Add test for command line programs and new files

src/dials/command_line/complete_full_sphere.py

@@ -64,12 +64,12 @@ def run(self, args=None):
         model_shadow = params.shadow
 
         experiments = flatten_experiments(params.input.experiments)
-
+        if experiments:
+            experiments, _ = Expeditor(experiments).filter_experiments_with_crystals()
         if len(experiments) != 1:
             self.parser.print_help()
             return
 
-        experiments, _ = Expeditor(experiments).filter_experiments_with_crystals()
         expt = experiments[0]
 
         axes = expt.goniometer.get_axes()

tests/command_line/test_handling_of_crystalless_experiment_models.py

@@ -0,0 +1,113 @@
+from __future__ import annotations
+
+import shutil
+import subprocess
+
+import pytest
+
+from dxtbx.serialize import load
+
+from dials.array_family import flex
+
+
+@pytest.fixture
+def indexed_data(dials_data, tmp_path):
+    loc = dials_data("semisynthetic_multilattice", pathlib=True)
+    result = subprocess.run(
+        [
+            shutil.which("dials.index"),
+            loc / "ag_imported_1_50.expt",
+            loc / "ag_strong_1_50.refl",
+            loc / "bh_imported_1_50.expt",
+            loc / "bh_strong_1_50.refl",
+            "max_lattices=2",
+            "joint_indexing=False",
+            "n_macro_cycles=2",
+            "output.retain_unindexed_experiments=True",
+        ],
+        cwd=tmp_path,
+        capture_output=True,
+    )
+    assert not result.returncode and not result.stderr
+    assert (tmp_path / "indexed.refl").is_file()
+    assert (tmp_path / "indexed.expt").is_file()
+    expts = load.experiment_list(tmp_path / "indexed.expt", check_format=False)
+    assert len(expts) == 6
+    assert len([c for c in expts.crystals() if c]) == 4
+    refls = flex.reflection_table.from_file(tmp_path / "indexed.refl")
+    refls.assert_experiment_identifiers_are_consistent(expts)
+    assert set(refls["imageset_id"]) == {0, 1}
+    return (tmp_path / "indexed.expt", tmp_path / "indexed.refl")
+
+
+def test_refine(indexed_data, tmp_path):
+    result = subprocess.run(
+        [
+            shutil.which("dials.refine"),
+            indexed_data[0],
+            indexed_data[1],
+        ],
+        cwd=tmp_path,
+        capture_output=True,
+    )
+    assert not result.returncode and not result.stderr
+    assert (tmp_path / "refined.refl").is_file()
+    assert (tmp_path / "refined.expt").is_file()
+    expts = load.experiment_list(tmp_path / "refined.expt", check_format=False)
+    assert len(expts) == 6
+    assert len([c for c in expts.crystals() if c]) == 4
+    refls = flex.reflection_table.from_file(tmp_path / "refined.refl")
+    refls.assert_experiment_identifiers_are_consistent(expts)
+    assert set(refls["imageset_id"]) == {0, 1}
+
+    result = subprocess.run(
+        [
+            shutil.which("dials.plot_scan_varying_model"),
+            tmp_path / "refined.expt",
+        ],
+        cwd=tmp_path,
+        capture_output=True,
+    )
+    assert not result.returncode and not result.stderr
+
+    result = subprocess.run(
+        [
+            shutil.which("dials.filter_reflections"),
+            tmp_path / "refined.expt",
+            tmp_path / "refined.refl",
+            "d_min=3.0",
+        ],
+        cwd=tmp_path,
+        capture_output=True,
+    )
+    assert not result.returncode and not result.stderr
+    refls = flex.reflection_table.from_file(tmp_path / "refined.refl")
+    assert set(refls["id"]) == {0, 1, 2, 3, 4, 5}
+
+
+@pytest.mark.parametrize(
+    "program,requires_refl,params",
+    [
+        ("dials.stereographic_projection", False, ["hkl=1,0,0"]),
+        ("dials.two_theta_offset", False, []),
+        ("dials.unit_cell_histogram", False, []),
+        ("dials.align_crystal", False, []),
+        ("dials.cluster_unit_cell", False, []),
+        ("dials.compare_orientation_matrices", False, []),
+        ("dials.refine_bravais_settings", True, ["crystal_id=0"]),
+        ("dials.indexed_as_integrated", True, []),
+        ("dials.reindex", True, ["change_of_basis_op=a,b,c"]),
+        ("dials.report", True, []),
+        ("dials.show", True, []),
+        ("dials.split_experiments", True, []),
+        ("dials.spot_resolution_shells", True, []),
+    ],
+)
+def test_programs(indexed_data, tmp_path, program, requires_refl, params):
+    cmd = [shutil.which(program), indexed_data[0]]
+    if requires_refl:
+        cmd.append(indexed_data[1])
+    if params:
+        cmd.extend(params)
+    result = subprocess.run(cmd, cwd=tmp_path, capture_output=True)
+    assert not result.returncode and not result.stderr