Minor error debugging and some new features

[AgnesBaud]

Description

1. Error when calling plot_one_graph on GroupBoxGraph class object

ValueError: Invalid value of type 'numpy.int64' received for the 'name' property of box Received value: 11

The 'name' property is a string and must be specified as:
  - A string
  - A number that will be converted to a string

2. Error when creating SunbeamKraken2Parser object with excel file (extension = .xlsx). Error not encountered with moonstone tests. Maybe because moonstone tests use an older version of pandas (1.0.1 =/= 1.3.5)

   TypeError: read_excel() got an unexpected keyword argument 'sep'`

3. Metaphlan parser:

• Check analysis_type -> warn if invalid value and set to default value = 'rel_ab'
• For Metaphlan3 parse, argument keep_NCBI_tax_col that allows to keep the NCBI tax column in the resulting dataframe
• Allows to compute a dataframe with less taxonomical level than expected

# Example: To compute a dataframe only up to the genus level meta2parser = Metaphlan3Parser(input_path, analysis_type='rel_ab', keep_NCBI_tax_col=True) meta2parser.taxonomical_names = meta2parser.taxonomical_names[:-2] # remove "species" and "sTrain" from taxonomical name observed_df = meta2parser.dataframe

Changelogs

• fixing name property error in plot_one_graph method in GroupBaseGraph class
• fixing unexpected keyword argument when loading excel file in SunbeamKraken2Parser
• moonstone needs python >= 3.8. Version requirements have been updated for numpy, scikit-bio, scikit-learn, pandas, statsmodels, hdmedians, scipy and plotly

Definition of Done

• [x] New code is tested with unit tests
• [ ] Documentation has been updated
• [ ] Pull Request has been revised by a maintainer of the project

[codecov-commenter]

Codecov Report

Base: 64.65% // Head: 64.65% // No change to project coverage :thumbsup:

Coverage data is based on head (3c8b8dc) compared to base (56db2cf). Patch coverage: 100.00% of modified lines in pull request are covered.

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Additional details and impacted files

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