diff --git a/.github/workflows/qiita-plugin-ci.yml b/.github/workflows/qiita-plugin-ci.yml index 54eb9ac..eaa8ef2 100644 --- a/.github/workflows/qiita-plugin-ci.yml +++ b/.github/workflows/qiita-plugin-ci.yml @@ -2,7 +2,7 @@ on: push: - branches: [ dev ] + branches: [dev] pull_request: jobs: @@ -90,10 +90,16 @@ jobs: conda deactivate # installing this plugin - conda create -q --yes -n qp-spades python=3.6 cmake clang zlib flash spades=3.15.2 + conda create -q --yes -n qp-spades python=3.11 cmake clang zlib flash # spades=3.15.4 conda activate qp-spades - # making sure the installed versions haven't changed + # installing cloudspades + wget https://github.com/ablab/spades/archive/refs/tags/cloudspades-0.1.tar.gz + tar -zxf cloudspades-0.1.tar.gz + cd cloudspades-0.1/assembler + sh spades_compile.sh + bin/spades.py --test + flash_version=`flash --version` spades_version=`spades.py --version` if [[ $flash_version != *"v1.2.11"* ]]; then echo "wrong flash version", $flash_version; exit 1; fi @@ -156,21 +162,21 @@ jobs: - uses: codecov/codecov-action@v1 with: - token: ${{ secrets.CODECOV_TOKEN }} - file: codecov.yml + token: ${{ secrets.CODECOV_TOKEN }} + file: codecov.yml lint: runs-on: ubuntu-latest steps: - - name: flake8 - uses: actions/setup-python@v2 - with: - python-version: 3.9 - - name: install dependencies - run: python -m pip install --upgrade pip - - name: Check out repository code - uses: actions/checkout@v2 - - name: lint - run: | - pip install -q flake8 - flake8 qp_spades setup.py scripts/* + - name: flake8 + uses: actions/setup-python@v2 + with: + python-version: 3.9 + - name: install dependencies + run: python -m pip install --upgrade pip + - name: Check out repository code + uses: actions/checkout@v2 + - name: lint + run: | + pip install -q flake8 + flake8 qp_spades setup.py scripts/*