Allow GBZ files to contain reference paths without haplotype numbers #1339
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| name: Test Mac | |
| # Run on our main branch and any PRs to it, and on release tags, but not every | |
| # commit in every branch. | |
| on: | |
| push: | |
| branches: | |
| - master | |
| tags: | |
| - "*" | |
| pull_request: | |
| branches: | |
| - master | |
| jobs: | |
| testmac: | |
| name: Test on Mac | |
| runs-on: macos-12 | |
| steps: | |
| - name: Use cache | |
| uses: actions/cache@v2 | |
| with: | |
| path: | | |
| deps | |
| lib | |
| include | |
| bin | |
| key: ${{ runner.os }}-12-${{ github.ref }} | |
| # Restore keys are a "list", but really only a multiline string is | |
| # accepted. Also we match by prefix. And the most recent cache is | |
| # used, not the most specific. | |
| # See: https://docs.github.com/en/actions/guides/caching-dependencies-to-speed-up-workflows#matching-a-cache-key | |
| restore-keys: | | |
| ${{ runner.os }}-12-${{ github.base_ref }} | |
| ${{ runner.os }}-12 | |
| - name: Checkout code without submodules | |
| uses: actions/checkout@v2 | |
| - name: Get or restore dependencies | |
| run: scripts/restore-deps.sh | |
| - name: Install packages | |
| # We don't use artemnovichkov/action-homebrew because that's for Linux. | |
| # We uninstall everything we don't need in order to prevent linking | |
| # conflicts with existing/outdated packages, which we can't resolve | |
| # because there's no way to tell Homebrew to force-link when installing | |
| # from a Brewfile. We also update Protobuf to make sure we have 3.21.3+ | |
| # to avoid problems with ABI changes with/without -DNDEBUG. | |
| # And we update libomp to make extra sure it will be picked up by the compiler. | |
| # We pre-install a pinned txm to work around https://github.com/anko/txm/issues/8 | |
| run: | | |
| brew bundle cleanup --force && \ | |
| brew bundle install && \ | |
| brew update && \ | |
| brew install protobuf && \ | |
| brew install libomp && \ | |
| npm install -g [email protected] && \ | |
| brew config && \ | |
| (brew doctor || echo "brew doctor is unhappy") | |
| - name: Run build and test | |
| run: | | |
| export VG_FULL_TRACEBACK=1 | |
| echo "Build with $(nproc) threads" | |
| set +e | |
| make -j$(nproc) test | |
| RETVAL=$? | |
| set -e | |
| # Whether vg testing succeeds or fails, see if we can get any Apple crash logs for it. | |
| ls ~/Library/Logs/DiagnosticReports/ | |
| for CRASH_FILE in $(ls ~/Library/Logs/DiagnosticReports/vg-* 2>/dev/null) ; do | |
| echo "vg crash report found: ${CRASH_FILE}" | |
| cat ${CRASH_FILE} | |
| done | |
| exit $RETVAL | |
| shell: bash |