Miscellaneous dials_regression --> dials-data test updates (dials#2907)

Author: dagewa

.conda-envs/linux.txt

@@ -5,7 +5,7 @@ c-compiler
 colorlog
 conda
 cxx-compiler
-dials-data>=2.4.102
+dials-data>=2.4.107
 docutils
 eigen
 ffbidx

.conda-envs/macos.txt

@@ -5,7 +5,7 @@ c-compiler
 colorlog
 conda
 cxx-compiler
-dials-data>=2.4.102
+dials-data>=2.4.107
 docutils
 eigen
 flexparser<0.4

.conda-envs/windows.txt

@@ -5,7 +5,7 @@ c-compiler
 colorlog
 conda
 cxx-compiler
-dials-data>=2.4.102
+dials-data>=2.4.107
 docutils
 eigen
 flexparser<0.4

newsfragments/2907.bugfix

@@ -0,0 +1 @@
+Updated miscellaneous tests to use data from ``dials-data`` rather than ``dials_regression``.

tests/algorithms/indexing/test_index.py

@@ -503,18 +503,15 @@ def test_index_small_molecule_multi_sequence_4(dials_data, tmp_path):
     assert len(result.indexed_reflections) > 1250, len(result.indexed_reflections)
 
 
-def test_index_small_molecule_multi_sequence_3(
-    dials_regression: pathlib.Path, tmp_path
-):
+def test_index_small_molecule_multi_sequence_3(dials_data, tmp_path):
     # test for small molecule multi-sequence indexing, 3 sequences with different values
     # of goniometer setting rotation (i.e. phi scans)
-    data_dir = dials_regression / "dials-191"
-    print(data_dir)
-    pickle_paths = [
-        sorted(data_dir.glob(f"*_SWEEP{i + 1}_strong.pickle"))[0] for i in range(3)
+    data_dir = dials_data("misc_regression", pathlib=True)
+    refl_paths = [
+        str(data_dir / f"dials-191_sweep{i + 1}_strong.refl") for i in range(3)
     ]
     sequence_paths = [
-        sorted(data_dir.glob(f"*_SWEEP{i + 1}_experiments.json"))[0] for i in range(3)
+        str(data_dir / f"dials-191_sweep{i + 1}_imported.expt") for i in range(3)
     ]
     extra_args = ["filter_ice=False"]
     expected_unit_cell = uctbx.unit_cell(
@@ -524,7 +521,7 @@ def test_index_small_molecule_multi_sequence_3(
     expected_hall_symbol = " P 1"
 
     result = run_indexing(
-        pickle_paths,
+        refl_paths,
         sequence_paths,
         tmp_path,
         extra_args,

tests/algorithms/spot_prediction/test_ray_predictor.py

@@ -1,15 +1,14 @@
 from __future__ import annotations
 
 import math
-import os
 
 import pytest
 
 from scitbx import matrix
 
 
 class RayPredictor:
-    def __init__(self, dials_regression):
+    def __init__(self, dials_data):
         import dxtbx
         from iotbx.xds import integrate_hkl, xparm
         from rstbx.cftbx.coordinate_frame_converter import coordinate_frame_converter
@@ -21,10 +20,9 @@ def __init__(self, dials_regression):
         from dials.util import ioutil
 
         # The XDS files to read from
-        integrate_filename = os.path.join(
-            dials_regression, "data", "sim_mx", "INTEGRATE.HKL"
-        )
-        gxparm_filename = os.path.join(dials_regression, "data", "sim_mx", "GXPARM.XDS")
+        data_dir = dials_data("misc_regression", pathlib=True)
+        integrate_filename = str(data_dir / "sim_mx-INTEGRATE.HKL")
+        gxparm_filename = str(data_dir / "sim_mx-GXPARM.XDS")
 
         # Read the XDS files
         self.integrate_handle = integrate_hkl.reader()
@@ -94,8 +92,8 @@ def __init__(self, dials_regression):
 
 
 @pytest.fixture(scope="session")
-def raypredictor(dials_regression):
-    return RayPredictor(dials_regression)
+def raypredictor(dials_data):
+    return RayPredictor(dials_data)
 
 
 def test_miller_index_set(raypredictor):

tests/algorithms/spot_prediction/test_scan_static_reflection_predictor.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import copy
-import os
 
 import pytest
 
@@ -12,7 +11,7 @@
 
 
 class Data:
-    def __init__(self, dials_data, dials_regression):
+    def __init__(self, dials_data):
         self.experiments = ExperimentListFactory.from_json_file(
             dials_data("centroid_test_data", pathlib=True) / "experiments.json"
         )
@@ -22,10 +21,9 @@ def __init__(self, dials_data, dials_regression):
         self.experiments[0].imageset.set_goniometer(self.experiments[0].goniometer)
         self.experiments[0].imageset.set_scan(self.experiments[0].scan)
 
-        reflection_filename = os.path.join(
-            dials_regression, "prediction_test_data", "expected_reflections.pickle"
+        reflection_filename = str(
+            dials_data("misc_regression", pathlib=True) / "prediction-expected.refl"
         )
-
         self.reflections = flex.reflection_table.from_file(reflection_filename)
 
     def predict_new(self, experiment=None, hkl=None, panel=None):
@@ -42,8 +40,8 @@ def predict_new(self, experiment=None, hkl=None, panel=None):
 
 
 @pytest.fixture(scope="session")
-def data(dials_data, dials_regression):
-    return Data(dials_data, dials_regression)
+def data(dials_data):
+    return Data(dials_data)
 
 
 def test_number_of_predictions(data):

tests/algorithms/spot_prediction/test_scan_varying_reflection_predictor.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import copy
-import os
 
 import pytest
 
@@ -11,16 +10,15 @@
 
 
 class Data:
-    def __init__(self, dials_regression):
-        path = os.path.join(
-            dials_regression,
-            "prediction_test_data",
-            "experiments_scan_varying_crystal.json",
-        )
+    def __init__(self, dials_data):
+        data_dir = dials_data("misc_regression", pathlib=True)
+        path = str(data_dir / "prediction-varying-crystal.expt")
 
         from dxtbx.model.experiment_list import ExperimentListFactory
 
-        self.experiments = ExperimentListFactory.from_json_file(path)
+        self.experiments = ExperimentListFactory.from_json_file(
+            path, check_format=False
+        )
         assert len(self.experiments) == 1
         assert (
             self.experiments[0].crystal.num_scan_points
@@ -55,8 +53,8 @@ def _predict_new(self, hkl=None, frame=None, panel=None):
 
 
 @pytest.fixture(scope="session")
-def data(dials_regression):
-    return Data(dials_regression)
+def data(dials_data):
+    return Data(dials_data)
 
 
 def test_regression(data):

tests/algorithms/spot_prediction/test_spot_prediction.py

@@ -1,15 +1,14 @@
 from __future__ import annotations
 
 import math
-import os
 
 import pytest
 
 from scitbx import matrix
 
 
 class SpotPredictor:
-    def __init__(self, dials_regression):
+    def __init__(self, dials_data):
         import dxtbx
         from iotbx.xds import integrate_hkl, xparm
         from rstbx.cftbx.coordinate_frame_converter import coordinate_frame_converter
@@ -22,10 +21,9 @@ def __init__(self, dials_regression):
         from dials.util import ioutil
 
         # The XDS files to read from
-        integrate_filename = os.path.join(
-            dials_regression, "data", "sim_mx", "INTEGRATE.HKL"
-        )
-        gxparm_filename = os.path.join(dials_regression, "data", "sim_mx", "GXPARM.XDS")
+        data_dir = dials_data("misc_regression", pathlib=True)
+        integrate_filename = str(data_dir / "sim_mx-INTEGRATE.HKL")
+        gxparm_filename = str(data_dir / "sim_mx-GXPARM.XDS")
 
         # Read the XDS files
         self.integrate_handle = integrate_hkl.reader()
@@ -93,8 +91,8 @@ def __init__(self, dials_regression):
 
 
 @pytest.fixture(scope="session")
-def spotpredictor(dials_regression):
-    return SpotPredictor(dials_regression)
+def spotpredictor(dials_data):
+    return SpotPredictor(dials_data)
 
 
 def test_dmin(spotpredictor):

tests/command_line/test_compute_delta_cchalf.py

@@ -2,10 +2,8 @@
 
 from __future__ import annotations
 
-import os
 import shutil
 import subprocess
-from pathlib import Path
 
 import pytest
 
@@ -84,12 +82,11 @@ def test_compute_delta_cchalf_scaled_data_mtz(dials_data, tmp_path):
         check_cchalf_result(f)
 
 
-def test_compute_delta_cchalf(dials_regression: Path):
+def test_compute_delta_cchalf(dials_data):
     """Test compute delta cchalf on an integrated mtz."""
 
-    filename = os.path.join(
-        dials_regression, "delta_cchalf_test_data", "test.XDS_ASCII.mtz"
-    )
+    data_dir = dials_data("misc_regression", pathlib=True)
+    filename = str(data_dir / "delta-cchalf-test_XDS_ASCII.mtz")
     params = phil_scope.extract()
     params.nbins = 1