Sourmash

Medium bug fixes:

* fix bug where `sourmash sketch ... --singleton -o output.sig` drops signatures (1810)
* fix `sourmash search --containment` with two abund signatures (1780)
* fix plot/labels/CSV ordering with `sourmash plot --csv` (1821)

Small bug fixes:

* fix `Index.search_abund` downsampling and filename output (1820)
* check to make sure that .zip files exist before trying to load from them (1777)
* fix and test and refactor output information during signature creation (1826)

Minor new functionality:

* adjust text output of gather to indicate weighted/unweighted results (1819)
* update `sourmash multigather` to save hash abundances to `.unassigned.sig` (1720)
* re-inflate prefetch output sketches (1827)

Cleanup and documentation fixes:

* fix 'sketch' output info (1794)
* fix PMID for mock metagenome (1811)
* check to make sure that = is in param strings where necessary (1775)

Developer updates:

* set pickfile on SourmashPicklist.load (1776)
* Fix new clippy lints in beta (1.59, next stable) (1791)
* Rust updates (clippy, MSRV, CI, wasm-pack) (1786)
* disable the `fix_lint` component of the py38 tests in `tox.ini` (1823)

Minor new features:

* Save prefetch csv directly from prefetch-gather with `--save-prefetch-csv` (1765)
* Added brief descriptions and `-h/--help` text to sourmash `gather`, `search`, and `compare` (1735)
* Adding bounds checking for `--scaled` and `--num` in `sourmash sketch` (1711)

Documentation updates:

* update release notes with -m for git tag (1754)
* update coverage from 10x to 20x per description in documentation page (1736)

Development updates:

* Update tests to use `runtmp` fixture instead of `utils.TempDirectory()` (1718)
* Refactor `ZipFileLinearCollection` and `SaveSignatures_ZipFile` to use `ZipStorage` (1598)
* Clippy fixes for 1.57 beta (1760)
* CI: Update cibuildwheel usage (1759)
* Replace `notify` format usage with f-strings instead (1723)
* CI: Fix build errors with cbindgen (1713)
* Change `sourmash compute` to `sourmash sketch` in test files (1712)
* Update tests to use `runtmp` fixture instead of `utils.TempDirectory()`

Major new features:

* added functionality to recover original k-mers given hashes - `sourmash sig kmers` et al. (1653, 1695, 1701)

Documentation updates:

* Updated picklist docs (1683)
* Updated the 'how to release' doc after 4.2.0 release (1649)

Minor new features:

* Adjusted dayhoff and hp encodings to tolerate stop codons in the protein sequence (1673)

Bug fixes and performance improvements:

* Fixed panic bug in `sourmash sketch` dna with bad input and `--check-sequence` (1702)

Refactoring and cleanup:

* Changed `sourmash compute` to `sourmash sketch` in `tests/test_sourmash.py` (1680, 1687)
* Tested and fixed `sourmash_args.load_many_signatures(...)` and `lca_db.load_single_database` (1684)

This is a bug-fix and performance release of sourmash.

There are no major new features.

`git log --oneline v4.2.0..latest`

Minor new features:

- new picklist coltypes for directly using `gather`, `prefetch`, and `manifest` outputs without specifying column name (1660)
- add `--from-file` to `sig cat` (1657)
- implement a lazy/on-demand `Index` loading class to support low memory tracking of a large index (1661)
- add `sourmash tax prepare` to build SQLite taxonomy databases for use with `tax` commands(1651)
- Support manifests in `MultiIndex` (1654)
- `tax` summarization additions and fixes, including reporting bp and unclassified (1667)
- add `--from-file`, improved sig selection to most `sig` commands (1672)


Bug fixes and performance improvements:

- fix bug in `gather` when run with `scaled=1` (1670)


Documentation updates:

- Add sourmash-bio/community Gitter badge to README (1658)


Refactoring and cleanup:

- add tests for `sourmash tax` `--containment-threshold` arg (1666)
- fix `sourmash tax` usage string (1655)
- add bounds checking for `--scaled` (1650)

Rust interface:

- Rust Core update (tag: r0.11.0) (1643)

This release adds several significant features: first, we've added a set of [`taxonomy` command-line functionality](https://sourmash.readthedocs.io/en/latest/command-line.html#sourmash-tax-subcommands-for-integrating-taxonomic-information-into-gather-results) for combining `sourmash gather` output with taxonomy databases, and we've also added a new "picklist" feature that enables [flexible selection of _subsets_ of databases](https://sourmash.readthedocs.io/en/latest/command-line.html#using-picklists-to-subset-large-collections-of-signatures). Finally, we've added manifests to databases to support picklists as well as faster database loading and signature selection.

As of this release, we've also formally moved development over to the [sourmash-bio organization](https://github.com/sourmash-bio/) on GitHub, and we've created a new gitter support channel, [sourmash-bio/community](https://gitter.im/sourmash-bio/community#notifications). Please join us there if you have any questions, comments, or feature requests!

Major new features:
* add `tax/taxonomy` submodule (1543, 1628, 1630, 1648)
* add picklists for subsetting databases and results (1587, 1588, 1623, 1590, 1639)
* Add manifests to support fast `Index.select(...)` and lazy loading (https://github.com/sourmash-bio/sourmash/pull/1590)

Documentation updates:
* Add new GTDB databases description to docs and start legacy databases page (1581)
* Change `dib-lab/` URLs to new `sourmash-bio/` URLs. (1629)
* Add notice for sustainable open source study (1580)

Minor new features:
* alias `--nucleotide`, `--no-nucleotide` for moltype args. (1632)
* add signature names to known/unknown hash sigs output by `sourmash prefetch` (1646)

Bug fixes and performance improvements:
* Speed up `sourmash gather` with prefetch by ignoring unidentifiable hashes (1613)
* Check for `MinHash` compatibility in `MinHash.intersection_and_union(...)` (1627)
* Fix selection w/abund and manifest column type conversions (1645)

Refactoring and cleanup:
* Fix Rust 1.59 lints (1600)
* Minor cleanup in `sourmash_args` & `sig` submodules (1586)
* Minor cleanup in minhash module (1585)
* Fix needless borrows as suggested by clippy (1636)

This is a bug-fix and performance release of sourmash.

There are no major new features.

Minor new features:
* add query info to gather CSV output (1565)

Bug fixes and performance improvements:

* Improved `MinHash.remove_many(...)` performance by five orders of magnitude (1571)
* Fix SBT index saving bug that arbitrarily replaced names (but not content) of identical signatures in `.sbt.zip` files (1568)
* Empty zipfiles should not cause `AssertionError` (https://github.com/dib-lab/sourmash/pull/1546)

Major refactoring and new internal functionality:
* update `MinHash.set_abundances` to remove hash if 0 abund; handle negative abundances (1575)

Refactoring and cleanup:
* Fix tests that fail to close files that they open (1550)
* Add "&" and " | " as alternate syntax for MinHash intersection merge (1533)
* Fix missing bracket in docs (1566)
* Updates for coverage tracking (1558)
* Provide a .copy() method for both `SourmashSignature()` and `MinHash` (1551, 1570)