Merge pull request #70 from stevenhua0320/c1

pre-commit run with no manual change

Author: sbillinge

.flake8

@@ -0,0 +1,16 @@
+[flake8]
+exclude =
+    .git,
+    __pycache__,
+    build,
+    dist,
+    doc/source/conf.py,
+    */doc/source/conf.py,
+    hooks/post_gen_project.py,
+    */__init__.py,
+    */debug.py
+builtins = cookiecutter
+max-line-length = 115
+# Ignore some style 'errors' produced while formatting by 'black' (see link below)
+# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings
+extend-ignore = E203

.pre-commit-config.yaml

@@ -0,0 +1,45 @@
+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: 'environment.yml'
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        exclude: '\.(rst|txt)$'
+  - repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+      - id: black
+        exclude: '.*\.py'
+  - 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]

conda-recipe/run_test.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
 
 import diffpy.srfit.tests
+
 assert diffpy.srfit.tests.test().wasSuccessful()

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))
 

doc/Makefile

@@ -31,4 +31,3 @@ clean:
 	rm -rf diffpy.srfitapi
 	rm -f srfit_examples.zip
 	$(MAKE) -C devmanual $@
-

doc/examples/coreshellnp.py

@@ -22,14 +22,11 @@
 """
 
 import numpy
-from scipy.optimize import leastsq
-
 from pyobjcryst import loadCrystal
+from scipy.optimize import leastsq
 
+from diffpy.srfit.fitbase import FitContribution, FitRecipe, FitResults, Profile
 from diffpy.srfit.pdf import PDFGenerator, PDFParser
-from diffpy.srfit.fitbase import Profile
-from diffpy.srfit.fitbase import FitContribution, FitRecipe
-from diffpy.srfit.fitbase import FitResults
 
 # Example Code
 
@@ -73,7 +70,7 @@ def makeRecipe(stru1, stru2, datname):
     # and a spherical shell CF for the shell. Since this is set up as two
     # phases, we implicitly assume that the core-shell correlations contribute
     # very little to the PDF.
-    from diffpy.srfit.pdf.characteristicfunctions import sphericalCF, shellCF
+    from diffpy.srfit.pdf.characteristicfunctions import shellCF, sphericalCF
     contribution.registerFunction(sphericalCF, name="f_CdS")
     contribution.registerFunction(shellCF, name="f_ZnS")
 

doc/examples/crystalpdf.py

@@ -26,14 +26,11 @@
 """
 
 import numpy
+from gaussianrecipe import scipyOptimize
 
-from diffpy.structure import Structure
+from diffpy.srfit.fitbase import FitContribution, FitRecipe, FitResults, Profile
 from diffpy.srfit.pdf import PDFGenerator, PDFParser
-from diffpy.srfit.fitbase import Profile
-from diffpy.srfit.fitbase import FitContribution, FitRecipe
-from diffpy.srfit.fitbase import FitResults
-
-from gaussianrecipe import scipyOptimize
+from diffpy.structure import Structure
 
 ####### Example Code
 

doc/examples/crystalpdfall.py

@@ -20,15 +20,11 @@
 """
 
 import numpy
-
+from gaussianrecipe import scipyOptimize
 from pyobjcryst import loadCrystal
 
+from diffpy.srfit.fitbase import FitContribution, FitRecipe, FitResults, Profile
 from diffpy.srfit.pdf import PDFGenerator, PDFParser
-from diffpy.srfit.fitbase import Profile
-from diffpy.srfit.fitbase import FitContribution, FitRecipe
-from diffpy.srfit.fitbase import FitResults
-
-from gaussianrecipe import scipyOptimize
 
 ####### Example Code
 

doc/examples/crystalpdfobjcryst.py

@@ -20,15 +20,12 @@
 by the ObjCrystCrystalParSet structure adapter.
 """
 
+from crystalpdf import plotResults
+from gaussianrecipe import scipyOptimize
 from pyobjcryst import loadCrystal
 
+from diffpy.srfit.fitbase import FitContribution, FitRecipe, FitResults, Profile
 from diffpy.srfit.pdf import PDFGenerator, PDFParser
-from diffpy.srfit.fitbase import Profile
-from diffpy.srfit.fitbase import FitContribution, FitRecipe
-from diffpy.srfit.fitbase import FitResults
-
-from gaussianrecipe import scipyOptimize
-from crystalpdf import plotResults
 
 ####### Example Code
 

doc/examples/crystalpdftwodata.py

@@ -22,15 +22,11 @@
 """
 
 import numpy
-
+from gaussianrecipe import scipyOptimize
 from pyobjcryst import loadCrystal
 
+from diffpy.srfit.fitbase import FitContribution, FitRecipe, FitResults, Profile
 from diffpy.srfit.pdf import PDFGenerator, PDFParser
-from diffpy.srfit.fitbase import Profile
-from diffpy.srfit.fitbase import FitContribution, FitRecipe
-from diffpy.srfit.fitbase import FitResults
-
-from gaussianrecipe import scipyOptimize
 
 ####### Example Code