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Jungfraujoch/licenses/COLLECT.sh
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leonarski_fandFilip Leonarski 19b135186d
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v1.0.0-rc.175 (#85)
* Rugnux: Processes a collection live while jfjoch_broker writes it (`rugnux <master.h5> <broker URL>`).
* Rugnux: Processing starts on the first images and confirms its choices once all are in, so analysis can begin during collection.
* Rugnux: Faster processing, especially on servers with several GPUs and CPU sockets and on computers without a GPU (`--no-gpu`, macOS).
* Rugnux: Uses much less GPU memory, so large data sets stay on the GPU of smaller cards, and a data set too large for the card is processed on the CPU instead.
* Rugnux: On macOS, Bragg integration runs on the Apple GPU.
* Rugnux: Better handling of twinning and pseudo-symmetry, with the twin hypothesis written as `<prefix>_twin_<SG>.mtz`, and a wrong `--model` no longer confirms the data or decides the hand.
* Rugnux: `--model` accepts predicted (AlphaFold) models and falls back to molecular replacement when the model is not placed as a rigid body (experimental `--mr` forces it), settling space group, hand and twinning and writing a different answer as `<prefix>_mr.mtz`.
* Rugnux: Molecular replacement is faster and settles the space group in more cases with several copies in the asymmetric unit.
* Rugnux: Deposition-ready mmCIF, a richer report, and numbered steps on the terminal with the full log in `<prefix>_log.txt`; `_P1.mtz`, `--estimate-beam-center` and `--beam-center-search` are removed.
* Rugnux: The beam-stop shadow is found correctly on tilted detectors.
* Rugnux: Stills files that record a stationary goniometer axis get the default stills geometry refinement.
* jfjoch_viewer: "Analyze dataset" uses the same defaults as a bare `rugnux <file>`, and shows the results of processed CBF, marCCD and SMV sweeps.
* jfjoch_viewer: The Files panel refreshes on F5 and every few seconds, and the plot type and other selections stay put during live collection.
* jfjoch_writer: Memory stays bounded and old data files are closed efficiently on long runs, any failure ends the run in an error state the broker is told about, and the master file appears only after its data files; the ZeroMQ pusher logs when a stalled writer makes it drop images.
* Fixes: The TCP image pusher no longer blocks the broker's receiver, GPU out-of-memory failures stop with a clear message, and the XDS plugin masks module and chip edges.

---------

Co-authored-by: Filip Leonarski <jungfrau@filips-mac-mini.home>
Reviewed-on: #85
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-10-16 15:34:43 +02:00

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#!/usr/bin/env bash
# Collect the verbatim license texts of all third-party components into this directory.
#
# This is the bulk reference material that accompanies THIRD_PARTY_NOTICES.md (the human-readable
# manifest at the repo root). Run from the repo root after a configure/build has populated the
# FetchContent source trees (build/_deps or cmake-build-*/_deps). Re-run when a dependency version
# changes. The output (licenses/*.txt) is committed so a source checkout needs no build to ship the
# notices.
#
# bash licenses/COLLECT.sh
#
set -euo pipefail
cd "$(dirname "$0")/.."
OUT=licenses
# Copy $1 to licenses/$2, trying each source path in $1 (space-separated) until one exists.
copy_license() {
local dest="$1"; shift
local src
for src in "$@"; do
if [[ -f "$src" ]]; then
cp "$src" "$OUT/$dest"
echo " $dest <- $src"
return 0
fi
done
echo " !! MISSING: $dest (none of: $*)" >&2
return 0
}
# Search the populated dependency trees in order of preference.
DEPS=(_deps cmake-build-release/_deps build/_deps cmake-build-debug/_deps)
find_dep() { # find_dep <relative-path-under-a-deps-dir>
local d
for d in "${DEPS[@]}"; do [[ -f "$d/$1" ]] && { echo "$d/$1"; return; }; done
}
echo "Collecting third-party license texts into $OUT/ ..."
# --- Fetched at build, statically linked into the C++ binaries -------------------------------
copy_license spdlog.txt "$(find_dep spdlog-src/LICENSE)"
copy_license zstd.txt "$(find_dep zstd-src/LICENSE)"
copy_license hdf5.txt "$(find_dep hdf5-src/LICENSE)"
copy_license catch2.txt "$(find_dep catch2-src/LICENSE.txt)"
copy_license cpp-httplib.txt "$(find_dep httplib-src/LICENSE)"
copy_license libzmq.txt "$(find_dep libzmq-src/LICENSE)"
copy_license libtiff.txt "$(find_dep tiff-src/LICENSE.md)"
copy_license fftw.txt "$(find_dep fftw-src/COPYING)"
copy_license ceres-solver.txt "$(find_dep ceres-src/LICENSE)"
copy_license abseil.txt "$(find_dep ceres-src/third_party/abseil-cpp/LICENSE)"
copy_license fast-feedback-indexer.txt "$(find_dep fast-indexer-src/LICENSE.md)"
copy_license eigen.txt "$(find_dep eigen3-src/COPYING.MPL2)"
copy_license eigen-README.txt "$(find_dep eigen3-src/COPYING.README)"
copy_license zlib.txt "$(find_dep zlib-src/LICENSE.md)"
# slsDetectorPackage is LGPL-3.0-or-later: ship both the GPL-3.0 base and the LGPL-3.0 addendum.
copy_license slsDetectorPackage-LGPL-3.0.txt "$(find_dep sls_detector_package-src/LICENSES/LGPL-3.0)"
copy_license slsDetectorPackage-GPL-3.0.txt "$(find_dep sls_detector_package-src/LICENSES/GPL-3.0)"
# libjpeg-turbo is built out-of-line by preview/ (ExternalProject), not under _deps.
# Mbed TLS is fetched only for viewer builds, so these are MISSING unless the configured tree
# had JFJOCH_VIEWER_BUILD / JFJOCH_VIEWER_ONLY on.
copy_license mbedtls.txt "$(find_dep mbedtls-src/LICENSE)"
copy_license tf-psa-crypto.txt "$(find_dep mbedtls-src/tf-psa-crypto/LICENSE)"
copy_license libjpeg-turbo.txt \
cmake-build-release/preview/libjpeg-turbo/src/libjpeg-turbo-project/LICENSE.md \
build/preview/libjpeg-turbo/src/libjpeg-turbo-project/LICENSE.md
# --- Vendored directly in the repository ----------------------------------------------------
copy_license nlohmann-json.txt include/nlohmann/LICENSE.MIT
copy_license tinycbor.txt frame_serialize/tinycbor/LICENSE
copy_license bitshuffle.txt compression/bitshuffle/LICENSE
copy_license bitshuffle-hperf.txt compression/bitshuffle_hperf/LICENSE-APACHE
copy_license lz4.txt compression/lz4/LICENSE
copy_license xilinx-hls-headers.txt fpga/include/LICENSE.HLS_Headers
copy_license gemmi.txt gemmi_gph/LICENSE.txt
# GEMMI bundles six third-party headers under its own include tree, each under its own licence
# (see THIRD_PARTY_NOTICES.md). Only PEGTL ships a LICENSE file; sajson, fast_float, half, pocketfft
# and tinydir carry their terms in a comment at the top of the header, so licenses/sajson.txt,
# fast-float.txt, half.txt, pocketfft.txt and tinydir.txt are kept by hand - re-extract them from the
# headers when GEMMI is updated.
copy_license pegtl.txt gemmi_gph/gemmi/third_party/tao/LICENSE
copy_license xbflash-qspi.txt tools/xbflash.qspi/LICENSE
copy_license wingetopt.txt tools/wingetopt/LICENSE
# --- Data files in the repository --------------------------------------------------------------
copy_license alphafold-db.txt tools/battery/models/LICENSE.txt
# --- Runtime SDK license texts, copied from their system install (best effort) ---------------
# These come from outside the build tree; the committed copies are authoritative if absent here.
copy_license Qt6-LGPL-3.0.txt /usr/share/common-licenses/LGPL-3
copy_license NVIDIA-CUDA-EULA.txt \
/usr/local/cuda/EULA.txt /usr/local/cuda-12.8/EULA.txt
echo "Done. base64-macaron.txt, traccc.txt, Qt6-NOTICE.txt and NVIDIA-CUDA-NOTICE.txt are maintained by hand."