Merge branch 'latest' of github.com:sourmash-bio/sourmash into fix_in…

…tersect_manifest
sourmash-bio · Dec 17, 2024 · c0165bd · c0165bd
2 parents d2300b7 + 61be936
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -10,7 +10,7 @@ repos:
       - id: check-toml
       - id: debug-statements
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.2
+    rev: v0.8.3
     hooks:
       - id: ruff-format
       - id: ruff

diff --git a/Cargo.lock b/Cargo.lock
diff --git a/doc/databases.md b/doc/databases.md
@@ -37,7 +37,7 @@ genomes. Among other uses, they can be used to detect host
 contamination in microbial metagenomes.
 
 Each file includes sketches at k=21, k=31, and k=51, at a scaled of
-1000, and is about 110 MB.
+1000, and is under 50 MB.
 
 * Human (hg38) - [hg38.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/hg38.sig.zip)
 * Cow (bosTau9) - [bosTau9.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/bosTau9.sig.zip)
@@ -49,6 +49,18 @@ Each file includes sketches at k=21, k=31, and k=51, at a scaled of
 * Goat (oviAri4) - [oviAri4.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/oviAri4.sig.zip)
 * Pig (susCr11) - [susScr11.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/susScr11.sig.zip)
 
+## Sketches for plant genomes
+
+These sketches are for the plant genomes available in GenBank as of 2024-07.
+
+| K-mer size | Zipfile collection |
+| -------- | -------- |
+| k21 | [download (7G)](https://farm.cse.ucdavis.edu/\~ctbrown/sourmash-db/genbank-plant-2024-07/genbank-plants-2024-07.k21.zip) |
+| k31 | [download (8.8G)](https://farm.cse.ucdavis.edu/\~ctbrown/sourmash-db/genbank-plant-2024-07/genbank-plants-2024-07.k31.zip) |
+| k51 | [download (11G)](https://farm.cse.ucdavis.edu/\~ctbrown/sourmash-db/genbank-plant-2024-07/genbank-plants-2024-07.k51.zip) |
+
+Lineage spreadsheet for sourmash `tax` commands: [download](https://farm.cse.ucdavis.edu/\~ctbrown/sourmash-db/genbank-plant-2024-07/genbank-plants-2024-07.lineages.csv.gz)
+
 ## GTDB R08-RS214 - DNA databases
 
 [GTDB R08-RS214](https://forum.gtdb.ecogenomic.org/t/announcing-gtdb-r08-rs214/456) consists of 402,709 genomes organized into 85,205 species clusters.

diff --git a/doc/support.md b/doc/support.md
@@ -81,6 +81,13 @@ you upgrade within a major sourmash release (barring bug fixes!). Moreover,
 if you rely on a feature introduced in v3.3.0, that feature will not break
 in v3.4.0, but will also not be backported to version 3.2.0.
 
+### Output file formats
+
+In particular, the CSV output file formats are guaranteed to be stable
+within major versions, with one caveat: we may add or rearrange
+columns between releases.  You should use column headers/column names
+to parse CSV files, and not depend on column order.
+
 ### Python API
 
 We intend to guarantee the Python API at the top level, i.e.

diff --git a/src/core/Cargo.toml b/src/core/Cargo.toml
@@ -55,7 +55,7 @@ rayon = { version = "1.10.0", optional = true }
 rkyv = { version = "0.7.44", optional = true }
 roaring = "0.10.8"
 roots = "0.0.8"
-serde = { version = "1.0.215", features = ["derive"] }
+serde = { version = "1.0.216", features = ["derive"] }
 serde_json = "1.0.133"
 statrs = "0.18.0"
 streaming-stats = "0.2.3"