fix travis config warnings

sourmash-bio · Apr 19, 2020 · 080f46b · 080f46b
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commit 080f46b
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Showing 5 changed files with 66 additions and 24 deletions.
diff --git a/.github/workflows/hypothesis.yml b/.github/workflows/hypothesis.yml
@@ -24,4 +24,11 @@ jobs:
 
       - name: Run Hypothesis tests
         run: |
-          python -m pytest --run-hypothesis --hypothesis-show-statistics --hypothesis-profile ci
+          python -m pytest --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
diff --git a/.github/workflows/khmer.yml b/.github/workflows/khmer.yml
@@ -0,0 +1,35 @@
+name: khmer compatibility tests
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v1
+
+      - name: Set up Python 3.7
+        uses: actions/setup-python@v1
+        with:
+          python-version: "3.7"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[test]
+          python -m pip install khmer
+
+      - name: Run khmer tests
+        run: |
+          python -m pytest -k test_nodegraph --cov-report=xml
+
+      - name: Upload coverage to Codecov  
+        uses: codecov/codecov-action@v1
+        with:
+            token: ${{ secrets.CODECOV_TOKEN }}
+            file: ./coverage.xml
+            fail_ci_if_error: true
diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
@@ -39,15 +39,19 @@ jobs:
           - build: macos
             os: macos-latest
             rust: stable
+            continue: false
           - build: windows
             os: windows-latest
             rust: stable
+            continue: true
           - build: beta
             os: ubuntu-latest
             rust: beta
+            continue: false
           - build: stable
             os: ubuntu-latest
             rust: stable
+            continue: false
     steps:
       - uses: actions/checkout@v1
 
@@ -57,13 +61,12 @@ jobs:
           override: true
 
       - name: Set up Python 3.8
-        if: matrix.os != 'windows-latest'
         uses: actions/setup-python@v1
         with:
           python-version: "3.8"
 
       - name: Install dependencies
-        if: matrix.os != 'windows-latest'
+        continue-on-error: ${{ matrix.continue }}
         run: |
           python -m pip install --upgrade pip
           python -m pip install -e .

diff --git a/.travis.yml b/.travis.yml
@@ -47,32 +47,31 @@ jobs:
         - "/snap/bin/ipfs --version"
         - "/snap/bin/ipfs daemon --init --offline &>/dev/null &"
       services:
-        - redis-server
+        - redis
         - docker
-    - <<: *test
-      python: 2.7
     - <<: *test
       python: 3.5
+    - <<: *test
+      python: 2.7
 
     - &wheel
       stage: build wheel and send to github releases
       python: 3.7
       services:
         - docker
       env:
-        - CIBW_BUILD='cp37-*'
-        - CIBW_SKIP='*-manylinux_i686'
+        - CIBW_BUILD: "'pp36* cp37-*'"    # build wheels for PyPy too
+        - CIBW_SKIP: "'*-win32 *-manylinux_i686'"
         - CIBW_BEFORE_BUILD='source .travis/install_cargo.sh'
         - CIBW_ENVIRONMENT='PATH="$HOME/.cargo/bin:$PATH"'
         - CIBW_ENVIRONMENT_MACOS='MACOSX_DEPLOYMENT_TARGET=10.11'
-      before_script: skip
+      before_script:
+        - python3 -m pip install cibuildwheel==1.3.0
       script:
-        - python -m pip install -U pip setuptools
-        - python -m pip install cibuildwheel==1.3.0
-        - python -m cibuildwheel --output-dir wheelhouse
+        - python3 -m cibuildwheel --output-dir wheelhouse
       deploy:
         provider: releases
-        api_key:
+        token:
           secure: "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"
         file_glob: true
         file: wheelhouse/sourmash*.whl
@@ -84,18 +83,16 @@ jobs:
       osx_image: xcode10.1
       language: shell
     - <<: *wheel
-      os: windows
-      language: shell
-      before_install:
-        - choco install python --version 3.8.0
-        - export PATH="/c/Python38:/c/Python38/Scripts:$PATH"
-        - ln -s /c/Python38/python.exe /c/Python38/python3.exe
-    - <<: *wheel
-      arch: aarch64
+      arch: arm64
     - <<: *wheel
       arch: ppc64le
-    - <<: *wheel
-      arch: s390x
+    #- <<: *wheel
+    #  os: windows
+    #  language: shell
+    #  before_install:
+    #    - choco install python --version 3.8.0
+    #    - export PATH="/c/Python38:/c/Python38/Scripts:$PATH"
+    #    - ln -s /c/Python38/python.exe /c/Python38/python3.exe
 
 stages:
   - check

diff --git a/setup.py b/setup.py
@@ -77,7 +77,7 @@ def build_native(spec):
     "zip_safe": False,
     "platforms": "any",
     "extras_require": {
-        'test' : ['pytest', 'pytest-cov', 'recommonmark', 'hypothesis', 'khmer>=2.1'],
+        'test' : ['pytest', 'pytest-cov', 'recommonmark', 'hypothesis'],
         'demo' : ['jupyter', 'jupyter_client', 'ipython'],
         'doc' : ['sphinx', 'recommonmark', 'alabaster',
                  "sphinxcontrib-napoleon", "nbsphinx",