Releases: Query-farm/vgi-scikit-bio
Releases · Query-farm/vgi-scikit-bio
Release list
v0.1.1 — docs: uvx / oci:// attach + logos
Patch release. The function surface is unchanged from
v0.1.0
(~90 functions across 5 schemas); this ships documentation and packaging
improvements:
- Attach with zero local install — the README now leads with
LOCATION 'uvx vgi-scikit-bio'(from PyPI) and
LOCATION 'oci://ghcr.io/query-farm/vgi-scikit-bio:0.1.1'(thevgiextension
pools the container asdocker run … stdio), alongside the installed console
script, source-checkout, and HTTP-server forms. - Project logos (VGI, scikit-bio, DuckDB) in the README header.
This upload refreshes the PyPI project page with the new README + logos.
INSTALL vgi FROM community; LOAD vgi;
ATTACH 'skbio' (TYPE vgi, LOCATION 'uvx vgi-scikit-bio');
SELECT skbio.sequence.gc_content('ATGCGGATTACAGG');
v0.1.0 — scikit-bio for DuckDB/SQL
First release of vgi-scikit-bio, a VGI worker exposing
scikit-bio to DuckDB/SQL — ~90 functions across 5 schemas:
sequence— GC content, reverse complement, complement, transcription,
translation (incl. six-frame), validation, sequence distances, k-mer & residue
compositionalignment— global/local pairwise alignment (scores and aligned strings)diversity— the full alpha-diversity metric family (aggregates),
beta-diversity distance matrices, phylogenetic Faith's PD & UniFrac, and
rarefactionstats— PCA/CA/PCoA ordination, PERMANOVA/ANOSIM/Mantel tests,
CLR/ILR/ALR (and inverse) compositional transforms, and ANCOM /
Dirichlet-multinomial differential abundancetree— neighbour joining / UPGMA / minimum evolution, Newick inspection,
and tree comparison (Robinson–Foulds, cophenetic)
Runs over stdio (DuckDB spawns it) or HTTP; a multi-arch container image is
published to ghcr.io/query-farm/vgi-scikit-bio. MIT licensed.
INSTALL vgi FROM community; LOAD vgi;
ATTACH 'skbio' (TYPE vgi, LOCATION 'vgi-scikit-bio');
SELECT skbio.sequence.gc_content('ATGCGGATTACAGG');