version 2020.8.6

Incompatible changes:

• Change random_seed to work with numpy.random.default_rng. This may cause different random numbers compared to the old versions using numpy.random.seed().
• Change parameter names in some functions
• Rename filter_abundance() to filter_sum(abundance)
• Other backwards incompatible function API changes and code refactoring.

New features:

• Add RatioExperiment for working with ratios between two groups of features
• Add random_seed option to tranforming.permute_data()
• Add bad_color parameter to heatmap() and derivative functions
• Add more methods for MS1Experiment
• Add q-values (correted p-values) to dsfdr and derivative functions. This is manifested in a new feature_metadata field ("qval") for results of diff_abundance() / correlation()
• improved GUI for qt5 heatmap database enrichment results.
• Add read_qiime2() function to enable reading of qiime2 feature tables artifacts with the associated representative sequences and taxonomy artifacts (without the need to install qiime2)
• Add Experiment.validate().
• Change default color scale in heatmap plot to linear scale for Experiment and log scale for AmpliconExperiment and MS1Experiment.
• Move to pytest for unit tests and doctests.
• Add new mechanism to register a function to a class as a method automatically. In order for a function to be registerred to a class, it must be a public function and has type hint of the class type for its first function parameter and return value.
• Clean and improve API documentation.

Other changes:

• make scikit-bio an optional dependency (needed only when processing dendrograms)

Version 2019.5.1

• Add reverse parameter to the sorting functions.
• Fix minor documentation formatting issues
• Update installation instruction with conda install from conda-forge
• Change the column names added to Experiment.feature_metadata after running Experiment.correlation or Experiment.diff_abundance

Version 2018.10.1

• Add notebook tutorial for calour.training module for classification and regression.
• Add notebook tutorial for metabolome data analysis
• Add plot functions in calour.training module
• Fix a bug in Expriment.aggregate_by_metadata when the number in the data table is overflow the int type.
• Add CONTRIBUTING.md as guidelines

Release 2019.5.1

This release has minor doc and functionality improvement.

release 2018.10.1

This release fixed a few minor bugs and improved documentation. The details is in change history

beta release

This is a beta release for calour. It provides interactive, exploratory analysis for 2 dimensional tables with metadata (like 16S microbiome table, gene abundance table, or metabolome table). The documentation is here.