add isort and flake8 and run pre-commit on all files

Author: Remi-Gau

.codespellrc

@@ -0,0 +1,4 @@
+[flake8]
+max-line-length=79
+exclude =
+    scripts/editProperties.py

.flake8

@@ -11,11 +11,29 @@ repos:
     -   id: check-ast
     -   id: check-added-large-files
     -   id: check-merge-conflict
+
+# Sorts Python imports alphabetically and by section with `isort`.
+-   repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+    -   id: isort
+        args: [--settings-path, pyproject.toml]
+
 -   repo: https://github.com/psf/black
     rev: 24.3.0
     hooks:
     -   id: black
+
 -   repo: https://github.com/codespell-project/codespell
     rev: v2.2.6
     hooks:
     -   id: codespell
+        args: [--toml, pyproject.toml]
+        additional_dependencies: [tomli]
+
+-   repo: https://github.com/pyCQA/flake8
+    rev: 7.1.0
+    hooks:
+    -   id: flake8
+        args: [--config, .flake8, --verbose]
+        additional_dependencies: [flake8-bugbear]

.pre-commit-config.yaml

@@ -0,0 +1,13 @@
+[tool.black]
+line-length = 79
+
+[tool.codespell]
+skip = "env,venv,*.svg,pyproject.toml"
+ignore-words-list = "HSI"
+builtin = "clear,rare"
+
+[tool.isort]
+combine_as_imports = true
+line_length = 79
+profile = "black"
+skip_gitignore = true

pyproject.toml

@@ -1,4 +1,5 @@
 import sys
+
 import rdflib as rl
 from pytablewriter import MarkdownTableWriter
 
@@ -81,7 +82,11 @@ def edit_properties(version):
         writer.value_matrix = []
         del props["klass_desc"]
         for val, comment in sorted(props.items()):
-            property = [val[2], comment, f"[{val[1]}{val[2]}]({val[1]}{val[2]})"]
+            property = [
+                val[2],
+                comment,
+                f"[{val[1]}{val[2]}]({val[1]}{val[2]})",
+            ]
             writer.value_matrix.append(property)
         writer.margin = 1  # add a whitespace for both sides of each cell
         doc.append("\n")

scripts/editProperties.py

@@ -1,9 +1,9 @@
-import os
 import json
+import os
 
 schema_dirs = ["contexts", "schemas", "terms"]
 tested = 0
-for root, dirs, files in os.walk(".", topdown=True):
+for root, _, files in os.walk(".", topdown=True):
     if os.path.basename(root) in schema_dirs:
         for name in files:
             with open(os.path.join(root, name)) as fp:

scripts/jsonParser.py

@@ -1,9 +1,11 @@
+import json
 import os
 import sys
-import json
-from pyld import jsonld
-import rdflib as rl
 from shutil import copyfile
+
+import rdflib as rl
+from pyld import jsonld
+
 from reproschema.jsonldutils import to_newformat
 
 
@@ -12,7 +14,9 @@ def create_release(version):
     terms = []
     for root, _, files in os.walk("terms"):
         for name in files:
-            terms.extend(json.loads(to_newformat(os.path.join(root, name), "jsonld")))
+            terms.extend(
+                json.loads(to_newformat(os.path.join(root, name), "jsonld"))
+            )
 
     kwargs = {"algorithm": "URDNA2015", "format": "application/n-quads"}
     data = jsonld.normalize(terms, kwargs)