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docs/cli/functions.md

@@ -13,4 +13,4 @@
    predict
    integrate
 
-```
+```

docs/cli/initial_solution.rst

@@ -21,4 +21,4 @@ Full parameter definitions
 
 .. phil:: laue_dials.command_line.initial_solution.working_phil
    :expert-level: 2
-   :attributes-level: 2
+   :attributes-level: 2

docs/cli/integrate.rst

@@ -21,4 +21,4 @@ Full parameter definitions
 
 .. phil:: laue_dials.command_line.integrate.working_phil
    :expert-level: 2
-   :attributes-level: 2
+   :attributes-level: 2

docs/cli/optimize_indexing.rst

@@ -21,4 +21,4 @@ Full parameter definitions
 
 .. phil:: laue_dials.command_line.optimize_indexing.working_phil
    :expert-level: 2
-   :attributes-level: 2
+   :attributes-level: 2

docs/cli/predict.rst

@@ -21,4 +21,4 @@ Full parameter definitions
 
 .. phil:: laue_dials.command_line.predict.working_phil
    :expert-level: 2
-   :attributes-level: 2
+   :attributes-level: 2

docs/cli/refine.rst

@@ -21,4 +21,4 @@ Full parameter definitions
 
 .. phil:: laue_dials.command_line.refine.working_phil
    :expert-level: 2
-   :attributes-level: 2
+   :attributes-level: 2

docs/cli/sequence_to_stills.rst

@@ -22,4 +22,3 @@ Full parameter definitions
 .. phil:: laue_dials.command_line.sequence_to_stills.phil_scope
    :expert-level: 2
    :attributes-level: 2
-

src/laue_dials/__init__.py

@@ -2,11 +2,9 @@
 
 if sys.version_info[:2] >= (3, 8):
     # TODO: Import directly (no need for conditional) when `python_requires = >= 3.8`
-    from importlib.metadata import (PackageNotFoundError,  # pragma: no cover
-                                    version)
+    from importlib.metadata import PackageNotFoundError, version  # pragma: no cover
 else:
-    from importlib_metadata import (PackageNotFoundError,  # pragma: no cover
-                                    version)
+    from importlib_metadata import PackageNotFoundError, version  # pragma: no cover
 
 try:
     # Change here if project is renamed and does not equal the package name

src/laue_dials/algorithms/laue.py

@@ -100,8 +100,9 @@ def gen_beam_models(expts, refls):
     # Imports
     from copy import deepcopy
 
-    from dials.algorithms.refinement.prediction.managed_predictors import \
-        ExperimentsPredictorFactory
+    from dials.algorithms.refinement.prediction.managed_predictors import (
+        ExperimentsPredictorFactory,
+    )
 
     # Instantiate new ExperimentList/reflection_table
     new_expts = ExperimentList()

src/laue_dials/command_line/initial_solution.py

@@ -11,8 +11,11 @@
 from dials.util import show_mail_handle_errors
 from dials.util.options import ArgumentParser
 
-from laue_dials.algorithms.monochromatic import (find_spots, initial_index,
-                                                 scan_varying_refine)
+from laue_dials.algorithms.monochromatic import (
+    find_spots,
+    initial_index,
+    scan_varying_refine,
+)
 
 logger = logging.getLogger("laue-dials.command_line.initial_solution")
 

src/laue_dials/command_line/integrate.py

@@ -17,8 +17,7 @@
 from cctbx import sgtbx
 from dials.array_family import flex
 from dials.util import show_mail_handle_errors
-from dials.util.options import (ArgumentParser,
-                                reflections_and_experiments_from_files)
+from dials.util.options import ArgumentParser, reflections_and_experiments_from_files
 
 from laue_dials.algorithms.integration import SegmentedImage
 

src/laue_dials/command_line/optimize_indexing.py

@@ -13,8 +13,7 @@
 import numpy as np
 from dials.array_family.flex import reflection_table
 from dials.util import show_mail_handle_errors
-from dials.util.options import (ArgumentParser,
-                                reflections_and_experiments_from_files)
+from dials.util.options import ArgumentParser, reflections_and_experiments_from_files
 from dxtbx.model import ExperimentList
 
 logger = logging.getLogger("laue-dials.command_line.optimize_indexing")

src/laue_dials/command_line/predict.py

@@ -16,8 +16,7 @@
 from dials.array_family import flex
 from dials.array_family.flex import reflection_table
 from dials.util import show_mail_handle_errors
-from dials.util.options import (ArgumentParser,
-                                reflections_and_experiments_from_files)
+from dials.util.options import ArgumentParser, reflections_and_experiments_from_files
 from dxtbx.model import ExperimentList
 
 from laue_dials.algorithms.outliers import gen_kde

src/laue_dials/command_line/refine.py

@@ -19,8 +19,11 @@
 from dxtbx.model import ExperimentList
 from dxtbx.model.experiment_list import ExperimentListFactory
 
-from laue_dials.algorithms.laue import (gen_beam_models, remove_beam_models,
-                                        store_wavelengths)
+from laue_dials.algorithms.laue import (
+    gen_beam_models,
+    remove_beam_models,
+    store_wavelengths,
+)
 
 logger = logging.getLogger("laue-dials.command_line.refine")
 
@@ -92,7 +95,7 @@
 
       min_nref_per_parameter = 1
     }
-    
+
     spherical_relp_model = True
   }
 }

src/laue_dials/command_line/sequence_to_stills.py

@@ -13,8 +13,7 @@
 from dials.array_family import flex
 from dials.array_family.flex import reflection_table
 from dials.util import show_mail_handle_errors
-from dials.util.options import (OptionParser,
-                                reflections_and_experiments_from_files)
+from dials.util.options import OptionParser, reflections_and_experiments_from_files
 from dxtbx.model import MosaicCrystalSauter2014
 from dxtbx.model.experiment_list import Experiment, ExperimentList
 from libtbx.phil import parse