0.1.0

Added

• bt.io.read_biom / bt.io.write_biom: read and write BIOM tables, both the
  1.0 (JSON) and 2.1 (HDF5) dialects.
• bt.io.read_qiime2: read QIIME 2 .qza artifacts (table, taxonomy, tree,
  sample metadata), with no QIIME 2 install needed.
• bt.io.read_dada2: read a DADA2 sequence table (CSV, TSV or .rds), with
  optional taxonomy and tree.
• bt.io.read_phyloseq: read a phyloseq object saved from R (.rds/.RData),
  with no R or rpy2 install needed.
• bt.datasets.toy: a tiny in-memory dataset for examples and tests.
• bt.datasets.global_patterns / bt.datasets.enterotype: phyloseq's example
  datasets, downloaded once and cached on disk with pooch.
• bt.pp.relative: per-sample relative abundance, added as a new layer.
• bt.pp.tax_glom: aggregate features that share a lineage to a taxonomic
  rank.
• bt.pp.filter_features / bt.pp.filter_samples: keep features by
  prevalence and total reads, and samples by depth.
• bt.pp.rarefy: subsample every sample to the same depth, without
  replacement.
• bt.datasets.esophagus: phyloseq's esophagus dataset, with a tree.
• bt.tl.alpha: observed features, Shannon, Simpson, Chao1 and Faith's PD.
• bt.tl.beta / bt.tl.unifrac: Bray-Curtis and Jaccard distances, and
  unweighted and weighted UniFrac.
• bt.tl.pcoa / bt.tl.nmds: principal coordinates and non-metric
  multidimensional scaling of a stored distance matrix.
• bt.tl.permanova: PERMANOVA of a stored distance matrix.
• R golden parity tests for pp.relative and pp.tax_glom against phyloseq
  on real data.
• New runtime dependencies: rdata, xarray, pooch, scikit-bio,
  biom-format, treedata, networkx, scipy, pandas.
• New runtime dependency: scikit-learn>=1.8, for tl.nmds.
• bt.pl.bar, bt.pl.heatmap, bt.pl.richness, bt.pl.ordination and
  bt.pl.scree: phyloseq's plots, drawn from the results tl and pp
  store, returning matplotlib axes.
• A Coming-from-R page, generated from every public docstring's R
  equivalent, and a test that keeps those docstrings parseable.
• Tutorials: getting started, and phyloseq's analysis vignette redone with
  biotapy. Every notebook now runs on each docs build.
• asv benchmarks on a synthetic 5,000 x 50,000 table, with the 0.1
  baselines in the docs.
• New runtime dependency: matplotlib>=3.8, for pl, imported only when a
  plot is drawn.
• New runtime dependency: threadpoolctl>=3.5, already required by
  scikit-learn, to limit tl.permanova's OpenMP threads.

Changed

• Feature-changing functions (pp.filter_features, pp.rarefy,
  pp.tax_glom) keep X and drop the ordination summaries
  uns["biotapy"]["pcoa"] and ["nmds"] along with the other derived slots.
• CI builds the docs, executing every notebook, and fails when total line
  coverage drops below 90%.
• bt.tl.permanova runs scikit-bio's OpenMP permutation test on one thread: on
  a machine with busy cores, its default thread pool was up to thousands of
  times slower.
• Package metadata declares the license as the SPDX expression BSD-3-Clause
  (PEP 639) and adds development status, audience and topic classifiers.
• The sdist no longer ships the tests that check the repository itself (CI
  config and knowledge bundle), so its test suite passes on its own.