v1.0.0-rc.178 (#88)

* Rugnux: Processes serial crystallography data from XFELs - SACLA (MPCCD), PAL-XFEL and European XFEL (CXI), LCLS (XTC) and SwissFEL Alvra (JUNGFRAU with a CrystFEL module geometry) - with several files or Jungfraujoch master files merged in one run (`rugnux *_master.h5`).
* Rugnux: Stills processing takes a known unit cell and space group as a starting point, finds the beam centre (and, with a cell, the detector distance) from the images, detects the saturation level in other facilities' files and refines the placement of individual detector panels.
* Rugnux: The stills report gives R_split and CC1/2 from frame half-sets, comparable with CrystFEL.
* jfjoch_viewer: Opens the same XFEL file formats.
* Validation: A stills battery checks Rugnux against deposited structures from SACLA, PAL-XFEL, LCLS, European XFEL and SwissFEL.
* Rugnux: More reliable convergence of rotation scaling, and live molecular replacement starts as soon as the model is uploaded.
* jfjoch_broker: Initialize clears the previous dataset's bearer tokens, image buffer and live Rugnux status, and a slow CUDA JIT cache is reported at start.

Reviewed-on: #88
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>

tests/MolecularReplacementTest.cpp

@@ -646,6 +646,54 @@ TEST_CASE("MolecularReplacement_RigidBodyBesideFixedCopy", "[MolecularReplacemen
 #endif
 }
 
+// A search made on one merge, carried over to another merge of the same crystal in a cell 0.5% longer: the
+// placement, a degree and half an angstrom out where it was found, is refined against the new merge onto the
+// truth and holds there; in another group it is not carried at all, and the merge is to be searched itself.
+TEST_CASE("MolecularReplacement_CarryToAnotherMerge", "[MolecularReplacement]") {
+    const SearchModel model = synthetic_model();
+    const gemmi::SpaceGroup &sg = gemmi::get_spacegroup_by_name("P 21 21 21");
+    const gemmi::UnitCell found_cell(52, 60, 70, 90, 90, 90), cell(52.26, 60.3, 70.35, 90, 90, 90);
+    const gemmi::Mat33 r = axis_angle({1, 2, 3}, 50);
+    const gemmi::Fractional t(0.17, 0.31, 0.09);
+    const gemmi::Structure truth = PlaceSearchModel(model, r, t, cell, sg);
+    auto merged = observed(truth);
+    for (size_t i = 0; i < merged.size(); i++)
+        merged[i].rfree_flag = i % 10 == 0;
+
+    MolecularReplacementResult early;
+    early.ok = true;
+    early.chosen = 0;
+    early.decision = "AGREES";
+    MRCandidate c;
+    c.space_group = sg;
+    c.copies = 1;
+    c.r_free = 0.30;
+    c.placed = std::make_shared<gemmi::Structure>(PlaceSearchModel(
+            model, axis_angle({0, 0, 1}, 1).multiply(r), gemmi::Fractional(t.x + 0.5 / 52, t.y, t.z), found_cell, sg));
+    early.candidates.push_back(c);
+
+    const UnitCell found_uc{52, 60, 70, 90, 90, 90}, uc{52.26f, 60.3f, 70.35f, 90, 90, 90};
+    const MRMerge searched{"first merge", &merged, found_uc, sg};
+    Logger logger("MolecularReplacement_CarryToAnotherMerge");
+    const auto carried = CarryMolecularReplacement(early, searched, {"MERGE", &merged, uc, sg}, logger, 4);
+    REQUIRE(carried);
+    CHECK(carried->decision == "AGREES");
+    CHECK(carried->r_free_searched == Catch::Approx(0.30));
+    CHECK(carried->candidates[0].placed->cell.a == Catch::Approx(52.26));
+    const auto worst = [&](const gemmi::Structure &st) {
+        const auto a = ModelPositions(st.models[0]), b = ModelPositions(truth.models[0]);
+        double w = 0;
+        for (size_t i = 0; i < a.size(); i++)
+            w = std::max(w, a[i].dist(b[i]));
+        return w;
+    };
+    CHECK(worst(*c.placed) > 0.5);
+    CHECK(worst(*carried->candidates[0].placed) < 0.2);
+
+    const gemmi::SpaceGroup &other = gemmi::get_spacegroup_by_name("P 2 21 21");
+    CHECK_FALSE(CarryMolecularReplacement(early, searched, {"MERGE", &merged, uc, other}, logger, 4));
+}
+
 #ifdef JFJOCH_USE_CUDA
 TEST_CASE("MolecularReplacement_GPUMatchesCPU", "[MolecularReplacement]") {
     if (get_gpu_count() == 0)