Merge broker-rugnux-live into rc176: rugnux in jfjoch_broker as a live thread during a DECTRIS rotation collection (off by default), the rugnux library without file I/O (results in ProcessResult::outputs, the CLI writes them through JFJochRugnuxOutput), END carrying the merged table, map coefficients and placed model

Branch reviewed at e16db07ff (review: owner's decisions accepted - _maps.mtz instead of .ccp4 in the
viewer, -o "" computes everything incl. MR/validation, Ctrl+C/error paths may leave fewer files, the
writer links gemmi/zlib) and merged at 55184eb09 with its review fixes (END size guard, frame drop as
in Lite, outputs released before re-runs, pool priority, docs, frontend gating).

Conflicts: rugnux/Rugnux.h (kept rc176's host_memory_budget_bytes, output_prefix removed as on the
branch), rugnux/RugnuxPipeline.h (MtzTable future + rc176's GPUMerge pointer), MolecularReplacement.h/.cpp
(rc176's GPU cost model, packed transform and split functions with the branch's RugnuxModel signature;
search_model with rc176's other_budgets, result.model_name). tests/RugnuxLargeTest.cpp: rc176's
host-budget test writes its files through WriteRugnuxOutputs now that the library writes none.
Generated code (broker/gen, frontend client, Python client docs, Redoc) regenerated from the merged
jfjoch_api.yaml with update_version.sh (version unchanged).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01PXc1zD1yxHqaR1DGdCTHL4

tests/MolecularReplacementTest.cpp

@@ -9,6 +9,7 @@
 #include <cstring>
 #include <fstream>
 #include <random>
+#include <sstream>
 
 #include <gemmi/dencalc.hpp>
 #include <gemmi/it92.hpp>
@@ -17,6 +18,7 @@
 #include "../image_analysis/structure_refinement/MolecularReplacement.h"
 #include "../image_analysis/structure_refinement/RigidBodyRefine.h"
 #include "../common/Logger.h"
+#include "../writer/RugnuxModelFile.h"
 #ifdef JFJOCH_USE_CUDA
 #include "../common/CUDAWrapper.h"
 #include "../image_analysis/structure_refinement/MolecularReplacementGPU.h"
@@ -448,7 +450,7 @@ TEST_CASE("MolecularReplacement_ModelKind", "[MolecularReplacement]") {
     const float plddt[3] = {90, 85, 95};
     write("MolecularReplacement_ModelKind_af.pdb", "CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1",
           plddt, false, false);
-    const SearchModel af = PrepareSearchModel("MolecularReplacement_ModelKind_af.pdb");
+    const SearchModel af = PrepareSearchModel(ReadRugnuxModelFile("MolecularReplacement_ModelKind_af.pdb"));
     CHECK(af.failure_reason.empty());
     CHECK(af.predicted);
     CHECK(af.residues_kept == 3);
@@ -457,7 +459,7 @@ TEST_CASE("MolecularReplacement_ModelKind", "[MolecularReplacement]") {
     const float refined[3] = {25, 112, 40};
     write("MolecularReplacement_ModelKind_xtal.pdb", "CRYST1   50.000   60.000   70.000  90.00  90.00  90.00 P 21 21 21    4",
           refined, true, true);
-    const SearchModel x = PrepareSearchModel("MolecularReplacement_ModelKind_xtal.pdb");
+    const SearchModel x = PrepareSearchModel(ReadRugnuxModelFile("MolecularReplacement_ModelKind_xtal.pdb"));
     CHECK(x.failure_reason.empty());
     CHECK(!x.predicted);
     CHECK(x.residues_kept == 3);
@@ -501,19 +503,20 @@ TEST_CASE("MolecularReplacement_PaeDomains", "[MolecularReplacement]") {
     m.st.models.push_back(model);
     m.residues_read = 120;
     m.residues_kept = 110;
-    const std::string path = "MolecularReplacement_PaeDomains.json";
-    {
-        std::ofstream out(path);
-        out << "[{\"predicted_aligned_error\":[";
-        for (int i = 0; i < 120; i++) {
-            out << (i ? "," : "") << "[";
-            for (int j = 0; j < 120; j++)
-                out << (j ? "," : "") << ((i < 55) == (j < 55) ? 2 : 25);
-            out << "]";
-        }
-        out << "],\"max_predicted_aligned_error\":31.75}]";
+    std::ostringstream json;
+    json << "[{\"predicted_aligned_error\":[";
+    for (int i = 0; i < 120; i++) {
+        json << (i ? "," : "") << "[";
+        for (int j = 0; j < 120; j++)
+            json << (j ? "," : "") << ((i < 55) == (j < 55) ? 2 : 25);
+        json << "]";
     }
-    const auto domains = PaeDomains(path, m);
+    json << "],\"max_predicted_aligned_error\":31.75}]";
+    const RugnuxModel parsed = ParseRugnuxModel(
+            "ATOM      1  CA  ALA A   1       0.000   0.000   0.000  1.00 90.00           C\nEND\n",
+            "AF-P12345-F1-model_v6.pdb", json.str());
+    REQUIRE(parsed.pae);
+    const auto domains = PaeDomains(*parsed.pae, m);
     REQUIRE(domains.size() == 2);
     CHECK(domains[0].size() == 60);
     CHECK(domains[0].front() == 60);
@@ -521,7 +524,6 @@ TEST_CASE("MolecularReplacement_PaeDomains", "[MolecularReplacement]") {
     const SearchModel d = DomainModel(m, domains[1]);
     CHECK(d.residues_kept == 50);
     CHECK(d.description == "PAE domain of 50 residues (1-50)");
-    std::remove(path.c_str());
 }
 
 // A placement of a group carried into a subgroup's merge: in P 21 21 21 read as P 1 21 1 on the same cell each