[MRG] backport github actions to stable branch (3.5.x)

.github/workflows/build_wheel.yml

@@ -0,0 +1,105 @@
+name: cibuildwheel
+
+on:
+  push:
+    branches: [stable]
+    tags: v*
+  pull_request:
+    branches: [stable]
+  schedule:
+    - cron: "0 0 * * *" # daily
+
+jobs:
+  build_wheels:
+    name: Build wheels for ${{ matrix.os }}-${{ matrix.arch }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        build: [
+          linux-x86_64,
+          linux-aarch64,
+          linux-ppc64le,
+          linux-s390x,
+          macos-x86_64,
+        ]
+        include:
+          - build: linux-x86_64
+            os: ubuntu-18.04
+            arch: x86_64
+            macos_target: ''
+          - build: linux-aarch64
+            os: ubuntu-18.04
+            arch: aarch64
+            macos_target: ''
+          - build: linux-ppc64le
+            os: ubuntu-18.04
+            arch: ppc64le
+            macos_target: ''
+          - build: linux-s390x
+            os: ubuntu-18.04
+            arch: s390x
+            macos_target: ''
+          - build: macos-x86_64
+            os: macos-latest
+            arch: x86_64
+            macos_target: 'MACOSX_DEPLOYMENT_TARGET=10.11'
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v2
+        name: Install Python
+        with:
+          python-version: '3.9'
+
+      - name: Install cibuildwheel
+        run: |
+          python -m pip install cibuildwheel==1.8.0
+
+      - name: Set up QEMU
+        if: runner.os == 'Linux'
+        uses: docker/setup-qemu-action@v1
+        with:
+          platforms: all
+
+      - name: Build wheels
+        env:
+          CIBW_BUILD: "cp39-*"
+          CIBW_SKIP: "*-win32 *-manylinux_i686"
+          CIBW_BEFORE_BUILD: 'source .ci/install_cargo.sh'
+          CIBW_ENVIRONMENT: 'PATH="$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
+        with:
+          path: './dist/sourmash*.whl'
+
+  release:
+    name: Publish wheels
+    runs-on: ubuntu-18.04
+    if: startsWith(github.ref, 'refs/tags/v')
+    needs: build_wheels
+
+    steps:
+      - name: Fetch wheels from artifacts
+        id: fetch_artifacts
+        uses: actions/download-artifact@v2
+        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/hypothesis.yml

@@ -2,9 +2,11 @@ name: Hypothesis tests
 
 on:
   push:
-    branches: [master]
+    branches: [latest]
   pull_request:
-    branches: [master]
+    branches: [latest]
+  schedule:
+    - cron: "0 0 * * *" # daily
 
 jobs:
   test:
@@ -20,15 +22,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install -e .[test]
+          pip install tox
 
       - name: Run Hypothesis tests
-        run: |
-          python -m pytest --cov=. --cov-report=xml --run-hypothesis --hypothesis-show-statistics --hypothesis-profile ci
-
-      - name: Upload coverage to Codecov  
-        uses: codecov/codecov-action@v1
-        with:
-            token: ${{ secrets.CODECOV_TOKEN }}
-            file: ./coverage.xml
-            fail_ci_if_error: true
+        run: tox -e hypothesis,coverage

.github/workflows/khmer.yml

@@ -2,9 +2,11 @@ name: khmer compatibility tests
 
 on:
   push:
-    branches: [master]
+    branches: [latest]
   pull_request:
-    branches: [master]
+    branches: [latest]
+  schedule:
+    - cron: "0 0 * * *" # daily
 
 jobs:
   test:
@@ -20,21 +22,10 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install -e .[test]
+          pip install tox
 
       - name: Run tests with latest released khmer
-        run: |
-          python -m pip install khmer
-          python -m pytest -k test_nodegraph --cov=. --cov-report=xml
-
-      - name: Run tests with khmer master tests
-        run: |
-          python -m pip install -U git+https://github.com/dib-lab/khmer.git#egg=khmer
-          python -m pytest -k test_nodegraph --cov=. --cov-report=xml
+        run: tox -e khmer,coverage
 
-      - name: Upload coverage to Codecov  
-        uses: codecov/codecov-action@v1
-        with:
-            token: ${{ secrets.CODECOV_TOKEN }}
-            file: ./coverage.xml
-            fail_ci_if_error: true
+      - name: Run tests with khmer master branch
+        run: tox -e khmer_master,coverage

.github/workflows/metadata.yml

@@ -2,9 +2,11 @@ name: Metadata checks
 
 on:
   push:
-    branches: [master]
+    branches: [latest]
   pull_request:
-    branches: [master]
+    branches: [latest]
+  schedule:
+    - cron: "0 0 * * *" # daily
 
 jobs:
   archive:

.github/workflows/python.yml

@@ -0,0 +1,75 @@
+name: Python tests
+
+on:
+  push:
+    branches: [stable]
+  pull_request:
+    branches: [stable]
+  schedule:
+    - cron: "0 0 * * *" # daily
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-18.04, macos-latest]
+        py: [3.9, 3.8, 3.7]
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.py }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.py }}
+
+      - name: Get pip cache dir
+        id: pip-cache
+        run: |
+          echo "::set-output name=dir::$(pip cache dir)"
+
+      - name: pip cache
+        uses: actions/cache@v2
+        with:
+          path: ${{ steps.pip-cache.outputs.dir }}
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox tox-gh-actions
+
+      - name: Set up Pandoc
+        uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Set up IPFS
+        if: startsWith(runner.os, 'Linux') && (matrix.py == '3.9')
+        uses: ibnesayeed/setup-ipfs@master
+        with:
+          ipfs_version: 0.6
+          run_daemon: true
+
+      - name: Start Redis
+        if: startsWith(runner.os, 'Linux') && (matrix.py == '3.9')
+        uses: supercharge/redis-github-action@4687e0c1d27b144de1dadc32967b7ce7e1227c7f
+        with:
+          redis-version: 6
+
+      - name: tox cache
+        uses: actions/cache@v2
+        with:
+          path: .tox/
+          key: ${{ runner.os }}-tox-${{ hashFiles('**/setup.py') }}
+          restore-keys: |
+            ${{ runner.os }}-tox-
+
+      - name: Test with tox
+        run: tox -e py
+        env:
+          PYTHONDEVMODE: 1

.github/workflows/rust.yml

@@ -2,10 +2,13 @@ name: Rust checks
 
 on:
   push:
-    branches: [master]
+    branches: [latest]
   pull_request:
     paths:
       - 'src/core/**'
+      - 'tests/test-data/**'
+  schedule:
+    - cron: "0 0 * * *" # daily
 
 jobs:
   check:
@@ -125,10 +128,9 @@ jobs:
         run: cargo tarpaulin --all --all-features --timeout 600 --out Xml -- --test-threads 1
 
       - name: Upload Rust coverage to codecov
-        uses: codecov/codecov-action@797e92895ec0eac368405352c0add9af878fe257
+        uses: codecov/codecov-action@v1
         with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          flags: rusttests
+          flags: rust
           fail_ci_if_error: true
 
   lints:
@@ -162,7 +164,7 @@ jobs:
     name: Check if wasm-pack builds a valid package for the sourmash crate
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@master
+      - uses: actions/checkout@v2
 
       - uses: actions-rs/toolchain@v1
         with:
@@ -190,7 +192,7 @@ jobs:
     name: Run tests under wasm32-wasi
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@master
+      - uses: actions/checkout@v2
       - name: Install wasm32-wasi target
         uses: actions-rs/toolchain@v1
         with:
@@ -199,7 +201,7 @@ jobs:
       - name: Install wasmtime
         run: "curl https://wasmtime.dev/install.sh -sSf | bash"
       - name: Add wasmtime to PATH
-        run: echo "::add-path::$HOME/.wasmtime/bin"
+        run: echo "$HOME/.wasmtime/bin" >> $GITHUB_PATH
       - name: Install cargo-wasi command
         uses: actions-rs/cargo@v1
         with:

.github/workflows/rust_publish.yml

@@ -10,7 +10,7 @@ jobs:
     name: Check if wasm-pack builds a valid package for the sourmash crate
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@master
+      - uses: actions/checkout@v2
       - uses: actions-rs/toolchain@v1
         with:
           toolchain: stable