v1.0.0-rc.166 (#76)

* `rugnux --mode calibration` writes `<prefix>.json` beside the `.poni`, whose `dataset_settings` member is a `jfjoch_broker` `dataset_settings` body as it stands.
* `rugnux` and `jfjoch_viewer` read PILATUS miniCBF sweeps natively, without conversion.
* Masters written by other facilities open, including Eiger 1.x and third-party NXmx variants.
* `rugnux` measures the beam centre on every run, and indexes with it when the file's value indexes nothing.
* A detector swung out on a 2theta arm is placed where the file says it stands, and the calibration can hold the tilt fixed.
* `rugnux` writes the unmerged MTZ by default, and a P1 merge beside it, so a wrong space group can be re-merged without reprocessing.
* Significant improvements to symmetry handling in `rugnux`: the lattice, the point group, the setting and the systematic absences.
* The `rugnux` report gives the resolution the CC1/2 fit reached, beside the range the reflections were written to.
* The `rugnux` report gives the twinning statistics measured before the space group was decided, beside the ones measured after.
* The `rugnux` report gives the strong-direction diffraction limit, and warns when CC1/2 is not monotone with resolution.
* `rugnux` ranks screw axes on the evidence their absences carry, rather than on how many control reflections a candidate happens to have.
* Twinning is no longer reported when the L-test contradicts it.
* The `rugnux` report gives the detector tilt, the measured tilt and the direct beam beside the beam centre, and a post-refined beam centre is judged against the run's own measurement rather than the file's.
* `--no-refine-tilt` holds the detector tilt at the value in the file, instead of zeroing it, when the calibration starts from the spots.
* The `jfjoch_viewer` grid scan view draws the cells in the proportion of the scan steps, so the map has the shape of the scanned area.

Reviewed-on: #76
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>

tests/WriteReflectionsTest.cpp

@@ -0,0 +1,72 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include <catch2/catch_all.hpp>
+
+#include <filesystem>
+#include <string>
+
+#include <gemmi/mtz.hpp>
+
+#include "../common/DiffractionExperiment.h"
+#include "../image_analysis/WriteReflections.h"
+#include "SyntheticMergedReflections.h"
+
+namespace {
+    // The wavelength CCP4's mtzlib substitutes when the data columns belong to dataset 0, which it
+    // takes for the reserved HKL_base: Cu K-alpha, and the wrong edge for anything reading f'/f''
+    // out of the file.
+    constexpr double CU_KALPHA_A = 1.54187;
+
+    constexpr UnitCell TETRAGONAL_CELL{47.0f, 47.0f, 63.0f, 90.0f, 90.0f, 90.0f};
+
+    DiffractionExperiment TestExperiment() {
+        DiffractionExperiment x;
+        x.IncidentEnergy_keV(12.7f);         // ~0.976 A, nowhere near the Cu K-alpha default
+        x.SpaceGroupNumber(96);              // P 43 21 2
+        x.SetUnitCell(TETRAGONAL_CELL);
+        return x;
+    }
+}
+
+TEST_CASE("Merged MTZ: the data dataset is id 1 and carries the wavelength", "[write_reflections]") {
+    jfjoch_test::SyntheticMergeParams params;
+    params.true_space_group = "P 43 21 2";
+    params.twin_supergroup = "P 43 21 2";
+    params.d_min_A = 5.0;
+    const auto reflections = jfjoch_test::GenerateSyntheticMerged(params);
+    REQUIRE(!reflections.empty());
+
+    const auto experiment = TestExperiment();
+    const auto path = (std::filesystem::temp_directory_path() / "rugnux_merged_wavelength.mtz").string();
+    WriteMtzReflections(reflections, TETRAGONAL_CELL, experiment, path);
+    const gemmi::Mtz mtz = gemmi::read_mtz_file(path);
+    std::filesystem::remove(path);
+
+    // HKL_base at id 0, the data at id 1. A data dataset written at id 0 occupies the id MTZ
+    // reserves for the base, and mtzlib then reports CU_KALPHA_A instead of the real wavelength.
+    REQUIRE(mtz.datasets.size() == 2);
+    CHECK(mtz.datasets[0].id == 0);
+    CHECK(mtz.datasets[0].dataset_name == "HKL_base");
+    CHECK(mtz.datasets[1].id == 1);
+    CHECK(mtz.datasets[1].wavelength == Catch::Approx(experiment.GetWavelength_A()).epsilon(1e-5));
+    CHECK(mtz.datasets[1].wavelength != Catch::Approx(CU_KALPHA_A).epsilon(1e-3));
+
+    // The wavelength is read off the dataset the data columns belong to, so they have to be on the
+    // data dataset and not on the base.
+    for (const char *label : {"IMEAN", "SIGIMEAN", "F", "SIGF", "FreeR_flag"}) {
+        const gemmi::Mtz::Column *col = mtz.column_with_label(label);
+        REQUIRE(col != nullptr);
+        CHECK(col->dataset_id == 1);
+    }
+
+    // Cell and space group travel in the same header.
+    CHECK(mtz.spacegroup != nullptr);
+    CHECK(mtz.spacegroup->number == 96);
+    CHECK(mtz.cell.a == Catch::Approx(TETRAGONAL_CELL.a).epsilon(1e-5));
+    CHECK(mtz.cell.c == Catch::Approx(TETRAGONAL_CELL.c).epsilon(1e-5));
+    CHECK(mtz.cell.gamma == Catch::Approx(90.0).epsilon(1e-5));
+    CHECK(mtz.datasets[1].cell.a == Catch::Approx(TETRAGONAL_CELL.a).epsilon(1e-5));
+
+    CHECK(mtz.nreflections == static_cast<int>(reflections.size()));
+}