skpkg: move over precommit files and create pre-commit auto fixes

.codespell/ignore_lines.txt

@@ -0,0 +1,2 @@
+;; Please include filenames and explanations for each ignored line.
+;; See https://docs.openverse.org/meta/codespell.html for docs.

.codespell/ignore_words.txt

@@ -0,0 +1,8 @@
+;; Please include explanations for each ignored word (lowercase).
+;; See https://docs.openverse.org/meta/codespell.html for docs.
+
+;; abbreviation for "materials" often used in a journal title
+mater
+
+;; Frobenius norm used in np.linalg.norm
+fro

.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

.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

@@ -2,6 +2,6 @@ This code is developed by:
 
 	Xiaohao Yang
 
-This code was developed as part of the xPDFsuite project to create software 
-and tools for general researchers to use PDF in their work. For more 
+This code was developed as part of the xPDFsuite project to create software
+and tools for general researchers to use PDF in their work. For more
 information on the DiffPy project email sb2896@columbia.edu

README.rst

@@ -17,13 +17,13 @@ INSTALLATION
 ------------------------------------------------------------------------
 
 We are going to release conda package for all platform. For general user
-please use the installation file and install software. For developor, 
+please use the installation file and install software. For developor,
 you can install dpx.confutils using
 
     python setup.py install
-    
-Note: the dependency is not specified in the setup.py. You need to install 
-them yourself. You can use Anaconda or other python enviroment.    
+
+Note: the dependency is not specified in the setup.py. You need to install
+them yourself. You can use Anaconda or other python enviroment.
 
 
 CONTACTS
@@ -33,4 +33,4 @@ For more information on diffpy.Structure please visit the project web-page
 
 http://www.diffpy.org/
 
-or email Prof. Simon Billinge at sb2896@columbia.edu.
+or email Prof. Simon Billinge at sb2896@columbia.edu.

requirements/pip.txt

@@ -1,4 +1,4 @@
 numpy
 configparser
 traits
-traitsui
+traitsui

src/diffpy/__init__.py

@@ -11,11 +11,8 @@
 # See LICENSENOTICE.txt for license information.
 #
 ##############################################################################
+"""Blank namespace package."""
 
-"""
-Blank namespace package.
-"""
-
-__import__('pkg_resources').declare_namespace(__name__)
+__import__("pkg_resources").declare_namespace(__name__)
 
 # End of file

src/diffpy/srxconfutils/__init__.py

@@ -12,18 +12,21 @@
 #
 ##############################################################################
 
+# some convenience imports
+from diffpy.srxconfutils.config import ConfigBase
+
 # package version
 from diffpy.srxconfutils.version import __version__
 
-# some convenience imports
-from diffpy.srxconfutils.config import ConfigBase, ConfigBase
 
 # unit tests
 def test():
-    '''Execute all unit tests for the diffpy.pdfgetx package.
+    """Execute all unit tests for the diffpy.pdfgetx package.
+
     Return a unittest TestResult object.
-    '''
+    """
     from dpx.confutils.tests import test
+
     return test()