Jungfraujoch/docs/THIRD_PARTY_NOTICES.md

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# Third-party software notices

Jungfraujoch is licensed under **GPL-3.0** (see [`LICENSE`](LICENSE.md)); the FPGA design is
licensed under **CERN-OHL-S-2.0** (see [`fpga/LICENSE`](FPGA_LICENSE.md)). It builds on a number of
third-party components, acknowledged below as required by their licenses.

This file is the human-readable manifest. The verbatim license texts live in the
[`licenses/`](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/) directory (regenerate with `bash licenses/COLLECT.sh`). The frontend's
bundled JavaScript dependencies are listed separately in
`frontend/dist/THIRD_PARTY_LICENSES.txt`, generated at build time (`npm run licenses`).

All licenses below are GPL-3.0-compatible, with one exception: the NVIDIA CUDA Toolkit is used under its own EULA (see the notes at the end of this file).

## Fetched at build time and statically linked into the C++ binaries

These are downloaded by CMake (`FetchContent` / `ExternalProject`) during the first configure and
linked into the Jungfraujoch executables.

| Component | Version | Copyright | License (SPDX) | License text |
|---|---|---|---|---|
| [spdlog](https://github.com/gabime/spdlog) | 1.17.0 | Gabi Melman | MIT | [spdlog.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/spdlog.txt) |
| [Zstandard](https://github.com/facebook/zstd) | 1.5.7 | Meta Platforms, Inc. | BSD-3-Clause | [zstd.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/zstd.txt) |
| [HDF5](https://github.com/HDFGroup/hdf5) | 2.2.0 | The HDF Group; UIUC | BSD-3-Clause-style + Apache-2.0 | [hdf5.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/hdf5.txt) |
| [slsDetectorPackage](https://github.com/slsdetectorgroup/slsDetectorPackage) | 8.0.2 / 9.2.0 | PSI | LGPL-3.0-or-later | [LGPL](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/slsDetectorPackage-LGPL-3.0.txt), [GPL](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/slsDetectorPackage-GPL-3.0.txt) |
| [cpp-httplib](https://github.com/yhirose/cpp-httplib) | 0.56.0 | Yuji Hirose | MIT | [cpp-httplib.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/cpp-httplib.txt) |
| [libzmq (ZeroMQ)](https://github.com/zeromq/libzmq) | 4.3.5 | iMatix and contributors | MPL-2.0 | [libzmq.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/libzmq.txt) |
| [libtiff](https://gitlab.com/libtiff/libtiff) | 4.7.2 | Sam Leffler; SGI | libtiff (BSD-like) | [libtiff.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/libtiff.txt) |
| [FFTW](https://www.fftw.org/) | 3.3.10 | Matteo Frigo; MIT | GPL-2.0-or-later | [fftw.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/fftw.txt) |
| [Ceres Solver](https://github.com/ceres-solver/ceres-solver) | (pinned) | Google Inc. and contributors | BSD-3-Clause | [ceres-solver.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/ceres-solver.txt) |
| [Abseil](https://github.com/abseil/abseil-cpp) | 20250127 (required by Ceres) | Google Inc. | Apache-2.0 | [abseil.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/abseil.txt) |
| [fast-feedback-indexer](https://github.com/paulscherrerinstitute/fast-feedback-indexer) | (pinned) | PSI | BSD-3-Clause | [fast-feedback-indexer.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/fast-feedback-indexer.txt) |
| [libjpeg-turbo](https://github.com/libjpeg-turbo/libjpeg-turbo) | 3.2.0 | D. R. Commander and others; IJG | IJG + BSD-3-Clause + Zlib | [libjpeg-turbo.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/libjpeg-turbo.txt) |
| [Mbed TLS](https://github.com/Mbed-TLS/mbedtls) (with TF-PSA-Crypto) | 4.2.0 | The Mbed TLS Contributors | Apache-2.0 OR GPL-2.0-or-later (used under Apache-2.0) | [mbedtls.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/mbedtls.txt), [tf-psa-crypto.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/tf-psa-crypto.txt) |
| [Catch2](https://github.com/catchorg/Catch2) | 3.16.0 | Catch2 Authors | BSL-1.0 | [catch2.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/catch2.txt) |
| [zlib-ng](https://github.com/zlib-ng/zlib-ng) | 2.3.3 | Jean-loup Gailly and Mark Adler; the zlib-ng contributors | Zlib | [zlib.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/zlib.txt) |
| [Eigen](https://gitlab.com/libeigen/eigen) | 3.4.1 | Benoit Jacob, Gael Guennebaud and contributors | MPL-2.0 (+ BSD parts) | [eigen.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/eigen.txt), [README](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/eigen-README.txt) |

Mbed TLS is fetched and statically linked only for viewer builds (`JFJOCH_VIEWER_BUILD` /
`JFJOCH_VIEWER_ONLY`), where it is the TLS backend of `jfjoch_viewer`'s cpp-httplib client; the
broker and writer never link it.

Catch2 is used only to build the test binary (`jfjoch_test`) and is not part of any shipped
artifact; it is listed here for completeness.

zlib is supplied by zlib-ng built in its zlib-compatible mode (same `zlib.h`, same API and symbol
names), so it is the zlib that HDF5, libtiff, cpp-httplib and GEMMI all link. It is
built during the configure rather than added as a subproject; the licence is the zlib licence
either way. Eigen is header-only: only its headers reach the binaries, and no Eigen CMake runs.

## Vendored directly in the repository

These live in the source tree (see the path) rather than being fetched; traccc and the Ceres-derived minimiser are the exceptions - code adapted into first-party files rather than a vendored directory, see the notes at the end of this file.

| Component | Path | Copyright | License (SPDX) | License text |
|---|---|---|---|---|
| [nlohmann/json](https://github.com/nlohmann/json) | `include/nlohmann/` | Niels Lohmann | MIT | [nlohmann-json.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/nlohmann-json.txt) |
| [Macaron Base64](https://gist.github.com/tomykaira/f0fd86b6c73063283afe550bc5d77594) | `include/base64/` | tomykaira | MIT | [base64-macaron.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/base64-macaron.txt) |
| [TinyCBOR](https://github.com/intel/tinycbor) | `frame_serialize/tinycbor/` | Intel Corporation | MIT | [tinycbor.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/tinycbor.txt) |
| [Bitshuffle](https://github.com/kiyo-masui/bitshuffle) | `compression/bitshuffle/` | Kiyoshi Masui | MIT | [bitshuffle.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/bitshuffle.txt) |
| [Bitshuffle (h-perf)](https://github.com/kalcutter/bitshuffle) | `compression/bitshuffle_hperf/` | Kal Conley | Apache-2.0 | [bitshuffle-hperf.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/bitshuffle-hperf.txt) |
| [LZ4](https://github.com/lz4/lz4) | `compression/lz4/` | Yann Collet | BSD-2-Clause | [lz4.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/lz4.txt) |
| [HLS arbitrary-precision types](https://github.com/Xilinx/HLS_arbitrary_Precision_Types) | `fpga/include/` | Xilinx, Inc. | Apache-2.0 | [xilinx-hls-headers.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/xilinx-hls-headers.txt) |
| [GEMMI](https://github.com/project-gemmi/gemmi) | `gemmi_gph/` | Global Phasing Ltd. | MPL-2.0 | [gemmi.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/gemmi.txt) |
| [PEGTL](https://github.com/taocpp/PEGTL) | `gemmi_gph/gemmi/third_party/tao/` | Dr. Colin Hirsch and Daniel Frey | MIT | [pegtl.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/pegtl.txt) |
| [sajson](https://github.com/chadaustin/sajson) | `gemmi_gph/gemmi/third_party/sajson.h` | Chad Austin | MIT | [sajson.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/sajson.txt) |
| [fast_float](https://github.com/fastfloat/fast_float) | `gemmi_gph/gemmi/third_party/fast_float.h` | The fast_float authors (Daniel Lemire et al.) | Apache-2.0 OR MIT OR BSL-1.0 | [fast-float.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/fast-float.txt) |
| [half](https://half.sourceforge.net/) | `gemmi_gph/gemmi/third_party/half.hpp` | Christian Rau | MIT | [half.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/half.txt) |
| [pocketfft](https://github.com/mreineck/pocketfft) | `gemmi_gph/gemmi/third_party/pocketfft_hdronly.h` | Max-Planck-Society; Peter Bell; MIT (FFTW-derived parts) | BSD-3-Clause | [pocketfft.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/pocketfft.txt) |
| [tinydir](https://github.com/cxong/tinydir) | `gemmi_gph/gemmi/third_party/tinydir.h` | Cong Xu, Lautis Sun, Baudouin Feildel, Andargor | BSD-2-Clause | [tinydir.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/tinydir.txt) |
| [traccc (ACTS)](https://github.com/acts-project/traccc) | `image_analysis/spot_finding/StrongPixelSet.cpp`, `SpotExtractorGPU.cu` | CERN, for the benefit of the ACTS project | MPL-2.0 | [traccc.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/traccc.txt) |
| [Ceres Solver](https://github.com/ceres-solver/ceres-solver) (adapted) | `image_analysis/geom_refinement/LMSolver.h`, `LMSolver.cpp` | Google Inc. | BSD-3-Clause | [ceres-solver.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/ceres-solver.txt) |
| [xbflash.qspi](https://github.com/Xilinx/XRT) | `tools/xbflash.qspi/` | Xilinx / AMD | Apache-2.0 | [xbflash-qspi.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/xbflash-qspi.txt) |
| [wingetopt](https://github.com/alex85k/wingetopt) | `tools/wingetopt/` | Todd C. Miller; The NetBSD Foundation | ISC AND BSD-2-Clause | [wingetopt.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/wingetopt.txt) |

## Data files in the repository

Not code and not linked into any binary: input files of the battery's timing benchmark
(`tools/battery/timing.json`), kept verbatim as downloaded.

| Component | Path | Copyright | License (SPDX) | License text |
|---|---|---|---|---|
| [AlphaFold Protein Structure Database](https://alphafold.ebi.ac.uk/) predictions AF-P68082-F1, AF-P62894-F1, AF-P17090-F1, AF-P32322-F1 and AF-Q65MG6-F1 (v6), with their predicted aligned error | `tools/battery/models/AF-*` | DeepMind Technologies Limited; EMBL-EBI | CC-BY-4.0 | [alphafold-db.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/alphafold-db.txt) |
| [wwPDB](https://www.wwpdb.org/) entries 4DC8, 4NWV, 9GJX, 9S02 and 9ZLO, deposited coordinates (mmCIF as the [RCSB PDB](https://www.rcsb.org/) serves them) | `tools/battery/models/pdb/` | the depositors; the wwPDB | CC0-1.0 | [wwPDB usage policy](https://www.wwpdb.org/about/usage-policies) |

The deposited entries are the reference models the benchmark's placements are checked against, and
4NWV's is also moved by a fixed transform at run time to make one start model.

## Runtime libraries and SDKs (shipped in binaries, not in the source tree)

| Component | Used by | License | Notice |
|---|---|---|---|
| [Qt 6](https://www.qt.io/) | `jfjoch_viewer` | LGPL-3.0 | [notice](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/Qt6-NOTICE.txt), [LGPL-3.0](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/Qt6-LGPL-3.0.txt) |
| [NVIDIA CUDA Toolkit](https://developer.nvidia.com/cuda-toolkit) (cudart, cuFFT) | CUDA builds | NVIDIA CUDA EULA | [notice](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/NVIDIA-CUDA-NOTICE.txt), [EULA](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/NVIDIA-CUDA-EULA.txt) |

## Frontend (npm) dependencies

The React/TypeScript frontend (`frontend/`) bundles a large transitive tree of npm packages,
overwhelmingly MIT/ISC/BSD/Apache-2.0 licensed. Their full notices are generated automatically:

```
cd frontend && npm run licenses     # writes dist/THIRD_PARTY_LICENSES.txt
```

The generated file is produced as part of the `frontend` build target and installed alongside the
served frontend, so the shipped web UI carries its own attribution.

## Notes on weak-copyleft and attribution-sensitive components

* **MPL-2.0** (Eigen, GEMMI, libzmq, traccc): file-level copyleft. GEMMI is vendored in `gemmi_gph/`
  in trimmed form; libzmq and Eigen are fetched at build time (Eigen is header-only). The
  corresponding source is available from each project upstream.
* **GEMMI's own bundled third-party headers** — PEGTL, sajson, fast_float, half, pocketfft and
  tinydir, all under `gemmi_gph/gemmi/third_party/` — are listed separately above rather than being
  absorbed into GEMMI's row: they are other authors' code under other licences (MIT, BSD and
  Apache/MIT/BSL), and GEMMI's MPL-2.0 does not speak for them. Their terms are carried in the
  headers themselves rather than in `LICENSE` files, so the `licenses/*.txt` copies are kept by hand;
  only PEGTL ships a `LICENSE`, which `COLLECT.sh` copies.
* **traccc** is the one entry that is not a vendored directory. Its sparse connected-component
  labelling enters two otherwise first-party files: `StrongPixelSet.cpp` adapts the SparseCCL source,
  and `SpotExtractorGPU.cu` follows the design of its GPU counterpart. MPL-2.0 is file-level, so both
  files name the origin at the top and are covered by `licenses/traccc.txt`. See
  [ACKNOWLEDGEMENT.md](ACKNOWLEDGEMENT.md) for the citation.
* **Ceres Solver** is also fetched and linked (table above); separately, `LMSolver.h`/`.cpp` re-implement
  its trust-region Levenberg-Marquardt minimiser, projected line search, polynomial step choice and
  sphere manifold for the crystal refinement, following its source. Both files name the origin at the
  top and are covered by `licenses/ceres-solver.txt`.
* **FFTW** is GPL-2.0-or-later — compatible with, and absorbed by, this project's GPL-3.0 license.
* **Apache-2.0** components: where upstream ships a `NOTICE` file, it is reproduced in the
  corresponding `licenses/` text.
* **Qt (LGPL-3.0)** and **NVIDIA CUDA (EULA)** carry redistribution conditions beyond a copyright
  notice; see their dedicated notice files. The verbatim LGPL-3.0 and CUDA EULA texts are bundled
  (`licenses/Qt6-LGPL-3.0.txt`, `licenses/NVIDIA-CUDA-EULA.txt`); the CUDA EULA is the one shipped
  with CUDA Toolkit 12.8 — replace it if you build against a different toolkit version.