note on input/output formats #75
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| on: | |
| push: | |
| branches: [master,benchmarking,fasten_normalize] | |
| name: benchmarking | |
| jobs: | |
| build_and_test: | |
| name: Benchmark with ${{matrix.os}} and python ${{ matrix.python-version }} | |
| runs-on: ${{matrix.os}} | |
| strategy: | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.7"] | |
| steps: | |
| - name: install hyperfine | |
| run: | | |
| wget https://github.com/sharkdp/hyperfine/releases/download/v1.13.0/hyperfine-v1.13.0-x86_64-unknown-linux-gnu.tar.gz | |
| tar zxvf hyperfine-v1.13.0-x86_64-unknown-linux-gnu.tar.gz | |
| echo | |
| ls -Fd hyperfine-v1.13.0-x86_64-unknown-linux-gnu/* | |
| echo hyperfine-v1.13.0-x86_64-unknown-linux-gnu >> $GITHUB_PATH | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| mamba-version: "*" | |
| channels: bioconda,conda-forge,defaults | |
| activate-environment: benchmarking | |
| - name: Conda info | |
| shell: bash -l {0} | |
| run: conda info | |
| - name: create conda env | |
| shell: bash -l {0} | |
| run: | | |
| conda info | |
| conda env list | |
| mamba install -n benchmarking seqkit seqtk | |
| - name: env | |
| shell: bash -l {0} | |
| run: | | |
| which seqkit | |
| tree -d | |
| - uses: actions/checkout@v3 | |
| with: | |
| path: fasten | |
| - uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| #- uses: actions-rs/cargo@v1 | |
| # with: | |
| # command: build | |
| # args: --release --all-features | |
| - name: cargo build | |
| run: | | |
| cd fasten && cargo build --release | |
| tree -d | |
| echo "fasten/target/release" >> $GITHUB_PATH | |
| - name: benchmark | |
| shell: bash -l {0} | |
| run: | | |
| export PATH=$PATH:fasten/target/release | |
| which fasten_clean | |
| bash fasten/tests/10_benchmark.sh | |