Merge pull request #200 from zmx27/migration

chore: pre-commit auto fixes from prettier

Author: sbillinge

.codecov.yml

@@ -1,14 +1,14 @@
 coverage:
   status:
-    project:  # more options at https://docs.codecov.com/docs/commit-status
+    project: # more options at https://docs.codecov.com/docs/commit-status
       default:
         target: auto # use the coverage from the base commit, fail if coverage is lower
-        threshold: 0%  # allow the coverage to drop by
+        threshold: 0% # allow the coverage to drop by
 
 comment:
   layout: " diff, flags, files"
   behavior: default
   require_changes: false
-  require_base: false  # [true :: must have a base report to post]
-  require_head: false  # [true :: must have a head report to post]
+  require_base: false # [true :: must have a base report to post]
+  require_head: false # [true :: must have a head report to post]
   hide_project_coverage: false # [true :: only show coverage on the git diff aka patch coverage]

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -12,7 +12,7 @@ assignees: ""
 - [ ] All the badges on the README are passing.
 - [ ] License information is verified as correct. If you are unsure, please comment below.
 - [ ] Locally rendered documentation contains all appropriate pages, including API references (check no modules are
-  missing), tutorials, and other human written text is up-to-date with any changes in the code.
+      missing), tutorials, and other human written text is up-to-date with any changes in the code.
 - [ ] Installation instructions in the README, documentation and on the website (e.g., diffpy.org) are updated.
 - [ ] Successfully run any tutorial examples or do functional testing with the latest Python version.
 - [ ] Grammar and writing quality are checked (no typos).
@@ -31,5 +31,5 @@ version information and details about the pre-release here:
 
 <!-- Before closing this issue, please complete the following: -->
 
-- [ ]  Run tutorial examples and conduct functional testing using the installation guide in the README. Attach screenshots/results as comments.
-- [ ]  Documentation (README, tutorials, API references, and websites) is deployed without broken links or missing figures.
+- [ ] Run tutorial examples and conduct functional testing using the installation guide in the README. Attach screenshots/results as comments.
+- [ ] Documentation (README, tutorials, API references, and websites) is deployed without broken links or missing figures.

.github/workflows/build-wheel-release-upload.yml

@@ -4,7 +4,7 @@ on:
   workflow_dispatch:
   push:
     tags:
-      - '*'  # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
+      - "*" # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
 
 jobs:
   release:

.github/workflows/check-news-item.yml

@@ -3,7 +3,7 @@ name: Check for News
 on:
   pull_request_target:
     branches:
-    - main
+      - main
 
 jobs:
   check-news-item:

.pre-commit-config.yaml

@@ -1,14 +1,14 @@
 default_language_version:
-    python: python3
+  python: python3
 ci:
-    autofix_commit_msg: |
-        [pre-commit.ci] auto fixes from pre-commit hooks
-    autofix_prs: true
-    autoupdate_branch: 'pre-commit-autoupdate'
-    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
-    autoupdate_schedule: monthly
-    skip: [no-commit-to-branch]
-    submodules: false
+  autofix_commit_msg: |
+    [pre-commit.ci] auto fixes from pre-commit hooks
+  autofix_prs: true
+  autoupdate_branch: "pre-commit-autoupdate"
+  autoupdate_commit_msg: "[pre-commit.ci] pre-commit autoupdate"
+  autoupdate_schedule: monthly
+  skip: [no-commit-to-branch]
+  submodules: false
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0
@@ -47,6 +47,6 @@ repos:
   - repo: https://github.com/codespell-project/codespell
     rev: v2.3.0
     hooks:
-    - id: codespell
-      additional_dependencies:
-        - tomli
+      - id: codespell
+        additional_dependencies:
+          - tomli

src/diffpy/__init__.py

@@ -12,7 +12,6 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
 """morph - tools for manipulating and comparing PDF data.
 
 """

src/diffpy/morph/__init__.py

@@ -12,8 +12,7 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
-"""Tools for manipulating and comparing PDF profiles"""
+"""Tools for manipulating and comparing PDF profiles."""
 
 # key used when saving multiple morphs
 __save_morph_as__ = "save_morph_as"

src/diffpy/morph/log.py

@@ -12,7 +12,6 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-
 """Configuration of loggers used in this package.
 
 Logger instances:

src/diffpy/morph/morph_api.py

@@ -54,7 +54,7 @@
 
 
 def morph_default_config(**kwargs):
-    """function to generate default morph configuration
+    """Function to generate default morph configuration.
 
     Parameters
     ----------
@@ -96,7 +96,7 @@ def morph(
     verbose=False,
     **kwargs,
 ):
-    """function to perform PDF morphing.
+    """Function to perform PDF morphing.
 
     Parameters
     ----------

src/diffpy/morph/morph_helpers/__init__.py

@@ -10,9 +10,8 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-
-"""List of helpers for certain morphing operations
-(currently only used for smear)."""
+"""List of helpers for certain morphing operations (currently only used for
+smear)."""
 
 from diffpy.morph.morph_helpers.transformpdftordf import TransformXtalPDFtoRDF
 from diffpy.morph.morph_helpers.transformrdftopdf import TransformXtalRDFtoPDF

src/diffpy/morph/morph_helpers/transformpdftordf.py

@@ -12,10 +12,7 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-
-
-"""class TransformXtalPDFtoRDF -- Transform crystal PDFs to RDFs.
-"""
+"""Class TransformXtalPDFtoRDF -- Transform crystal PDFs to RDFs."""
 
 
 from diffpy.morph.morphs.morph import LABEL_GR, LABEL_RA, LABEL_RR, Morph
@@ -34,7 +31,6 @@ class TransformXtalPDFtoRDF(Morph):
 
     With s = baselineslope,
     R(r) = r * (G(r) - r * s)
-
     """
 
     # Define input output types

src/diffpy/morph/morph_helpers/transformrdftopdf.py

@@ -12,10 +12,7 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-
-
-"""class TransformXtalRDFtoPDF -- Transform crystal RDFs to PDFs.
-"""
+"""Class TransformXtalRDFtoPDF -- Transform crystal RDFs to PDFs."""
 
 
 import numpy
@@ -36,7 +33,6 @@ class TransformXtalRDFtoPDF(Morph):
 
     With s = baselineslope,
     G(r) = R(r) / r + r * s
-
     """
 
     # Define input output types

src/diffpy/morph/morph_io.py

@@ -34,8 +34,8 @@ def single_morph_output(
     verbose=False,
     stdout_flag=False,
 ):
-    """Helper function for printing details about a single morph.
-    Handles both printing to terminal and printing to a file.
+    """Helper function for printing details about a single morph. Handles both
+    printing to terminal and printing to a file.
 
     Parameters
     ----------
@@ -136,9 +136,9 @@ def create_morphs_directory(save_directory):
 
 def get_multisave_names(target_list: list, save_names_file=None, mm=False):
     """Create or import a dictionary that specifies names to save morphs as.
-    First attempt to import names from a specified file.
-    If names for certain morphs not found, use default naming scheme:
-    'Morph_with_Target_<target file name>.cgr'.
+    First attempt to import names from a specified file. If names for certain
+    morphs not found, use default naming scheme: 'Morph_with_Target_<target
+    file name>.cgr'.
 
     Used when saving multiple morphs.
 

src/diffpy/morph/morphapp.py

@@ -42,8 +42,8 @@ def __init__(self, *args, **kwargs):
         def custom_error(self, msg):
             """custom_error(msg : string)
 
-            Print a message incorporating 'msg' to stderr and exit.
-            Does not print usage.
+            Print a message incorporating 'msg' to stderr and exit. Does
+            not print usage.
             """
             self.exit(2, "%s: error: %s\n" % (self.get_prog_name(), msg))
 

src/diffpy/morph/morphs/__init__.py

@@ -12,9 +12,7 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-
-"""Definition of morphs.
-"""
+"""Definition of morphs."""
 
 
 from diffpy.morph.morphs.morph import Morph  # noqa: F401

src/diffpy/morph/morphs/morph.py

@@ -12,8 +12,6 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-
-
 """Morph -- base class for defining a morph.
 """
 
@@ -198,7 +196,7 @@ def checkConfig(self):
         return
 
     def plotInputs(self, xylabels=True):
-        """Plot input arrays using matplotlib.pyplot
+        """Plot input arrays using matplotlib.pyplot.
 
         Parameters
         ----------
@@ -220,7 +218,7 @@ def plotInputs(self, xylabels=True):
         return rv
 
     def plotOutputs(self, xylabels=True, **plotargs):
-        """Plot output arrays using matplotlib.pyplot
+        """Plot output arrays using matplotlib.pyplot.
 
         Parameters
         ----------

src/diffpy/morph/morphs/morphchain.py

@@ -12,7 +12,6 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-
 """MorphChain -- Chain of morphs executed in order.
 """
 

src/diffpy/morph/morphs/morphfuncy.py

@@ -3,7 +3,7 @@
 
 class MorphFuncy(Morph):
     """Apply the user-supplied Python function to the y-coordinates of the
-    morph data"""
+    morph data."""
 
     # Define input output types
     summary = "Apply a Python function to the y-axis data"

src/diffpy/morph/morphs/morphishape.py

@@ -12,11 +12,8 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-
-
-"""class MorphISphere -- apply inverse spherical shape function
-class MorphISpheroid -- apply inverse spheroidal shape function
-"""
+"""Class MorphISphere -- apply inverse spherical shape function class
+MorphISpheroid -- apply inverse spheroidal shape function."""
 
 
 import numpy
@@ -26,7 +23,7 @@ class MorphISpheroid -- apply inverse spheroidal shape function
 
 
 class MorphISphere(Morph):
-    """Apply inverse spherical characteristic function to the morph
+    """Apply inverse spherical characteristic function to the morph.
 
     Configuration Variables
     -----------------------
@@ -56,7 +53,7 @@ def morph(self, x_morph, y_morph, x_target, y_target):
 
 
 class MorphISpheroid(Morph):
-    """Apply inverse spherical characteristic function to the morph
+    """Apply inverse spherical characteristic function to the morph.
 
     Configuration Variables
     -----------------------

src/diffpy/morph/morphs/morphresolution.py

@@ -12,10 +12,7 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-
-
-"""class MorphResolutionDamping -- apply resolution broadening to the morph
-"""
+"""Class MorphResolutionDamping -- apply resolution broadening to the morph."""
 
 
 import numpy

src/diffpy/morph/morphs/morphrgrid.py

@@ -12,10 +12,7 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-
-
-"""class MorphRGrid -- put morph and target on desired grid.
-"""
+"""Class MorphRGrid -- put morph and target on desired grid."""
 
 
 import numpy

src/diffpy/morph/morphs/morphscale.py

@@ -12,10 +12,7 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-
-
-"""class MorphScale -- scale the morph data
-"""
+"""Class MorphScale -- scale the morph data."""
 
 
 from diffpy.morph.morphs.morph import LABEL_GR, LABEL_RA, Morph

src/diffpy/morph/morphs/morphshape.py

@@ -12,11 +12,8 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-
-
-"""class MorphSphere -- apply a spherical shape function to the morph
-class MorphSpheroid -- apply a spheroidal shape function to the morph
-"""
+"""Class MorphSphere -- apply a spherical shape function to the morph class
+MorphSpheroid -- apply a spheroidal shape function to the morph."""
 
 
 import numpy
@@ -28,7 +25,7 @@ class MorphSpheroid -- apply a spheroidal shape function to the morph
 
 
 class MorphSphere(Morph):
-    """Apply a spherical characteristic function to the morph
+    """Apply a spherical characteristic function to the morph.
 
     Configuration Variables
     -----------------------
@@ -56,7 +53,7 @@ def morph(self, x_morph, y_morph, x_target, y_target):
 
 
 class MorphSpheroid(Morph):
-    """Apply a spherical characteristic function to the morph
+    """Apply a spherical characteristic function to the morph.
 
     Configuration Variables
     -----------------------
@@ -143,7 +140,6 @@ def _spheroidalCF2(r, psize, axrat):
     axrat  --  The ratio of axis lengths
 
     From Lei et al., Phys. Rev. B, 80, 024118 (2009)
-
     """
     pelpt = axrat
 

src/diffpy/morph/morphs/morphshift.py

@@ -12,10 +12,7 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-
-
-"""class MorphShift -- shift the morph
-"""
+"""Class MorphShift -- shift the morph."""
 
 
 import numpy