Move fasta concatnate codes to phylotree module #14
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| name: Conda build | |
| on: | |
| push: | |
| branches: ["main", "dev"] | |
| paths: ["**.py", "environment.yml"] | |
| pull_request: | |
| branches: ["main", "dev"] | |
| paths: ["**.py", "environment.yml"] | |
| workflow_dispatch: | |
| jobs: | |
| build_ASTER: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Cache ASTER binary | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.local/bin/astral | |
| key: ASTER-Linux | |
| - name: Install dependencies | |
| run: | | |
| if ! [ -f ~/.local/bin/astral ]; \ | |
| then sudo apt-get install build-essential cmake g++ wget unzip; \ | |
| fi | |
| - name: Build ASTER | |
| run: | | |
| if ! [ -f ~/.local/bin/astral ]; \ | |
| then \ | |
| wget https://github.com/chaoszhang/ASTER/archive/refs/heads/Linux.zip; \ | |
| unzip Linux.zip; \ | |
| cd ASTER-Linux; \ | |
| make; \ | |
| fi | |
| - name: Move Binary | |
| run: | | |
| if ! [ -f ~/.local/bin/astral ]; \ | |
| then \ | |
| mkdir -p ~/.local/bin; \ | |
| cp ASTER-Linux/bin/astral ~/.local/bin/; \ | |
| chmod +x ~/.local/bin/astral; \ | |
| fi | |
| working-directory: ${{ github.workspace }} | |
| - name: Export ASTER to PATH and verify | |
| run: | | |
| export PATH=$PATH:$HOME/.local/bin | |
| which astral | |
| build-conda: | |
| runs-on: ubuntu-latest | |
| needs: build_ASTER | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: environment.yml | |
| create-args: >- | |
| python=3.10 | |
| flake8 | |
| pytest | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=130 --statistics | |
| shell: micromamba-shell {0} | |
| - name: Install package | |
| run: | | |
| pip install . | |
| shell: micromamba-shell {0} | |
| - name: Cache ASTER binary | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.local/bin/astral | |
| key: ASTER-Linux | |
| - name: Test with pytest | |
| run: | | |
| pytest | |
| shell: micromamba-shell {0} |