MRG: force continue past tax genome classification errors
#3100
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## latest #3100 +/- ##
==========================================
+ Coverage 86.89% 86.90% +0.01%
==========================================
Files 136 136
Lines 15542 15554 +12
Branches 2637 2640 +3
==========================================
+ Hits 13505 13517 +12
Misses 1735 1735
Partials 302 302
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. |
… into allow-classif-errs
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
bluegenes
changed the title
tax genome classification errorstax genome classification errors
for more information, see https://pre-commit.ci
|
@sourmash-bio/devs ready for review |
ctb
added a commit
that referenced
this pull request
Jun 11, 2024
Minor new features: * add `--set-name` to `sig intersect` and `sig subtract` (#3162) * upgrade `sig overlap` and `sig subtract` to load more than JSON signatures (#3153) * force continue past `tax genome` classification errors (#3100) Bug fixes: * fix `remaining_bp` output from sourmash gather (#3195) * fix RocksDB-based gather & other rust-based infelicities revealed by plugins (#3193, #3197) * use correct denominator in f_unique_to_query (#3138) Cleanup and documentation updates: * update JOSS for sourmash v4 (#3114, #3203, #3209) * fix links to taxonomy spreadsheets (#3119) * fix description of `f_unique_weighted` (#3164) Developer updates: * transition internal signature loading functions (#3161) * allow get/set record.filename (#3121) * round a number that is losing precision in 15th place in `test_distance_utpy` (#3126) * disable ppc64le wheel building (#3127) * prepare to remove `sourmash compute` for sourmash v5.0 (#3103) * add rustup target x86_64-apple-darwin (#3148) * mv `.cargo/config` to `config.toml` (#3147) * fix clippy warnings about max_value (#3146) * bump to v4.8.9-dev (#3135) * update src/core/CHANGELOG.md for sourmash-rs core release r0.14.0 (#3199) Dependabot updates: * Bump DeterminateSystems/nix-installer-action from 11 to 12 (#3184) * Bump DeterminateSystems/magic-nix-cache-action from 6 to 7 (#3185) * Bump statrs from 0.16.0 to 0.16.1 (#3186) * Bump serde from 1.0.202 to 1.0.203 (#3175) * Bump ouroboros from 0.18.3 to 0.18.4 (#3176) * Bump itertools from 0.12.1 to 0.13.0 (#3166) * Bump camino from 1.1.6 to 1.1.7 (#3169) * Bump serde from 1.0.201 to 1.0.202 (#3168) * Bump thiserror from 1.0.60 to 1.0.61 (#3167) * Bump pypa/cibuildwheel from 2.18.0 to 2.18.1 (#3165) * Bump DeterminateSystems/magic-nix-cache-action from 4 to 6 (#3157) * Bump DeterminateSystems/nix-installer-action from 10 to 11 (#3156) * Bump pypa/cibuildwheel from 2.17.0 to 2.18.0 (#3155) * Bump serde_json from 1.0.116 to 1.0.117 (#3159) * Bump thiserror from 1.0.59 to 1.0.60 (#3158) * Bump serde from 1.0.200 to 1.0.201 (#3160) * Bump roaring from 0.10.3 to 0.10.4 (#3142) * Bump histogram from 0.10.0 to 0.10.1 (#3141) * Bump getrandom from 0.2.14 to 0.2.15 (#3143) * Bump num-iter from 0.1.44 to 0.1.45 (#3140) * Bump jinja2 from 3.1.3 to 3.1.4 (#3145) * Bump serde from 1.0.199 to 1.0.200 (#3144) * Bump serde from 1.0.198 to 1.0.199 (#3130) * Bump conda-incubator/setup-miniconda from 3.0.3 to 3.0.4 (#3131) * Update pytest requirement from <8.2.0,>=6.2.4 to >=6.2.4,<8.3.0 (#3132) * Bump myst-parser from 2.0.0 to 3.0.1 (#3133) * Bump thiserror from 1.0.58 to 1.0.59 (#3123) * Bump serde_json from 1.0.115 to 1.0.116 (#3124) * Bump serde from 1.0.197 to 1.0.198 (#3122) * Update docutils requirement from <0.21,>=0.17.1 to >=0.17.1,<0.22 (#3116)
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
When we were doing one or a few genome classifications, it made sense to error out completely if there was an issue. Now that we have fastmultigather and can do 10s of thousands at once, It would be nice to be able to continue past errors (logging them).
Changed behavior: