Cleanup configs (#58)

* Move flake8 config into tox.ini

* Remove W503 ignore as it is defaulted to be set

* Fix tox.ini typo, create pyproject.toml

* Remove reorder-python-imports

Author: RemyLau

.flake8

@@ -1,9 +1,4 @@
 repos:
--   repo: https://github.com/asottile/reorder_python_imports
-    rev: v2.6.0
-    hooks:
-    -   id: reorder-python-imports
-
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.0.1
     hooks:

.pre-commit-config.yaml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools>=42.0", "wheel"]
+build-backend = "setuptools.build_meta"

pyproject.toml

@@ -1,5 +1,4 @@
 """Different strategies for generating node2vec walks."""
-
 import numpy as np
 from gensim.models import Word2Vec
 from numba import njit, prange

src/pecanpy/pecanpy.py

@@ -1,5 +1,4 @@
 """Dense Graph object equipped with random walk computation."""
-
 import numpy as np
 from numba import njit
 from pecanpy.graph import DenseGraph
@@ -96,7 +95,8 @@ def get_extended_normalized_probs(
             # print("NUM INOUT: ", inout_ind.sum(), "\n")
 
             t = prev_nbrs_weight[inout_ind] / average_weight_ary[inout_ind]
-            # b = 1; t = b * t / (1 - (b - 1) * t)  # optional nonlinear parameterization
+            # optional nonlinear parameterization
+            # b = 1; t = b * t / (1 - (b - 1) * t)
 
             # compute out biases
             alpha = 1 / q + (1 - 1 / q) * t

src/pecanpy/rw/dense_rw.py

@@ -1,5 +1,4 @@
 """Sparse Graph equipped with random walk computation."""
-
 import numpy as np
 from numba import boolean, njit
 from pecanpy.graph import SparseGraph

src/pecanpy/rw/sparse_rw.py

@@ -1,7 +1,7 @@
 [tox]
 minversion = 3.8.0
 envlist = python3.8, python3.9, flake8
-isolated_buiold = true
+isolated_build = true
 
 [gh-actions]
 python =
@@ -39,3 +39,19 @@ description = Run the flake8 tool with several plugins (bandit, docstrings, impo
 [flake8]
 max-line-length = 88
 extend-ignore = E203
+exclude =
+    .tox,
+    .git,
+    __pycache__,
+    build,
+    dist,
+    *.pyc,
+    *.egg-info,
+    .cache,
+    .eggs
+import-order-style = pycharm
+application-import-names =
+    pybel
+    bel_resources
+    tests
+format = ${cyan}%(path)s${reset}:${yellow_bold}%(row)d${reset}:${green_bold}%(col)d${reset}: ${red_bold}%(code)s${reset} %(text)s