add precommit and fix related checks

Author: Tieqiong

Diff for: .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.

Diff for: .codespell/ignore_words.txt

@@ -0,0 +1,29 @@
+;; 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
+
+;; alternative use of socioeconomic
+socio-economic
+
+;; Frobenius norm used in np.linalg.norm
+fro
+
+;; abbreviation for "structure"
+struc
+
+;; method name within JournalPanel class
+onText
+
+;; a method name within JournalPanel class
+delt
+
+;; structure file format
+discus
+
+;; variable name within pdfbaseline module
+aline
+
+;; variable name within TestSFAverageObjCryst class
+fo

Diff for: .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,
+    doc/source/conf.py
+max-line-length = 115
+# 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

Diff for: .isort.cfg

@@ -0,0 +1,5 @@
+[settings]
+# Keep import statement below line_length character limit
+line_length = 115
+multi_line_output = 3
+include_trailing_comma = True

Diff for: .pre-commit-config.yaml

@@ -0,0 +1,67 @@
+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
+        exclude: ^conda-recipe/meta\.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]

Diff for: .prettierignore

@@ -0,0 +1 @@
+/conda-recipe/*

Diff for: .travis.yml

@@ -114,7 +114,7 @@ parallel jobs (-j4) ::
 
    sudo scons -j4 install
 
-See ``scons -h`` for decription of build targets and options.
+See ``scons -h`` for description of build targets and options.
 
 
 DEVELOPMENT

Diff for: README.rst

@@ -1,52 +1,56 @@
 #!/usr/bin/env python
 
-'''Create source distribution tar.gz archive, where each file belongs
-to a root user and modification time is set to the git commit time.
-'''
+"""Create source distribution tar.gz archive, where each file belongs to a root
+user and modification time is set to the git commit time."""
 
-import sys
+import glob
+import gzip
 import os
 import subprocess
-import glob
+import sys
 import tarfile
-import gzip
+
+from setup import FALLBACK_VERSION, versiondata
 
 BASEDIR = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
 sys.path.insert(0, BASEDIR)
 
-from setup import versiondata, FALLBACK_VERSION
-timestamp = versiondata.getint('DEFAULT', 'timestamp')
+timestamp = versiondata.getint("DEFAULT", "timestamp")
 
-vfb = versiondata.get('DEFAULT', 'version').split('.post')[0] + '.post0'
+vfb = versiondata.get("DEFAULT", "version").split(".post")[0] + ".post0"
 emsg = "Invalid FALLBACK_VERSION. Expected %r got %r."
 assert vfb == FALLBACK_VERSION, emsg % (vfb, FALLBACK_VERSION)
 
+
 def inform(s):
     sys.stdout.write(s)
     sys.stdout.flush()
     return
 
+
 inform('Run "setup.py sdist --formats=tar" ')
-cmd_sdist = ([sys.executable, '-Wignore:Cannot detect name suffix'] +
-             'setup.py sdist --formats=tar'.split())
-ec = subprocess.call(cmd_sdist, cwd=BASEDIR, stdout=open(os.devnull, 'w'))
-if ec:  sys.exit(ec)
+cmd_sdist = [sys.executable, "-Wignore:Cannot detect name suffix"] + "setup.py sdist --formats=tar".split()
+ec = subprocess.call(cmd_sdist, cwd=BASEDIR, stdout=open(os.devnull, "w"))
+if ec:
+    sys.exit(ec)
 inform("[done]\n")
 
-tarname = max(glob.glob(BASEDIR + '/dist/*.tar'), key=os.path.getmtime)
+tarname = max(glob.glob(BASEDIR + "/dist/*.tar"), key=os.path.getmtime)
 
 tfin = tarfile.open(tarname)
-fpout = gzip.GzipFile(tarname + '.gz', 'w', mtime=0)
-tfout = tarfile.open(fileobj=fpout, mode='w')
+fpout = gzip.GzipFile(tarname + ".gz", "w", mtime=0)
+tfout = tarfile.open(fileobj=fpout, mode="w")
+
 
 def fixtarinfo(tinfo):
     tinfo.uid = tinfo.gid = 0
-    tinfo.uname = tinfo.gname = 'root'
+    tinfo.uname = tinfo.gname = "root"
     tinfo.mtime = timestamp
     tinfo.mode &= ~0o022
     return tinfo
 
-inform('Filter %s --> %s.gz ' % (2 * (os.path.basename(tarname),)))
+
+inform("Filter %s --> %s.gz " % (2 * (os.path.basename(tarname),)))
 for ti in tfin:
     tfout.addfile(fixtarinfo(ti), tfin.extractfile(ti))
 

Diff for: devutils/makesdist

@@ -1,11 +1,21 @@
 #!/usr/bin/env python
 
-"""Tune the peak precision parameter so that PDFCalculator
-gives equivalent results to diffpy.pdffit2.
+"""Tune the peak precision parameter so that PDFCalculator gives equivalent
+results to diffpy.pdffit2.
 
 Usage: tunePeakPrecision.py [qmax] [peakprecision] [createplot]
 """
 
+# global imports
+import sys
+import time
+
+import numpy
+
+import diffpy.pdffit2
+from diffpy.srreal.pdf_ext import PDFCalculator
+from diffpy.structure import Structure
+
 # Results:
 # Qmax  peakprecision   CPU     Notes
 # 15    3.2e-6                  clear minimum
@@ -21,16 +31,6 @@
 peakprecision = None
 createplot = False
 
-# global imports
-import sys
-import time
-
-import numpy
-
-from diffpy.structure import Structure
-from diffpy.srreal.pdf_ext import PDFCalculator
-import diffpy.pdffit2
-
 # make PdfFit silent
 diffpy.pdffit2.redirect_stdout(open("/dev/null", "w"))
 
@@ -52,7 +52,7 @@
 
 
 def Gpdffit2(qmax):
-    """Calculate reference nickel PDF using diffpy.pdffit2
+    """Calculate reference nickel PDF using diffpy.pdffit2.
 
     qmax    -- vawevector cutoff value in 1/A
 
@@ -68,7 +68,7 @@ def Gpdffit2(qmax):
 
 
 def Gsrreal(qmax, peakprecision=None):
-    """Calculate nickel PDF using PDFCalculator from diffpy.srreal
+    """Calculate nickel PDF using PDFCalculator from diffpy.srreal.
 
     qmax            -- vawevector cutoff value in 1/A
     peakprecision   -- precision factor affecting peak cutoff,