0.2.0

Added

• bt.io.read_humann: read HUMAnN 3 and 4 tables (gene families, reactions
  or pathway abundance, also after regrouping or renormalising) into a
  MuData with a community modality, "function", and a per-taxon one,
  "function_by_taxon".
• bt.io.read_metaphlan: read MetaPhlAn 3 and 4 profiles, one or merged, as
  relative abundances of the leaf clades with the seven taxonomic ranks.
• bt.io.read_picrust2 / bt.io.read_picrust2_traits: read PICRUSt2's
  predicted metagenomes and pathways, with the per-ASV contributions as the
  per-taxon modality, and its per-ASV gene copy numbers. PICRUSt2 itself is
  not needed.
• bt.fn.load_hierarchy: read a function hierarchy (HUMAnN or PICRUSt2
  mapping files, or your own) from a local file.
• bt.fn.func_glom: aggregate functions to one level of a hierarchy, as
  humann_regroup_table does.
• bt.fn.renorm: renormalise a function table to copies per million or
  relative abundance, as humann_renorm_table does. func_glom and renorm
  are tested against HUMAnN 3.9's own output.
• bt.fn.contributions and bt.pl.contributions: one function's abundance
  per taxon in every sample, as a table and as stacked bars.
• bt.fn.functional_redundancy: taxonomic diversity, functional diversity
  and functional redundancy per sample (Tian et al. 2020).
• bt.datasets.toy_humann: a tiny in-memory function table for examples and
  tests.
• bt.datasets.enzyme: the ENZYME EC hierarchy (CC BY 4.0), downloaded once
  and cached.
• bt.datasets.hmp2: the HMP2 inflammatory bowel disease cohort's pathways,
  species and metadata, one stool metagenome per participant, downloaded once
  and cached.
• A function guide and a tutorial on the HMP2 cohort.
• asv benchmarks for fn.func_glom, io.read_humann and
  fn.functional_redundancy, with their baselines in the docs.
• New runtime dependency: mudata>=0.4, for function tables.

Changed

• bt.pp.relative divides each value by its sample total, summed in float64:
  a sample whose total is subnormal no longer gives inf, and a float32 table
  is no longer off by about 1e-7.
• bt.pl.bar no longer gives a group the grey that marks missing values, so
  with eight or more groups plus missing values the colours change.
• The Coming-from-R page marks the phyloseq calls biotapy does not cover yet
  "not in 0.2".
• The docs build gives each notebook cell up to 5 minutes, enough for the
  function tutorial to download the HMP2 tables on a cold cache.