Merge branch 'latest' into joss-ani

.cargo/config

@@ -0,0 +1,5 @@
+[target.x86_64-unknown-linux-musl]
+rustflags = ["-C", "target-feature=-crt-static"]
+
+[target.aarch64-unknown-linux-musl]
+rustflags = ["-C", "target-feature=-crt-static"]

.ci/install_cargo.sh

@@ -1,4 +1,10 @@
 #! /bin/sh
-curl https://sh.rustup.rs -sSf | sh -s -- -y --default-toolchain stable
+curl https://sh.rustup.rs -sSf | sh -s -- -y --default-toolchain=stable
+rustup show
 export PATH="$HOME/.cargo/bin:$PATH"
 rustc -V
+rustup target add aarch64-apple-darwin
+
+# update crates.io index without updating Cargo.lock
+export CARGO_NET_GIT_FETCH_WITH_CLI=true
+cargo update --dry-run

.envrc

@@ -0,0 +1 @@
+use flake

.github/PULL_REQUEST_TEMPLATE.md

@@ -8,8 +8,10 @@ Please also be sure to note here if file formats, command-line
 interface, and/or the top-level sourmash API will change because of
 this PR.
 
-If you are a new contributor, please provide
-[your ORCID](https://orcid.org).  If you don't have one, please
+If you are a new contributor, please add your name and
+[your ORCID](https://orcid.org) to the `pyproject.toml` author list
+(maintaining alphabetical order by last name).
+If you don't have an ORCID, please
 [register for one](https://orcid.org/register).
 
 Once the items above are done, and all checks pass, request a review!

.github/dependabot.yml

@@ -3,12 +3,17 @@ updates:
 - package-ecosystem: pip
   directory: "/"
   schedule:
-    interval: daily
-    time: "13:00"
+    interval: weekly
   open-pull-requests-limit: 10
 - package-ecosystem: cargo
   directory: "/"
   schedule:
-    interval: daily
-    time: "13:00"
+    interval: weekly
+  allow:
+    - dependency-type: "direct"
   open-pull-requests-limit: 10
+  rebase-strategy: "disabled"  
+- package-ecosystem: "github-actions"
+  directory: "/"
+  schedule:
+    interval: weekly

.github/workflows/asv.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 0
 
@@ -22,10 +22,10 @@ jobs:
         git checkout latest
         git checkout -
 
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v1
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.7
+        python-version: "3.10"
 
     - uses: actions-rs/toolchain@v1
       with:

.github/workflows/build_wheel.yml

@@ -16,82 +16,55 @@ jobs:
       matrix:
         build: [
           linux-x86_64,
-          linux-aarch64,
-          linux-ppc64le,
-          linux-s390x,
           macos-x86_64,
+          macos-arm64,
         ]
         include:
           - build: linux-x86_64
-            os: ubuntu-18.04
+            os: ubuntu-20.04
             arch: x86_64
             macos_target: ''
-          - build: linux-aarch64
-            os: ubuntu-18.04
-            arch: aarch64
-            macos_target: ''
-          - build: linux-ppc64le
-            os: ubuntu-18.04
-            arch: ppc64le
-            macos_target: ''
-          - build: linux-s390x
-            os: ubuntu-18.04
-            arch: s390x
-            macos_target: ''
           - build: macos-x86_64
             os: macos-latest
             arch: x86_64
-            macos_target: 'MACOSX_DEPLOYMENT_TARGET=10.11'
+            macos_target: 'MACOSX_DEPLOYMENT_TARGET=10.11 CARGO_BUILD_TARGET=x86_64-apple-darwin'
+          - build: macos-arm64
+            os: macos-latest
+            arch: arm64
+            macos_target: 'MACOSX_DEPLOYMENT_TARGET=11 CARGO_BUILD_TARGET=aarch64-apple-darwin'
       fail-fast: false
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
         name: Install Python
         with:
           python-version: '3.9'
 
-      - name: Install cibuildwheel
-        run: |
-          python -m pip install cibuildwheel==1.8.0
-
-      - name: Set up QEMU
-        if: runner.os == 'Linux'
-        uses: docker/setup-qemu-action@v1
-        with:
-          platforms: all
-
       - name: Build wheels
+        uses: pypa/cibuildwheel@v2.11.3
         env:
-          CIBW_BUILD: "cp39-*"
-          CIBW_SKIP: "*-win32 *-manylinux_i686"
-          CIBW_BEFORE_BUILD: 'source .ci/install_cargo.sh'
-          CIBW_ENVIRONMENT: 'PATH="$HOME/.cargo/bin:$PATH"'
           CIBW_ENVIRONMENT_MACOS: ${{ matrix.macos_target }}
-          CIBW_BUILD_VERBOSITY: 3
           CIBW_ARCHS_LINUX: ${{ matrix.arch }}
           CIBW_ARCHS_MACOS: ${{ matrix.arch }}
-        run: |
-          python -m cibuildwheel --output-dir dist
-          ls -lR ./dist
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
-          path: './dist/sourmash*.whl'
+          path: './wheelhouse/sourmash*.whl'
 
   release:
     name: Publish wheels
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-20.04
     if: startsWith(github.ref, 'refs/tags/v')
     needs: build_wheels
 
     steps:
       - name: Fetch wheels from artifacts
         id: fetch_artifacts
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           path: 'wheels/'
 

.github/workflows/build_wheel_all_archs.yml

@@ -0,0 +1,99 @@
+name: cibuildwheel_ubuntu
+
+on:
+  #pull_request:        # use for testing modifications to this action
+  push:
+    branches: [latest]
+    tags: v*
+  schedule:
+    - cron: "0 0 * * *" # daily
+
+jobs:
+  build_wheels:
+    name: Build wheels for ${{ matrix.os }}-${{ matrix.arch }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        build: [
+          linux-aarch64,
+          linux-ppc64le,
+          linux-s390x,
+        ]
+        include:
+          - build: linux-aarch64
+            os: ubuntu-20.04
+            arch: aarch64
+            macos_target: ''
+          - build: linux-ppc64le
+            os: ubuntu-20.04
+            arch: ppc64le
+            macos_target: ''
+          - build: linux-s390x
+            os: ubuntu-20.04
+            arch: s390x
+            macos_target: ''
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v4
+        name: Install Python
+        with:
+          python-version: '3.9'
+
+      # Added due to weird error when building inside docker container
+      # for other platforms...
+      # https://github.com/JonasAlfredsson/docker-nginx-certbot/issues/30
+      - name: Set Swap Space
+        if: runner.os == 'Linux'
+        uses: pierotofy/set-swap-space@v1.0
+        with:
+          swap-size-gb: 10
+      - run: |
+          # Workaround for https://github.com/rust-lang/cargo/issues/8719
+          sudo mkdir -p /var/lib/docker
+          sudo mount -t tmpfs -o size=10G none /var/lib/docker
+          sudo systemctl restart docker
+        if: runner.os == 'Linux'
+
+      - name: Set up QEMU
+        if: runner.os == 'Linux'
+        uses: docker/setup-qemu-action@v2
+        with:
+          platforms: all
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.11.3
+        env:
+          CIBW_ENVIRONMENT_MACOS: ${{ matrix.macos_target }}
+          CIBW_ARCHS_LINUX: ${{ matrix.arch }}
+          CIBW_ARCHS_MACOS: ${{ matrix.arch }}
+          CARGO_NET_GIT_FETCH_WITH_CLI: true
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: './wheelhouse/sourmash*.whl'
+
+  release:
+    name: Publish wheels
+    runs-on: ubuntu-20.04
+    if: startsWith(github.ref, 'refs/tags/v')
+    needs: build_wheels
+
+    steps:
+      - name: Fetch wheels from artifacts
+        id: fetch_artifacts
+        uses: actions/download-artifact@v3
+        with:
+          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}}/artifact
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/dev_envs.yml

@@ -7,32 +7,39 @@ jobs:
   nix:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2.3.4
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 0
 
     - name: Cache nix store
       id: cache-nix
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
-        path: /nix/store
-        key: nix-${{ hashFiles('shell.nix') }}-${{ hashFiles('nix/**') }}
+        path: |
+          ~/.nix-portable/store
+          ~/bin/nix-portable
+        key: nix-${{ hashFiles('shell.nix') }}-${{ hashFiles('nix/**') }}-v009
 
-    - uses: cachix/install-nix-action@v12
-      with:
-        nix_path: nixpkgs=channel:nixos-20.09
+    - name: Install nix-portable
+      if: steps.cache-nix.outputs.cache-hit != 'true'
+      run: |
+        mkdir ~/bin
+        wget -qO ~/bin/nix-portable https://github.com/DavHau/nix-portable/releases/download/v009/nix-portable
+        chmod +x ~/bin/nix-portable
+
+    - run: ~/bin/nix-portable nix-shell --command "tox -e py39"
 
-    - run: nix-shell --command "tox -e py39"
+    - run: ~/bin/nix-portable nix run . -- --version
 
   mamba:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2.3.4
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 0
 
     - name: cache conda
-      uses: actions/cache@v1
+      uses: actions/cache@v3
       env:
         CACHE_NUMBER: 0
       with:
@@ -41,7 +48,7 @@ jobs:
           ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
 
     - name: setup conda
-      uses: conda-incubator/setup-miniconda@e23d871804685e8c52189e5bd45e9145019f10af
+      uses: conda-incubator/setup-miniconda@3b0f2504dd76ef23b6d31f291f4913fb60ab5ff3
       with:
         auto-update-conda: true
         python-version: 3.9

.github/workflows/hypothesis.yml

@@ -11,12 +11,14 @@ jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
 
-      - name: Set up Python 3.7
-        uses: actions/setup-python@v1
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
         with:
-          python-version: "3.7"
+          python-version: "3.10"
 
       - name: Install dependencies
         run: |

.github/workflows/metadata.yml

@@ -12,8 +12,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout sources
-        uses: actions/checkout@v1
+        uses: actions/checkout@v3
 
       - name: Trigger new archival in software heritage on new tags
         if: startsWith(github.ref, 'refs/tags/')
-        run: curl https://archive.softwareheritage.org/api/1/origin/save/git/url/https://github.com/dib-lab/sourmash.git/
+        run: curl https://archive.softwareheritage.org/api/1/origin/save/git/url/https://github.com/sourmash-bio/sourmash.git/