flake8

.gitlab-ci.yml

@@ -16,10 +16,10 @@ check_style:
   stage: style
   image: docker-registry.esrf.fr/dau/est:python3.7_stretch_pyqt5_gtk3_wxpython
   before_script:
-    - pip install black  
+    - pip install black flake8
   script:
-    # run black
     - LC_ALL=C.UTF-8 black --check --safe .
+    - flake8
 
 
 # build

est/__main__.py

@@ -36,9 +36,6 @@ __date__ = "10/12/2020"
 
 
 import logging
-
-logging.basicConfig()
-
 import sys
 from silx.utils.launcher import Launcher
 
@@ -50,6 +47,9 @@ except ImportError:
     import_version = False
 
 
+logging.basicConfig()
+
+
 def main():
     """Main function of the launcher
 

est/app/canvas_launcher/launcher.py

@@ -10,7 +10,8 @@ except ImportError:
 else:
     old_config = False
 from .splash import splash_screen, getIcon
-import os, sys
+import os
+import sys
 from Orange.misc import environ
 import pkg_resources
 

est/core/process/larch/pre_edge.py

@@ -152,7 +152,7 @@ class Larch_pre_edge(
             _xas_obj,
             data_keys=(
                 _NexusDatasetDef(
-                    "flat", units="{}(E)".format(MU_CHAR), units_latex="\mu(E)"
+                    "flat", units="{}(E)".format(MU_CHAR), units_latex=r"\mu(E)"
                 ),
                 _NexusDatasetDef("dmude"),
                 _NexusDatasetDef("edge_step_poly"),
@@ -162,11 +162,11 @@ class Larch_pre_edge(
                 _NexusDatasetDef("pre_edge_details"),
                 _NexusDatasetDef("e0", "eV"),
                 _NexusDatasetDef(
-                    "Mu", units="{}(E)".format(MU_CHAR), units_latex="\mu(E)"
+                    "Mu", units="{}(E)".format(MU_CHAR), units_latex=r"\mu(E)"
                 ),
                 _NexusDatasetDef("energy", "eV"),
                 _NexusDatasetDef(
-                    "mu_ref", units="{}(E)".format(MU_CHAR), units_latex="\mu(E)"
+                    "mu_ref", units="{}(E)".format(MU_CHAR), units_latex=r"\mu(E)"
                 ),
                 _NexusDatasetDef("I0"),
                 _NexusDatasetDef("I1"),
@@ -179,7 +179,7 @@ class Larch_pre_edge(
                     auxiliary_signals=None,
                     silx_style={"signal_scale_type": "linear"},
                     title="Mu",
-                    title_latex="\mu",
+                    title_latex=r"\mu",
                 ),
                 _NexusSpectrumDef(
                     signal="Mu",
@@ -196,7 +196,7 @@ class Larch_pre_edge(
                     auxiliary_signals=("mu_ref",),
                     silx_style={"signal_scale_type": "linear"},
                     title="Mu vs Mu ref",
-                    title_latex="\mu \quad vs \quad \mu_{ref}",
+                    title_latex=r"\mu \quad vs \quad \mu_{ref}",
                 ),
                 _NexusSpectrumDef(
                     signal="flat",
@@ -204,7 +204,7 @@ class Larch_pre_edge(
                     auxiliary_signals=None,
                     silx_style={"signal_scale_type": "linear"},
                     title="Mu flat",
-                    title_latex="\mu_{flat}",
+                    title_latex=r"\mu_{flat}",
                 ),
             ),
         )

est/core/process/larch/xftf.py

@@ -188,41 +188,41 @@ class Larch_xftf(
                 _NexusDatasetDef(
                     "chir_im",
                     units="{}^(-3)".format(ANGSTROM_CHAR),
-                    units_latex="\mathring{A}^{-3}",
+                    units_latex=r"\mathring{A}^{-3}",
                 ),
                 _NexusDatasetDef("chir_re"),
                 _NexusDatasetDef(
                     "chir_mag",
                     units="{}^(-3)".format(ANGSTROM_CHAR),
-                    units_latex="\mathring{A}^{-3}",
+                    units_latex=r"\mathring{A}^{-3}",
                 ),
                 _NexusDatasetDef(
                     "masked_chir_mag",
                     units="{}".format(ANGSTROM_CHAR),
-                    units_latex="\mathring{A}",
+                    units_latex=r"\mathring{A}",
                 ),
                 _NexusDatasetDef(
-                    "r", units="{}".format(ANGSTROM_CHAR), units_latex="\mathring{A}"
+                    "r", units="{}".format(ANGSTROM_CHAR), units_latex=r"\mathring{A}"
                 ),
                 _NexusDatasetDef(
                     "masked_r",
                     units="{}".format(ANGSTROM_CHAR),
-                    units_latex="\mathring{A}",
+                    units_latex=r"\mathring{A}",
                 ),
                 _NexusDatasetDef(
                     "k",
                     units="{}^(-1)".format(ANGSTROM_CHAR),
-                    units_latex="\mathring{A}^{-1}",
+                    units_latex=r"\mathring{A}^{-1}",
                 ),
                 _NexusDatasetDef(
                     "masked_k",
                     units="{}^(-1)".format(ANGSTROM_CHAR),
-                    units_latex="\mathring{A}^{-1}",
+                    units_latex=r"\mathring{A}^{-1}",
                 ),
                 _NexusDatasetDef(
                     "masked_chi_weighted_k",
                     units="{}^(-2)".format(ANGSTROM_CHAR),
-                    units_latex="\mathring{A}^{-2}",
+                    units_latex=r"\mathring{A}^{-2}",
                 ),
             ),
             plots=(
@@ -232,7 +232,7 @@ class Larch_xftf(
                     auxiliary_signals=None,
                     silx_style={"signal_scale_type": "linear"},
                     title="chi(k)*k^k_weight",
-                    title_latex="\chi(k).k^{k\_weight}",
+                    title_latex=r"\chi(k).k^{k\_weight}",
                 ),
                 _NexusSpectrumDef(
                     signal="masked_chir_mag",

est/core/process/pymca/normalization.py

@@ -32,7 +32,7 @@ import functools
 import logging
 import multiprocessing
 from PyMca5.PyMcaPhysics.xas.XASClass import XASClass
-from est.core.process.process import Process, Progress
+from est.core.process.process import Process
 from est.core.process.process import _NexusDatasetDef
 from est.core.types import Spectrum, XASObject
 

est/core/process/pymca/test/test_workflow.py

@@ -23,7 +23,7 @@
 #
 # ###########################################################################*/
 """
-unit test for workflow composed of pymca process 
+unit test for workflow composed of pymca process
 """
 __authors__ = ["H. Payno"]
 __license__ = "MIT"

est/gui/noise.py

@@ -70,7 +70,7 @@ class _SavitskyGolayNoiseOpts(qt.QWidget):
         qt.QWidget.__init__(self, parent)
         self.setLayout(qt.QFormLayout())
 
-        ## Inputs
+        # Inputs
         self.layout().addRow(qt.QLabel("Inputs", self))
 
         # add window size
@@ -104,8 +104,9 @@ class _SavitskyGolayNoiseOpts(qt.QWidget):
         self._eEnd.setValue(10000000000)
         self.layout().addRow(qt.QLabel("     - E end", self), self._eEnd)
 
-        ## Outputs
+        # Outputs
         self.layout().addRow(qt.QLabel("Outputs", self))
+
         # raw data average noise
         self._rawData = qt.QLineEdit("", self)
         self._rawData.setReadOnly(True)

est/gui/qtapplicationmanager.py

@@ -20,7 +20,7 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 # THE SOFTWARE.
 #
-#############################################################################*/
+# ############################################################################*/
 
 """
 This module is used to manage the rsync between files for transfert.

est/gui/roiselector.py

@@ -64,8 +64,7 @@ class ROISelector(qt.QWidget):
         self._roi.setName("ROI")
         self._roiManager.addRoi(self._roi)
         self.__roi_first_definition = True
-        """flag used make sure the roi is clearly visible at least during the 
-        first processing"""
+        """flag used make sure the roi is clearly visible at least during the first processing"""
 
         # Create the table widget displaying
         self._roiTable = RegionOfInterestTableWidget()

est/io/io.py

@@ -161,6 +161,7 @@ def load_data(
         assert name == "spectra"
         # TODO: might need to be improved because this is redefined each
         #  time. Not sure about the cost
+
         @silx.io.h5py_utils.retry(retry_timeout=timeout)
         def read_dataset(url):
             spectra = []

est/version.py

@@ -50,6 +50,7 @@ Thus 2.1.0a3 is hexversion 0x020100a3.
 """
 
 from __future__ import absolute_import, print_function, division
+from collections import namedtuple
 
 __authors__ = ["Jérôme Kieffer", "H.Payno"]
 __license__ = "MIT"
@@ -83,8 +84,6 @@ SERIAL = 1  # <16
 
 date = __date__
 
-from collections import namedtuple
-
 _version_info = namedtuple(
     "version_info", ["major", "minor", "micro", "releaselevel", "serial"]
 )

orangecontrib/est/test/__init__.py

@@ -20,7 +20,7 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 # THE SOFTWARE.
 #
-#############################################################################*/
+# ############################################################################*/
 
 
 __authors__ = ["H.Payno"]

run_tests.py

@@ -44,6 +44,7 @@ import time
 import unittest
 import collections
 from argparse import ArgumentParser
+import warnings
 
 
 class StreamHandlerUnittestReady(logging.StreamHandler):
@@ -79,7 +80,6 @@ logging.root.addHandler(createBasicHandler())
 
 # Capture all default warnings
 logging.captureWarnings(True)
-import warnings
 
 warnings.simplefilter("default")
 

snippets/raw_bm23_analysis.py

@@ -57,10 +57,8 @@ class AnalysisThread(threading.Thread):
         max_raw_energy = max(self.spectrum.energy)
         if HAS_REACH_END_VALUE:
             norm2 = max_raw_energy - 100
-            spline_range_end = max_raw_energy - 50
         else:
             norm2 = max_raw_energy
-            spline_range_end = max_raw_energy
         ft_k_range_end = etok(norm2)  # here ft_k value seems really strange no ?
 
         return {
@@ -155,7 +153,7 @@ class AnalysisThread(threading.Thread):
                 with HDF5File(filename=url.file_path(), mode="r") as h5f:
                     if url.data_path() in h5f:
                         setattr(input_information, set_fct, url)
-            except:
+            except Exception:
                 _logger.warning("{} not set because not found".format(set_fct))
 
         self.mu_ref_url = DataUrl(
@@ -173,19 +171,19 @@ class AnalysisThread(threading.Thread):
         # TODO: add a process attact to attach informations from an url.
         try:
             xas_obj.spectra.data.flat[0].I0 = get_data(self.I0_url)
-        except:
+        except Exception:
             pass
         try:
             xas_obj.spectra.data.flat[0].I1 = get_data(self.I1_url)
-        except:
+        except Exception:
             pass
         try:
             xas_obj.spectra.data.flat[0].I2 = get_data(self.I2_url)
-        except:
+        except Exception:
             pass
         try:
             xas_obj.spectra.data.flat[0].mu_ref = get_data(self.mu_ref_url)
-        except:
+        except Exception:
             pass
 
         configuration = self.get_configuration()
@@ -267,7 +265,7 @@ class AnalysisThread(threading.Thread):
         ):
             try:
                 I_data = silx_utils.get_data(IX_url)
-            except:
+            except Exception:
                 pass
             else:
                 concurrent.submitToQtMainThread(