Merge pull request #6 from 8bitsam/black

Black, flake8, and pre-commit fixes

Author: sbillinge

.codecov.yml

@@ -1,4 +1,4 @@
-# show coverage in CI status, not as a comment. 
+# show coverage in CI status, not as a comment.
 comment: off
 coverage:
   status:

.flake8

@@ -4,7 +4,8 @@ exclude =
     __pycache__,
     build,
     dist,
-    versioneer.py,
-    fourigui/_version.py,
-    docs/source/conf.py
+    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

.pre-commit-config.yaml

@@ -1,15 +1,44 @@
 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$'
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        exclude: '\.(rst|txt)$'
   - repo: https://github.com/psf/black
-    rev: 24.8.0
+    rev: 24.4.2
     hooks:
       - id: black
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.0.0
+  - 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]

AUTHORS.rst

@@ -31,5 +31,3 @@ Contributors
 ------------
 
 None yet. Why not be the first? See: CONTRIBUTING.rst
-
-

CONTRIBUTING.rst

@@ -101,4 +101,3 @@ Before you submit a pull request, check that it meets these guidelines:
 3. The pull request should work for Python 2.7, 3.3, 3.4, 3.5 and for PyPy. Check
    https://travis-ci.org/sbillinge/fourigui/pull_requests
    and make sure that the tests pass for all supported Python versions.
-

README.rst

@@ -98,4 +98,3 @@ For more information on diffpy.structure please visit the project web-page
 http://www.diffpy.org/
 
 or email Prof. Simon Billinge at [email protected].
-

conda-recipe/meta.yaml

@@ -58,7 +58,7 @@ test:
 about:
   home: https://github.com/diffpy/diffpy.fourigui
   #TODO add short description
-  summary: 
+  summary:
   license: Modified BSD License
   license_file: LICENSE.txt
 

devutils/makesdist

@@ -4,18 +4,18 @@
 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")
 
 vfb = versiondata.get("DEFAULT", "version").split(".post")[0] + ".post0"

further_processing_code/FFT.py

@@ -1,5 +1,5 @@
-import numpy as np
 import h5py
+import numpy as np
 
 
 def fourier_transformation(fftholder):

further_processing_code/symm_op.py

@@ -11,10 +11,11 @@
 # for different cubic structures one can easily change the symmetry operation parameters in line 106
 # more complex textures or crystal strucutes require more effort to derive appropriate symmetry operations
 
-import numpy as np
+from time import time
+
 import h5py
+import numpy as np
 from scipy.ndimage import rotate
-from time import time
 
 
 def load_data(fname):
@@ -37,10 +38,11 @@ def save_data(fname, arr):
 
 def symm_op(arr, angle, inversion):
     """
-    Perform symmetry operations on data set "arr". arr will be inverted about the center voxel and rotated with "angle"
-    about the z axis by iterating the 2D planes in the 3D data set arr along the z axis. rotation of the planes in the
-    data set is perfomed by scipy.ndimage.rotate. arr might contain nan values which scipy.ndimage.rotate cannot
-    operate. therefore the nan values in arr will be converted to float values 0.0 and denoted by 3D array "isnanarr_so".
+    Perform symmetry operations on data set "arr". arr will be inverted about the center voxel and rotated with
+    "angle" about the z axis by iterating the 2D planes in the 3D data set arr along the z axis. rotation of the
+    planes in the data set is perfomed by scipy.ndimage.rotate. arr might contain nan values which
+    scipy.ndimage.rotate cannot operate. therefore the nan values in arr will be converted to float values 0.0 and
+    denoted by 3D array "isnanarr_so".
     :param arr: data set in h5 type
     :param angle: rotate arr angle degrees about the z axis. put False if no rotation is intended.
     :param inversion: Boolian variable if arr is supposed to be inverted about center voxel.
@@ -107,8 +109,8 @@ def main(arr, symm_op_params):
     """
     Perform symmertry operations specified in symm_op_params and bin together the symmetry operated data sets.
     :param arr: data set in h5 type
-    :param symm_op_params: list of tuples with the supposed angle for the rotation in degree and False if no rotation
-    is intended and True or False if data set should be inverted or not.
+    :param symm_op_params: list of tuples with the supposed angle for the rotation in degree and False if no
+    rotation is intended and True or False if data set should be inverted or not.
     :return arr: average of all symmetry operated data sets
     """
     holder = np.zeros_like(arr)

requirements/run.txt

@@ -1,4 +1,3 @@
 matplotlib
 h5py
 scipy
-

setup.py

@@ -7,14 +7,14 @@
 in reciprocal space
 
 Packages:   diffpy.fourigui
-Scripts:    fourgui - 
+Scripts:    fourgui -
 """
 
-import sys
 import os
 import re
-from setuptools import setup, find_packages
+import sys
 
+from setuptools import find_packages, setup
 
 # Use this version when git data are not available, like in git zip archive.
 # Update when tagging a new release.
@@ -31,7 +31,7 @@
 
 
 def gitinfo():
-    from subprocess import Popen, PIPE
+    from subprocess import PIPE, Popen
 
     kw = dict(stdout=PIPE, cwd=MYDIR, universal_newlines=True)
     proc = Popen(["git", "describe", "--match=v[[:digit:]]*"], **kw)
@@ -90,8 +90,11 @@ def getversioncfg():
     long_description = fp.read()
 
 
+def dest(p):
+    return os.path.normpath(p.replace("_build", ""))
+
+
 def datafiles_html():
-    dest = lambda p: os.path.normpath(p.replace("_build", ""))
     rv = [
         (dest(t), [os.path.join(t, f) for f in fl])
         for t, d, fl in os.walk("doc/manual/_build/html")

src/diffpy/fourigui/__init__.py

@@ -16,7 +16,3 @@
 """\
 '{{cookiecutter.short_description}}'
 """
-# package version
-from diffpy.fourigui.version import __version__
-
-from diffpy.fourigui.fourigui import main