/gh/MoseleyBioinformaticsLab/mwtab).

- Changes build and codecov badges to match new sources.

~~~~~~~~~~~~~~~~~~

**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.

~~~~~~~~~~~~~~~~~~

**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.