skpkg: apply pre-commit to project directory with no manual edits

.flake8

@@ -0,0 +1,13 @@
+# As of now, flake8 does not natively support configuration via pyproject.toml
+# https://github.com/microsoft/vscode-flake8/issues/135
+[flake8]
+exclude =
+    .git,
+    __pycache__,
+    build,
+    dist,
+    docs/source/conf.py
+max-line-length = 79
+# Ignore some style 'errors' produced while formatting by 'black'
+# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings
+extend-ignore = E203

.gitignore

@@ -45,4 +45,4 @@ setup.cfg
 /DistancePrinter/gitarchive.cfg
 
 # test output
-actual.res
+actual.res

.isort.cfg

@@ -0,0 +1,5 @@
+[settings]
+# Keep import statement below line_length character limit
+line_length = 79
+multi_line_output = 3
+include_trailing_comma = True

.pre-commit-config.yaml

@@ -0,0 +1,66 @@
+default_language_version:
+  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
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: check-added-large-files
+  - repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+      - id: black
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.7.1
+    hooks:
+      - id: nbstripout
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: no-commit-to-branch
+        name: Prevent Commit to Main Branch
+        args: ["--branch", "main"]
+        stages: [pre-commit]
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli
+  # prettier - multi formatter for .json, .yml, and .md files
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: f12edd9c7be1c20cfa42420fd0e6df71e42b51ea # frozen: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+        additional_dependencies:
+          - "prettier@^3.2.4"
+  # docformatter - PEP 257 compliant docstring formatter
+  - repo: https://github.com/s-weigand/docformatter
+    rev: 5757c5190d95e5449f102ace83df92e7d3b06c6c
+    hooks:
+      - id: docformatter
+        additional_dependencies: [tomli]
+        args: [--in-place, --config, ./pyproject.toml]

AUTHORS.txt

@@ -1 +1 @@
-Xiaohao Yang
+Xiaohao Yang

MANIFEST.in

@@ -1,3 +1,3 @@
 recursive-include DistancePrinter *
 prune doc
-exclude MANIFEST.in
+exclude MANIFEST.in

README.rst

@@ -18,10 +18,10 @@ To install the DistancePrinter package:
 
     python setup.py install
 
-By default the files are installed in the system directories, which are 
-usually only writeable by the root.  See the usage info "./setup.py install 
---help" for options to install as a normal user under a different location.  
-Note that installation to non-standard directories you may require adjustments 
+By default the files are installed in the system directories, which are
+usually only writeable by the root.  See the usage info "./setup.py install
+--help" for options to install as a normal user under a different location.
+Note that installation to non-standard directories you may require adjustments
 to the PATH and PYTHONPATH environment variables.
 
 CONTACTS

src/diffpy/distanceprinter/__init__.py

@@ -12,9 +12,7 @@
 #
 ##############################################################################
 
-"""
-Blank namespace package.
-"""
+"""Blank namespace package."""
 
 __import__("pkg_resources").declare_namespace(__name__)
 

src/diffpy/distanceprinter/distanceprinter.py

@@ -13,6 +13,7 @@
 ##############################################################################
 
 import sys
+
 import numpy as np
 
 from diffpy.pdffit2 import PdfFit
@@ -70,9 +71,7 @@ def calDistance(strufile, atomi, atomj, lb, ub, complete):
 
 
 def formatResults(stru, distlist, complete, all0ddij, **kw):
-    """
-    format the distlist to string
-    """
+    """Format the distlist to string."""
     lines = []
     # header
     lines.append("# Structure file: %s" % kw["strufile"])

src/diffpy/distanceprinter/version.py

@@ -15,8 +15,8 @@
 
 """Definition of __version__, __date__, __gitsha__."""
 
-from pkg_resources import resource_filename
 from ConfigParser import RawConfigParser
+from pkg_resources import resource_filename
 
 # obtain version information from the version.cfg file
 cp = RawConfigParser(dict(version="", date="", commit="", timestamp=0))

tests/outputs/expected.res

@@ -1,11 +1,11 @@
 # Structure file: /home/zthatcher/GitLab/dev/dpx.distanceprinter/tests/test_files/Ni-9008476.cif
-# 
+#
 # lattice=Lattice(a=3.52387, b=3.52387, c=3.52387, alpha=90, beta=90, gamma=90)
 #  0 Ni   0.000000 0.000000 0.000000 1.0000
 #  1 Ni   0.000000 0.500000 0.500000 1.0000
 #  2 Ni   0.500000 0.000000 0.500000 1.0000
 #  3 Ni   0.500000 0.500000 0.000000 1.0000
-# 
+#
 # Inter-atomic distance of (all, all) in (1.00, 10.00) A
 
 Ni.0-Ni.1:	2.491752
@@ -1527,4 +1527,4 @@ Ni.3-Ni.3:	9.967009
 Ni.3-Ni.3:	9.967009
 Ni.3-Ni.3:	9.967009
 Ni.3-Ni.3:	9.967009
-Ni.3-Ni.3:	9.967009
+Ni.3-Ni.3:	9.967009