MRG: upgrade sig overlap and sig subtract to load more than JSON signatures
#3153
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 #3153 +/- ##
==========================================
+ Coverage 86.64% 86.65% +0.01%
==========================================
Files 136 136
Lines 15807 15821 +14
Branches 2713 2713
==========================================
+ Hits 13696 13710 +14
Misses 1801 1801
Partials 310 310
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. |
for more information, see https://pre-commit.ci
ctb
changed the title
sig overlap and sig subtractsig overlap and sig subtract
|
Ready for review @sourmash-bio/devs |
5 tasks
ctb
changed the title
sig overlap and sig subtractsig overlap and sig subtract to load more than JSON signatures
|
@ccbaumler @AnneliektH would either of you be able to look at this and (potentially) approve it? lmk if you don't have review privileges. |
ctb
added a commit
that referenced
this pull request
Jun 4, 2024
Note: PR into #3153 Tackles some signature loading and saving cleanup throughout the codebase. Most changes are in the tests, and this is a significant cleanup of the test code! Fixes #1062. --- Goals: * deprecate external use of `sourmash.signature` load/save functions, because they are JSON-specific and inflexible. * simplify and standardize signature load/save function usage during tests; * get rid of deprecation messages during tests; In brief, * rename `sourmash.signature.load_signatures` to `load_signatures_from_json`; * rename `sourmash.signature.load_one_signature` to `load_one_signature_from_json`; * rename `sourmash.signature.save_signatures` to `save_signatures_to_json`; * deprecate `sourmash.save_signatures` and `sourmash.load_one_signature` for 5.0 (joining `load_signatures`, which was already deprecated); * reduce/eliminate deprecations by transitioning internal test code to use these three functions directly from `sourmash.signature` instead of from the top-level sourmash import. * **bonus**: eliminate zipfile UserWarning around overwriting files, which causes lots of warnings when running tests. --- Done: - [x] in sourmash.signature submodule, rename `load_signatures` to `load_signatures_from_json`, `load_one_signature` to `load_one_signatures_from_json`, and `save_signatures` to `save_signatures_to_json`; make tests pass. - [x] deprecate `sourmash.load_one_signature` and `sourmash.save_signatures`. - [x] catch zipfile UserWarning for duplicate filenames in ZipStorage.save TODO: - [x] transition internal sourmash code+tests away from deprecated functions - [ ] create issue around changing API documentation prior to 5.0; --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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.
Fix
sig overlapandsig subtractto take more than just JSON signatures.Also, adds a function
sourmash_args.load_one_signaturethat I think should (eventually) replace the now-deprecatedsourmash.signature.load_one_signature. This will be the topic of a new PR - for now, I think it's a nice quick fix!Fixes #3136
Related issues:
load_one_signatureuseload_file_as_signaturesAPI #1062 - will do another PR to close this issueload_*sig/db functions insourmash_args.py#1877TODO: