MRG: add utilities for using ictv taxonomic ranks with sourmash tax
#2608
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## latest #2608 +/- ##
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+ Coverage 86.59% 86.63% +0.04%
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Files 135 135
Lines 15329 15390 +61
Branches 2605 2624 +19
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+ Hits 13274 13333 +59
- Misses 1755 1756 +1
- Partials 300 301 +1
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ok @sourmash-bio/devs ready for review! |
bluegenes
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release notes: https://hackmd.io/SCoVcWS1RhCH-ndQNWF-1A?view # sourmash release v4.8.6 - release notes Minor new features: * re-establish `tax` gather reading flexibility (#2986) * update JOSS paper per pyopensci review (#2964) * Clean up and refactor `KmerMinHash::merge` in core (#2973) * add label output & input options to `compare` and `plot`, for better customization (#2598) * add utilities for using ictv taxonomic ranks with `sourmash tax` (#2608) Bug fixes: * Fix `tax metagenome` to work on gather output created with `--estimate-ani-ci` (#2952) * fix gather memory usage issue by not accumulating `GatherResult` (#2962) * update the CLI docs and help for `search --containment` and `prefetch` (#2971) Documentation updates: * update tutorial to remove bioconda & use sourmash-minimal (#2972) * update readme with maintainers & sourmash comparison info (#2965) * add branchwater reference; make FAQ more visible (#2984) * update FAQ answer on k-mer size (#2899) * update README with repostatus and pyver badges, and Windows support (#2928) * add full column descriptions for `gather` and `prefetch` output (#2954) * add scaled FAQ, adjust ksize answer (#2921) * minor refactoring of gather code, small doc updates (#2953) * Add threshold-bp and scaled relationship to faqs (#2930) Developer updates: * nix updates for pyopensci review (#2975) * add scaled selection to manifest; add helper functions for collection and sig/sketch usage (#2948) * Pre-commit updates (#2427) * fix upload wheel CI (#2974) * release core; bump rust core version to r0.12.1 (#2988) * CI: macos deployment target and maturin updates (#2879) * MRG: bump version to 4.8.6-dev, post-release (#2877) * fix benchmark code & a few other small issues from pyOpenSci review (#2920) * fix uploading of wheels after upload-artifact upgrade. (#2887) * in core, enable downsample within select (#2931) Dependabot updates: * Bump pypa/cibuildwheel from 2.16.4 to 2.16.5 (#2981) * Bump tempfile from 3.9.0 to 3.10.0 (#2979) * Bump rkyv from 0.7.43 to 0.7.44 (#2978) * Bump actions/cache from 3 to 4 (#2933) * Bump actions/download-artifact from 3 to 4 (#2884) * Bump actions/upload-artifact from 3 to 4 (#2883) * Bump cachix/cachix-action from 13 to 14 (#2926) * Bump cachix/install-nix-action from 24 to 25 (#2927) * Bump chrono from 0.4.31 to 0.4.33 (#2957) * Bump getrandom from 0.2.11 to 0.2.12 (#2924) * Bump histogram from 0.8.3 to 0.8.4 (#2923) * Bump histogram from 0.8.4 to 0.9.0 (#2935) * Bump jinja2 from 3.1.2 to 3.1.3 (#2922) * Bump memmap2 from 0.9.0 to 0.9.2 (#2882) * Bump memmap2 from 0.9.2 to 0.9.3 (#2889) * Bump memmap2 from 0.9.3 to 0.9.4 (#2958) * Bump mymindstorm/setup-emsdk from 13 to 14 (#2934) * Bump ouroboros from 0.18.1 to 0.18.2 (#2894) * Bump ouroboros from 0.18.2 to 0.18.3 (#2936) * Bump pypa/cibuildwheel from 2.16.2 to 2.16.4 (#2960) * Bump rayon from 1.8.0 to 1.8.1 (#2937) * Bump rkyv from 0.7.42 to 0.7.43 (#2880) * Bump serde from 1.0.194 to 1.0.195 (#2901) * Bump serde from 1.0.195 to 1.0.196 (#2956) * Bump serde_json from 1.0.108 to 1.0.110 (#2896) * Bump serde_json from 1.0.110 to 1.0.111 (#2902) * Bump serde_json from 1.0.111 to 1.0.113 (#2955) * Bump shlex from 1.1.0 to 1.3.0 (#2940) * Bump supercharge/redis-github-action from 1.7.0 to 1.8.0 (#2885) * Bump tempfile from 3.8.1 to 3.9.0 (#2893) * Bump thiserror from 1.0.50 to 1.0.51 (#2881) * Bump thiserror from 1.0.51 to 1.0.56 (#2897) * Bump wasm-bindgen from 0.2.89 to 0.2.90 (#2925) * Bump wasm-bindgen-test from 0.3.39 to 0.3.40 (#2938) * Bump web-sys from 0.3.66 to 0.3.67 (#2939) * Update pytest requirement from <7.5.0,>=6.2.4 to >=6.2.4,<8.1.0 (#2959)
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This PR adds taxonomic utilities for ICTV taxonomies.
ICTVLineageInfoclass to handle 15-rank ICTV taxonomies.--ictvuser option to relevant tax commands (metagenome,genome,annotate,summarize) to enable ICTV usage.Note that since NCBI ranks are a subset of ICTV ranks, if users forget to specify
--ictv, everything will "work", but won't use all available taxonomic ranks. This isn't really a bug, just noting it.