more pre-commit checks

.pre-commit-config.yaml

@@ -1,6 +1,23 @@
 repos:
+ - repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: v4.0.1
+ hooks:
+ - id: check-merge-conflict
+ - id: debug-statements
+ - id: mixed-line-ending
+ - id: check-case-conflict
+ - id: check-yaml
+ - repo: https://github.com/timothycrosley/isort
+ rev: 5.8.0
+ hooks:
+ - id: isort
  - repo: https://github.com/ambv/black
- rev: stable
+ rev: 21.6b0
  hooks:
  - id: black
  language_version: python3
+ - repo: https://gitlab.com/pycqa/flake8
+ rev: 3.9.2
+ hooks:
+ - id: flake8
+ language_version: python3

hetnetpy/matrix.py

@@ -1,6 +1,6 @@
+import logging
 from collections import OrderedDict
 
-import logging
 import numpy
 import scipy.sparse
 

hetnetpy/pathtools.py

@@ -1,5 +1,5 @@
-import itertools
 import functools
+import itertools
 import operator
 
 from hetnetpy.hetnet import Node, Path

hetnetpy/permute.py

@@ -1,6 +1,6 @@
 import collections
-import random
 import logging
+import random
 
 from hetnetpy.hetnet import Graph
 

hetnetpy/readwrite.py

@@ -1,7 +1,7 @@
 import collections
 import csv
-import io
 import importlib
+import io
 import json
 import mimetypes
 import operator

hetnetpy/stats.py

@@ -1,6 +1,6 @@
-import pandas
 import matplotlib
 import matplotlib.backends.backend_pdf
+import pandas
 import seaborn
 
 

setup.cfg

@@ -0,0 +1,15 @@
+[flake8]
+ignore =
+ E203
+ E402
+ E501
+ E731
+ W503
+
+[isort]
+profile = black
+multi_line_output = 3
+include_trailing_comma = True
+force_grid_wrap = 0
+use_parentheses = True
+line_length = 88

setup.py

@@ -1,5 +1,4 @@
 import pathlib
-import re
 
 import setuptools
 

test/graph_test.py

@@ -6,7 +6,7 @@
 import hetnetpy.hetnet
 import hetnetpy.readwrite
 
-from .readwrite_test import formats, extensions
+from .readwrite_test import extensions, formats
 
 
 def test_creation(tmpdir):

test/matrix_test.py

@@ -4,8 +4,8 @@
 import pytest
 import scipy.sparse
 
-from hetnetpy.matrix import metaedge_to_adjacency_matrix, sparsify_or_densify
 import hetnetpy.readwrite
+from hetnetpy.matrix import metaedge_to_adjacency_matrix, sparsify_or_densify
 
 directory = os.path.dirname(os.path.abspath(__file__))
 

test/neo4j_test.py

@@ -1,8 +1,8 @@
 import pathlib
 import textwrap
 
-from neo4j import GraphDatabase
 import pytest
+from neo4j import GraphDatabase
 
 import hetnetpy.neo4j
 import hetnetpy.readwrite

test/pathtools_test.py

@@ -3,7 +3,7 @@
 import pytest
 
 import hetnetpy.readwrite
-from hetnetpy.pathtools import paths_between, DWPC
+from hetnetpy.pathtools import DWPC, paths_between
 
 directory = os.path.dirname(os.path.abspath(__file__))
 

test/readwrite_test.py

@@ -2,7 +2,6 @@
 
 import hetnetpy.readwrite
 
-
 directory = os.path.dirname(os.path.abspath(__file__))
 
 formats = ["json", "pkl"]