Merge pull request #2 from ericpre/add_pre_commit

Add pre-commit for running black excluding database files

.pre-commit-config.yaml

@@ -0,0 +1,6 @@
+repos:
+  - repo: https://github.com/psf/black
+    # Version can be updated by running "pre-commit autoupdate"
+    rev: 23.10.1
+    hooks:
+    - id: black

doc/conf.py

@@ -91,11 +91,13 @@
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-html_logo = '_static/hyperspy_logo.png'
+html_logo = "_static/hyperspy_logo.png"
 
 # -- Options for sphinx_favicon extension -----------------------------------
 
-favicons = ["hyperspy.ico", ]
+favicons = [
+    "hyperspy.ico",
+]
 
 # Check links to API when building documentation
 nitpicky = False
@@ -110,10 +112,10 @@
 if Version(numpydoc.__version__) >= Version("1.6.0rc0"):
     numpydoc_validation_checks = {"all", "ES01", "EX01", "GL02", "GL03", "SA01", "SS06"}
 
-autoclass_content = 'both'
+autoclass_content = "both"
 
 autodoc_default_options = {
-    'show-inheritance': True,
+    "show-inheritance": True,
 }
 toc_object_entries_show_parents = "hide"
 

examples/model_fitting/EELS_curve_fitting.py

@@ -14,10 +14,8 @@
 
 s.add_elements(("Mn", "O"))
 s.set_microscope_parameters(
-    beam_energy=300,
-    convergence_angle=24.6,
-    collection_angle=13.6
-    )
+    beam_energy=300, convergence_angle=24.6, collection_angle=13.6
+)
 
 m = s.create_model(ll=ll)
 m.enable_fine_structure()

examples/model_fitting/plot_residual.py

@@ -9,28 +9,28 @@
 import numpy as np
 import hyperspy.api as hs
 
-#%%
+# %%
 # Create a signal:
 data = np.arange(1000, dtype=np.int64).reshape((10, 100))
 s = hs.signals.Signal1D(data)
 
-#%%
+# %%
 # Add noise:
 s.add_poissonian_noise(random_state=0)
 
-#%%
+# %%
 # Create model:
 m = s.create_model()
 line = hs.model.components1D.Expression("a * x + b", name="Affine")
 m.append(line)
 
-#%%
+# %%
 # Fit for all navigation positions:
 m.multifit()
 
-#%%
+# %%
 # Plot the fitted model with residual:
 m.plot(plot_residual=True)
 
-#%%
+# %%
 # sphinx_gallery_thumbnail_number = 2

exspy/__init__.py

@@ -1,4 +1,3 @@
-
 from . import components
 from . import data
 from . import models
@@ -11,7 +10,7 @@
     "components",
     "data",
     "preferences",
-    "material"
+    "material",
     "models",
     "signals",
 ]

exspy/_defaults_parser.py

@@ -27,7 +27,7 @@
 
 config_path = Path("~/.exspy").expanduser()
 config_path.mkdir(parents=True, exist_ok=True)
-defaults_file = Path(config_path, 'exspyrc')
+defaults_file = Path(config_path, "exspyrc")
 
 _logger = logging.getLogger(__name__)
 
@@ -37,52 +37,56 @@ def guess_gos_path():
         # If DM is installed, use the GOS tables from the default
         # installation
         # location in windows
-        program_files = os.environ['PROGRAMFILES']
-        gos = 'Gatan\\DigitalMicrograph\\EELS Reference Data\\H-S GOS Tables'
+        program_files = os.environ["PROGRAMFILES"]
+        gos = "Gatan\\DigitalMicrograph\\EELS Reference Data\\H-S GOS Tables"
         gos_path = Path(program_files, gos)
 
         # Else, use the default location in the .hyperspy forlder
-        if not gos_path.is_dir() and 'PROGRAMFILES(X86)' in os.environ:
-            program_files = os.environ['PROGRAMFILES(X86)']
+        if not gos_path.is_dir() and "PROGRAMFILES(X86)" in os.environ:
+            program_files = os.environ["PROGRAMFILES(X86)"]
             gos_path = Path(program_files, gos)
             if not gos_path.is_dir():
-                gos_path = Path(config_path, 'EELS_GOS')
+                gos_path = Path(config_path, "EELS_GOS")
     else:
-        gos_path = Path(config_path, 'EELS_GOS')
+        gos_path = Path(config_path, "EELS_GOS")
     return gos_path
 
 
 class EELSConfig(t.HasTraits):
     eels_gos_files_path = t.Directory(
         guess_gos_path(),
-        label='Hartree-Slater GOS directory',
-        desc='The GOS files are used to create the EELS edge components')
+        label="Hartree-Slater GOS directory",
+        desc="The GOS files are used to create the EELS edge components",
+    )
 
 
 class EDSConfig(t.HasTraits):
-    eds_mn_ka = t.CFloat(130.,
-                         label='Energy resolution at Mn Ka (eV)',
-                         desc='default value for FWHM of the Mn Ka peak in eV,'
-                         'This value is used as a first approximation'
-                         'of the energy resolution of the detector.')
+    eds_mn_ka = t.CFloat(
+        130.0,
+        label="Energy resolution at Mn Ka (eV)",
+        desc="default value for FWHM of the Mn Ka peak in eV,"
+        "This value is used as a first approximation"
+        "of the energy resolution of the detector.",
+    )
     eds_tilt_stage = t.CFloat(
-        0.,
-        label='Stage tilt',
-        desc='default value for the stage tilt in degree.')
+        0.0, label="Stage tilt", desc="default value for the stage tilt in degree."
+    )
     eds_detector_azimuth = t.CFloat(
-        0.,
-        label='Azimuth angle',
-        desc='default value for the azimuth angle in degree. If the azimuth'
-        ' is zero, the detector is perpendicular to the tilt axis.')
+        0.0,
+        label="Azimuth angle",
+        desc="default value for the azimuth angle in degree. If the azimuth"
+        " is zero, the detector is perpendicular to the tilt axis.",
+    )
     eds_detector_elevation = t.CFloat(
-        35.,
-        label='Elevation angle',
-        desc='default value for the elevation angle in degree.')
+        35.0,
+        label="Elevation angle",
+        desc="default value for the elevation angle in degree.",
+    )
 
 
 template = {
-    'EELS': EELSConfig(),
-    'EDS': EDSConfig(),
+    "EELS": EELSConfig(),
+    "EDS": EDSConfig(),
 }
 
 
@@ -97,9 +101,9 @@ def config2template(template, config):
     for section, traited_class in template.items():
         config_dict = {}
         for name, value in config.items(section):
-            if value == 'True':
+            if value == "True":
                 value = True
-            elif value == 'False':
+            elif value == "False":
                 value = False
             config_dict[name] = value
         traited_class.trait_set(True, **config_dict)
@@ -128,7 +132,7 @@ def config2template(template, config):
             rewrite = True
 
 if not defaults_file_exists or rewrite is True:
-    _logger.info('Writing the config file')
+    _logger.info("Writing the config file")
     with open(defaults_file, "w") as df:
         config.write(df)
 
@@ -144,10 +148,10 @@ class Preferences(t.HasTraits):
     def save(self):
         config = configparser.ConfigParser(allow_no_value=True)
         template2config(template, config)
-        config.write(open(defaults_file, 'w'))
+        config.write(open(defaults_file, "w"))
 
 
 preferences = Preferences(
-    EELS=template['EELS'],
-    EDS=template['EDS'],
+    EELS=template["EELS"],
+    EDS=template["EDS"],
 )

exspy/components/__init__.py

@@ -19,7 +19,7 @@
     "SEE",
     "Vignetting",
     "VolumePlasmonDrude",
-    ]
+]
 
 
 def __dir__():

exspy/components/eels_arctan.py

@@ -21,7 +21,6 @@
 
 
 class EELSArctan(Expression):
-
     r"""Arctan function component for EELS (with minimum at zero).
 
     .. math::
@@ -52,7 +51,7 @@ class EELSArctan(Expression):
 
     """
 
-    def __init__(self, A=1., k=1., x0=1., module=["numpy", "scipy"], **kwargs):
+    def __init__(self, A=1.0, k=1.0, x0=1.0, module=["numpy", "scipy"], **kwargs):
         # To be able to still read old file versions that contain this argument
         if "minimum_at_zero" in kwargs:
             del kwargs["minimum_at_zero"]

exspy/components/eels_cl_edge.py

@@ -17,7 +17,6 @@
 # along with exSpy. If not, see <https://www.gnu.org/licenses/#GPL>.
 
 
-
 import functools
 import logging
 import math
@@ -141,7 +140,9 @@ class EELSCLEdge(Component):
     fine_structure_components : set, default ``set()``
         A set containing components to model the fine structure region
         of the EELS ionization edge.
-    """.format(_GOSH_DOI)
+    """.format(
+        _GOSH_DOI
+    )
 
     _fine_structure_smoothing = 0.3
     _fine_structure_coeff_free = True
@@ -200,11 +201,9 @@ def __init__(self, element_subshell, GOS="gosh", gos_file_path=None):
         self._whitelist["fine_structure_spline_onset"] = None
         self._whitelist["fine_structure_spline_active"] = None
         self._whitelist["_fine_structure_coeff_free"] = None
-        self.effective_angle.events.value_changed.connect(
-            self._integrate_GOS, [])
+        self.effective_angle.events.value_changed.connect(self._integrate_GOS, [])
         self.onset_energy.events.value_changed.connect(self._integrate_GOS, [])
-        self.onset_energy.events.value_changed.connect(
-            self._calculate_knots, [])
+        self.onset_energy.events.value_changed.connect(self._calculate_knots, [])
         self._fine_structure_spline_onset = 0
         self.events.active_changed.connect(self._set_active_fine_structure_components)
 
@@ -249,25 +248,25 @@ def fine_structure_width(self, arg):
     @property
     def E0(self):
         return self.__E0
-    
+
     @E0.setter
     def E0(self, arg):
         self.__E0 = arg
         self._calculate_effective_angle()
-    
+
     @property
     def collection_angle(self):
         return self.__collection_angle
-    
+
     @collection_angle.setter
     def collection_angle(self, arg):
         self.__collection_angle = arg
         self._calculate_effective_angle()
-    
+
     @property
     def convergence_angle(self):
         return self.__convergence_angle
-    
+
     @convergence_angle.setter
     def convergence_angle(self, arg):
         self.__convergence_angle = arg
@@ -306,7 +305,7 @@ def fine_structure_smoothing(self, value):
         if 0 <= value <= 1:
             self._fine_structure_smoothing = value
             self._set_fine_structure_coeff()
-            if self.fine_structure_active and  self.model:
+            if self.fine_structure_active and self.model:
                 self.model.update_plot()
         else:
             raise ValueError("The value must be a number between 0 and 1")
@@ -324,7 +323,7 @@ def fine_structure_spline_onset(self, value):
         if not np.allclose(value, self._fine_structure_spline_onset):
             self._fine_structure_spline_onset = value
             self._set_fine_structure_coeff()
-            if self.fine_structure_active and  self.model:
+            if self.fine_structure_active and self.model:
                 self.model.update_plot()
 
     @property
@@ -341,16 +340,22 @@ def fine_structure_spline_active(self, value):
             self._fine_structure_coeff_free = self.fine_structure_coeff.free
             self.fine_structure_coeff.free = False
             self._fine_structure_spline_active = value
-        if self.fine_structure_active and  self.model:
+        if self.fine_structure_active and self.model:
             self.model.update_plot()
 
     def _set_fine_structure_coeff(self):
         if self.energy_scale is None:
             return
-        self.fine_structure_coeff._number_of_elements = int(
-            round(self.fine_structure_smoothing *
-                  (self.fine_structure_width - self.fine_structure_spline_onset) /
-                  self.energy_scale)) + 4
+        self.fine_structure_coeff._number_of_elements = (
+            int(
+                round(
+                    self.fine_structure_smoothing
+                    * (self.fine_structure_width - self.fine_structure_spline_onset)
+                    / self.energy_scale
+                )
+            )
+            + 4
+        )
         self.fine_structure_coeff.bmin = None
         self.fine_structure_coeff.bmax = None
         self._calculate_knots()
@@ -376,10 +381,10 @@ def fix_fine_structure(self):
     def free_fine_structure(self):
         """Frees the parameters of the fine structure
 
-        If there are fine structure components, only the 
+        If there are fine structure components, only the
         parameters that have been previously fixed with
         ``fix_fine_structure`` will be set free.
-        
+
         The spline parameters set free only if
         ``fine_structure_spline_active`` is ``True``.
 
@@ -468,7 +473,8 @@ def function(self, E):
                 if np.any(bifs):
                     cts[bifs] = splev(
                         E[bifs],
-                        (self.__knots, self.fine_structure_coeff.value + (0,) * 4, 3))
+                        (self.__knots, self.fine_structure_coeff.value + (0,) * 4, 3),
+                    )
             # The cross-section is set to 0 in the fine structure region
             itab = (E < Emax) & (E >= ifsx2)
         else:
@@ -530,6 +536,8 @@ def get_fine_structure_as_signal1D(self):
 
     def as_dictionary(self, fullcopy=True):
         dic = super().as_dictionary(fullcopy=fullcopy)
-        dic["fine_structure_components"] = [t.name for t in self.fine_structure_components]
+        dic["fine_structure_components"] = [
+            t.name for t in self.fine_structure_components
+        ]
         dic["_whitelist"]["fine_structure_components"] = ""
         return dic