Use CalVer #45
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| name: Build and test | |
| on: | |
| push: | |
| branches: | |
| - "main" | |
| - "staging" | |
| - "dev" | |
| pull_request: | |
| branches: | |
| - "*" | |
| env: | |
| PROGRAM_NAME: InteinFinder | |
| jobs: | |
| build: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: | |
| - macos-11 | |
| - ubuntu-20.04 | |
| ocaml-compiler: | |
| - 4.14.1 | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v2 | |
| - run: brew install tree | |
| if: matrix.os == 'macos-11' | |
| - run: echo "LOCAL_PATH=$HOME/.local/bin" >> $GITHUB_ENV | |
| - name: Setup path | |
| run: | | |
| mkdir -p "$LOCAL_PATH" | |
| echo "$LOCAL_PATH" >> $GITHUB_PATH | |
| - name: Setup just | |
| run: | | |
| \curl \ | |
| --proto '=https' \ | |
| --tlsv1.2 \ | |
| -sSf \ | |
| https://just.systems/install.sh \ | |
| | bash -s -- \ | |
| --to "$LOCAL_PATH" \ | |
| --tag 1.13.0 | |
| - name: Download MAFFT | |
| run: | | |
| \curl -L \ | |
| https://mafft.cbrc.jp/alignment/software/mafft-7.490-without-extensions-src.tgz \ | |
| | tar xz \ | |
| && cd mafft-*/core/ && make clean && make && sudo make install | |
| - name: Download & Install MMseqs2 (ubuntu) | |
| run: | | |
| \curl -L \ | |
| https://github.com/soedinglab/MMseqs2/releases/download/13-45111/mmseqs-linux-sse2.tar.gz \ | |
| | tar xz \ | |
| && mv mmseqs/bin/mmseqs "$LOCAL_PATH" | |
| if: matrix.os == 'ubuntu-20.04' | |
| - name: Download & Install MMseqs2 (macOS) | |
| run: | | |
| \curl -L \ | |
| https://github.com/soedinglab/MMseqs2/releases/download/13-45111/mmseqs-osx-universal.tar.gz \ | |
| | tar xz \ | |
| && mv mmseqs/bin/mmseqs "$LOCAL_PATH" | |
| if: matrix.os == 'macos-11' | |
| - name: Download & Install NCBI BLAST+ (ubuntu) | |
| run: | | |
| \curl -L \ | |
| https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.12.0/ncbi-blast-2.12.0+-x64-linux.tar.gz \ | |
| | tar xz \ | |
| && mv ncbi-blast-2.12.0+/bin/rpsblast "${LOCAL_PATH}/rpsblast+" \ | |
| && mv ncbi-blast-2.12.0+/bin/makeprofiledb "${LOCAL_PATH}/makeprofiledb" | |
| if: matrix.os == 'ubuntu-20.04' | |
| - name: Download & Install NCBI BLAST+ (macOS) | |
| run: | | |
| \curl -L \ | |
| https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.12.0/ncbi-blast-2.12.0+-x64-macosx.tar.gz \ | |
| | tar xz \ | |
| && mv ncbi-blast-2.12.0+/bin/rpsblast "${LOCAL_PATH}/rpsblast+" \ | |
| && mv ncbi-blast-2.12.0+/bin/makeprofiledb "${LOCAL_PATH}/makeprofiledb" | |
| if: matrix.os == 'macos-11' | |
| - name: Use OCaml ${{ matrix.ocaml-compiler }} (ubuntu) | |
| uses: ocaml/setup-ocaml@v2 | |
| with: | |
| ocaml-compiler: ${{ matrix.ocaml-compiler }} | |
| dune-cache: true | |
| cache-prefix: v1-${{ matrix.os }} | |
| opam-pin: false | |
| opam-depext: false | |
| if: matrix.os == 'ubuntu-20.04' | |
| - name: Use OCaml ${{ matrix.ocaml-compiler }} (macOS) | |
| uses: ocaml/setup-ocaml@v2 | |
| with: | |
| ocaml-compiler: ${{ matrix.ocaml-compiler }} | |
| dune-cache: false | |
| cache-prefix: v1-${{ matrix.os }} | |
| opam-pin: false | |
| opam-depext: false | |
| if: matrix.os == 'macos-11' | |
| - name: Install tiny_config | |
| run: | | |
| git clone https://github.com/mooreryan/tiny_config.git | |
| cd tiny_config | |
| opam install base otoml yaml | |
| opam pin add tiny_config . | |
| opam pin add tiny_toml . | |
| opam install tiny_config | |
| opam install tiny_toml | |
| - run: opam install --locked . --deps-only --with-doc --with-test | |
| - name: Check dev profile | |
| run: | | |
| opam exec -- just clean | |
| opam exec -- just build_dev | |
| opam exec -- just test_dev | |
| opam exec -- just install_dev | |
| if: matrix.ocaml-compiler == '4.14.1' | |
| # Send the coverage. | |
| - name: Send coverage | |
| run: | | |
| opam install bisect_ppx | |
| opam exec -- just send_coverage | |
| if: matrix.ocaml-compiler == '4.14.1' && matrix.os == 'ubuntu-20.04' | |
| env: | |
| COVERALLS_REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Check release profile | |
| run: | | |
| opam exec -- just clean | |
| opam exec -- just build_release | |
| opam exec -- just test_release | |
| opam exec -- just install_release | |
| if: matrix.ocaml-compiler == '4.14.1' | |
| - name: Upload InteinFinder artifact | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: ${{ env.PROGRAM_NAME }}-${{ matrix.os }} | |
| path: _build/install/default/bin/${{ env.PROGRAM_NAME }} | |
| if: matrix.ocaml-compiler == '4.14.1' | |
| - name: Upload RemoveInteins artifact | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: RemoveInteins-${{ matrix.os }} | |
| path: _build/install/default/bin/RemoveInteins | |
| if: matrix.ocaml-compiler == '4.14.1' |