pre-commit fixes

Author: 8bitsam

.flake8

@@ -8,4 +8,4 @@ exclude =
 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
+extend-ignore = E203

.github/workflows/build.yaml

@@ -59,7 +59,7 @@ jobs:
 
     # This step will upload tagged commits to pypi.
     # The pypi token must be added to GH secrets
-    # 
+    #
     # - name: Publish package
     #   if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
     #   uses: pypa/gh-action-pypi-publish@release/v1

.pre-commit-config.yaml

@@ -0,0 +1,43 @@
+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
+        exclude: '\.(rst|txt)$'
+  - 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]

CHANGELOG.md

@@ -13,5 +13,5 @@ No notable functional changes from 1.4.1
 ### Deprecated
 
 ### Removed
- 
+
 ### Fixed

devutils/makesdist

@@ -1,51 +1,57 @@
 #!/usr/bin/env python
 
-'''Create source distribution tar.gz archive, where each file belongs
+"""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
 
 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')
+from setup import FALLBACK_VERSION, versiondata
 
-vfb = versiondata.get('DEFAULT', 'version').split('.post')[0] + '.post0'
+timestamp = versiondata.getint("DEFAULT", "timestamp")
+
+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] + '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] + "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))
 

diffpy/pdffit2/ipy_ext.py

@@ -54,7 +54,6 @@ def showfit(self, offset=None):
         No return value.
         """
         from matplotlib.pyplot import gca
-        from math import floor
 
         cr = self.r
         cGobs = self.Gobs

diffpy/pdffit2/pdffit.py

@@ -148,7 +148,10 @@ def intro():
         date = __date__[:10]
         d = {"version": __version__, "date": date, "year": date[:4] or "2019"}
         msg = __intro_message__ % d
-        def filler(mx): return mx.group(0).rstrip(" *").ljust(77) + "*"
+
+        def filler(mx):
+            return mx.group(0).rstrip(" *").ljust(77) + "*"
+
         msg_ljust = re.sub("(?m)^(.{1,77}|.{79}.*)$", filler, msg)
         print(msg_ljust, file=output.stdout)
         return
@@ -1288,6 +1291,7 @@ def __getRef(self, var_string):
             retval = f(self._handle, arg_int)
         return retval
 
+
 # End of class PdfFit
 
 

diffpy/pdffit2/tests/ExceptionsTest.py

@@ -16,8 +16,7 @@
 
 import unittest
 
-from diffpy.pdffit2 import PdfFit
-from diffpy.pdffit2 import pdffit2
+from diffpy.pdffit2 import PdfFit, pdffit2
 from diffpy.pdffit2.tests.pdffit2testutils import datafile
 
 

diffpy/pdffit2/tests/TestPdfFit.py

@@ -5,13 +5,10 @@
 
 import unittest
 
+from diffpy.pdffit2 import PdfFit, pdffit2
+from diffpy.pdffit2.tests.pdffit2testutils import capture_output, datafile
 from diffpy.structure import loadStructure
 
-from diffpy.pdffit2 import PdfFit
-from diffpy.pdffit2 import pdffit2
-from diffpy.pdffit2.tests.pdffit2testutils import datafile, capture_output
-
-
 # ----------------------------------------------------------------------------
 
 
@@ -324,7 +321,7 @@ def test_getcrw(self):
         self.assertAlmostEqual(self.P.getrw(), rw19, self.places)
         # renormalize cumulative Rw and compare with Rw at r=15
         Gobs19 = numpy.array(self.P.getpdf_obs())
-        Gnorm19 = numpy.sqrt(numpy.sum(Gobs19 ** 2))
+        Gnorm19 = numpy.sqrt(numpy.sum(Gobs19**2))
         r = numpy.array(self.P.getR())
         idx = numpy.nonzero(r <= 15)[0]
         Gnorm15 = numpy.sqrt(numpy.sum(Gobs19[idx] ** 2))
@@ -353,7 +350,7 @@ def test_getcrw_two_datasets(self):
         rw1 = self.P.getcrw()[-1]
         self.P.setdata(2)
         rw2 = self.P.getcrw()[-1]
-        self.assertAlmostEqual(rwtot ** 2, rw1 ** 2 + rw2 ** 2, self.places)
+        self.assertAlmostEqual(rwtot**2, rw1**2 + rw2**2, self.places)
         return
 
     #   def test_getpar(self):

diffpy/pdffit2/tests/TestPhaseFractions.py

@@ -29,7 +29,7 @@ def test_xray_fractions(self):
         """test_xray_fractions -- check phase fractions in x-ray dataset."""
         self.P.setdata(1)
         ph = self.P.phase_fractions()
-        bb1 = 28 ** 2
+        bb1 = 28**2
         bb2 = ((8 * 82 + 24 * 8 + 4 * 21 + 2 * 74 + 2 * 22) / 40.0) ** 2
         self.assertAlmostEqual(1.0, sum(ph["atom"]), self.places)
         self.assertAlmostEqual(1.0, sum(ph["cell"]), self.places)
@@ -57,7 +57,7 @@ def test_neutron_fractions(self):
         """test_neutron_fractions -- check phase fractions in neutron dataset."""
         self.P.setdata(2)
         ph = self.P.phase_fractions()
-        bb1 = 10.31 ** 2
+        bb1 = 10.31**2
         bPb = 9.4012
         bO = 5.8054
         bSc = 12.11

diffpy/pdffit2/tests/__init__.py

@@ -35,8 +35,9 @@ def testsuite(pattern=""):
         The TestSuite object containing the matching tests.
     """
     import re
-    from os.path import dirname
     from itertools import chain
+    from os.path import dirname
+
     from pkg_resources import resource_filename
 
     loader = unittest.defaultTestLoader

diffpy/pdffit2/tests/debug.py

@@ -25,6 +25,7 @@
 
 if __name__ == "__main__":
     import sys
+
     from diffpy.pdffit2.tests import testsuite
 
     pattern = sys.argv[1] if len(sys.argv) > 1 else ""

diffpy/pdffit2/tests/pdffit2testutils.py

@@ -19,7 +19,9 @@
 
 
 import os.path
+
 import six
+
 import diffpy.pdffit2
 
 # silence the C++ engine output

diffpy/pdffit2/tests/rundeps.py

@@ -21,6 +21,7 @@
 
 if __name__ == "__main__":
     import sys
+
     from diffpy.pdffit2.tests import testdeps
 
     # produce zero exit code for a successful test

diffpy/pdffit2/tests/testdata/300K.gr

@@ -1,5 +1,5 @@
 History written: Fri Apr 30 13:05:36 2004
-produced by 
+produced by
 ##### Run Information     runCorrection=T
 prep=gsas     machine=npdf
 run=300K     background=npdf_00907
@@ -27,12 +27,12 @@ density=     effDensity=3.4138
 
 ##### Banks=6  deltaQ=0.01  matchRef=0  matchScal=T  matchOffset=T
 bank   angle   blendQmin   blendQmax       (0.0 means no info)
-  1     90.0        1.62    29.42   
-  2    -90.0        1.62    29.42   
-  3    119.0        1.97    35.85   
-  4    -119.0        1.97    35.85   
-  5    148.0        2.20    40.00   
-  6    -148.0        2.20    40.00   
+  1     90.0        1.62    29.42
+  2    -90.0        1.62    29.42
+  3    119.0        1.97    35.85
+  4    -119.0        1.97    35.85
+  5    148.0        2.20    40.00
+  6    -148.0        2.20    40.00
 
 ##### Program Specific Information
 ## Ft     calcError=1     (1 for true, 0 for false)

diffpy/pdffit2/version.py

@@ -28,7 +28,6 @@
 
 from pkg_resources import resource_filename
 
-
 # obtain version information from the version.cfg file
 cp = dict(version="", date="", commit="", timestamp="0")
 fcfg = resource_filename(__name__, "version.cfg")