Update tests

src/dials/command_line/index.py

@@ -158,7 +158,8 @@ def _index_single_imageset(experiments, reflections, params, log_text=None):
     # update the identifiers so that the unindexed has id 0, and the rest 1,2,3.. etc
     idxr.unindexed_reflections["id"] = flex.int(idxr.unindexed_reflections.size(), 0)
     idxr.unindexed_reflections.experiment_identifiers()[0] = unindexed[0].identifier
-    idxr.unindexed_reflections.clean_experiment_identifiers_map()
+    if idxr.unindexed_reflections.size():
+        idxr.unindexed_reflections.clean_experiment_identifiers_map()
 
     idx_refl = idxr.refined_reflections
     for id_ in sorted(set(idx_refl["id"]), reverse=True):
@@ -179,7 +180,8 @@ def _index_single_imageset(experiments, reflections, params, log_text=None):
     indexed_experiments = ExperimentList(unindexed)
     indexed_experiments.extend(idxr.refined_experiments)
     idx_refl.extend(idxr.unindexed_reflections)
-    idx_refl.assert_experiment_identifiers_are_consistent()
+    idx_refl.assert_experiment_identifiers_are_consistent(indexed_experiments)
+
     return indexed_experiments, idx_refl
 
 

tests/algorithms/indexing/test_index.py

@@ -68,12 +68,14 @@ def run_indexing(
     assert out_refls.is_file()
 
     experiments_list = load.experiment_list(out_expts, check_format=False)
-    assert len(experiments_list.crystals()) == n_expected_lattices
+    assert len([c for c in experiments_list.crystals() if c]) == n_expected_lattices
     indexed_reflections = flex.reflection_table.from_file(out_refls)
     indexed_reflections.assert_experiment_identifiers_are_consistent(experiments_list)
     rmsds = None
 
     for i, experiment in enumerate(experiments_list):
+        if experiment.crystal is None:
+            continue
         assert unit_cells_are_similar(
             experiment.crystal.get_unit_cell(),
             expected_unit_cell,
@@ -609,7 +611,7 @@ def test_refinement_failure_on_max_lattices_a15(dials_data, tmp_path):
     experiments_list = load.experiment_list(
         tmp_path / "indexed.expt", check_format=False
     )
-    assert len(experiments_list) == 2
+    assert len([c for c in experiments_list.crystals() if c]) == 2
 
     # now try to reindex with existing model
     result = subprocess.run(
@@ -628,7 +630,7 @@ def test_refinement_failure_on_max_lattices_a15(dials_data, tmp_path):
     experiments_list = load.experiment_list(
         tmp_path / "indexed.expt", check_format=False
     )
-    assert len(experiments_list) == 2
+    assert len([c for c in experiments_list.crystals() if c]) == 2
 
 
 @pytest.mark.parametrize(
@@ -688,6 +690,7 @@ def test_index_multi_lattice_multi_sweep(dials_data, tmp_path):
             "max_lattices=2",
             "joint_indexing=False",
             "n_macro_cycles=2",
+            "output.retain_unindexed_experiment=False",
         ],
         cwd=tmp_path,
         capture_output=True,
@@ -959,7 +962,8 @@ def test_index_known_orientation(dials_data, tmp_path):
     )
 
 
-def test_all_expt_ids_have_expts(dials_data, tmp_path):
+@pytest.mark.parametrize("retain_unindexed", [True, False])
+def test_all_expt_ids_have_expts(dials_data, tmp_path, retain_unindexed):
     result = subprocess.run(
         [
             shutil.which("dials.index"),
@@ -972,6 +976,7 @@ def test_all_expt_ids_have_expts(dials_data, tmp_path):
             "max_lattices=8",
             "beam.fix=all",
             "detector.fix=all",
+            f"retain_unindexed_experiment={retain_unindexed}",
         ],
         cwd=tmp_path,
         capture_output=True,
@@ -982,9 +987,18 @@ def test_all_expt_ids_have_expts(dials_data, tmp_path):
 
     refl = flex.reflection_table.from_file(tmp_path / "indexed.refl")
     expt = ExperimentList.from_file(tmp_path / "indexed.expt", check_format=False)
-    assert (refl["id"] != -1).count(True) == refl.get_flags(refl.flags.indexed).count(
-        True
-    )
+    if retain_unindexed:
+        id_ = None
+        for i in refl.experiment_identifiers().keys():
+            if refl.experiment_identifiers()[i] == expt[0].identifier:
+                id_ = i
+                break
+        sel = refl["id"] == id_
+        assert sel.count(False) == refl.get_flags(refl.flags.indexed).count(True)
+    else:
+        assert (refl["id"] != -1).count(True) == refl.get_flags(
+            refl.flags.indexed
+        ).count(True)
     refl.assert_experiment_identifiers_are_consistent(expt)
 
     assert flex.max(refl["id"]) + 1 == len(expt)
@@ -1002,6 +1016,7 @@ def test_multi_lattice_multi_sweep_joint(dials_data, tmp_path):
             dials_data("l_cysteine_dials_output", pathlib=True) / "indexed.expt",
             dials_data("l_cysteine_dials_output", pathlib=True) / "indexed.refl",
             "max_lattices=2",
+            "output.retain_unindexed_experiment=False",
         ],
         cwd=tmp_path,
         capture_output=True,