happy linter

httomo/common.py

@@ -2,6 +2,7 @@
 from enum import IntEnum, unique
 from pathlib import Path
 
+
 @unique
 class PipelineTasks(IntEnum):
     """An enumeration of available pipeline stages."""

httomo/data/hdf/loaders.py

@@ -11,7 +11,6 @@
 from httomo.utils import Colour, _parse_preview, log_once, log_rank
 
 
-
 @dataclass
 class LoaderData:
     data: ndarray

httomo/task_runner.py

@@ -490,7 +490,9 @@ def _get_method_funcs(yaml_config: Path, comm: MPI.Comm) -> List[MethodFunc]:
                 parameters=method_conf,
                 cpu=True if not is_httomolibgpu else wrapper_init_module.meta.cpu,
                 gpu=False if not is_httomolibgpu else wrapper_init_module.meta.gpu,
-                calc_max_slices=None if not is_httomolibgpu else wrapper_init_module.calc_max_slices,
+                calc_max_slices=None
+                if not is_httomolibgpu
+                else wrapper_init_module.calc_max_slices,
                 reslice_ahead=False,
                 pattern=Pattern.all,
                 is_loader=False,
@@ -810,7 +812,9 @@ def run_method(
             recon_algorithm = None
             if recon_center is not None:
                 slice_dim = 1
-                recon_algorithm = dict_params_method.pop("algorithm", None) # covers tomopy case
+                recon_algorithm = dict_params_method.pop(
+                    "algorithm", None
+                )  # covers tomopy case
             else:
                 slice_dim = _get_slicing_dim(current_func.pattern)
 
@@ -1121,7 +1125,7 @@ def _get_available_gpu_memory(safety_margin_percent: float = 10.0) -> int:
 def _update_max_slices(
     section: PlatformSection,
     process_data_shape: Optional[Tuple[int, int, int]],
-    input_data_type: Optional[np.dtype]
+    input_data_type: Optional[np.dtype],
 ) -> Tuple[np.dtype, Tuple[int, int]]:
     if process_data_shape is None or input_data_type is None:
         return
@@ -1142,20 +1146,19 @@ def _update_max_slices(
     output_dims = non_slice_dims_shape
     if section.gpu:
         available_memory = _get_available_gpu_memory(10.0)
-        available_memory_in_GB = round(available_memory/(1024**3),2)
-        max_slices_methods = [max_slices]*len(section.methods)
+        available_memory_in_GB = round(available_memory / (1024**3), 2)
+        max_slices_methods = [max_slices] * len(section.methods)
         idx = 0
         for m in section.methods:
             if m.calc_max_slices is not None:
                 (slices_estimated, data_type, output_dims) = m.calc_max_slices(
-                    slice_dim,
-                    non_slice_dims_shape,
-                    data_type,
-                    available_memory
+                    slice_dim, non_slice_dims_shape, data_type, available_memory
                 )
                 max_slices_methods[idx] = min(max_slices, slices_estimated)
                 idx += 1
-            non_slice_dims_shape = output_dims # overwrite input dims with estimated output ones
+            non_slice_dims_shape = (
+                output_dims  # overwrite input dims with estimated output ones
+            )
         section.max_slices = min(max_slices_methods)
     else:
         # TODO: How do we determine the output dtype in functions that aren't on GPU, tomopy, etc.

httomo/wrappers_class.py

@@ -7,6 +7,7 @@
 
 from mpi4py.MPI import Comm
 
+
 def _gpumem_cleanup():
     """cleans up GPU memory and also the FFT plan cache"""
     if gpu_enabled:
@@ -358,9 +359,5 @@ def calc_max_slices(
                 default_args[name] = par.default
         kwargs = {**default_args, **self.dict_params}
         return self.meta.calc_max_slices(
-            slice_dim, 
-            non_slice_dims_shape,
-            dtype,
-            available_memory,
-            **kwargs
+            slice_dim, non_slice_dims_shape, dtype, available_memory, **kwargs
         )

tests/conftest.py

@@ -124,6 +124,7 @@ def sample_pipelines():
 def gpu_pipeline():
     return "samples/pipeline_template_examples/03_basic_gpu_pipeline_tomo_standard.yaml"
 
+
 @pytest.fixture
 def merge_yamls():
     def _merge_yamls(*yamls) -> None:

tests/test_method_query.py

@@ -21,6 +21,7 @@ def test_get_invalid_method():
     with pytest.raises(KeyError, match="key doesntexist is not present"):
         get_method_info("tomopy.misc.corr", "doesntexist", "pattern")
 
+
 def test_get_invalid_attr():
     with pytest.raises(KeyError, match="attribute doesntexist is not present"):
         get_method_info("tomopy.misc.corr", "median_filter", "doesntexist")
@@ -45,7 +46,9 @@ def test_httomolibgpu_memfunc():
 def test_httomolibgpu_meta():
     from httomolibgpu import MethodMeta
 
-    assert isinstance(get_httomolibgpu_method_meta("prep.normalize.normalize"), MethodMeta)
+    assert isinstance(
+        get_httomolibgpu_method_meta("prep.normalize.normalize"), MethodMeta
+    )
 
 
 def test_httomolibgpu_meta_incomplete_path():

tests/test_pipeline.py

@@ -239,6 +239,7 @@ def test_i12_testing_pipeline_output(
     assert "Saving intermediate file: 6-tomopy-recon-tomo-gridrec.h5" in log_contents
     assert "INFO | ~~~ Pipeline finished ~~~" in log_contents
 
+
 def test_diad_testing_pipeline_output(
     cmd, diad_data, diad_loader, testing_pipeline, output_folder, merge_yamls
 ):
@@ -383,6 +384,7 @@ def test_sweep_pipeline_with_save_all_using_mpi(
     log_files = list(filter(lambda x: ".log" in x, files))
     assert len(log_files) == 2
 
+
 """
 #   Something weird going on here with the logs 
 
@@ -403,6 +405,7 @@ def test_sweep_pipeline_with_save_all_using_mpi(
     )
 """
 
+
 def test_sweep_range_pipeline_with_step_absent(
     cmd, standard_data, sample_pipelines, output_folder
 ):
@@ -440,13 +443,13 @@ def test_multi_inputs_pipeline(cmd, standard_data, sample_pipelines, output_fold
 
     with h5py.File(h5_files[0], "r") as f:
         arr = np.array(f["data"])
-        assert arr.shape == (20, 128, 160)          
+        assert arr.shape == (20, 128, 160)
         assert arr.dtype == np.uint16
     with h5py.File(h5_files[1], "r") as f:
         arr = np.array(f["data"])
         assert arr.shape == (20, 128, 160)
         assert arr.dtype == np.uint16
     with h5py.File(h5_files[2], "r") as f:
         arr = np.array(f["data"])
-        assert arr.shape == (180, 128, 160) 
+        assert arr.shape == (180, 128, 160)
         assert arr.dtype == np.uint16

tests/test_task_runner.py

@@ -113,7 +113,7 @@ def test_determine_platform_sections_platform_change() -> None:
         "sino-all-sino",
         "all-sino-sino",
         "all-all-all",
-    ]
+    ],
 )
 def test_determine_platform_sections_pattern_all_combine(
     pattern1: Pattern, pattern2: Pattern, expected: Pattern