Precommit rework (wright-group#978)

* Update pre commit config

* plot_colorbar docstring formatting

* Rm trailing whitespace from mostly rst and yml files

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/PULL_REQUEST_TEMPLATE

@@ -5,7 +5,7 @@ please describe your changes here :smiley:
 ## Checklist
 
 - [ ] added tests, if applicable
-- [ ] updated documentation, if applicable 
+- [ ] updated documentation, if applicable
 - [ ] updated CHANGELOG.md
-- [ ] tests pass 
- 
+- [ ] tests pass
+

.github/workflows/codeql-analysis.yml

@@ -47,7 +47,7 @@ jobs:
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
-        # By default, queries listed here will override any specified in a config file. 
+        # By default, queries listed here will override any specified in a config file.
         # Prefix the list here with "+" to use these queries and those in the config file.
         queries: +security-and-quality
 

.pre-commit-config.yaml

@@ -1,9 +1,18 @@
 repos:
--   repo: https://github.com/psf/black
-    rev: master
+  - repo: https://github.com/psf/black
+    rev: 20.8b1 # Replace by any tag/version: https://github.com/psf/black/tags
     hooks:
-    - id: black
-      name: black
-      language: system
-      args: [--line-length=99, --safe]
-      entry: black
+      - id: black
+        language_version: python3 # Should be a command that runs python3.6+
+        args: ["--line-length", "99"]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.3.0
+    hooks:
+      - id: trailing-whitespace
+        exclude: datasets|.data$
+      - id: no-commit-to-branch
+        args: [-b master]
+
+default_language_version:
+  python: python3

.readthedocs.yml

@@ -7,7 +7,7 @@ python:
   version: 3.6
   pip_install: true
   extra_requirements: [docs]
-  
+
 formats:
   - epub
   - pdf

.zenodo.json

@@ -1,48 +1,48 @@
 {
-    "license": {"id": "MIT"}, 
-    "title": "WrightTools", 
-    "upload_type": "software", 
+    "license": {"id": "MIT"},
+    "title": "WrightTools",
+    "upload_type": "software",
     "creators": [
         {
-            "orcid": "0000-0002-3845-824X", 
-            "affiliation": "University of Wisconsin–Madison", 
+            "orcid": "0000-0002-3845-824X",
+            "affiliation": "University of Wisconsin–Madison",
             "name": "Blaise J. Thompson"
-        }, 
+        },
         {
-            "orcid": "0000-0001-6167-8059", 
-            "affiliation": "University of Wisconsin–Madison", 
+            "orcid": "0000-0001-6167-8059",
+            "affiliation": "University of Wisconsin–Madison",
             "name": "Kyle F. Sunden"
-        }, 
+        },
         {
-            "orcid": "0000-0002-8922-8049", 
-            "affiliation": "University of Wisconsin–Madison", 
+            "orcid": "0000-0002-8922-8049",
+            "affiliation": "University of Wisconsin–Madison",
             "name": "Darien J. Morrow"
-        }, 
+        },
         {
-            "orcid": "0000-0003-4602-2961", 
-            "affiliation": "University of Wisconsin–Madison", 
+            "orcid": "0000-0003-4602-2961",
+            "affiliation": "University of Wisconsin–Madison",
             "name": "Daniel D. Kohler"
-        }, 
+        },
         {
-            "orcid": "0000-0002-9453-3590", 
-            "affiliation": "University of Wisconsin–Madison", 
+            "orcid": "0000-0002-9453-3590",
+            "affiliation": "University of Wisconsin–Madison",
             "name": "Nathan Andrew Neff-Mallon"
-        }, 
+        },
         {
-            "affiliation": "University of Wisconsin–Madison", 
+            "affiliation": "University of Wisconsin–Madison",
             "name": "Kyle J. Czech"
-        }, 
+        },
         {
-            "orcid": "0000-0001-6718-8341", 
-            "affiliation": "University of Wisconsin–Madison", 
+            "orcid": "0000-0001-6718-8341",
+            "affiliation": "University of Wisconsin–Madison",
             "name": "Emily M. Kaufman"
-        }, 
+        },
         {
             "name": "Thomas Parker"
-        }, 
+        },
         {
             "name": "Rachel Swedin"
         }
-    ], 
+    ],
     "access_right": "open"
 }

CHANGELOG.md

@@ -117,7 +117,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/).
 ## [3.2.0]
 
 ### Added
-- new method: moment - Take the Nth moment of a channel along an axis 
+- new method: moment - Take the Nth moment of a channel along an axis
 - new method: trim - Use statistical test in channels to remove outlier points
 - Support for remote files in `from_` functions
 
@@ -154,7 +154,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/).
 ### Added
 - Plotting functions like plot, pcolor, and contour now will plot channels e.g. 2D channels within a 3D data object
 - Quick plotting methods now have lines and labels for constants
-- π release 
+- π release
 
 ## [3.1.3]
 
@@ -273,5 +273,5 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/).
 [2.13.8]: https://github.com/wright-group/WrightTools/compare/2.13.7...2.13.8
 [2.13.7]: https://github.com/wright-group/WrightTools/compare/2.13.6...2.13.7
 [2.13.6]: https://github.com/wright-group/WrightTools/compare/2.13.5...2.13.6
-[2.13.5]: https://github.com/wright-group/WrightTools/releases/tag/2.13.5 
+[2.13.5]: https://github.com/wright-group/WrightTools/releases/tag/2.13.5
 

WrightTools/artists/_helpers.py

@@ -202,7 +202,7 @@ def corner_text(
     -------
     text
         The matplotlib text object.
-    
+
     Other Parameters
     ----------------
     **kwargs : matplotlib.text.Text properties.
@@ -623,22 +623,22 @@ def plot_colorbar(
         Colorbar orientation. Default is vertical.
     ticklocation : {'auto', 'left', 'right', 'top', 'bottom'} (optional)
         Tick location. Default is auto.
-    extend : {‘neither’, ‘both’, ‘min’, ‘max’} (optional)
-        If not ‘neither’, make pointed end(s) for out-of- range values.
+    extend : {'neither', 'both', 'min', 'max'} (optional)
+        If not 'neither', make pointed end(s) for out-of- range values.
         These are set for a given colormap using the colormap set_under and set_over methods.
-    extendfrac :	{None, ‘auto’, length, lengths} (optional)
+    extendfrac : {None, 'auto', length, lengths} (optional)
         If set to None, both the minimum and maximum triangular colorbar extensions
         have a length of 5% of the interior colorbar length (this is the default setting).
-        If set to ‘auto’, makes the triangular colorbar extensions the same lengths
+        If set to 'auto', makes the triangular colorbar extensions the same lengths
         as the interior boxes
-        (when spacing is set to ‘uniform’) or the same lengths as the respective adjacent
-        interior boxes (when spacing is set to ‘proportional’).
+        (when spacing is set to 'uniform') or the same lengths as the respective adjacent
+        interior boxes (when spacing is set to 'proportional').
         If a scalar, indicates the length of both the minimum and maximum triangular
         colorbar extensions as a fraction of the interior colorbar length.
         A two-element sequence of fractions may also be given, indicating the lengths
         of the minimum and maximum colorbar extensions respectively as a fraction
         of the interior colorbar length.
-    extendrect :	bool (optional)
+    extendrect : bool (optional)
         If False the minimum and maximum colorbar extensions will be triangular (the default).
         If True the extensions will be rectangular.
 

WrightTools/artists/_interact.py

@@ -139,7 +139,7 @@ def norm(arr, signed, ignore_zero=True):
 
 
 def interact2D(data, xaxis=0, yaxis=1, channel=0, local=False, verbose=True):
-    """ Interactive 2D plot of the dataset.
+    """Interactive 2D plot of the dataset.
     Side plots show x and y projections of the slice (shaded gray).
     Left clicks on the main axes draw 1D slices on side plots at the coordinates selected.
     Right clicks remove the 1D slices.

WrightTools/data/_data.py

@@ -540,7 +540,7 @@ def moment(self, axis, channel=0, moment=1, *, resultant=None):
         resultant : tuple of int
             The resultant shape after the moment operation.
             By default, it is intuited by the axis along which the moment is being taken.
-            This default only works if that axis is 1D, so resultant is required if a 
+            This default only works if that axis is 1D, so resultant is required if a
             multidimensional axis is passed as the first argument.
             The requirement of monotonicity applies on a per pixel basis.
 
@@ -1325,7 +1325,7 @@ def print_tree(self, *, verbose=True):
 
     def prune(self, keep_channels=True, *, verbose=True):
         """Remove unused variables and (optionally) channels from the Data object.
-            
+
         Unused variables are those that are not included in either axes or constants.
         Unused channels are those not specified in keep_channels, or the first channel.
 
@@ -1848,7 +1848,7 @@ def create_constant(self, expression, *, verbose=True):
             Expression for the new constant.
         verbose : boolean (optional)
             Toggle talkback. Default is True
-            
+
         See Also
         --------
         set_constants
@@ -1878,7 +1878,7 @@ def remove_constant(self, constant, *, verbose=True):
             Expression for the new constant.
         verbose : boolean (optional)
             Toggle talkback. Default is True
-            
+
         See Also
         --------
         set_constants

WrightTools/data/_join.py

@@ -277,7 +277,7 @@ def combine(data, out, item_name, new_idx, transpose, slice_):
         print("  channels:")
         for channel in out.channels:
             percent_nan = np.around(
-                100. * (np.isnan(channel[:]).sum() / float(channel.size)), decimals=2
+                100.0 * (np.isnan(channel[:]).sum() / float(channel.size)), decimals=2
             )
             print(
                 "    {0} : {1} to {2} ({3}% NaN)".format(

WrightTools/diagrams/delay.py

@@ -115,7 +115,7 @@ def label_sectors(
         labelbottom="off",
     )
 
-    ax.set_aspect(1.)
+    ax.set_aspect(1.0)
 
     plt.savefig("TRIEE_delay_space.png", transparent=True)
 
@@ -160,6 +160,6 @@ def label_sectors(
         labelbottom="off",
     )
 
-    ax.set_aspect(1.)
+    ax.set_aspect(1.0)
 
     plt.savefig("TRIEE_delay_space_as_collected.png", transparent=True)

WrightTools/kit/_lineshapes.py

@@ -33,7 +33,7 @@ def gaussian(x, x0, FWHM, norm="height"):
         Type of normalization.
         height specifies that the maximum value is 1.
         area specifies that the lineshape integrates to 1.
-        Default is height.        
+        Default is height.
 
     Returns
     -------
@@ -63,7 +63,7 @@ def lorentzian_complex(x, x0, G, norm="height_imag"):
         Type of normalization.
         height_imag specifies that the maximum value of the imaginary component is 1.
         area_int specifies that the square magnitude of the lineshape integrates to 1.
-        Default is height_imag.       
+        Default is height_imag.
 
     Returns
     -------
@@ -92,7 +92,7 @@ def lorentzian_real(x, x0, G, norm="height"):
         Type of normalization.
         height specifies that the maximum value is 1.
         area specifies that the lineshape integrates to 1.
-        Default is height.        
+        Default is height.
 
     Returns
     -------
@@ -108,10 +108,10 @@ def lorentzian_real(x, x0, G, norm="height"):
 
 def voigt(x, x0, FWHM, G):
     """Calculate an unnormalized Voigt lineshape using Scipy's Faddeeva function
-    
+
     `Link to Voigt article on Wikipedia`__
 
-    __ https://en.wikipedia.org/wiki/Voigt_profile  
+    __ https://en.wikipedia.org/wiki/Voigt_profile
 
     Parameters
     ----------
@@ -122,7 +122,7 @@ def voigt(x, x0, FWHM, G):
     FHWM : array_like or number
         Full-width-at-half-maximum of Gaussian part of lineshape.
     G : array_like or number
-        Half-width-at-half-maximum of Lorentzian part of lineshape.  
+        Half-width-at-half-maximum of Lorentzian part of lineshape.
 
     Returns
     -------

docs/api/WrightTools.artists.Axes.rst

@@ -6,12 +6,12 @@ WrightTools.artists.Axes
 .. autoclass:: Axes
    :show-inheritance:
 
-   
+
    .. rubric:: Methods
 
    .. autosummary::
       :toctree: WrightTools.artists.Axes
-   
+
       ~Axes.add_sideplot
       ~Axes.contour
       ~Axes.contourf

docs/api/WrightTools.artists.GridSpec.rst

@@ -6,9 +6,9 @@ WrightTools.artists.GridSpec
 .. autoclass:: GridSpec
    :show-inheritance:
 
-
-
 
-
-
-
+
+
+
+
+

docs/api/WrightTools.collection.Collection.rst

@@ -6,10 +6,10 @@ WrightTools.collection.Collection
 .. autoclass:: Collection
    :show-inheritance:
 
-   
+
    .. automethod:: __init__
 
-   
+
    .. rubric:: Methods
 
    .. autosummary::
@@ -22,15 +22,15 @@ WrightTools.collection.Collection
       ~Collection.flush
       ~Collection.print_tree
       ~Collection.save
-
 
-
-
+
+
+
    .. rubric:: Attributes
 
    .. autosummary::
       :toctree: WrightTools.collection.Collection
-   
+
       ~Collection.attrs
       ~Collection.class_name
       ~Collection.created
@@ -40,5 +40,5 @@ WrightTools.collection.Collection
       ~Collection.name
       ~Collection.natural_name
       ~Collection.parent
-   
-   
+
+