v1.0.0-rc.170 (#80)

* Fixed a `jfjoch_broker` crash during indexing: sorting no longer misbehaves on non-finite values, and GPU FFT indexer kernel launches are now error-checked.
* rugnux needs about a third less peak memory to scale, merge and post-refine rotation data, with identical results.
* `rugnux --model`: the placed coordinate file carries the space group its own coordinates obey, and says so when that is not the group the reflection files beside it carry.
* `jfjoch_viewer`: fixes in the dataset plots, inspector and layout; spot markers lose their black outline by default (a checkbox under "Image features" restores it) and the highest-pixel markers are white boxes around the pixel.

Reviewed-on: #80
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>

tests/ModelValidationTest.cpp

@@ -398,9 +398,12 @@ TEST_CASE("WriteModel_KeepsTheContentAndTakesTheGivenFrame", "[ModelValidation]"
 
     const auto input = WriteTemp("write_model_test_input.pdb", kPdbRich);
     gemmi::Structure st = gemmi::read_structure_gz(input, gemmi::CoorFormat::Detect);
+    // The model in the data's own group, which is the ordinary case: the frame it is written in is
+    // then wholly the caller's. The cell it arrives in (40/50/60) is not the data's and is replaced.
+    st.spacegroup_hm = "P 43 21 2";
 
-    // A frame that is neither the model's (P 1, 40/50/60) nor anything derived from it: the tetragonal
-    // lysozyme cell and one enantiomorph of its group, standing in for what AdoptModelFrame settled.
+    // The tetragonal lysozyme cell and one enantiomorph of its group, standing in for what
+    // AdoptModelFrame settled.
     const UnitCell data_cell{.a = 79, .b = 79, .c = 38, .alpha = 90, .beta = 90, .gamma = 90};
     const gemmi::SpaceGroup *sg = gemmi::find_spacegroup_by_name("P 43 21 2");
     REQUIRE(sg != nullptr);
@@ -441,6 +444,63 @@ TEST_CASE("WriteModel_KeepsTheContentAndTakesTheGivenFrame", "[ModelValidation]"
     std::filesystem::remove(written);
 }
 
+// A model cannot be labelled with a group its own coordinates do not obey. Where the data were merged
+// in a supergroup of the model's - an over-merge across a pseudo-symmetry operation, or the hand the
+// model's fit did not earn - that operation would generate atoms the model does not contain, and a
+// refinement program acts on it silently. The model keeps its own group and the caller is warned.
+TEST_CASE("WriteModel_DoesNotStampAGroupTheCoordinatesDoNotObey", "[ModelValidation]") {
+    Logger logger("WriteModel_DoesNotStampAGroupTheCoordinatesDoNotObey");
+
+    const auto input = WriteTemp("write_model_sg_test_input.pdb", kPdbRich);   // P 1
+    const gemmi::Structure st = gemmi::read_structure_gz(input, gemmi::CoorFormat::Detect);
+
+    const UnitCell data_cell{.a = 79, .b = 79, .c = 38, .alpha = 90, .beta = 90, .gamma = 90};
+    const gemmi::SpaceGroup *sg = gemmi::find_spacegroup_by_name("P 43 21 2");
+    REQUIRE(sg != nullptr);
+
+    WritePlacedModel(st, data_cell, *sg, "write_model_sg_test", logger);
+    const std::string written = "write_model_sg_test_model.cif";
+    REQUIRE(std::filesystem::exists(written));
+
+    const gemmi::Structure back = gemmi::read_structure_gz(written, gemmi::CoorFormat::Detect);
+    // The cell is still the data's - the coordinates do sit in it - but the group is the model's own.
+    CHECK(back.cell.a == Catch::Approx(79.0));
+    CHECK(back.cell.c == Catch::Approx(38.0));
+    REQUIRE(back.find_spacegroup() != nullptr);
+    CHECK(back.find_spacegroup()->number == 1);
+
+    std::filesystem::remove(input);
+    std::filesystem::remove(written);
+    std::filesystem::remove("write_model_sg_test_model.pdb");
+}
+
+// The other direction is not a mismatch at all: a model whose coordinates obey more symmetry than the
+// data were merged in obeys the data's group too - the file simply holds more than one asymmetric unit
+// of it, which is what a model in P1 always does. The reflection files' group is kept, as before.
+TEST_CASE("WriteModel_KeepsTheDataGroupWhenItIsASubgroup", "[ModelValidation]") {
+    Logger logger("WriteModel_KeepsTheDataGroupWhenItIsASubgroup");
+
+    const auto input = WriteTemp("write_model_sub_test_input.pdb", kPdbRich);
+    gemmi::Structure st = gemmi::read_structure_gz(input, gemmi::CoorFormat::Detect);
+    st.spacegroup_hm = "P 43 21 2";
+
+    const UnitCell data_cell{.a = 79, .b = 79, .c = 38, .alpha = 90, .beta = 90, .gamma = 90};
+    const gemmi::SpaceGroup *p1 = gemmi::find_spacegroup_by_name("P 1");
+    REQUIRE(p1 != nullptr);
+
+    WritePlacedModel(st, data_cell, *p1, "write_model_sub_test", logger);
+    const std::string written = "write_model_sub_test_model.cif";
+    REQUIRE(std::filesystem::exists(written));
+
+    const gemmi::Structure back = gemmi::read_structure_gz(written, gemmi::CoorFormat::Detect);
+    REQUIRE(back.find_spacegroup() != nullptr);
+    CHECK(back.find_spacegroup()->number == 1);
+
+    std::filesystem::remove(input);
+    std::filesystem::remove(written);
+    std::filesystem::remove("write_model_sub_test_model.pdb");
+}
+
 // CC(model, data) has to follow where the signal actually is, or it cannot support the one-sided
 // claim it exists for. The check is closed: the "observed" intensities are the model's own with
 // Gaussian noise added, and how much noise is chosen per shell - almost none in the first, some in