Allow changing storage location for a collection in RevIndex #3015
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Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## latest #3015 +/- ##
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+ Coverage 86.62% 86.70% +0.08%
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Files 135 135
Lines 15392 15395 +3
Branches 2624 2624
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+ Hits 13333 13349 +16
+ Misses 1758 1745 -13
Partials 301 301
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) Updates `src/core/CHANGELOG.md` with release notes; see below. ## Release checklist from #2987 (comment): - [x] verify minimum supported rust version (MSRV) for writing release notes (see #2988 for an example); MSRV is checked by CI in `.github/workflows/rust.yml`, `minimum_rust_version` - [x] write release notes using `git log --oneline r0.12.0..latest src/core | cut -d\ -f2- > /tmp/out.txt` - [x] verify that the ChangeLog is up to date: https://github.com/sourmash-bio/sourmash/blob/latest/src/core/CHANGELOG.md - [x] bump version in `src/core/Cargo.toml` ## Release notes for r0.13.0 MSRV: 1.65 Changes/additions: * Calculate all gather stats in rust; use for rocksdb gather (#2943) * adjust protein ksize for record/manifest (#3019) * Allow changing storage location for a collection in RevIndex (#3015) * make core Manifest booleans python compatible (core) (#3007) Updates: * Bump roaring from 0.10.2 to 0.10.3 (#3014) * Bump histogram from 0.9.0 to 0.9.1 (#3002) * Bump chrono from 0.4.33 to 0.4.34 (#3000) * Bump web-sys from 0.3.67 to 0.3.68 (#2998) * Bump num-iter from 0.1.43 to 0.1.44 (#2997) * Bump wasm-bindgen-test from 0.3.40 to 0.3.41 (#2996)
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# 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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As part of sourmash-bio/branchwater#4 I hit a pretty big drawback on the
RevIndex::openAPI: it has no way of dealing with theCollectionstorage moving to another location.This also means that the index is non-relocatable if the
Collectionuses a relative path to where the index was built originally =(I started by making a test that build an index, move the sigs to another location, then try to open the index without passing a new location (should error), and then passing an updated location (should work).
This break semantic versioning (added argument to
open), so requires a version bump. Since it will be a version bump, I also added the[non_exhaustive]annotation toSourmashError, even tho this PR is not updating it, because it would always be a breaking change if we add a new error and don't require users to check for all cases (if matching explicitly).I didn't dump the RevIndex version because there are no changes to the file format, should be compatible with existing DBs