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

…abot/pip/sphinx-gte-6-and-lt-9

.github/workflows/build_wheel.yml

@@ -46,7 +46,7 @@ jobs:
           python-version: '3.10'
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.19.2
+        uses: pypa/cibuildwheel@v2.20.0
         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/cibuildwheel@v2.19.2
+        uses: pypa/cibuildwheel@v2.20.0
         env:
           CIBW_PLATFORM: pyodide 
           CIBW_BUILD: 'cp312-pyodide_wasm32'
@@ -73,7 +73,6 @@ jobs:
           name: wheel-wasm
           path: './wheelhouse/sourmash*.whl'
 
-
   release:
     name: Publish wheels
     runs-on: ubuntu-20.04
@@ -88,9 +87,8 @@ jobs:
           path: 'wheels/'
 
       # if it matches a Python release tag, upload to github releases
-      # TODO: In the future, use the create-release and upload-release-assets actions
       - name: Release
-        uses: fnkr/github-action-ghr@v1
-        env:
-          GHR_PATH: ${{steps.fetch_artifacts.outputs.download-path}}
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        uses: softprops/action-gh-release@v2
+        with:
+          files: |
+            ${{steps.fetch_artifacts.outputs.download-path}}/wheel-*/*

.github/workflows/build_wheel_all_archs.yml

@@ -80,9 +80,8 @@ jobs:
           path: 'wheels/'
 
       # if it matches a Python release tag, upload to github releases
-      # TODO: In the future, use the create-release and upload-release-assets actions
       - name: Release
-        uses: fnkr/github-action-ghr@v1
-        env:
-          GHR_PATH: ${{steps.fetch_artifacts.outputs.download-path}}
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        uses: softprops/action-gh-release@v2
+        with:
+          files: |
+            ${{steps.fetch_artifacts.outputs.download-path}}/wheel-*/*

.github/workflows/codspeed.yml

@@ -15,10 +15,10 @@ jobs:
   benchmarks-rust:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Setup rust toolchain, cache and cargo-codspeed binary
-        uses: moonrepo/setup-rust@v0
+        uses: moonrepo/setup-rust@v1
         with:
           channel: stable
           cache-target: release
@@ -28,7 +28,7 @@ jobs:
         run: cargo codspeed build -p sourmash
 
       - name: Run the benchmarks
-        uses: CodSpeedHQ/action@v2
+        uses: CodSpeedHQ/action@v3
         with:
           run: "cd src/core && cargo codspeed run"
           token: ${{ secrets.CODSPEED_TOKEN }}

.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: v0.5.4
+    rev: v0.5.6
     hooks:
       - id: ruff-format
       - id: ruff

doc/command-line.md

@@ -2324,7 +2324,7 @@ fast selection and lazy loading of sketches in many situations.
 The `sig check` command can also be used to create standalone manifests
 from collections using a picklist, with the `-m/--save-manifest-matching`
 option. This is useful for commands that don't support picklists natively,
-e.g. plugins and extensions.
+such as commands in plugins.
 
 Note that `sig collect` and `sig check` will generate manifests containing the
 pathnames given to them - so if you use relative paths, the references
@@ -2345,7 +2345,7 @@ file.
 You can read more about the details of zip files and manifests in
 [the advanced usage information for databases](databases-advanced.md).
 
-### Using sourmash plugins
+## Using sourmash plugins
 
 As of sourmash v4.7.0, sourmash has an experimental plugins interface!
 The plugin interface supports extending sourmash to load and save
@@ -2359,4 +2359,28 @@ is installed in.
 In the future, we will include a list of available sourmash plugins in
 the documentation, and also provide a way to list available plugins.
 
-You can list all installed plugins with `sourmash info -v`.
+You can list all installed plugins and their versions with `sourmash info -v`.
+
+Below are some useful plugins that the sourmash team uses regularly
+and supports!
+
+### The `branchwater` plugin - multithreaded and optimized sourmash operations
+
+(Installable via conda and pip as `sourmash_plugin_branchwater`.)
+
+The
+[`branchwater` plugin](https://github.com/sourmash-bio/sourmash_plugin_branchwater)
+provides faster and lower memory versions of `search`, `gather`, and
+`sketch`, as well as large-scale metagenome search
+(used for [petabyte-scale sequence search](https://www.biorxiv.org/content/10.1101/2022.11.02.514947v1))
+and large-scale clustering.
+
+Read [the branchwater plugin docs](https://github.com/sourmash-bio/sourmash_plugin_branchwater/tree/main/doc/) for more information, and ask questions on [the sourmash issue tracker!](https://github.com/sourmash-bio/sourmash/issues)
+
+### The `betterplot` plugin - improved plotting and visualization
+
+(Installable via pip as `sourmash_plugin_betterplot`.)
+
+The [`betterplot` plugin](https://github.com/sourmash-bio/sourmash_plugin_betterplot/) provides a variety of new plotting outputs for sourmash, including improved distance matrices, MDS plots, tSNE plots, upset plots, and Venn diagrams. It also supports cluster-cutting and extraction, as well as improved labeling and coloring by category.
+
+Read [the betterplot docs](https://github.com/sourmash-bio/sourmash_plugin_betterplot/) for more information, and ask questions on [the sourmash issue tracker!](https://github.com/sourmash-bio/sourmash/issues).

doc/dev_plugins.md

@@ -69,7 +69,7 @@ Some (early stage) plugins are also available as examples:
 
 ## Debugging plugins
 
-`sourmash info -v` will list all installed plugins.
+`sourmash info -v` will list all installed plugins and their versions.
 
 `sourmash sig cat <input sig> -o <output sig>` is a simple way to
 invoke a `save_to` plugin. Use `-d` to turn on debugging output.

flake.nix

@@ -62,7 +62,7 @@
 
           sourmash = python.buildPythonPackage ( commonArgs // rec {
             pname = "sourmash";
-            version = "4.8.10";
+            version = "4.8.11";
             format = "pyproject";
 
             cargoDeps = rustPlatform.importCargoLock {

pyproject.toml

@@ -9,7 +9,7 @@ build-backend = 'maturin'
 name = "sourmash"
 description = "tools for comparing biological sequences with k-mer sketches"
 readme = "README.md"
-version = "4.8.11-dev"
+version = "4.8.11"
 
 authors = [
   { name="Luiz Irber", orcid="0000-0003-4371-9659" },
@@ -117,12 +117,12 @@ demo = [
 ]
 doc = [
   "sphinx>=6,<9",
-  "myst-parser==3.0.1",
+  "myst-parser",
   "Jinja2",
   "alabaster",
   "sphinxcontrib-napoleon",
   "nbsphinx",
-  "sphinx-design==0.5.0",
+  "sphinx-design==0.6.1",
   "ipython",
   "docutils>=0.17.1,<0.22",
 ]

src/core/Cargo.toml

@@ -56,7 +56,7 @@ rkyv = { version = "0.7.44", optional = true }
 roaring = "0.10.6"
 roots = "0.0.8"
 serde = { version = "1.0.204", features = ["derive"] }
-serde_json = "1.0.120"
+serde_json = "1.0.122"
 statrs = "0.17.1"
 streaming-stats = "0.2.3"
 thiserror = "1.0"
@@ -68,7 +68,7 @@ vec-collections = "0.4.3"
 codspeed-criterion-compat = "2.6.0"
 proptest = { version = "1.5.0", default-features = false, features = ["std"]}
 rand = "0.8.2"
-tempfile = "3.10.1"
+tempfile = "3.11.0"
 
 [[bench]]
 name = "compute"