Resolve sourmash gather --help issue #3032
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## latest #3032 +/- ##
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Coverage 86.76% 86.76%
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Files 136 136
Lines 15509 15509
Branches 2624 2624
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Hits 13457 13457
Misses 1751 1751
Partials 301 301
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thanks @bnelsj! Assuming all the test pass, I would like to merge this - can I update the PR from Also, we would like to invite you to join the author list on future JOSS papers. If this is of interest, can you provide us with an ORCID, please? Thanks! |
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Feel free to update the PR. My ORCID is 0009-0001-1553-932X. Glad I could help! |
This was referenced Feb 23, 2024
Closed
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ctb
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Feb 23, 2024
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ok! if you merge bnelsj#1 then this should auto-merge after tests pass! |
MRG: add bnelsj orcid
auto-merge was automatically disabled
February 23, 2024 18:20
Head branch was pushed to by a user without write access
ctb
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Mar 21, 2024
# Release notes for sourmash v4.8.7 Note: This release changes the way `sourmash multigather` names output files in some situations. Please see #2722 for details. Minor new features: * support proper manifest creation with `--relpath` for `sig check` and `sig collect` (#3054) * fix `multigather` output by adding md5sum along with `-U/--output-add-query-md5sum` (#2722) * enable loading lineages from annotated gather with match_name instead of name (#3078) Bug fixes: * fix output for `sketch ... --singleton` (#3066) * fix `calculate_gather_stats` `threshold=0` bug (#3052) Cleanup and documentation updates: * adjust protein ksize for record/manifest (#3019) * Resolve `sourmash gather --help` issue (#3032) * rework the manifest documentation; do misc cleanup (#3027) * add branchwater web to docs (#3018) Developer updates: * make core Manifest booleans python compatible (core) (#3007) * safer ksize selection while still accommodating k=k*3 (#3028) * fix clippy beta issues (#3088) * tell dependabot to ignore upgrades to `byteorder`, `chrono`, `once_cell`, and `wasm-bindgen` (#3065) * update rust changelog for r0.13.0 in preparation for release (#3033) * Allow changing storage location for a collection in RevIndex (#3015) * Fix tox and nix configs so all tox tests execute correctly (#2992) * Calculate all gather stats in rust; use for rocksdb gather (#2943) * bump screed req to 1.1.3 (#3067) * bump to v4.8.7-dev (#2989) Dependabot updates: * Bump DeterminateSystems/magic-nix-cache-action from 1 to 3 (#2994) * Bump DeterminateSystems/magic-nix-cache-action from 3 to 4 (#3085) * Bump DeterminateSystems/nix-installer-action from 4 to 9 (#2995) * Bump DeterminateSystems/nix-installer-action from 9 to 10 (#3083) * Bump chrono from 0.4.33 to 0.4.34 (#3000) * Bump conda-incubator/setup-miniconda from 3.0.1 to 3.0.2 (#3046) * Bump conda-incubator/setup-miniconda from 3.0.2 to 3.0.3 (#3057) * Bump histogram from 0.9.0 to 0.9.1 (#3002) * Bump itertools from 0.12.0 to 0.12.1 (#3043) * Bump log from 0.4.20 to 0.4.21 (#3062) * Bump num-iter from 0.1.43 to 0.1.44 (#2997) * Bump pypa/cibuildwheel from 2.16.5 to 2.17.0 (#3084) * Bump rayon from 1.8.1 to 1.9.0 (#3058) * Bump roaring from 0.10.2 to 0.10.3 (#3014) * Bump serde from 1.0.196 to 1.0.197 (#3045) * Bump serde_json from 1.0.113 to 1.0.114 (#3044) * Bump tempfile from 3.10.0 to 3.10.1 (#3059) * Bump thiserror from 1.0.56 to 1.0.57 (#2999) * Bump thiserror from 1.0.57 to 1.0.58 (#3082) * Bump wasm-bindgen from 0.2.91 to 0.2.92 (#3060) * Bump wasm-bindgen-test from 0.3.40 to 0.3.41 (#2996) * Bump wasm-bindgen-test from 0.3.41 to 0.3.42 (#3063) * Bump web-sys from 0.3.67 to 0.3.68 (#2998) * Bump web-sys from 0.3.68 to 0.3.69 (#3061) * Revert "Bump wasm-bindgen from 0.2.91 to 0.2.92 (#3060)" (#3064) * Update asv to 0.6.2 (#3025) * Update pytest requirement from <8.1.0,>=6.2.4 to >=6.2.4,<8.2.0 (#3075)
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This PR escapes
%characters in the usage string for sourmash gather, which was causing a ValueError when invoked on the command line withsourmash gather --help.Fixes #3031