PEP8

nxtomomill/__main__.py

@@ -36,15 +36,14 @@ __date__ = "04/01/2018"
 
 
 import logging
-
-logging.basicConfig()
-
 import sys
 from silx.utils.launcher import Launcher as _Launcher
 import nxtomomill.version
 from collections import namedtuple
 import traceback
 
+logging.basicConfig()
+
 
 DeprecationWarning = namedtuple(
     "DeprecationWarning", ["since", "reason", "replacement"]

nxtomomill/app/test/test_dxfile2nx_app.py

@@ -38,7 +38,6 @@ import tempfile
 from nxtomomill.test.utils.dxfile import MockDxFile
 from nxtomomill.app.dxfile2nx import main
 import os
-import subprocess
 
 
 def test_dxfile2nx_application():
@@ -50,7 +49,7 @@ def test_dxfile2nx_application():
         n_darks = 2
         n_flats = 4
 
-        mock = MockDxFile(
+        MockDxFile(
             file_path=dx_file_path,
             n_projection=n_projections,
             n_darks=n_darks,

nxtomomill/app/test/test_edf2nx_app.py

@@ -38,7 +38,6 @@ import tempfile
 from tomoscan.esrf.mock import MockEDF
 from nxtomomill.app.edf2nx import main
 import os
-import subprocess
 
 
 def test_edf2nx_application():

nxtomomill/app/test/test_h52nx_app.py

@@ -38,7 +38,6 @@ import tempfile
 from nxtomomill.test.utils.bliss import MockBlissAcquisition
 from nxtomomill.app.h52nx import main
 import os
-import subprocess
 
 
 def test_h52nx_application():

nxtomomill/app/test/test_patch_nx_app.py

@@ -37,9 +37,7 @@ __date__ = "30/08/2021"
 import tempfile
 from tomoscan.esrf.mock import MockHDF5
 from nxtomomill.app.patch_nx import main
-import h5py
 import os
-import subprocess
 
 
 def test_patch_nx_application():

nxtomomill/converter/__init__.py

-from .edf.edfconverter import edf_to_nx
-from .hdf5.hdf5converter import from_h5_to_nx
-from .hdf5.hdf5converter import h5_to_nx
-from .hdf5.hdf5converter import get_bliss_tomo_entries
-from .edf.edfconverter import EDFFileKeys
-from .dxfile.dxfileconverter import from_dx_to_nx
+from .edf.edfconverter import edf_to_nx  # noqa F401
+from .hdf5.hdf5converter import from_h5_to_nx  # noqa F401
+from .hdf5.hdf5converter import h5_to_nx  # noqa F401
+from .hdf5.hdf5converter import get_bliss_tomo_entries  # noqa F401
+from .edf.edfconverter import EDFFileKeys  # noqa F401
+from .dxfile.dxfileconverter import from_dx_to_nx  # noqa F401

nxtomomill/converter/dxfile/__init__.py

@@ -31,4 +31,4 @@ __authors__ = ["H. Payno"]
 __date__ = "07/06/2020"
 __license__ = "MIT"
 
-from .dxfileconverter import from_dx_to_nx
+from .dxfileconverter import from_dx_to_nx  # noqa F401

nxtomomill/converter/dxfile/dxfileconverter.py

@@ -329,7 +329,7 @@ class _DxFileToNxConverter(BaseConverter):
         if self.energy is None:
             try:
                 self._configuration.energy = self._read_energy()
-            except Exception as e:
+            except Exception:
                 self._configuration.energy = None
         if self.energy is None:
             self._configuration.energy = self.DEFAULT_BEAM_ENERGY
@@ -552,7 +552,7 @@ class _DxFileToNxConverter(BaseConverter):
                 where="end",
                 logger=_logger,
             ).process()
-        except Exception as e:
+        except Exception:
             _logger.warning(
                 "No projections found in {} or unable to add them to the dataset".format(
                     self._data_proj_url.path()

nxtomomill/converter/edf/edfconverter.py

@@ -46,10 +46,10 @@ from nxtomomill.settings import Tomo
 from tomoscan.esrf.edfscan import EDFTomoScan
 from tomoscan.unitsystem import metricsystem
 from tomoscan.io import HDF5File
-import datetime
 import fabio
 import numpy
 import os
+import logging
 
 EDF_MOTOR_POS = Tomo.EDF.MOTOR_POS
 EDF_MOTOR_MNE = Tomo.EDF.MOTOR_MNE
@@ -61,8 +61,6 @@ EDF_X_TRANS = Tomo.EDF.X_TRANS
 EDF_Y_TRANS = Tomo.EDF.Y_TRANS
 EDF_Z_TRANS = Tomo.EDF.Z_TRANS
 
-import logging
-
 _logger = logging.getLogger(__name__)
 
 
@@ -181,7 +179,7 @@ def edf_to_nx(
                         .split(" ")
                         .index(file_keys.rot_angle_key)
                     )
-                except:
+                except (KeyError, ValueError):
                     rotangle_index = -1
                 try:
                     xtrans_index = (
@@ -189,7 +187,7 @@ def edf_to_nx(
                         .split(" ")
                         .index(file_keys.x_trans_key)
                     )
-                except:
+                except (KeyError, ValueError):
                     xtrans_index = -1
                 try:
                     ytrans_index = (
@@ -197,7 +195,7 @@ def edf_to_nx(
                         .split(" ")
                         .index(file_keys.y_trans_key)
                     )
-                except:
+                except (KeyError, ValueError):
                     ytrans_index = -1
                 try:
                     ztrans_index = (
@@ -205,7 +203,7 @@ def edf_to_nx(
                         .split(" ")
                         .index(file_keys.z_trans_key)
                     )
-                except:
+                except (KeyError, ValueError):
                     ztrans_index = -1
 
                 if hasattr(fid, "bytecode"):
@@ -248,7 +246,7 @@ def edf_to_nx(
         if sample_name is None:
             try:
                 sample_name = os.path.abspath(scan.path).split(os.sep)[-3:]
-            except:
+            except Exception:
                 sample_name = "unknow"
         h5d["/entry/sample/name"] = sample_name
         if instrument_name is not None:
@@ -363,7 +361,7 @@ def edf_to_nx(
                 else:
                     data = fabio_file.getframe(index).data
                     header = fabio_file.getframe(index).header
-            except Exception as e:
+            except Exception:
                 data = None
                 header = None
             finally:
@@ -614,7 +612,7 @@ def edf_to_nx(
     # create beam group at root for compatibility
     try:
         link_nxbeam_to_root(file_path=output_file, entry_path="entry")
-    except Exception as e:
+    except Exception:
         pass
 
     return fileout_h5, "entry"

nxtomomill/converter/edf/test/test_edf2nx.py

@@ -28,7 +28,6 @@ __license__ = "MIT"
 __date__ = "09/10/2020"
 
 
-import shutil
 import tempfile
 import os
 from nxtomomill import converter
@@ -52,7 +51,7 @@ def test_edf_to_nx_converter(progress):
         n_proj = 120
         n_alignment_proj = 5
         dim = 100
-        mock = MockEDF(
+        MockEDF(
             scan_path=scan_path,
             n_radio=n_proj,
             n_ini_radio=n_proj,

nxtomomill/converter/hdf5/acquisition/baseacquisition.py

@@ -36,7 +36,7 @@ __date__ = "27/11/2020"
 import h5py
 
 try:
-    import hdf5plugin
+    import hdf5plugin  # noqa F401
 except ImportError:
     pass
 from nxtomomill.plugins import (
@@ -525,7 +525,7 @@ class BaseAcquisition:
                     info_retrieve=resource_name,
                     expected_unit=None,
                 )
-            except (ValueError, KeyError) as e:
+            except (ValueError, KeyError):
                 pass
             else:
                 return values, None

nxtomomill/converter/hdf5/acquisition/standardacquisition.py

@@ -52,7 +52,7 @@ from silx.io.url import DataUrl
 from typing import Union
 
 try:
-    import hdf5plugin
+    import hdf5plugin  # noqa F401
 except ImportError:
     pass
 import logging

nxtomomill/converter/hdf5/acquisition/utils.py

@@ -37,7 +37,7 @@ import typing
 import h5py
 
 try:
-    import hdf5plugin
+    import hdf5plugin  # noqa F401
 except ImportError:
     pass
 import logging
@@ -84,7 +84,7 @@ def get_entry_type(
 
         try:
             title = h5py_read_dataset(entry["title"])
-        except Exception as e:
+        except Exception:
             _logger.error("fail to find title for %s, skip this group" % entry.name)
         else:
             init_titles = list(configuration.init_titles)

nxtomomill/converter/hdf5/acquisition/xrdctacquisition.py

@@ -42,7 +42,7 @@ import h5py
 from silx.io.url import DataUrl
 
 try:
-    import hdf5plugin
+    import hdf5plugin  # noqa F401
 except ImportError:
     pass
 import logging
@@ -137,4 +137,4 @@ class XRDCTAcquisition(StandardAcquisition):
 
     def _write_beam(self, root_node, request_input, input_callback):
         instrument_node = root_node.require_group("instrument")
-        beam_node = instrument_node.require_group("beam")
+        instrument_node.require_group("beam")

nxtomomill/converter/hdf5/acquisition/zseriesacquisition.py

@@ -46,7 +46,7 @@ import h5py
 from silx.io.url import DataUrl
 
 try:
-    import hdf5plugin
+    import hdf5plugin  # noqa F401
 except ImportError:
     pass
 
@@ -59,7 +59,7 @@ def is_z_series_frm_titles(entry: h5py.Group, configuration: TomoHDF5Config) ->
     """
     try:
         title = h5py_read_dataset(entry["title"])
-    except Exception as e:
+    except Exception:
         return False
     else:
         return title in configuration.zserie_init_titles

nxtomomill/converter/hdf5/hdf5converter.py

@@ -60,10 +60,10 @@ import os
 import h5py
 
 try:
-    import hdf5plugin
+    import hdf5plugin  # noqa F401
 except ImportError:
     pass
-## import that should be removed when h5_to_nx will be removed
+# import that should be removed when h5_to_nx will be removed
 from nxtomomill.converter.hdf5.utils import H5FileKeys
 from nxtomomill.converter.hdf5.utils import H5ScanTitles
 

nxtomomill/io/__init__.py

-from .config import *
+from .config import *  # noqa F401,F403

nxtomomill/io/config.py

@@ -22,7 +22,7 @@
 # THE SOFTWARE.
 #
 #
-# ###########################################################################*/
+# ###########################################################################
 
 """
 contains the HDF5Config
@@ -1099,7 +1099,7 @@ class TomoHDF5Config:
         ]
         flat_titles_dks.extend(TomoHDF5Config.FLAT_TILES_ALIASES)
         flat_title_key_picked = None
-        ## handle flat titles
+        # handle flat titles
         for alias in flat_titles_dks:
             flat_titles = dict_.get(alias, None)
             if flat_titles is not None:

nxtomomill/io/framegroup.py

@@ -107,8 +107,6 @@ class FrameGroup:
     @url.setter
     def url(self, url: Union[DataUrl, str]):
         if isinstance(url, str):
-            from nxtomomill.io.utils import is_url_path
-
             # handle if the string path is not a "full url" then we consider
             # this is only the data path.
             self._url = DataUrl(path=url)
@@ -200,7 +198,7 @@ class FrameGroup:
             urls_str = ",\n".join(["{}".format(str(url)) for url in urls])
             return """(
 {}
-)           
+)
             """.format(
                 urls_str
             )
@@ -211,7 +209,7 @@ class FrameGroup:
         Create an instance of FrameGroup from it string representation.
         """
         if not isinstance(input_str, str):
-            raise TypeError("input_str should be a string".format(input_str))
+            raise TypeError(f"{input_str} should be a string")
 
         from nxtomomill.io.utils import (
             remove_parenthesis_or_brackets,
@@ -333,7 +331,7 @@ def filter_acqui_frame_type(
     frame_types = frame_types[current_acqui_idx + 1 :]
     try:
         next_acqui = frame_types.index(AcquisitionStep.INITIALIZATION) - 1
-    except ValueError as e:
+    except ValueError:
         next_acqui = -1
     sequence_target = sequence_target[:next_acqui]
     filter_fct = lambda a: a.frame_type is frame_type

nxtomomill/io/test/test_config.py

@@ -31,7 +31,7 @@ __date__ = "23/02/2021"
 import unittest
 import shutil
 import tempfile
-from nxtomomill.io.config import TomoHDF5Config, generate_default_h5_config
+from nxtomomill.io.config import TomoHDF5Config
 from nxtomomill import settings
 import os