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r0.12.0

r0.12.0
@luizirber luizirber tagged this 01 Dec 00:58 
MSRV: 1.64

Added:

- Initial implementation for `Manifest`, `Selection`, and `Picklist` following
  the Python API. (#2230)
- `Collection` is a new abstraction for working with a set of signatures. A
  collection needs a `Storage` for holding the signatures (on-disk, in-memory,
  or remotely), and a `Manifest` to describe the metadata for each signature. (#2230)
- Expose CSV parsing and RocksDB errors. (#2230)
- New module `sourmash::index::revindex::disk_revindex` with the on-disk
  RevIndex implementation based on RocksDB. (#2230)
- Add `iter` and `iter_mut` methods for `Signature`. (#2230)
- Add `load_sig` and `save_sig` methods to `Storage` trait for higher-level data
  manipulation and caching. (#2230)
- Add `spec` method to `Storage` to allow constructing a concrete `Storage` from
  a string description. (#2230)
- Add `InnerStorage` for synchronizing parallel access to `Storage`
  implementations. (#2230)
- Add `MemStorage` for keeping signatures in-memory (mostly for debugging and
  testing). (#2230)
- Add new `branchwater` feature (enabled by default), which can be disabled by
  downstream projects to limit bringing heavy dependencies like rocksdb. (#2230)
- Add new `rkyv` feature (disabled by default), making `MinHash` serializable
  with the `rkyv` crate. (#2230)
- Add semver checks for CI (so we bump versions accordingly, or avoid breaking
  changes). (#2230)
- Add cargo deny config. (#2724)
- Benchmarks for seq_to_hashes in protein mode. (#1944)
- Oxidize ZipStorage. (#1909)
- Move greyhound-core into sourmash. (#1238)
- add `MinHash.kmers_and_hashes(...)` and `sourmash sig kmers`. (#1695)
- Produce list of hashes from a sequence. (#1653)

Changed:

- Rename `HashFunctions` variants to follow camel-case, so `Murmur64Protein`
  instead of `murmur64_protein`. (#2230)
- `LinearIndex` is now implemented as a thin layer on top of `Collection`. (#2230)
- Move `GatherResult` to `sourmash::index` module. (#2230)
- Move `sourmash::index::revindex` to `sourmash::index::mem_revindex` (this is
  the Greyhound version of revindex, in-memory only). It was also refactored
  internally to build a version of a `LinearIndex` that will be merged in the
  future with `sourmash::index::LinearIndex`. (#2230)
- Move `select` method from `Index` trait into a separate `Select` trait,
  and implement it for `Signature` based on the new `Selection` API. (#2230)
- Move `SigStore` into `sourmash::storage` module, and remove the generic. Now
  it always stores `Signature`. Also implement `Select` for it. (#2230)
- Disable `musllinux` wheels (need to figure out how to build rocksdb for it). (#2230)
- Reorganize traits for easier wasm and native compilation. (#1836)
- Adjust dayhoff and hp encodings to tolerate stop codons in the protein sequence. (#1673)

Fixed:

- Reduce features combinations on Rust checks (takes much less time to run). (#2230)
- Build: MSRV check for 1.64. (#2680)
- maturin: move deprecated definition from Cargo.toml to pyproject.toml. (#2597)
- Fix broken crates.io badge. (#2556)
- Fix unnecessary typecasts in Rust. (#2366)
- Fix `Signature.minhash` API during `sourmash sketch`. (#2329)
- Return Err for angular_similarity when abundance tracking is off. (#2327)
- Update various descriptions to talk about k-mers, not just DNA. (#2137)
- Fix downsample_scaled in `core`. (#2108)
- speed up `SeqToHashes` `translate`. (#1946)
- Speed-up `SeqToHashes()`. (#1938)
- Fix containment calculation for nodegraphs. (#1862)
- Fix panic bug in `sourmash sketch` dna with bad input and `--check-sequence`. (#1702)
- Fix Rust panic in `MinHash.seq_to_hashes`. (#1701)
- Beta lints. (#2841 #2630 #2596 #2298 #1791 #1786 #1760)

Removed:

- Remove BIGSI and SBT code. (#2732)
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