OpenMS Homebrew tap

Nightly Homebrew bottles of OpenMS built from the nightly branch of OpenMS/OpenMS.

brew install openms/openms/openms      # TOPP command-line tools (pulls in libopenms)
brew install openms/openms/openms-gui  # TOPPView, TOPPAS, INIFileEditor
brew install openms/openms/libopenms   # only the C++ library, e.g. to build against it

Or brew tap openms/openms and then brew install openms.

Formula	Contents	Depends on
libopenms	libOpenMS, libOpenSwathAlgo, libOpenMS_CLI, headers, CMake package, share/OpenMS (incl. PeptDeep models)	—
openms	TOPP command-line tools, share/OpenMS/TOOLS/OpenMS-TOPP.tsv (keg-only)	libopenms
openms-gui	libOpenMS_GUI, TOPPView, TOPPAS, INIFileEditor (app bundles on macOS), ExecutePipeline, ImageCreator; only these entry points are linked into bin	libopenms, openms, Qt

openms is keg-only: its ~150 tools have generic names (FileInfo clashes with leptonica's fileinfo on case-insensitive file systems) and are not linked into HOMEBREW_PREFIX/bin. To use them, add them to PATH:

export PATH="$(brew --prefix openms)/bin:$PATH"

They find their tool registry relative to themselves, so no other setup is needed. openms-gui lays out the GUI in libexec as a merged installation (libexec/bin holds the GUI tools plus links to all TOPP tools, libexec/share/OpenMS/TOOLS both registries), so TOPPView and TOPPAS find the TOPP tools without openms being linked. On macOS, link the apps with ln -sf "$(brew --prefix openms-gui)"/Applications/*.app /Applications/.

The three formulae are built from the same OpenMS commit: libopenms with BUILD_TOPP_TOOLS=OFF WITH_GUI=OFF, the other two against the installed libopenms with OPENMS_USE_INSTALLED_LIBRARY=ON (OpenMS#10339). Their versions must always match exactly. pyOpenMS is intentionally not packaged here.

Upgrading from the earlier all-in-one openms formula: libopenms takes over the library files (link_overwrite), so brew upgrade openms works without manual unlinking.

How bottles are built

Bottles are built with the same brew commands brew test-bot runs (install --build-bottle, bottle --json, audit, reinstall from the bottle, linkage --test, test; see build-bottles.sh) and published with brew pr-upload to GitHub Packages, like homebrew-core. brew test-bot --only-formulae itself is not used, because it uninstalls and reinstalls the whole dependency tree around every formula, which took about half of each CI run. The bottle downloads of the dependency trees are kept in the Actions cache, keyed on the exact dependency versions.

• nightly.yml: triggered by OpenMS/OpenMS after the nightly branch moves (repository_dispatch, type openms-nightly), with a daily fallback at 04:00 UTC and manual workflow_dispatch. It
  1. pins all three formulae to the nightly commit (bump-nightly.py): source tarball, version X.Y.Z-pre.YYYYMMDD, and resources for everything OpenMS' CMake would download (FetchContent deps, PeptDeep ONNX models; only libopenms needs them), read from OpenMS' CMake files at that commit;
  2. builds bottles on macOS and Linux (build.yml);
  3. uploads them to ghcr.io/openms/openms and pushes the bottle commit to main.
• tests.yml / publish.yml: the standard brew tap-new pull request flow (build as above, then brew pr-pull) for manual formula changes.

Compiler cache

A full OpenMS build takes hours on hosted runners, so CI keeps a ccache per runner OS in the Actions cache. The formulae only use it when HOMEBREW_OPENMS_CCACHE and HOMEBREW_OPENMS_CCACHE_DIR are set (CI only). The cache is saved by the nightly run (default-branch scope, saved even on failure) and restored by every run, including pull requests.

Triggering from OpenMS/OpenMS

Add to .github/workflows/update_nightly.yml after the nightly branch is updated, using a token (e.g. the OpenMS GitHub App) with contents: write on this repository:

    - name: Build Homebrew bottles
      if: steps.compare_branches.outputs.behind == 'true' || inputs.force
      run: gh api repos/OpenMS/homebrew-openms/dispatches -f event_type=openms-nightly -f "client_payload[sha]=$(git rev-parse HEAD)"
      env:
        GH_TOKEN: ${{ steps.app-token.outputs.token }}

Upstreaming to homebrew-core

The formulae are written to homebrew-core rules (offline build, no vendored downloads, tests). For submission, replace the nightly url/version with a release tarball, drop livecheck skip and the ccache_args hook.