lint with flake8 rules

Author: scottgigante

python/magic/__init__.py

@@ -1,4 +1,4 @@
-import magic.plot
-
 from .magic import MAGIC
 from .version import __version__
+
+import magic.plot

python/magic/magic.py

@@ -6,21 +6,21 @@
 (C) 2018 Krishnaswamy Lab GPLv2
 """
 
-import numbers
-import warnings
+from . import utils
+from scipy import sparse
+from scipy import spatial
+from sklearn.base import BaseEstimator
+from sklearn.decomposition import PCA
+from sklearn.exceptions import NotFittedError
 
 import graphtools
 import matplotlib.pyplot as plt
+import numbers
 import numpy as np
 import pandas as pd
 import scprep
 import tasklogger
-from scipy import sparse, spatial
-from sklearn.base import BaseEstimator
-from sklearn.decomposition import PCA
-from sklearn.exceptions import NotFittedError
-
-from . import utils
+import warnings
 
 try:
     import anndata

python/magic/plot.py

@@ -1,17 +1,17 @@
 # author: Scott Gigante <[email protected]>
 # (C) 2017 Krishnaswamy Lab GPLv2
 
-import numbers
+from .magic import MAGIC
+from .utils import in_ipynb
+from matplotlib import animation
+from matplotlib import rc
+from scipy import sparse
 
 import matplotlib.pyplot as plt
+import numbers
 import numpy as np
 import pandas as pd
 import scprep
-from matplotlib import animation, rc
-from scipy import sparse
-
-from .magic import MAGIC
-from .utils import in_ipynb
 
 
 def _validate_gene(gene, data):

python/magic/utils.py

@@ -1,9 +1,9 @@
-import numbers
+from scipy import sparse
 
+import numbers
 import numpy as np
 import pandas as pd
 import scprep
-from scipy import sparse
 
 try:
     import anndata

python/setup.py

@@ -1,7 +1,7 @@
-import os
-import sys
+from setuptools import find_packages
+from setuptools import setup
 
-from setuptools import find_packages, setup
+import os
 
 install_requires = [
     "numpy>=1.14.0",

python/test/test.py

@@ -1,11 +1,11 @@
 #!/usr/bin/env python
 
 
-import os
-import scprep
-import numpy as np
 import magic
 import matplotlib as mpl
+import numpy as np
+import os
+import scprep
 
 mpl.use("agg")
 

setup.cfg

@@ -0,0 +1,24 @@
+[flake8]
+ignore =
+    # top-level module docstring
+    D100, D104,
+    # space before : conflicts with black
+    E203
+per-file-ignores =
+    # imported but unused
+    __init__.py: F401
+    # missing docstring in public function for methods, metrics, datasets
+    openproblems/tasks/*/*/*.py: D103, E203
+    openproblems/tasks/*/*/__init__.py: F401, D103
+max-line-length = 88
+exclude =
+    .git,
+    __pycache__,
+    build,
+    dist,
+    Snakefile
+
+[isort]
+profile = black
+force_single_line = true
+force_alphabetical_sort = true