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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,195 @@ | ||
| name: Build and test | ||
|
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||
| on: | ||
| push: | ||
| branches: | ||
| - "*" | ||
| pull_request: | ||
| branches: | ||
| - "*" | ||
|
|
||
| jobs: | ||
| build: | ||
| strategy: | ||
| matrix: | ||
| name: [ubuntu-gcc-10, | ||
| ubuntu-gcc-11, | ||
| # ubuntu-gcc-11-sanitize, | ||
| ubuntu-gcc-12, | ||
| ubuntu-gcc-12-debugoptimized, | ||
| ubuntu-clang-13, | ||
| # macos-xcode-12.5 | ||
| ] | ||
|
|
||
| include: | ||
| - name: ubuntu-gcc-9 | ||
| os: ubuntu-latest | ||
| compiler: gcc | ||
| version: "9" | ||
| buildtype: "release" | ||
|
|
||
| - name: ubuntu-gcc-10 | ||
| os: ubuntu-latest | ||
| compiler: gcc | ||
| version: "10" | ||
| buildtype: "release" | ||
|
|
||
| - name: ubuntu-gcc-11 | ||
| os: ubuntu-latest | ||
| compiler: gcc | ||
| version: "11" | ||
| buildtype: "release" | ||
|
|
||
| - name: ubuntu-gcc-12 | ||
| os: ubuntu-latest | ||
| compiler: gcc | ||
| version: "12" | ||
| buildtype: "release" | ||
|
|
||
| # To enable this, we'd probably need to add `export ASAN_OPTIONS=detect_odr_violation=0`. | ||
| # | ||
| # - name: ubuntu-gcc-11-sanitize | ||
| # os: ubuntu-latest | ||
| # compiler: gcc | ||
| # version: "11" | ||
| # buildtype: "release" | ||
| # sanitize: "address" | ||
| # | ||
|
|
||
| - name: ubuntu-gcc-12-debugoptimized | ||
| os: ubuntu-latest | ||
| compiler: gcc | ||
| version: "12" | ||
| buildtype: "debugoptimized" | ||
|
|
||
| - name: ubuntu-clang-13 | ||
| os: ubuntu-latest | ||
| compiler: clang | ||
| version: "13" | ||
| buildtype: "release" | ||
|
|
||
| # Currently we get "dyld: Library not loaded: @rpath/librestbed.4.dylib" | ||
| # when attempting to run executables. | ||
| # | ||
| # - name: macos-xcode-12.5 | ||
| # os: macos-latest | ||
| # compiler: xcode | ||
| # version: "12.5" | ||
| # buildtype: "release" | ||
|
|
||
| runs-on: ${{ matrix.os }} | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: 3.8 | ||
|
|
||
| - name: Install (Linux) | ||
| if: runner.os == 'Linux' | ||
| run: | | ||
| sudo apt install -y ccache libboost-all-dev | ||
| sudo rm -rf /usr/local/share/boost | ||
| if [ "${{ matrix.compiler }}" = "gcc" ]; then | ||
| sudo apt-get install -y g++-${{ matrix.version }} | ||
| echo "CC=ccache gcc-${{ matrix.version }}" >> $GITHUB_ENV | ||
| echo "CXX=ccache g++-${{ matrix.version }}" >> $GITHUB_ENV | ||
| else | ||
| sudo apt-get install -y clang-${{ matrix.version }} | ||
| echo "CC=ccache clang-${{ matrix.version }}" >> $GITHUB_ENV | ||
| echo "CXX=ccache clang++-${{ matrix.version }}" >> $GITHUB_ENV | ||
| fi | ||
| - name: Install (macOS) | ||
| if: runner.os == 'macOS' | ||
| run: | | ||
| brew install pkg-config boost ccache coreutils | ||
| echo "DEVELOPER_DIR=/Applications/Xcode_${{ matrix.version }}.app/Contents/Developer" >> $GITHUB_ENV | ||
| echo "CC=ccache clang" >> $GITHUB_ENV | ||
| echo "CXX=ccache clang++" >> $GITHUB_ENV | ||
| - name: Install meson | ||
| run: | | ||
| python3 -mpip install meson ninja | ||
| # Caches for different branches are isolated, so we don't need to put the branch name into the key. | ||
|
|
||
| - name: Prepare ccache timestamp | ||
| id: ccache_cache_timestamp | ||
| run: | | ||
| ccache --set-config=cache_dir=$HOME/.ccache | ||
| if [ "${{ runner.os }}" = "Linux" ]; then | ||
| stamp=$(date '+%s') | ||
| else | ||
| stamp=$(gdate '+%s') | ||
| fi | ||
| echo "${stamp}" | ||
| echo "timestamp=${stamp}" >> $GITHUB_OUTPUT | ||
| - name: ccache cache files | ||
| uses: pat-s/[email protected] | ||
| with: | ||
| path: ~/.ccache | ||
| key: ${{ matrix.name }}-ccache-${{ steps.ccache_cache_timestamp.outputs.timestamp }} | ||
| restore-keys: | | ||
| ${{ matrix.name }}-ccache- | ||
| - name: build restbed | ||
| run: | | ||
| cd | ||
| git clone --recursive https://github.com/corvusoft/restbed.git | ||
| mkdir restbed/build | ||
| cd restbed/build | ||
| cmake .. -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DBUILD_TESTS=NO -DBUILD_SSL=NO -DCMAKE_INSTALL_PREFIX="${HOME}/local/" -G Ninja | ||
| ninja install | ||
| echo "LD_LIBRARY_PATH=${HOME}/local/library:$LD_LIBRARY_PATH" >> $GITHUB_ENV | ||
| - name: build g3log | ||
| run: | | ||
| cd | ||
| git clone https://github.com/KjellKod/g3log.git | ||
| mkdir g3log/build | ||
| cd g3log/build | ||
| cmake .. -DCMAKE_INSTALL_PREFIX="/usr/" -DUSE_DYNAMIC_LOGGING_LEVELS=ON -G Ninja | ||
| ninja package | ||
| sudo dpkg -i g3log*.deb | ||
| - name: Configure otcetera | ||
| run: | | ||
| cd ${GITHUB_WORKSPACE} | ||
| ARGS="${ARGS} -Drestbed_dir=${HOME}/local/" | ||
| if [ "${{ runner.os }}" = "Linux" ] && [ "${{ matrix.name }}" != "windows" ] && [ "${{ matrix.sanitize }}" != "" ] ; then | ||
| # Address sanitizer can't find its dylibs on OS X? | ||
| ARGS="${ARGS} -Db_sanitize=${{ matrix.sanitize }}" | ||
| fi | ||
| echo "CPPFLAGS=-g $CPPFLAGS" >> $GITHUB_ENV | ||
| echo meson setup build --prefix=$HOME/local --buildtype=${{ matrix.buildtype }} ${ARGS} | ||
| meson setup build --prefix=$HOME/local --buildtype=${{ matrix.buildtype }} ${ARGS} | ||
| - name: Build otcetera | ||
| run: | | ||
| ccache -p | ||
| ninja -C build install -j4 | ||
| ccache -s | ||
| - name: Run otcetera tests | ||
| run: | | ||
| $HOME/local/bin/otc-version-reporter | ||
| $HOME/local/bin/otc-solve-subproblem -h | ||
| python3 -mpip install requests | ||
| ninja -C build test | ||
| - name: Upload test files if they failed | ||
| uses: actions/upload-artifact@v3 | ||
| if: failure() | ||
| with: | ||
| name: test-results-${{ matrix.name }} | ||
| path: expected | ||
|
|
||
| - name: Upload test files if they failed | ||
| uses: actions/upload-artifact@v3 | ||
| if: failure() | ||
| with: | ||
| name: test-resultsws-${{ matrix.name }} | ||
| path: expected-ws | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,6 @@ | ||
| *~ | ||
| #*# | ||
| .#* | ||
| build* | ||
| COPYING | ||
| INSTALL | ||
| *gmon.out | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,9 @@ | ||
| [ | ||
| { | ||
| "action": "edit", | ||
| "taxon": { | ||
| "ott_id": 2, | ||
| "flags": "edited,hybrid,hidden" | ||
| } | ||
| } | ||
| ] |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,9 @@ | ||
| [ | ||
| { | ||
| "action": "add", | ||
| "forward": { | ||
| "former": 6520249, | ||
| "redirect_to": 100 | ||
| } | ||
| } | ||
| ] |
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