Update dials-data pathlib references

newsfragments/862.misc

@@ -0,0 +1 @@
+Update dials-data uses for the new always-pathlib dials-data.

tests/command_line/test_average.py

@@ -14,9 +14,7 @@ def test_average(dials_data, tmp_path, use_mpi):
     if use_mpi:
         pytest.importorskip("mpi4py")
 
-    data = (
-        dials_data("image_examples", pathlib=True) / "SACLA-MPCCD-run266702-0-subset.h5"
-    )
+    data = dials_data("image_examples") / "SACLA-MPCCD-run266702-0-subset.h5"
     if use_mpi:
         command = "mpirun"
         mpargs = "-n 2 dxtbx.image_average --mpi=True".split()

tests/command_line/test_dlsnxs2cbf.py

@@ -16,7 +16,7 @@
 
 @pytest.mark.xfail(reason="Broken for old data while collecting new data")
 def test_dlsnxs2cbf(dials_data, tmp_path, capsys):
-    screen = dials_data("thaumatin_eiger_screen", pathlib=True)
+    screen = dials_data("thaumatin_eiger_screen")
     master = screen / "Therm_6_1_master.h5"
     run([str(master), "junk_%04d.cbf"])
 
@@ -48,7 +48,7 @@ def test_dlsnxs2cbf(dials_data, tmp_path, capsys):
 @pytest.mark.parametrize("remove_axis", ["phi", "chi"], ids=["no phi", "no chi"])
 def test_dlsnxs2cbf_deleted_axis(dials_data, tmp_path, remove_axis):
     """Check that a master file without φ or χ axes processes OK."""
-    screen = dials_data("thaumatin_eiger_screen", pathlib=True)
+    screen = dials_data("thaumatin_eiger_screen")
     master = "Therm_6_1_master.h5"
     links = (path.name for path in screen.glob("*") if path.name != master)
     try:

tests/command_line/test_plot_detector_models.py

@@ -6,7 +6,7 @@
 
 
 def test_plot_models_noninteractive_to_pdf(dials_data, tmp_path):
-    ssx = dials_data("cunir_serial_processed", pathlib=True)
+    ssx = dials_data("cunir_serial_processed")
     expts = str(ssx / "imported_no_ref_5.expt")
     subprocess.run(
         [shutil.which("dxtbx.plot_detector_models"), expts, "pdf_file=plot_test.pdf"],

tests/command_line/test_print_header.py

@@ -4,7 +4,7 @@
 
 
 def test_print_header(dials_data, capsys):
-    screen = dials_data("thaumatin_eiger_screen", pathlib=True)
+    screen = dials_data("thaumatin_eiger_screen")
     master = screen / "Therm_6_1_master.h5"
     print_header.run([str(master)])
 

tests/command_line/test_show_mask_info.py

@@ -4,7 +4,7 @@
 
 
 def test_show_mask_info(dials_data, capsys):
-    data = dials_data("image_examples", pathlib=True) / "dectris_eiger_master.h5"
+    data = dials_data("image_examples") / "dectris_eiger_master.h5"
 
     show_mask_info.run([str(data)])
     captured = capsys.readouterr()

tests/format/test_FormatCBFFullPilatusDLS6MSN126.py

@@ -8,9 +8,7 @@
 
 
 def test_DLS_I03_smargon(dials_data):
-    filename = (
-        dials_data("image_examples", pathlib=True) / "DLS_I03_smargon_0001.cbf.gz"
-    )
+    filename = dials_data("image_examples") / "DLS_I03_smargon_0001.cbf.gz"
     assert FormatCBFFullPilatusDLS6MSN126.understand(filename)
     expts = ExperimentListFactory.from_filenames(
         [filename], format_kwargs={"dynamic_shadowing": True}

tests/format/test_FormatCBFMiniEigerDLS16MSN160.py

@@ -8,9 +8,7 @@
 
 
 def test_dlsnxs2cbf_therm(dials_data):
-    filename = (
-        dials_data("image_examples", pathlib=True) / "dlsnxs2cbf_therm_0001.cbf.gz"
-    )
+    filename = dials_data("image_examples") / "dlsnxs2cbf_therm_0001.cbf.gz"
 
     assert FormatCBFMiniEigerDLS16MSN160.understand(filename)
     expts = ExperimentListFactory.from_filenames(

tests/format/test_FormatCBFMiniPilatus.py

@@ -7,7 +7,7 @@
 
 
 def test_single_panel(dials_data, tmpdir):
-    filename = dials_data("x4wide", pathlib=True) / "X4_wide_M1S4_2_0001.cbf"
+    filename = dials_data("x4wide") / "X4_wide_M1S4_2_0001.cbf"
 
     assert FormatCBFMiniPilatus.understand(filename)
     expts = ExperimentListFactory.from_filenames([filename])
@@ -17,7 +17,7 @@ def test_single_panel(dials_data, tmpdir):
 
 
 def test_multi_panel(dials_data, tmpdir):
-    filename = dials_data("x4wide", pathlib=True) / "X4_wide_M1S4_2_0001.cbf"
+    filename = dials_data("x4wide") / "X4_wide_M1S4_2_0001.cbf"
 
     assert FormatCBFMiniPilatus.understand(filename)
     expts = ExperimentListFactory.from_filenames(

tests/format/test_FormatCBFMiniPilatusDLS12M.py

@@ -56,9 +56,7 @@ def test_bad_pixel_mask(timestamp, multi_panel, masked_pixel_count, dials_data,
         )
         mocked_timestamp.return_value = timestamp
 
-    image_path = str(
-        dials_data("image_examples", pathlib=True) / "DLS_I23-germ_13KeV_0001.cbf.bz2"
-    )
+    image_path = str(dials_data("image_examples") / "DLS_I23-germ_13KeV_0001.cbf.bz2")
     experiments = ExperimentListFactory.from_filenames(
         [image_path], format_kwargs={"multi_panel": multi_panel}
     )

tests/format/test_FormatHDF5EigerNearlyNexus.py

@@ -33,7 +33,7 @@ def test_biomax_vertical_goniometer_at_diamond(tmpdir):
 
 
 def test_semi_synthetic_dectris_eiger_nearly_nexus(dials_data, tmpdir):
-    master_h5 = dials_data("image_examples", pathlib=True) / "dectris_eiger_master.h5"
+    master_h5 = dials_data("image_examples") / "dectris_eiger_master.h5"
 
     if not os.access(master_h5, os.R_OK):
         pytest.skip("Test images not available")

tests/format/test_FormatHDF5EigerNearlyNexusSPring8.py

@@ -11,7 +11,7 @@
 
 def test_spring8_ccp4_2018_zenodo_1443110_data03(dials_data):
     master_h5 = (
-        dials_data("spring8_ccp4_2018", pathlib=True)
+        dials_data("spring8_ccp4_2018")
         / "ccp4school2018_bl41xu"
         / "05"
         / "data03"

tests/format/test_FormatHDF5SaclaMPCCD.py

@@ -15,10 +15,7 @@
 
 
 def test_static_mask(dials_data):
-    master_h5 = (
-        dials_data("image_examples", pathlib=True)
-        / "SACLA-MPCCD-Phase3-21528-5images.h5"
-    )
+    master_h5 = dials_data("image_examples") / "SACLA-MPCCD-Phase3-21528-5images.h5"
     assert FormatHDF5SaclaMPCCD.understand(master_h5)
 
     expts_from_filename = ExperimentListFactory.from_filenames([master_h5])
@@ -35,10 +32,7 @@ def test_static_mask(dials_data):
 
 
 def test_MPCCD_Phase3_21528(dials_data):
-    master_h5 = (
-        dials_data("image_examples", pathlib=True)
-        / "SACLA-MPCCD-Phase3-21528-5images.h5"
-    )
+    master_h5 = dials_data("image_examples") / "SACLA-MPCCD-Phase3-21528-5images.h5"
     assert FormatHDF5SaclaMPCCD.understand(master_h5)
     expts = ExperimentListFactory.from_filenames([master_h5])
     imageset = expts[0].imageset
@@ -81,10 +75,7 @@ def test_MPCCD_RECONST_MODE(dials_data, monkeypatch):
         else:
             monkeypatch.delenv("MPCCD_RECONST_MODE", raising=False)
 
-        master_h5 = (
-            dials_data("image_examples", pathlib=True)
-            / "SACLA-MPCCD-Phase3-21528-5images.h5"
-        )
+        master_h5 = dials_data("image_examples") / "SACLA-MPCCD-Phase3-21528-5images.h5"
         expts = ExperimentListFactory.from_filenames([master_h5])
         imageset = expts[0].imageset
         # Horrible hack to work around format_instance caching
@@ -107,10 +98,7 @@ def test_MPCCD_RECONST_MODE(dials_data, monkeypatch):
 
 
 def test_combine_with_user_static_mask(dials_data, tmpdir):
-    master_h5 = (
-        dials_data("image_examples", pathlib=True)
-        / "SACLA-MPCCD-Phase3-21528-5images.h5"
-    )
+    master_h5 = dials_data("image_examples") / "SACLA-MPCCD-Phase3-21528-5images.h5"
     assert FormatHDF5SaclaMPCCD.understand(master_h5)
 
     expts_from_filename = ExperimentListFactory.from_filenames([master_h5])
@@ -154,7 +142,7 @@ def test_HDF5_format_caching(dials_data, clear_cache):
     xfail: see https://github.com/cctbx/dxtbx/issues/245
     """
     img_file = "SACLA-MPCCD-Phase3-21528-5images.h5"
-    master_h5 = dials_data("image_examples", pathlib=True) / img_file
+    master_h5 = dials_data("image_examples") / img_file
 
     expts1 = ExperimentListFactory.from_filenames([master_h5])
     expts1[0].imageset.get_mask(0)

tests/format/test_FormatISISSXD.py

@@ -9,7 +9,7 @@
 
 @pytest.fixture(scope="session")
 def nacl(dials_data):
-    location = dials_data("isis_sxd_example_data", pathlib=True)
+    location = dials_data("isis_sxd_example_data")
     nacl_filename = join(location, "sxd_nacl_run.nxs")
     return nacl_filename
 

tests/format/test_FormatNXmxDLS16M.py

@@ -182,9 +182,7 @@ def test_grid_scan_i04():
     raises=AssertionError, reason="https://github.com/cctbx/dxtbx/issues/13"
 )
 def test_screening(dials_data):
-    master_h5 = (
-        dials_data("thaumatin_eiger_screen", pathlib=True) / "Therm_6_1_master.h5"
-    )
+    master_h5 = dials_data("thaumatin_eiger_screen") / "Therm_6_1_master.h5"
     assert FormatNXmxDLS16M.understand(master_h5)
 
     expts = ExperimentListFactory.from_filenames([master_h5])

tests/format/test_FormatPYunspecified.py

@@ -5,7 +5,7 @@
 
 
 def test_static_mask(dials_data):
-    data_dir = dials_data("image_examples", pathlib=True)
+    data_dir = dials_data("image_examples")
     filename = str(
         data_dir / "LCLS_CXI-shot-s00-2011-12-02T21_07Z29.723_00569.pickle",
     )

tests/format/test_FormatSMVADSC.py

@@ -6,7 +6,7 @@
 
 
 def test_noninteger_pedestal(dials_data, tmpdir):
-    data_dir = dials_data("image_examples", pathlib=True)
+    data_dir = dials_data("image_examples")
     filename = str(data_dir / "APS_14BMC-q315_1_001.img.bz2")
     # Read this file in as data
     with bz2.open(filename, "rb") as f:

tests/format/test_cbf_mini_as_file.py

@@ -20,7 +20,7 @@
     ],
 )
 def test_cbf_writer(image_file, dials_data, tmp_path):
-    data_dir = dials_data("image_examples", pathlib=True)
+    data_dir = dials_data("image_examples")
     filename = str(data_dir / image_file)
     imageset = ExperimentListFactory.from_filenames([filename])[0].imageset
     output_file = tmp_path / "image_0001.cbf"

tests/format/test_format.py

@@ -4,7 +4,7 @@
 
 
 def test_reading_refl_failure(dials_data):
-    test_data = dials_data("centroid_test_data", pathlib=True)
+    test_data = dials_data("centroid_test_data")
 
     assert Registry.get_format_class_for_file(test_data / "indexed.refl") is None
     # Check .expt while here

tests/format/test_nexus.py

@@ -67,7 +67,7 @@ def nexus_file(tmp_path_factory) -> Path:
 
 
 def test_data_factory_nxs(dials_data):
-    nxs_file = dials_data("vmxi_thaumatin", pathlib=True) / "image_15799.nxs"
+    nxs_file = dials_data("vmxi_thaumatin") / "image_15799.nxs"
     with h5py.File(nxs_file) as fh:
         data = fh["/entry/data"]
         data_factory = nexus.DataFactory(nexus.NXdata(data))

tests/imagelist.py

@@ -5,7 +5,7 @@
 import dials_data.download
 
 df = dials_data.download.DataFetcher()
-data_dir = df("image_examples", pathlib=True)
+data_dir = df("image_examples")
 image_examples = []
 for f in data_dir.iterdir():
     ext = os.path.splitext(f)[1]

tests/masking/test_masking.py

@@ -121,8 +121,7 @@ def _construct_shadow_masker(goniometer):
 @pytest.fixture
 def dls_i23_experiment(dials_data):
     experiments_file = str(
-        dials_data("shadow_test_data", pathlib=True)
-        / "DLS_I23_Kappa-data_1_0400.cbf.gz"
+        dials_data("shadow_test_data") / "DLS_I23_Kappa-data_1_0400.cbf.gz"
     )
     experiments = ExperimentListFactory.from_filenames([experiments_file])
     return experiments[0]

tests/model/test_detector.py

@@ -333,7 +333,7 @@ def test_get_detector_projection_2d_axes():
 def test_get_panel_projection_2d_from_axes(dials_data):
     # Get test data
     pytest.importorskip("h5py")
-    filename = dials_data("image_examples", pathlib=True) / "dectris_eiger_master.h5"
+    filename = dials_data("image_examples") / "dectris_eiger_master.h5"
     experiment = ExperimentListFactory.from_filenames([filename])[0]
     detector = experiment.detector