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/ResultReportTest.cpp

@@ -59,7 +59,7 @@ TEST_CASE("ResultReport_Render", "[Diagnostics]") {
     result.indexing_rate = 0.87f;
     result.consensus_cell = UnitCell{.a = 79.0f, .b = 79.0f, .c = 38.0f,
                                      .alpha = 90.0f, .beta = 90.0f, .gamma = 90.0f};
-    result.space_group_number = 96;
+    result.space_group = *gemmi::find_spacegroup_by_number(96);
     result.used_beam_x_pxl = 766.62f;
     result.used_beam_y_pxl = 846.87f;
     result.used_distance_mm = 243.53f;
@@ -69,10 +69,15 @@ TEST_CASE("ResultReport_Render", "[Diagnostics]") {
     const auto text = RenderResultReport("prefix", "in.h5", x, result);
 
     // The stable keys a consumer greps for.
-    CHECK(text.find("\nREPORT_VERSION= 4\n") != std::string::npos);
+    CHECK(text.find("\nREPORT_VERSION= 6\n") != std::string::npos);
     CHECK(text.find("\nOUTPUT_PREFIX= prefix\n") != std::string::npos);
     CHECK(text.find("\nINDEXING_RATE= 0.8700\n") != std::string::npos);
     CHECK(text.find("\nSPACE_GROUP_NUMBER= 96\n") != std::string::npos);
+    // What the data could NOT decide, beside what they did. The group here was given rather
+    // than searched for, and it is one of the 22 that come in enantiomorphic pairs.
+    CHECK(text.find("\nSPACE_GROUP_ALTERNATIVES= NONE\n") != std::string::npos);
+    CHECK(text.find("\nSPACE_GROUP_ENANTIOMORPH= GIVEN\n") != std::string::npos);
+    CHECK(text.find("\nSPACE_GROUP_REFUSED_POINT_GROUP= NONE\n") != std::string::npos);
     CHECK(text.find("\nSWEEP_QUALITY_STATUS= COMPUTED\n") != std::string::npos);
     CHECK(text.find("\nSWEEP_QUALITY_COUNT= 2\n") != std::string::npos);
     CHECK(text.find("\nSWEEP_QUALITY_REASONS= no_diffraction crystal_out_of_beam weak_diffraction "
@@ -246,14 +251,62 @@ TEST_CASE("ResultReport_ModelValidationSection", "[Diagnostics]") {
     good.n_work = 16682;
     good.n_free = 928;
     good.mean_atom_density_sigma = 1.42;
+    good.fit_tested = true;
+    good.model_fits = true;
+    good.null_replicates = 5;
+    good.null_r_work_mean = 0.6031;
+    good.null_r_work_sd = 0.0094;
+    good.r_work_sigma = 4.12;
+    good.model_enantiomorph_candidate = true;
+    good.adopted_model_enantiomorph = true;
     result.model_validation = good;
+    result.space_group = *gemmi::find_spacegroup_by_number(96);
 
     const auto text = RenderResultReport("p", "in.h5", x, result);
     CHECK(text.find("10. MODEL VALIDATION") != std::string::npos);
     CHECK(text.find("\nMODEL_FILE= model.cif\n") != std::string::npos);
     CHECK(text.find("\nR_FREE= 0.2145\n") != std::string::npos);
     CHECK(text.find("\nR_FREE_REFLECTIONS= 928\n") != std::string::npos);
+    CHECK(text.find("\nMODEL_VALIDATION= PERFORMED\n") != std::string::npos);
     CHECK(text.find("MODEL_VALIDATION= NOT_PERFORMED") == std::string::npos);
+    CHECK(text.find("\nMODEL_FIT= ACCEPTED\n") != std::string::npos);
+    CHECK(text.find("\nMODEL_FIT_STATISTIC= R_WORK\n") != std::string::npos);
+    CHECK(text.find("\nMODEL_FIT_NULL_REPLICATES= 5\n") != std::string::npos);
+    CHECK(text.find("\nMODEL_FIT_SIGMA= +4.12\n") != std::string::npos);
+    CHECK(text.find("\nMODEL_DECISIONS_TAKEN= ENANTIOMORPH\n") != std::string::npos);
+    // The hand is ASSUMED from the model, never determined: merged intensities cannot see it.
+    CHECK(text.find("\nSPACE_GROUP_ENANTIOMORPH= ASSUMED_FROM_MODEL\n") != std::string::npos);
+
+    // The same model, not accepted by the data: it still has R-factors and maps, but it decides
+    // nothing - the reflections stay in the group and the indexing they were merged in.
+    ModelValidationResult rejected = good;
+    rejected.model_fits = false;
+    rejected.r_work_sigma = 0.59;
+    rejected.adopted_model_enantiomorph = false;
+    result.model_validation = rejected;
+    const auto rejected_text = RenderResultReport("p", "in.h5", x, result);
+    CHECK(rejected_text.find("\nMODEL_FIT= REJECTED\n") != std::string::npos);
+    CHECK(rejected_text.find("\nMODEL_DECISIONS_TAKEN= NONE\n") != std::string::npos);
+    CHECK(rejected_text.find("\nR_WORK= 0.1823\n") != std::string::npos);
+    CHECK(rejected_text.find("\nSPACE_GROUP_ENANTIOMORPH= ASSUMED_FROM_MODEL\n") == std::string::npos);
+    CHECK(rejected_text.find("byte for byte") != std::string::npos);
+
+    // A model that claims nothing - already in the data's group, no merohedral ambiguity - is never
+    // put to the null, and NOT_TESTED has to be distinguishable from a model the data refused.
+    ModelValidationResult untested = good;
+    untested.fit_tested = false;
+    untested.model_fits = false;
+    untested.model_enantiomorph_candidate = false;
+    untested.adopted_model_enantiomorph = false;
+    result.model_validation = untested;
+    const auto untested_text = RenderResultReport("p", "in.h5", x, result);
+    CHECK(untested_text.find("\nMODEL_FIT= NOT_TESTED\n") != std::string::npos);
+    CHECK(untested_text.find("\nMODEL_DECISIONS_TAKEN= NONE\n") != std::string::npos);
+    CHECK(untested_text.find("\nR_WORK= 0.1823\n") != std::string::npos);
+    CHECK(untested_text.find("MODEL_FIT_NULL_MEAN=") == std::string::npos);
+    CHECK(untested_text.find("was tried and REJECTED") == std::string::npos);
+
+    result.model_validation = good;
 
     ModelValidationResult failed;
     failed.model_path = "broken.pdb";