trying to induce new life to this repo

.pre-commit-config.yaml

@@ -19,3 +19,8 @@ repos:
     hooks:
     -   id: ruff
         args: [ --fix ]
+
+  - repo: https://github.com/pre-commit/mirrors-isort
+    rev: v5.10.1
+    hooks:
+      - id: isort

.vscode/extensions.json

@@ -9,5 +9,6 @@
         "ms-python.mypy-type-checker",
         "eamodio.gitlens",
         "ms-vscode.makefile-tools",
+        "ms-python.isort",
     ]
 }

.vscode/settings.json

@@ -42,7 +42,6 @@
 
     // ==== Linting ===
     // linter
-    "flake8.enabled" : false,
     "isort.enabled" : false,
     "ruff.enable": true,
     "ruff.lint.args": [
@@ -66,14 +65,12 @@
 
     // === Integrated terminal ====
     "terminal.integrated.profiles.linux": {
-        // Ensure the default integrated terminal (bash) respects .bash_profile
-        // https://superuser.com/questions/1209366/win10-vs-code-integrated-bash-not-loading-bash-profile
         "bash": {
             "path": "bash",
             "args": ["--init-file", "${workspaceFolder}/.vscode/start-terminal.sh"],
         },
     },
-
+    "terminal.integrated.defaultProfile.linux": "bash",
     "python.defaultInterpreterPath": "${workspaceFolder}/.venv/bin/python",
     "python.envFile": "${workspaceFolder}/.env",
 

.vscode/start-terminal.sh

@@ -3,7 +3,7 @@
 echo "Init vscode integrated terminal"
 
 ENV_FILE=".env"
-VENV_DIR=".venv/bin/activate"
+VENV_DIR="./.venv/bin/activate"
 
 if test -f ~/.bash_profile; then
     echo "Running ~/.bash_profile"

Makefile

@@ -27,8 +27,9 @@ endif
 format:
 	@echo "formatting..."
 	@poetry install
+	# add isort
+	@poetry run isort .
 	@poetry run black .
-	# ruff fix
 	@poetry run pre-commit run --all-files --config .pre-commit-config.yaml
 
 .PHONY: run_tests

graph_ml/_ext/Trie.pxd

@@ -1,7 +1,7 @@
 # distutils: language = c++
 
-from libcpp.string cimport string
 from libcpp.list cimport list
+from libcpp.string cimport string
 
 
 cdef extern from "Trie.cpp":

graph_ml/_ext/cytrie.pyx

@@ -2,6 +2,7 @@
 
 from Trie cimport Trie
 
+
 cdef class CyTrie:
     cdef Trie c_trie;
 

graph_ml/datasets/polbooks.py

@@ -1,8 +1,7 @@
-import pandas as pd
 import networkx as nx
+import pandas as pd
 from torch_geometric.data import extract_zip
 
-
 from ..datasets import dataset
 
 

graph_ml/models/torch_node2vec.py

@@ -1,6 +1,7 @@
 import numpy as np
-from torch_geometric.nn import Node2Vec as PyGNode2Vec
 import torch
+from torch_geometric.nn import Node2Vec as PyGNode2Vec
+
 from ..models.node2vec import Node2Vec
 
 

graph_ml/transformations/sampler.py

@@ -1,7 +1,9 @@
+import random
 from typing import Optional
+
 import numpy as np
 import pytorch_lightning as pl
-import random
+
 from ..utils import utils
 
 

graph_ml/transformations/samplers.py

@@ -8,6 +8,7 @@
 
 import numpy as np
 from scipy import sparse
+
 from ..utils import utils
 
 

graph_ml/utils/config.py

@@ -1,8 +1,9 @@
 import os
 import sys
+
 import torch
-from ..utils import utils
 
+from ..utils import utils
 
 OS = os.name
 PLATFORM = sys.platform

graph_ml/utils/utils.py

@@ -1,7 +1,8 @@
 import os
+
 import numpy as np
-from scipy import sparse
 from numba import njit
+from scipy import sparse
 
 
 def get_formatted_environ_variable(name, dtype, default):

pyproject.toml

@@ -49,6 +49,7 @@ codeium-jupyter = "^1.1.21"
 jupyter-contrib-nbextensions = "^0.7.0"
 pre-commit = "^3.6.2"
 black = "^24.2.0"
+isort = "^5.13.2"
 
 
 [tool.poetry.build]

tests/test_config.py

@@ -1,7 +1,9 @@
 import os
-from graph_ml.utils import config
+
 import pytest
 
+from graph_ml.utils import config
+
 
 @pytest.fixture()
 def OS():

tests/test_cython.py

@@ -1,6 +1,7 @@
-from graph_ml import CyTrie
 import pytest
 
+from graph_ml import CyTrie
+
 
 @pytest.fixture()
 def trie():

tests/test_samplers.py

@@ -1,7 +1,8 @@
-from graph_ml.transformations import samplers
-from graph_ml.datasets import polbooks
 import pytest
 
+from graph_ml.datasets import polbooks
+from graph_ml.transformations import samplers
+
 
 @pytest.fixture()
 def dataset():