From d22b8609c8f0bef3bab3f258d6f54a200bceaa8a Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Mon, 16 Dec 2024 06:50:57 -0800 Subject: [PATCH 1/4] MRG: add comment about semver and column headings (#3433) This PR updates the docs to make it clear that we may rearrange or add columns within major versions, and suggests that people parse based on CSV headings. Fixes https://github.com/sourmash-bio/sourmash/issues/3432 --- doc/support.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/doc/support.md b/doc/support.md index f4ee4f492..84ea41380 100644 --- 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. From 872351de3994625dcfeac34d2e0376e698ed991b Mon Sep 17 00:00:00 2001 From: Tessa Pierce Ward Date: Mon, 16 Dec 2024 15:18:53 -0800 Subject: [PATCH 2/4] MRG: add genbank plant db to docs (#3429) created with directsketch; see https://github.com/bluegenes/2024-ds-plant for details ref https://github.com/sourmash-bio/sourmash/issues/3172 --------- Co-authored-by: C. Titus Brown --- doc/databases.md | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/doc/databases.md b/doc/databases.md index 3d607bdb9..efdd7a55d 100644 --- 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. From e7cf9e228f6ab4e21de53db11e96a7480b8faa5b Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 16 Dec 2024 15:21:53 -0800 Subject: [PATCH 3/4] [pre-commit.ci] pre-commit autoupdate (#3439) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.8.2 → v0.8.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.8.2...v0.8.3) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: C. Titus Brown --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c50d4e626..69362be16 100644 --- 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 From 61be9365c1a6af078f6456a6d068aa1e39bebf1f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 16 Dec 2024 16:33:31 -0800 Subject: [PATCH 4/4] Bump serde from 1.0.215 to 1.0.216 (#3436) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Bumps [serde](https://github.com/serde-rs/serde) from 1.0.215 to 1.0.216.
Release notes

Sourced from serde's releases.

v1.0.216

  • Mark all generated impls with #[automatically_derived] to exclude from code coverage (#2866, #2868, thanks @​tdittr)
Commits
  • ad8dd41 Release 1.0.216
  • f91d2ed Merge pull request #2868 from dtolnay/automaticallyderived
  • 9497463 Mark all generated trait impls as #[automatically_derived]
  • 46e9ecf Merge pull request #2866 from tdittr/mark-visitors-as-generated
  • e9c399c Mark generated impl de::Visitor blocks as #[automatically_derived]
  • b9dbfcb Switch out fnv in favor of foldhash in test
  • c270e27 Use BuildHasher instead of Hasher in collection macros
  • 0307f60 Resolve question_mark clippy lint in build script
  • See full diff in compare view

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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- Cargo.lock | 8 ++++---- src/core/Cargo.toml | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 853a3f9eb..dbfa03d53 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1560,18 +1560,18 @@ checksum = "1c107b6f4780854c8b126e228ea8869f4d7b71260f962fefb57b996b8959ba6b" [[package]] name = "serde" -version = "1.0.215" +version = "1.0.216" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6513c1ad0b11a9376da888e3e0baa0077f1aed55c17f50e7b2397136129fb88f" +checksum = "0b9781016e935a97e8beecf0c933758c97a5520d32930e460142b4cd80c6338e" dependencies = [ "serde_derive", ] [[package]] name = "serde_derive" -version = "1.0.215" +version = "1.0.216" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ad1e866f866923f252f05c889987993144fb74e722403468a4ebd70c3cd756c0" +checksum = "46f859dbbf73865c6627ed570e78961cd3ac92407a2d117204c49232485da55e" dependencies = [ "proc-macro2", "quote", diff --git a/src/core/Cargo.toml b/src/core/Cargo.toml index a45d03481..fcb1407e0 100644 --- 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"