Merge branch 'latest' into better-summarized-lingroups

sourmash-bio · Oct 24, 2024 · e3c3bb6 · e3c3bb6
2 parents cffbf38 + 5acf698
commit e3c3bb6
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diff --git a/.github/workflows/build_wheel.yml b/.github/workflows/build_wheel.yml
@@ -46,7 +46,7 @@ jobs:
           python-version: '3.10'
 
       - name: Build wheels
-        uses: pypa/[email protected].1
+        uses: pypa/[email protected].3
         env:
           CIBW_ENVIRONMENT_MACOS: ${{ matrix.macos_target }}
           CIBW_ARCHS_LINUX: ${{ matrix.arch }}
@@ -63,7 +63,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Build wheels
-        uses: pypa/[email protected].1
+        uses: pypa/[email protected].3
         env:
           CIBW_PLATFORM: pyodide 
           CIBW_BUILD: 'cp312-pyodide_wasm32'

diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml
@@ -13,7 +13,7 @@ on:
 
 jobs:
   benchmarks-rust:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v4
 

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-ast
       - id: check-builtin-literals
@@ -10,7 +10,7 @@ repos:
       - id: check-toml
       - id: debug-statements
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.5
+    rev: v0.7.0
     hooks:
       - id: ruff-format
       - id: ruff

diff --git a/Cargo.lock b/Cargo.lock
diff --git a/flake.lock b/flake.lock
diff --git a/include/sourmash.h b/include/sourmash.h
@@ -30,6 +30,10 @@ enum SourmashErrorCode {
   SOURMASH_ERROR_CODE_NON_EMPTY_MIN_HASH = 106,
   SOURMASH_ERROR_CODE_MISMATCH_NUM = 107,
   SOURMASH_ERROR_CODE_NEEDS_ABUNDANCE_TRACKING = 108,
+  SOURMASH_ERROR_CODE_CANNOT_UPSAMPLE_SCALED = 109,
+  SOURMASH_ERROR_CODE_NO_MIN_HASH_FOUND = 110,
+  SOURMASH_ERROR_CODE_EMPTY_SIGNATURE = 111,
+  SOURMASH_ERROR_CODE_MULTIPLE_SKETCHES_FOUND = 112,
   SOURMASH_ERROR_CODE_INVALID_DNA = 1101,
   SOURMASH_ERROR_CODE_INVALID_PROT = 1102,
   SOURMASH_ERROR_CODE_INVALID_CODON_LENGTH = 1103,

diff --git a/src/core/CHANGELOG.md b/src/core/CHANGELOG.md
@@ -7,6 +7,40 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [unreleased]
 
+## [0.16.0] - 2024-10-15
+
+MSRV: 1.65
+
+Changes/additions:
+
+* refactor `calculate_gather_stats` to disallow repeated downsampling (#3352)
+* improve downsampling behavior on `KmerMinHash`; fix `RevIndex::gather` bug around `scaled`. (#3342)
+* derive Hash for `HashFunctions` (#3344)
+
+Updates:
+
+* Bump web-sys from 0.3.70 to 0.3.72 (#3354)
+* Bump tempfile from 3.12.0 to 3.13.0 (#3340)
+
+
+## [0.15.2] - 2024-09-25
+
+MSRV: 1.65
+
+Changes/additions:
+* add `Manifest::intersect_manifest` to Rust core (#3305)
+* propagate error from `RocksDB::open` on bad directory (#3306, #3307)
+
+Updates:
+
+* Bump getset from 0.1.2 to 0.1.3 (#3328)
+* Bump memmap2 from 0.9.4 to 0.9.5 (#3326)
+* Bump codspeed-criterion-compat from 2.6.0 to 2.7.2 (#3324)
+* Bump serde_json from 1.0.127 to 1.0.128 (#3316)
+* Bump serde from 1.0.209 to 1.0.210 (#3318)
+* Bump serde from 1.0.208 to 1.0.209 (#3310)
+* Bump serde_json from 1.0.125 to 1.0.127 (#3309)
+
 ## [0.15.1] - 2024-08-20
 
 MSRV: 1.65

diff --git a/src/core/Cargo.toml b/src/core/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "sourmash"
-version = "0.15.1"
+version = "0.16.0"
 authors = ["Luiz Irber <[email protected]>", "N. Tessa Pierce-Ward <[email protected]>"]
 description = "tools for comparing biological sequences with k-mer sketches"
 repository = "https://github.com/sourmash-bio/sourmash"
@@ -56,7 +56,7 @@ rkyv = { version = "0.7.44", optional = true }
 roaring = "0.10.6"
 roots = "0.0.8"
 serde = { version = "1.0.210", features = ["derive"] }
-serde_json = "1.0.128"
+serde_json = "1.0.132"
 statrs = "0.17.1"
 streaming-stats = "0.2.3"
 thiserror = "1.0"
@@ -68,7 +68,7 @@ vec-collections = "0.4.3"
 codspeed-criterion-compat = "2.7.2"
 proptest = { version = "1.5.0", default-features = false, features = ["std"]}
 rand = "0.8.2"
-tempfile = "3.12.0"
+tempfile = "3.13.0"
 
 [[bench]]
 name = "compute"
@@ -97,7 +97,7 @@ skip_feature_sets = [
 
 [target.'cfg(all(target_arch = "wasm32", target_os="unknown"))'.dependencies]
 js-sys = "0.3.68"
-web-sys = { version = "0.3.70", features = ["console", "File", "FileReaderSync"] }
+web-sys = { version = "0.3.72", features = ["console", "File", "FileReaderSync"] }
 wasm-bindgen = "0.2.89"
 getrandom = { version = "0.2", features = ["js"] }