Merge branch 'latest' into update/joss

.github/dependabot.yml

@@ -12,7 +12,6 @@ updates:
   allow:
     - dependency-type: "direct"
   open-pull-requests-limit: 10
-  rebase-strategy: "disabled"  
 - package-ecosystem: "github-actions"
   directory: "/"
   schedule:

.github/workflows/build_wheel.yml

@@ -45,7 +45,7 @@ jobs:
           python-version: '3.9'
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.12.0
+        uses: pypa/cibuildwheel@v2.15.0
         env:
           CIBW_ENVIRONMENT_MACOS: ${{ matrix.macos_target }}
           CIBW_ARCHS_LINUX: ${{ matrix.arch }}
@@ -55,11 +55,40 @@ jobs:
         with:
           path: './wheelhouse/sourmash*.whl'
 
+  build_wasm:
+    runs-on: ubuntu-20.04
+    env:
+        PYODIDE_VERSION: "0.23.0"
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+           python-version: "3.11.2"
+      - run: |
+          pip install pyodide-build==${PYODIDE_VERSION} "pydantic<2"
+          pyodide config get emscripten_version  # trigger setup
+          echo EMSCRIPTEN_VERSION=$(pyodide config get emscripten_version) >> $GITHUB_ENV
+      - uses: mymindstorm/setup-emsdk@v12
+        with:
+           version: ${{ env.EMSCRIPTEN_VERSION }}
+      - uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          target: wasm32-unknown-emscripten
+      - run: |
+          export RUSTC_BOOTSTRAP=1
+          pyodide build
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: './dist/sourmash*.whl'
+
+
   release:
     name: Publish wheels
     runs-on: ubuntu-20.04
     if: startsWith(github.ref, 'refs/tags/v')
-    needs: build_wheels
+    needs: [build_wheels, build_wasm]
 
     steps:
       - name: Fetch wheels from artifacts

.github/workflows/build_wheel_all_archs.yml

@@ -66,7 +66,7 @@ jobs:
           platforms: all
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.12.0
+        uses: pypa/cibuildwheel@v2.15.0
         env:
           CIBW_ENVIRONMENT_MACOS: ${{ matrix.macos_target }}
           CIBW_ARCHS_LINUX: ${{ matrix.arch }}

.github/workflows/dev_envs.yml

@@ -11,14 +11,19 @@ jobs:
       with:
         fetch-depth: 0
 
-    - uses: cachix/install-nix-action@v18
+    - uses: cachix/install-nix-action@v22
       with:
         extra_nix_config: |
           access-tokens = github.com=${{ secrets.GITHUB_TOKEN }}
 
+    - uses: cachix/cachix-action@v12
+      with:
+        name: sourmash-bio
+        authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
+
     - run: nix run .# -- --version
 
-    - run: nix-shell --command "tox -e py39"
+    - run: nix-shell --command "tox -e py310"
 
   mamba:
     runs-on: ubuntu-latest

.github/workflows/hypothesis.yml

@@ -27,3 +27,10 @@ jobs:
 
       - name: Run Hypothesis tests
         run: tox -e hypothesis,coverage
+
+      - name: Upload Python coverage to codecov
+        uses: codecov/codecov-action@v3
+        with:
+          flags: hypothesis-py
+          fail_ci_if_error: true
+          files: .tox/coverage.xml

.github/workflows/python.yml

@@ -57,7 +57,7 @@ jobs:
 
       - name: Start Redis
         if: startsWith(runner.os, 'Linux') && (matrix.py == '3.9')
-        uses: supercharge/redis-github-action@4b67a313c69bc7a90f162e8d810392fffe10d3b5
+        uses: supercharge/redis-github-action@1.6.0
         with:
           redis-version: 6
 
@@ -73,3 +73,10 @@ jobs:
         run: tox
         env:
           PYTHONDEVMODE: 1
+
+      - name: Upload Python coverage to codecov
+        uses: codecov/codecov-action@v3
+        with:
+          flags: python
+          fail_ci_if_error: true
+          files: .tox/coverage.xml

.github/workflows/rust.yml

@@ -268,17 +268,17 @@ jobs:
 
       - uses: actions-rs/toolchain@v1
         with:
-          toolchain: 1.56.1
+          toolchain: "1.64.0"
           override: true
 
       - name: check if README matches MSRV defined here
-        run: grep '1.56.1' src/core/README.md
+        run: grep '1.64.0' src/core/README.md
 
       - name: Check if it builds properly
         uses: actions-rs/cargo@v1
         with:
           command: build
-          args: --all-features
+          args: --all-features --tests
 
   check_cbindgen:
     name: "Check if cbindgen runs cleanly for generating the C headers"

.gitignore

@@ -17,14 +17,13 @@ sourmash.egg-info
 *.so
 .coverage
 .pytest_cache
+**/*.pyc
 .python-version
 src/sourmash/version.py
 *.DS_Store
 .tox
-src/sourmash/_lowlevel*.py
+src/sourmash/_lowlevel/*
 .env
-Pipfile
-Pipfile.lock
 target/
 .eggs
 .asv

.pre-commit-config.yaml

@@ -28,10 +28,10 @@ repos:
 # format using black
 # when the full codebase is black, use it directly;
 #  while it isn't, let's use darker to format new/changed code
--   repo: https://github.com/akaihola/darker
-    rev: 1.2.1
-    hooks:
-    -   id: darker
+- repo: https://github.com/akaihola/darker
+  rev: 1.7.1
+  hooks:
+    - id: darker
 #- repo: https://github.com/psf/black
 #  rev: 20.8b1
 #  hooks: