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…olumn for lingroup name
bluegenes
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## latest #3758 +/- ##
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- Coverage 88.19% 88.17% -0.02%
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Files 137 137
Lines 22552 22553 +1
Branches 2298 2298
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- Hits 19889 19887 -2
- Misses 2348 2351 +3
Partials 315 315
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@ctb ready for review |
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Seems good to me - downstream scripts can check for presence of header.
This was referenced Aug 7, 2025
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Major new features: * start writing v4->v5 migration docs (#3721) * adjust warnings around tax abund and provide v5 upgrades to `tax metagenome` (#3711) Minor new features: * try setting up --v4 and --v5 behavior differences for `sig check` (#3072) * update `sig manifest` default rebuilding behavior for v5. (#3074) * handle (ignore) empty taxids for `bioboxes` format (#3748) * improve summary_csv for lingroups (#3758) Cleanup and documentation updates: * use auto-generated database list (#3754) Developer updates: * CI: fix dependabot config syntax, and clippy beta lints (#3762) * CI: update to cibuildwheel 3.1.1 (#3738) * ci: group dependabot updates by language (#3749) * Remove docutils dep (#3769) * bump version to 4.9.4-dev (#3715) * disable WebAssembly builds, for now (#3724) Dependabot updates: * Build(ci): Bump actions/download-artifact from 4 to 5 (#3766) * Build(deps): Bump DeterminateSystems/nix-installer-action from 17 to 18 (#3727) * Build(deps): Bump DeterminateSystems/nix-installer-action from 18 to 19 (#3746) * Build(deps): Bump criterion from 0.6.0 to 0.7.0 (#3741) * Build(deps): Bump md5 from 0.7.0 to 0.8.0 (#3719) * Build(deps): Bump memmap2 from 0.9.5 to 0.9.7 (#3732) * Build(deps): Bump prefix-dev/setup-pixi from 0.8.10 to 0.8.11 (#3733) * Build(deps): Bump prefix-dev/setup-pixi from 0.8.11 to 0.8.14 (#3747) * Build(deps): Bump rand from 0.9.1 to 0.9.2 (#3743) * Build(deps): Bump serde_json from 1.0.140 to 1.0.141 (#3742) * [pre-commit.ci] pre-commit autoupdate (#3718) * [pre-commit.ci] pre-commit autoupdate (#3725) * [pre-commit.ci] pre-commit autoupdate (#3731) * [pre-commit.ci] pre-commit autoupdate (#3737) * [pre-commit.ci] pre-commit autoupdate (#3740) * [pre-commit.ci] pre-commit autoupdate (#3756)
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Fixes
tax metagenomewith lins/lingroup: need to write LIN, not lingroup name #3757, needed for sankey plots from csv_summary w/ LINs and LINgroups #MRG: sankey modifications for LINs and LINgroups sourmash_plugin_betterplot#81ref: improve sourmash tax metagenome lingroup output #3361
summary_csv: revert to lingroup LIN in lineage column (change in MRG: when lingroups are provided, use them for
csv_summary#3311 introduced this ~bug)add lingroup column for lingroup name
NOTE: this PR adds the
lingroupcolumn to thecsv_summaryoutput fortax metagenomeONLY when we're using LINs and lingroups. I'm not sure this is the best approach, but I also don't want to add an empty useless column for everybody else? We could leave out the lingroup names, but then we're left with the LIN only, e.g.0;1;1;8;1;0rather than a nice, human-readable name (which is one of the key reasons to uselingroupfile).