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

…rocksdb_open

.envrc

@@ -1 +1,6 @@
-use flake
+#use flake
+
+PATH=~/.pixi/bin:$PATH
+
+watch_file pixi.lock
+eval "$(pixi shell-hook)"

.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

@@ -0,0 +1,34 @@
+name: codspeed-benchmarks
+
+on:
+  # Run on pushes to the main branch
+  push:
+    branches:
+      - "latest"
+  # Run on pull requests
+  pull_request:
+  # `workflow_dispatch` allows CodSpeed to trigger backtest
+  # performance analysis in order to generate initial data.
+  workflow_dispatch:
+
+jobs:
+  benchmarks-rust:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup rust toolchain, cache and cargo-codspeed binary
+        uses: moonrepo/setup-rust@v1
+        with:
+          channel: stable
+          cache-target: release
+          bins: cargo-codspeed
+
+      - name: Build the benchmark target(s)
+        run: cargo codspeed build -p sourmash
+
+      - name: Run the benchmarks
+        uses: CodSpeedHQ/action@v3
+        with:
+          run: "cd src/core && cargo codspeed run"
+          token: ${{ secrets.CODSPEED_TOKEN }}

.github/workflows/dev_envs.yml

@@ -3,6 +3,9 @@ on:
   pull_request:
   push:
     branches: [latest]
+concurrency:
+  group: ${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/latest' }}
 jobs:
   nix:
     runs-on: ${{ matrix.os }}
@@ -15,16 +18,40 @@ jobs:
         fetch-depth: 0
 
     - name: Install Nix
-      uses: DeterminateSystems/nix-installer-action@v12
+      uses: DeterminateSystems/nix-installer-action@v13
     - name: Run the Magic Nix Cache
       uses: DeterminateSystems/magic-nix-cache-action@v7
 
     - run: nix run .# -- --version
 
     - run: nix develop --command bash -c "tox -e py310"
 
+  pixi:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-14]
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: set up pixi
+      uses: prefix-dev/[email protected]
+      with:
+        pixi-version: v0.26.1
+        cache: true
+        frozen: true
+
+    - name: run tests for 3.10
+      shell: pixi run bash {0}
+      run: tox -e py310
+
   mamba:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-14]
     steps:
     - uses: actions/checkout@v4
       with:
@@ -42,20 +69,11 @@ jobs:
     - name: setup conda
       uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca
       with:
-        auto-update-conda: true
         python-version: "3.10"
-        channels: conda-forge,bioconda
-        miniforge-variant: Mambaforge
         miniforge-version: latest
-        use-mamba: true
-        mamba-version: "*"
+        environment-file: dev.yml
         activate-environment: sourmash_dev
         auto-activate-base: false
-        use-only-tar-bz2: true
-
-    - name: install dependencies
-      shell: bash -l {0}
-      run: mamba install 'tox>=3.27,<4' tox-conda rust git compilers pandoc libstdcxx-ng
 
     - name: run tests for 3.10
       shell: bash -l {0}

.github/workflows/rust.yml

@@ -260,7 +260,7 @@ jobs:
         uses: actions-rs/cargo@v1
         with:
           command: build
-          args: --all-features --tests
+          args: --all-features
 
   check_cbindgen:
     name: "Check if cbindgen runs cleanly for generating the C headers"

.gitignore

@@ -37,3 +37,6 @@ wasm-pack.log
 # nix
 .direnv/
 result
+
+# pixi
+.pixi/

.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: v0.5.1
+    rev: v0.5.6
     hooks:
       - id: ruff-format
       - id: ruff