From 080f46b6835d4f02d7fc8254575e8ed4b1f35f3c Mon Sep 17 00:00:00 2001 From: Luiz Irber Date: Fri, 17 Apr 2020 17:42:33 -0700 Subject: [PATCH] fix travis config warnings --- .github/workflows/hypothesis.yml | 9 +++++++- .github/workflows/khmer.yml | 35 ++++++++++++++++++++++++++++++ .github/workflows/rust.yml | 7 ++++-- .travis.yml | 37 +++++++++++++++----------------- setup.py | 2 +- 5 files changed, 66 insertions(+), 24 deletions(-) create mode 100644 .github/workflows/khmer.yml diff --git a/.github/workflows/hypothesis.yml b/.github/workflows/hypothesis.yml index ad01aee6dd..37c11cc6e7 100644 --- 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 new file mode 100644 index 0000000000..e06fe678d8 --- /dev/null +++ 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 index df68c43690..1f10368bfa 100644 --- 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: ${{ matrix.continue }} run: | python -m pip install --upgrade pip python -m pip install -e . diff --git a/.travis.yml b/.travis.yml index 738bd5bf75..180ce0f3ce 100644 --- a/.travis.yml +++ b/.travis.yml @@ -47,12 +47,12 @@ jobs: - "/snap/bin/ipfs --version" - "/snap/bin/ipfs daemon --init --offline &>/dev/null &" services: - - redis-server + - redis - docker - - <<: *test - python: 2.7 - <<: *test python: 3.5 + - <<: *test + python: 2.7 - &wheel stage: build wheel and send to github releases @@ -60,19 +60,18 @@ jobs: services: - docker env: - - CIBW_BUILD='cp37-*' - - CIBW_SKIP='*-manylinux_i686' + - CIBW_BUILD: "'pp36* cp37-*'" # build wheels for PyPy too + - CIBW_SKIP: "'*-win32 *-manylinux_i686'" - CIBW_BEFORE_BUILD='source .travis/install_cargo.sh' - CIBW_ENVIRONMENT='PATH="$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 index 3aac0f2228..99f23bdde5 100644 --- 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",