v1.0.0-rc.160 (#70)

This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use.

* rugnux: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell.
* rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged.
* rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set.
* rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme.
* rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free.
* rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry.
* Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md.
* Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #70

Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>

docker/build_images.sh

@@ -0,0 +1,98 @@
+#!/usr/bin/env bash
+# Build (and optionally push) the jungfraujoch build-environment images, in parallel.
+#
+# Each docker/<variant>/Dockerfile is a *self-contained build environment* (toolchain, static Qt,
+# static libdbus, static OpenSSL, Eigen, DIALS, XDS, Node, ...). It does NOT copy the project in --
+# the source is mounted and built at run time (see build_in_rocky9.sh). So the build context is just
+# the per-variant directory; the huge repo is never sent to the Docker daemon.
+#
+# Images are tagged  gitea.psi.ch/leonarski_f/jfjoch_<variant>:<TAG>  (matches the CI runner images).
+#
+# Concurrency (JOBS):
+#   JOBS controls how many image builds run at once (default 2). Each build internally runs
+#   `make -j$(nproc)` for Qt/dbus, so J parallel builds ~= J*nproc compile threads and several GB of
+#   RAM each at link time. JOBS=2 is a safe default that overlaps the (network-bound) base-image
+#   pull / package-install / source-download phases across builds without thrashing the CPU. Bump to
+#   4 for full parallelism on a big machine (enough RAM + disk for 4 CUDA bases), or JOBS=1 for serial.
+#
+# Usage:
+#   docker/build_images.sh                     # all four, JOBS=2
+#   docker/build_images.sh rocky9 rocky8       # subset
+#   JOBS=4 docker/build_images.sh              # all four at once
+#   JOBS=1 docker/build_images.sh              # serial
+#   TAG=2607b docker/build_images.sh           # override the tag (default 2607b)
+#   PUSH=1   docker/build_images.sh            # build (parallel) then push (serial; needs docker login)
+#
+# Parallel stdout would be an unreadable interleave, so each build streams to its own log file:
+#   docker/build-logs/<variant>-<TAG>.log      (follow live with:  tail -f docker/build-logs/*.log)
+set -euo pipefail
+
+REGISTRY="${REGISTRY:-gitea.psi.ch/leonarski_f}"
+TAG="${TAG:-2607b}"
+PUSH="${PUSH:-0}"
+JOBS="${JOBS:-2}"
+
+here="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+logdir="$here/build-logs"
+mkdir -p "$logdir"
+
+all=(rocky8 rocky9 ubuntu2204 ubuntu2404)
+variants=("$@"); [ "${#variants[@]}" -eq 0 ] && variants=("${all[@]}")
+
+for v in "${variants[@]}"; do
+    [ -f "$here/$v/Dockerfile" ] || { echo "!! no Dockerfile for variant '$v' ($here/$v/Dockerfile)"; exit 1; }
+done
+
+# One image build. Records OK/FAIL to a status file so the parent can summarise after wait; never
+# returns non-zero itself, so the job-pool's `wait -n` under `set -e` stays happy.
+build_one() {
+    local v="$1"
+    local img="$REGISTRY/jfjoch_$v:$TAG"
+    local log="$logdir/${v}-${TAG}.log"
+    if docker build --pull -t "$img" "$here/$v" >"$log" 2>&1; then
+        echo OK   > "$logdir/${v}-${TAG}.status"
+    else
+        echo FAIL > "$logdir/${v}-${TAG}.status"
+    fi
+}
+
+echo "==> building ${#variants[@]} image(s): ${variants[*]}"
+echo "==> JOBS=$JOBS  TAG=$TAG  REGISTRY=$REGISTRY"
+echo "==> logs in $logdir/  (follow: tail -f $logdir/*.log)"
+echo
+
+# Launch with a concurrency cap of JOBS. `wait -n` reaps exactly one finished build before the next
+# is started once we are at the cap; the trailing `wait` drains the rest.
+running=0
+for v in "${variants[@]}"; do
+    if [ "$running" -ge "$JOBS" ]; then wait -n || true; running=$((running - 1)); fi
+    : > "$logdir/${v}-${TAG}.status"          # clear any stale status from a previous run
+    echo "==> [$v] started -> $REGISTRY/jfjoch_$v:$TAG"
+    build_one "$v" &
+    running=$((running + 1))
+done
+wait
+
+echo
+echo "===================== build summary ====================="
+rc=0; ok_variants=()
+for v in "${variants[@]}"; do
+    s="$(cat "$logdir/${v}-${TAG}.status" 2>/dev/null || echo '??')"
+    printf "  %-12s %s\n" "$v" "$s"
+    if [ "$s" = OK ]; then ok_variants+=("$v"); else rc=1; fi
+done
+[ "$rc" -eq 0 ] || echo "!! one or more builds FAILED -- see the per-variant logs above"
+
+echo
+if [ "$PUSH" = "1" ]; then
+    for v in "${ok_variants[@]}"; do
+        img="$REGISTRY/jfjoch_$v:$TAG"
+        echo "==> push $img"
+        docker push "$img"
+    done
+else
+    echo "Built locally. To push the successful ones (after 'docker login gitea.psi.ch'):"
+    for v in "${ok_variants[@]}"; do echo "  docker push $REGISTRY/jfjoch_$v:$TAG"; done
+fi
+
+exit "$rc"

docker/build_in_rocky9.sh

@@ -0,0 +1,61 @@
+#!/usr/bin/env bash
+# Manually build the viewer inside one of the build-environment images and inspect its runtime .so
+# deps -- the quick way to confirm the static-libdbus + glib-off changes actually dropped the
+# dbus/systemd/glib/selinux tail. Defaults to the rocky9 image built by build_images.sh.
+#
+# The repo is mounted read-write at /workspace, but the CMake build tree lives in the container's
+# /tmp (thrown away with --rm), so nothing root-owned is left in your working copy. Building needs
+# network (FetchContent pulls curl/zstd/hdf5/...) but NOT a GPU.
+#
+# Usage:
+#   docker/build_in_rocky9.sh                 # build viewer in jfjoch_rocky9:$TAG, then ldd it
+#   docker/build_in_rocky9.sh rocky8          # use a different variant's image
+#   TAG=2607b docker/build_in_rocky9.sh
+set -euo pipefail
+
+REGISTRY="${REGISTRY:-gitea.psi.ch/leonarski_f}"
+TAG="${TAG:-2607b}"
+VARIANT="${1:-rocky9}"
+IMG="$REGISTRY/jfjoch_$VARIANT:$TAG"
+
+repo="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"   # repo root = docker/..
+
+echo "==> image $IMG"
+echo "==> repo  $repo  (mounted at /workspace; build tree in container /tmp)"
+
+docker run --rm \
+    -v "$repo":/workspace -w /workspace \
+    "$IMG" bash -lc '
+        set -eux
+        git config --global --add safe.directory /workspace || true
+        # If this image predates the CMAKE_PREFIX_PATH fix, point cmake at the static libdbus config
+        # dir so the viewer (Qt6::DBus -> find_package(DBus1)) resolves WrapDBus1. Harmless once the
+        # image ENV already carries it.
+        dbus_dir=$(ls -d /opt/dbus-*-static/lib/cmake/DBus1 2>/dev/null | head -1)
+        cmake -G Ninja -S /workspace -B /tmp/build \
+            -DJFJOCH_VIEWER_ONLY=ON -DJFJOCH_USE_CUDA=ON \
+            ${dbus_dir:+-DDBus1_DIR=$dbus_dir} \
+            -DCMAKE_BUILD_TYPE=Release \
+            -DCMAKE_CXX_FLAGS="-march=x86-64-v3" -DCMAKE_C_FLAGS="-march=x86-64-v3"
+        ninja -C /tmp/build -j"$(nproc)" jfjoch_viewer
+        bin=/tmp/build/viewer/jfjoch_viewer
+
+        echo "===================== ldd jfjoch_viewer ====================="
+        ldd "$bin" | sort
+        echo "========== dbus/systemd tail (what the static libdbus removes) =========="
+        # These only ever entered via the system libdbus-1.so -> libsystemd chain, so they MUST be gone.
+        tail_re="libdbus-1|libsystemd|libzstd|liblz4|libgcrypt|libgpg-error|libcap\."
+        if ldd "$bin" | grep -Ei "$tail_re"; then
+            echo ">>> FAIL: the dbus/systemd tail is still linked"
+        else
+            echo ">>> OK: libdbus/libsystemd/zstd/lz4/cap/gcrypt/gpg-error all gone"
+        fi
+        echo "========== residual glib/selinux (expected on RHEL9, NOT from us) =========="
+        # libglib here is pulled by the system harfbuzz/fontconfig/freetype text stack (glib-linked on
+        # RHEL9), not by Qt -- QT_FEATURE_glib=OFF is honoured (Qt is off the glib event loop) but cannot
+        # drop the font-stack glib. libselinux/libpcre2-8 come from the krb5/GSSAPI stack that static
+        # curl links for auth (kept for the reverse-proxy Kerberos plan) -- same bucket as libcrypto.
+        # Shedding these would mean static-linking the whole font stack / dropping krb5. (libpcre2-16 is
+        # Qt-owned and legitimately stays.)
+        ldd "$bin" | grep -Ei "libglib|gthread|selinux|libpcre\.|libpcre2-8" || echo "(none)"
+    '

docker/rocky8/Dockerfile

@@ -3,6 +3,7 @@ LABEL authors="leonarski_f"
 
 ARG OPENSSL_VERSION=3.5.4
 ARG QT_VERSION=6.9.1
+ARG DBUS_VERSION=1.14.10
 ARG NODE_MAJOR=22
 ARG EIGEN_VERSION=3.4.0
 # HDF5, libtiff and libjpeg-turbo are built by the jungfraujoch CMake itself (FetchContent /
@@ -47,11 +48,10 @@ RUN dnf -y install epel-release && \
       libXinerama-devel \
       mesa-libGL-devel \
       mesa-libEGL-devel \
-      dbus-devel \
+      expat-devel \
       krb5-devel \
       zlib-devel \
       zlib-static \
-      glib2-devel \
       fontconfig-devel \
       zlib-static \
       java-21-openjdk-headless \
@@ -96,6 +96,35 @@ ENV CXX=${GCC_TOOLSET_ROOT}/usr/bin/g++
 
 ENV PKG_CONFIG_PATH=${OPENSSL_ROOT_DIR}/lib/pkgconfig:${OPENSSL_ROOT_DIR}/lib64/pkgconfig
 
+# Static libdbus: link D-Bus into the viewer (Qt6::DBus) instead of pulling libdbus-1.so.3 at runtime.
+# A distro libdbus-1.so drags in libsystemd (-> libzstd/liblz4/libcap/libgcrypt/libgpg-error) and
+# libselinux (-> libpcre2). Disabling those integrations makes libdbus-1.a depend on ~libc alone, so
+# that whole runtime .so tail disappears while the viewer keeps its single-instance / remote-control
+# D-Bus feature -- it is a pure session-bus client (registers a name + exports an adaptor), so the
+# daemon-side systemd/selinux features are irrelevant. Static-only install (no .so); the Qt build
+# finds it through find_package(DBus1) via the -DDBus1_DIR hint (the CMake package config dbus
+# installs, which imports libdbus-1.a). Built -fPIC (--with-pic) so the archive links into Qt's PIE
+# tools (qdbusxml2cpp). expat is only a configure-time dep of the dbus daemon; the client libdbus-1
+# links neither expat nor systemd.
+RUN set -eux; \
+    cd /tmp; \
+    curl -LO https://dbus.freedesktop.org/releases/dbus/dbus-${DBUS_VERSION}.tar.xz; \
+    tar -xf dbus-${DBUS_VERSION}.tar.xz; \
+    cd dbus-${DBUS_VERSION}; \
+    ./configure --prefix=/opt/dbus-${DBUS_VERSION}-static \
+      --enable-static --disable-shared --with-pic \
+      --disable-systemd --without-systemdsystemunitdir \
+      --disable-selinux --disable-apparmor --disable-libaudit \
+      --disable-tests --disable-asserts \
+      --disable-doxygen-docs --disable-xml-docs --disable-ducktype-docs \
+      CFLAGS="-fPIC"; \
+    make -j"$(nproc)"; \
+    make install; \
+    cd /; rm -rf /tmp/dbus-${DBUS_VERSION} /tmp/dbus-${DBUS_VERSION}.tar.xz
+
+# Put the static libdbus pkgconfig ahead of the system one so Qt6::DBus resolves to the .a
+ENV PKG_CONFIG_PATH=/opt/dbus-${DBUS_VERSION}-static/lib/pkgconfig:${PKG_CONFIG_PATH}
+
 ARG QT_PREFIX=/opt/qt-${QT_VERSION}-static
 RUN set -eux; \
     cd /tmp; \
@@ -108,6 +137,8 @@ RUN set -eux; \
       -DQT_BUILD_TESTS=OFF \
       -DQT_BUILD_EXAMPLES=OFF \
       -DQT_FEATURE_dbus=ON \
+      -DQT_FEATURE_dbus_linked=ON \
+      -DDBus1_DIR=/opt/dbus-${DBUS_VERSION}-static/lib/cmake/DBus1 \
       -DQT_FEATURE_xcb=ON \
       -DQT_FEATURE_xcb_xlib=OFF \
       -DQT_FEATURE_xkbcommon_x11=ON \
@@ -115,6 +146,7 @@ RUN set -eux; \
       -DQT_FEATURE_opengl_desktop=ON \
       -DQT_FEATURE_opengl_dynamic=OFF \
       -DQT_FEATURE_vulkan=OFF \
+      -DQT_FEATURE_glib=OFF \
       -DCMAKE_BUILD_TYPE=Release \
       -DCMAKE_INSTALL_PREFIX=${QT_PREFIX} \
       -DCMAKE_C_COMPILER=${CC} \
@@ -136,8 +168,10 @@ RUN set -eux; \
     cmake --install eigen-build; \
     cd /; rm -rf /tmp/eigen /tmp/eigen-build
 
-# Make Qt and Eigen discoverable by CMake
-ENV CMAKE_PREFIX_PATH=/opt/qt-${QT_VERSION}-static:/opt/eigen-3.4
+# Make Qt, the static libdbus, and Eigen discoverable by CMake. The static libdbus prefix is
+# required here (not only at Qt build time): every Qt6::DBus consumer re-runs find_package(DBus1)
+# through Qt's exported config, so DBus1Config.cmake must be on CMAKE_PREFIX_PATH for the viewer build.
+ENV CMAKE_PREFIX_PATH=/opt/qt-${QT_VERSION}-static:/opt/dbus-${DBUS_VERSION}-static:/opt/eigen-3.4
 
 # Set workdir for your project
 WORKDIR /workspace

docker/rocky9/Dockerfile

@@ -3,6 +3,7 @@ LABEL authors="leonarski_f"
 
 ARG OPENSSL_VERSION=3.5.4
 ARG QT_VERSION=6.9.1
+ARG DBUS_VERSION=1.14.10
 ARG NODE_MAJOR=22
 ARG EIGEN_VERSION=3.4.0
 # HDF5, libtiff and libjpeg-turbo are built by the jungfraujoch CMake itself (FetchContent /
@@ -57,11 +58,10 @@ RUN dnf -y update && \
       libXinerama-devel \
       mesa-libGL-devel \
       mesa-libEGL-devel \
-      dbus-devel \
+      expat-devel \
       krb5-devel \
       zlib-devel \
       zlib-static \
-      glib2-devel \
       zlib-static \
       fontconfig-devel \
       mesa-dri-drivers \
@@ -99,6 +99,35 @@ ENV PATH=${GCC_TOOLSET_ROOT}/usr/bin:${PATH}
 ENV CC=${GCC_TOOLSET_ROOT}/usr/bin/gcc
 ENV CXX=${GCC_TOOLSET_ROOT}/usr/bin/g++
 
+# Static libdbus: link D-Bus into the viewer (Qt6::DBus) instead of pulling libdbus-1.so.3 at runtime.
+# A distro libdbus-1.so drags in libsystemd (-> libzstd/liblz4/libcap/libgcrypt/libgpg-error) and
+# libselinux (-> libpcre2). Disabling those integrations makes libdbus-1.a depend on ~libc alone, so
+# that whole runtime .so tail disappears while the viewer keeps its single-instance / remote-control
+# D-Bus feature -- it is a pure session-bus client (registers a name + exports an adaptor), so the
+# daemon-side systemd/selinux features are irrelevant. Static-only install (no .so); the Qt build
+# finds it through find_package(DBus1) via the -DDBus1_DIR hint (the CMake package config dbus
+# installs, which imports libdbus-1.a). Built -fPIC (--with-pic) so the archive links into Qt's PIE
+# tools (qdbusxml2cpp). expat is only a configure-time dep of the dbus daemon; the client libdbus-1
+# links neither expat nor systemd.
+RUN set -eux; \
+    cd /tmp; \
+    curl -LO https://dbus.freedesktop.org/releases/dbus/dbus-${DBUS_VERSION}.tar.xz; \
+    tar -xf dbus-${DBUS_VERSION}.tar.xz; \
+    cd dbus-${DBUS_VERSION}; \
+    ./configure --prefix=/opt/dbus-${DBUS_VERSION}-static \
+      --enable-static --disable-shared --with-pic \
+      --disable-systemd --without-systemdsystemunitdir \
+      --disable-selinux --disable-apparmor --disable-libaudit \
+      --disable-tests --disable-asserts \
+      --disable-doxygen-docs --disable-xml-docs --disable-ducktype-docs \
+      CFLAGS="-fPIC"; \
+    make -j"$(nproc)"; \
+    make install; \
+    cd /; rm -rf /tmp/dbus-${DBUS_VERSION} /tmp/dbus-${DBUS_VERSION}.tar.xz
+
+# Put the static libdbus pkgconfig ahead of the system one so Qt6::DBus resolves to the .a
+ENV PKG_CONFIG_PATH=/opt/dbus-${DBUS_VERSION}-static/lib/pkgconfig:${PKG_CONFIG_PATH}
+
 # Build and install static Qt 6.9 with Core, Gui, Widgets, Charts, DBus
 ARG QT_PREFIX=/opt/qt-${QT_VERSION}-static
 RUN set -eux; \
@@ -112,6 +141,8 @@ RUN set -eux; \
       -DQT_BUILD_TESTS=OFF \
       -DQT_BUILD_EXAMPLES=OFF \
       -DQT_FEATURE_dbus=ON \
+      -DQT_FEATURE_dbus_linked=ON \
+      -DDBus1_DIR=/opt/dbus-${DBUS_VERSION}-static/lib/cmake/DBus1 \
       -DQT_FEATURE_xcb=ON \
       -DQT_FEATURE_xcb_xlib=OFF \
       -DQT_FEATURE_xkbcommon_x11=ON \
@@ -119,6 +150,7 @@ RUN set -eux; \
       -DQT_FEATURE_opengl_desktop=ON \
       -DQT_FEATURE_opengl_dynamic=OFF \
       -DQT_FEATURE_vulkan=OFF \
+      -DQT_FEATURE_glib=OFF \
       -DCMAKE_BUILD_TYPE=Release \
       -DCMAKE_INSTALL_PREFIX=${QT_PREFIX} \
       -DCMAKE_C_COMPILER=${CC} \
@@ -175,8 +207,10 @@ RUN set -eux; \
     cmake --install eigen-build; \
     cd /; rm -rf /tmp/eigen /tmp/eigen-build
 
-# Make Qt and Eigen discoverable by CMake
-ENV CMAKE_PREFIX_PATH=/opt/qt-${QT_VERSION}-static:/opt/eigen-3.4
+# Make Qt, the static libdbus, and Eigen discoverable by CMake. The static libdbus prefix is
+# required here (not only at Qt build time): every Qt6::DBus consumer re-runs find_package(DBus1)
+# through Qt's exported config, so DBus1Config.cmake must be on CMAKE_PREFIX_PATH for the viewer build.
+ENV CMAKE_PREFIX_PATH=/opt/qt-${QT_VERSION}-static:/opt/dbus-${DBUS_VERSION}-static:/opt/eigen-3.4
 
 ENV LANG=en_US.UTF-8
 ENV LANGUAGE=en_US:en

docker/ubuntu2204/Dockerfile

@@ -6,6 +6,7 @@ ENV DEBIAN_FRONTEND=noninteractive
 
 ARG OPENSSL_VERSION=3.5.4
 ARG QT_VERSION=6.9.1
+ARG DBUS_VERSION=1.14.10
 ARG NODE_MAJOR=22
 ARG EIGEN_VERSION=3.4.0
 # HDF5, libtiff and libjpeg-turbo are built by the jungfraujoch CMake itself (FetchContent /
@@ -71,9 +72,8 @@ RUN set -eux; \
       libgl1-mesa-dev \
       libglx-dev \
       libegl1-mesa-dev \
-      libdbus-1-dev \
+      libexpat1-dev \
       zlib1g-dev \
-      libglib2.0-dev \
       libfontconfig1-dev \
       libdrm-dev \
       mesa-utils \
@@ -123,6 +123,35 @@ RUN set -eux; \
     rm -rf /var/lib/apt/lists/*; \
     node --version; npm --version; (corepack enable || true)
 
+# Static libdbus: link D-Bus into the viewer (Qt6::DBus) instead of pulling libdbus-1.so.3 at runtime.
+# A distro libdbus-1.so drags in libsystemd (-> libzstd/liblz4/libcap/libgcrypt/libgpg-error) and
+# libselinux (-> libpcre2). Disabling those integrations makes libdbus-1.a depend on ~libc alone, so
+# that whole runtime .so tail disappears while the viewer keeps its single-instance / remote-control
+# D-Bus feature -- it is a pure session-bus client (registers a name + exports an adaptor), so the
+# daemon-side systemd/selinux features are irrelevant. Static-only install (no .so); the Qt build
+# finds it through find_package(DBus1) via the -DDBus1_DIR hint (the CMake package config dbus
+# installs, which imports libdbus-1.a). Built -fPIC (--with-pic) so the archive links into Qt's PIE
+# tools (qdbusxml2cpp). expat is only a configure-time dep of the dbus daemon; the client libdbus-1
+# links neither expat nor systemd.
+RUN set -eux; \
+    cd /tmp; \
+    curl -LO https://dbus.freedesktop.org/releases/dbus/dbus-${DBUS_VERSION}.tar.xz; \
+    tar -xf dbus-${DBUS_VERSION}.tar.xz; \
+    cd dbus-${DBUS_VERSION}; \
+    ./configure --prefix=/opt/dbus-${DBUS_VERSION}-static \
+      --enable-static --disable-shared --with-pic \
+      --disable-systemd --without-systemdsystemunitdir \
+      --disable-selinux --disable-apparmor --disable-libaudit \
+      --disable-tests --disable-asserts \
+      --disable-doxygen-docs --disable-xml-docs --disable-ducktype-docs \
+      CFLAGS="-fPIC"; \
+    make -j"$(nproc)"; \
+    make install; \
+    cd /; rm -rf /tmp/dbus-${DBUS_VERSION} /tmp/dbus-${DBUS_VERSION}.tar.xz
+
+# Put the static libdbus pkgconfig ahead of the system one so Qt6::DBus resolves to the .a
+ENV PKG_CONFIG_PATH=/opt/dbus-${DBUS_VERSION}-static/lib/pkgconfig:${PKG_CONFIG_PATH}
+
 # Build and install static Qt with Core, Gui, Widgets, Charts, DBus
 ARG QT_PREFIX=/opt/qt-${QT_VERSION}-static
 RUN set -eux; \
@@ -136,6 +165,8 @@ RUN set -eux; \
       -DQT_BUILD_TESTS=OFF \
       -DQT_BUILD_EXAMPLES=OFF \
       -DQT_FEATURE_dbus=ON \
+      -DQT_FEATURE_dbus_linked=ON \
+      -DDBus1_DIR=/opt/dbus-${DBUS_VERSION}-static/lib/cmake/DBus1 \
       -DQT_FEATURE_xcb=ON \
       -DQT_FEATURE_xcb_xlib=OFF \
       -DQT_FEATURE_xkbcommon_x11=ON \
@@ -143,6 +174,7 @@ RUN set -eux; \
       -DQT_FEATURE_opengl_desktop=ON \
       -DQT_FEATURE_opengl_dynamic=OFF \
       -DQT_FEATURE_vulkan=OFF \
+      -DQT_FEATURE_glib=OFF \
       -DCMAKE_BUILD_TYPE=Release \
       -DCMAKE_INSTALL_PREFIX=${QT_PREFIX} \
       -DCMAKE_C_COMPILER=${CC} \
@@ -164,8 +196,10 @@ RUN set -eux; \
     cmake --install eigen-build; \
     cd /; rm -rf /tmp/eigen /tmp/eigen-build
 
-# Make Qt and Eigen discoverable by CMake
-ENV CMAKE_PREFIX_PATH=/opt/qt-${QT_VERSION}-static:/opt/eigen-3.4
+# Make Qt, the static libdbus, and Eigen discoverable by CMake. The static libdbus prefix is
+# required here (not only at Qt build time): every Qt6::DBus consumer re-runs find_package(DBus1)
+# through Qt's exported config, so DBus1Config.cmake must be on CMAKE_PREFIX_PATH for the viewer build.
+ENV CMAKE_PREFIX_PATH=/opt/qt-${QT_VERSION}-static:/opt/dbus-${DBUS_VERSION}-static:/opt/eigen-3.4
 
 # Set workdir for your project
 WORKDIR /workspace

docker/ubuntu2404/Dockerfile

@@ -6,6 +6,7 @@ ENV DEBIAN_FRONTEND=noninteractive
 
 ARG OPENSSL_VERSION=3.5.4
 ARG QT_VERSION=6.9.1
+ARG DBUS_VERSION=1.14.10
 ARG NODE_MAJOR=22
 ARG EIGEN_VERSION=3.4.0
 # HDF5, libtiff and libjpeg-turbo are built by the jungfraujoch CMake itself (FetchContent /
@@ -71,9 +72,8 @@ RUN set -eux; \
       libgl1-mesa-dev \
       libglx-dev \
       libegl1-mesa-dev \
-      libdbus-1-dev \
+      libexpat1-dev \
       zlib1g-dev \
-      libglib2.0-dev \
       libfontconfig1-dev \
       libdrm-dev \
       libglvnd-dev \
@@ -110,6 +110,35 @@ RUN set -eux; \
     rm -rf /var/lib/apt/lists/*; \
     node --version; npm --version; (corepack enable || true)
 
+# Static libdbus: link D-Bus into the viewer (Qt6::DBus) instead of pulling libdbus-1.so.3 at runtime.
+# A distro libdbus-1.so drags in libsystemd (-> libzstd/liblz4/libcap/libgcrypt/libgpg-error) and
+# libselinux (-> libpcre2). Disabling those integrations makes libdbus-1.a depend on ~libc alone, so
+# that whole runtime .so tail disappears while the viewer keeps its single-instance / remote-control
+# D-Bus feature -- it is a pure session-bus client (registers a name + exports an adaptor), so the
+# daemon-side systemd/selinux features are irrelevant. Static-only install (no .so); the Qt build
+# finds it through find_package(DBus1) via the -DDBus1_DIR hint (the CMake package config dbus
+# installs, which imports libdbus-1.a). Built -fPIC (--with-pic) so the archive links into Qt's PIE
+# tools (qdbusxml2cpp). expat is only a configure-time dep of the dbus daemon; the client libdbus-1
+# links neither expat nor systemd.
+RUN set -eux; \
+    cd /tmp; \
+    curl -LO https://dbus.freedesktop.org/releases/dbus/dbus-${DBUS_VERSION}.tar.xz; \
+    tar -xf dbus-${DBUS_VERSION}.tar.xz; \
+    cd dbus-${DBUS_VERSION}; \
+    ./configure --prefix=/opt/dbus-${DBUS_VERSION}-static \
+      --enable-static --disable-shared --with-pic \
+      --disable-systemd --without-systemdsystemunitdir \
+      --disable-selinux --disable-apparmor --disable-libaudit \
+      --disable-tests --disable-asserts \
+      --disable-doxygen-docs --disable-xml-docs --disable-ducktype-docs \
+      CFLAGS="-fPIC"; \
+    make -j"$(nproc)"; \
+    make install; \
+    cd /; rm -rf /tmp/dbus-${DBUS_VERSION} /tmp/dbus-${DBUS_VERSION}.tar.xz
+
+# Put the static libdbus pkgconfig ahead of the system one so Qt6::DBus resolves to the .a
+ENV PKG_CONFIG_PATH=/opt/dbus-${DBUS_VERSION}-static/lib/pkgconfig:${PKG_CONFIG_PATH}
+
 # Build and install static Qt with Core, Gui, Widgets, Charts, DBus
 ARG QT_PREFIX=/opt/qt-${QT_VERSION}-static
 RUN set -eux; \
@@ -123,6 +152,8 @@ RUN set -eux; \
       -DQT_BUILD_TESTS=OFF \
       -DQT_BUILD_EXAMPLES=OFF \
       -DQT_FEATURE_dbus=ON \
+      -DQT_FEATURE_dbus_linked=ON \
+      -DDBus1_DIR=/opt/dbus-${DBUS_VERSION}-static/lib/cmake/DBus1 \
       -DQT_FEATURE_xcb=ON \
       -DQT_FEATURE_xcb_xlib=OFF \
       -DQT_FEATURE_xkbcommon_x11=ON \
@@ -130,6 +161,7 @@ RUN set -eux; \
       -DQT_FEATURE_opengl_desktop=ON \
       -DQT_FEATURE_opengl_dynamic=OFF \
       -DQT_FEATURE_vulkan=OFF \
+      -DQT_FEATURE_glib=OFF \
       -DCMAKE_BUILD_TYPE=Release \
       -DCMAKE_INSTALL_PREFIX=${QT_PREFIX} \
       -DCMAKE_C_COMPILER=${CC} \
@@ -151,8 +183,10 @@ RUN set -eux; \
     cmake --install eigen-build; \
     cd /; rm -rf /tmp/eigen /tmp/eigen-build
 
-# Make Qt and Eigen discoverable by CMake
-ENV CMAKE_PREFIX_PATH=/opt/qt-${QT_VERSION}-static:/opt/eigen-3.4
+# Make Qt, the static libdbus, and Eigen discoverable by CMake. The static libdbus prefix is
+# required here (not only at Qt build time): every Qt6::DBus consumer re-runs find_package(DBus1)
+# through Qt's exported config, so DBus1Config.cmake must be on CMAKE_PREFIX_PATH for the viewer build.
+ENV CMAKE_PREFIX_PATH=/opt/qt-${QT_VERSION}-static:/opt/dbus-${DBUS_VERSION}-static:/opt/eigen-3.4
 
 # Set workdir for your project
 WORKDIR /workspace