Install the license files of the libraries into share/licenses; fix the macOS Arrow build

[timosachsenberg]

Description

Software that is built against the contrib and redistributes its libraries has to ship their license texts. The pyOpenMS wheels for Linux and Windows are such software, and OpenMS/OpenMS#10292 so far adds its own copies of the texts for them. This PR installs the texts in the contrib instead, taken straight from the source archives, so OpenMS can pick them up from the contrib build.

• Building a library installs its license and notice files, as its source archive has them, to share/licenses/<library>/ in the build directory. This covers:
  • zlib, bzip2, boost, curl, arrow, libsvm, xerces-c;
  • glpk, coin-or (Cbc, Cgl, Clp, CoinMP, CoinUtils, Osi), eigen;
  • hdf5, libzip, openmp.
• SOURCE.txt in each folder names the source archive, its SHA-256 and where it is published. It also points to this repository for the build scripts and patches. MPL-2.0 (Eigen) and EPL-1.0 (COIN-OR, which the contrib patches) ask for this.
• Arrow builds and links some dependencies itself: Snappy, zstd, Thrift, xsimd, RapidJSON, mimalloc, and the AWS SDK where S3 is on.
  • share/licenses/arrow/bundled/<dependency>/ gets the license files from the top of their source trees in Arrow's build directory, plus Arrow's thirdparty/versions.txt.
  • The set follows what Arrow fetched on each platform.
• A missing file fails the build with FATAL_ERROR, as the other macros do.
• The release tarballs (lib bin include share) and the manylinux image keep share/, so both carry the files.
• Library_Licences.txt and licensetexts/ are removed. They linked to web pages for libraries the contrib no longer builds, and the installed files replace them.

macOS build

The macOS job of this workflow has failed on master since July; the last green run was on 2026-07-03.

• Cause: newer Xcode versions report their libtool as Apple Inc. version cctools_ld-<version>, but Arrow 23.0.0 only accepts cctools-<version>. Its configuration therefore stops with libtool found appears not to be Apple's libtool: /usr/bin/libtool.
• Fix: on macOS, patches/arrow/BuildUtils.cmake.diff changes that check to the regex of GH-49369: [C++][R] Deal with validating libtool again apache/arrow#49370. That regex accepts both forms and still rejects GNU libtool.

Testing

• Small libraries (Linux): a contrib build of ZLIB, BZIP2, LIBSVM, EIGEN and LIBZIP installs the five folders.
  • The SHA-256 in SOURCE.txt matches the archive.
  • The texts are byte-identical to the copies in [BUILD] Ship the third-party licenses with packages and wheels; drop ProteoWizard and SpectraST OpenMS#10292, which came from upstream.
• Arrow 23.0.0, configured like the Unix build here but with S3 off:
  • The new macro installs Snappy, zstd, Thrift and versions.txt from the real build tree.
  • The sandbox could not download mimalloc, xsimd or RapidJSON. The macro found their folders at the expected paths and failed because they were empty.
• Arrow patch:
  • OPENMS_PATCH applies it to the Arrow 23.0.0 source and skips it on a second run.
  • The new regex accepts Apple Inc. version cctools_ld-1266.5 and Apple Inc. version cctools-1010.6, and rejects GNU libtool's output and empty output.
• Edge cases:
  • COIN-OR's subfolders are kept.
  • A missing file fails the build.
  • A second run replaces the folder.
• Not run locally: the full build, with Boost, Xerces-C, COIN-OR, HDF5, curl, Arrow with S3, and Windows and macOS. This PR's CI runs it. Each platform's log should show Installing ... license files .. done.

After merging

• The merge to master rebuilds ghcr.io/openms/contrib_manylinux_2_34:latest, which the Linux wheels use.
• A manual run of the CI workflow creates a release with contrib_build-*.tar.gz, which the Windows wheels download.
• [BUILD] Ship the third-party licenses with packages and wheels; drop ProteoWizard and SpectraST OpenMS#10292 then takes the texts from <contrib>/share/licenses/ and drops its copies.

🤖 Generated with Claude Code

https://claude.ai/code/session_01YC1T2K9HQEUk2kQMZqC8h7

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Generated by Claude Code

Summary by CodeRabbit

• New Features

  • Contrib library builds now install available license and notice files under share/licenses/<library>/.
  • Arrow’s bundled dependency licenses and version information are included in a dedicated subfolder.
  • Installed license folders include a SOURCE.txt with archive and source details.

• Documentation

  • The README explains where license files are installed and notes that redistributions should include the folders for linked libraries.

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ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Advanced

Run ID: 8b5745b5-24fc-4085-8be7-5572a8f0e50d

📥 Commits

Reviewing files that changed from the base of the PR and between 6aff676 and 99190d6.

📒 Files selected for processing (12)

• CMakeLists.txt
• Library_Licences.txt
• README.md
• libraries.cmake/arrow.cmake
• licensetexts/License.bzip2.txt
• licensetexts/License.gpl-2.0.txt
• licensetexts/License.gpl-3.0.txt
• licensetexts/License.hdf5.txt
• licensetexts/License.lgpl-2.1.txt
• licensetexts/License.libSVM.txt
• licensetexts/README.md
• macros.cmake

💤 Files with no reviewable changes (8)

• licensetexts/License.gpl-3.0.txt
• licensetexts/License.gpl-2.0.txt
• licensetexts/README.md
• licensetexts/License.lgpl-2.1.txt
• licensetexts/License.hdf5.txt
• licensetexts/License.libSVM.txt
• Library_Licences.txt
• licensetexts/License.bzip2.txt

Included review availability: This review used your included allowance. Your plan provides up to 1 included review per hour; 0 remain after this review.

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📝 Walkthrough

Walkthrough

Contrib build blocks now install license and notice files for selected libraries. A shared macro records source archive metadata. Arrow builds also collect bundled dependency licenses. The README describes the installed license directories and their distribution.

Changes

License distribution

Layer / File(s)	Summary
Shared installation macro and archive metadata macros.cmake	Adds OPENMS_INSTALL_LICENSES to replace a library’s license directory, copy requested files while preserving subdirectories, fail when a requested file is missing, and write SOURCE.txt. The archive release URL is defined once and used by download_contrib_archive.
Library license installation and documentation CMakeLists.txt, libraries.cmake/arrow.cmake, README.md, Library_Licences.txt, licensetexts/*	Build blocks install license and notice files for selected libraries. Arrow’s bundled dependency licenses and versions.txt are copied into the license directory. The README documents the layout and distribution. The former license reference list and local license texts are removed.

Priority: ➖ Normal

Change: Feature

Merge Risk: ⚪ Minimal · up to 99190

No concrete issue has been established that should block merging. Arrow’s bundled-license collection and pyOpenMS wheel packaging remain unverified.

Architecture Summary

Architecture risk: 🔵 Low · up to 99190

The change affects 6 systems.

Changed systems: licensetexts, CMakeLists.txt, libraries.cmake, Library_Licences.txt, macros.cmake, README.md

Architecture concerns
No architecture-level concerns identified.

Review details

Systems and components

• observed — licensetexts (service) was modified; 7 changed files map to changed impact.
• observed — CMakeLists.txt (service) was modified; 1 changed file maps to changed impact.
• observed — libraries.cmake (service) was modified; 1 changed file maps to changed impact.
• observed — Library_Licences.txt (service) was modified; 1 changed file maps to changed impact.

Before / after behavior

• observed — Modified behavior in CMakeLists.txt: After building ZLIB, the block installs its LICENSE file.
• observed — Modified behavior in CMakeLists.txt: After building BZIP2, the block installs its LICENSE file.
• observed — Modified behavior in CMakeLists.txt: After building BOOST, the block installs LICENSE_1_0.txt.
• observed — Modified behavior in CMakeLists.txt: After building and copying CURL libraries, the block installs COPYING.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff. Analyzed 0 functions across 0…
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly summarizes the main changes: installing library license files and fixing the macOS Arrow build.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Commit to this branch
• Create a new PR

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_{I’m a rabbit; I hop by the build,
Where license files now are filled.
From source paths to folders they go,
With archive details set below.
Arrow’s bundled notices join the ride,
And version notes sit by their side.}

_{Comment @coderabbitai help to get the list of available commands.}