Migrate linting from flake8+isort to ruff

Makefile

@@ -10,15 +10,12 @@ coverage.xml: testcov
 coverage-report: testcov
 	coverage report
 
-flake8:
-	flake8 streamflow tests
-
 format:
-	isort streamflow tests
+	ruff check --fix streamflow tests
 	black --target-version py310 streamflow tests
 
 format-check:
-	isort --check-only streamflow tests
+	ruff check streamflow tests
 	black --target-version py310 --diff --check streamflow tests
 
 pyupgrade:

pyproject.toml

@@ -53,9 +53,8 @@ bandit = [
 lint = [
     "black==26.3.1",
     "codespell==2.4.2",
-    "flake8-bugbear==25.11.29",
-    "isort==8.0.1",
-    "pyupgrade==3.21.2"
+    "pyupgrade==3.21.2",
+    "ruff==0.15.12"
 ]
 test = [
     "cwltest==2.6.20251216093331",
@@ -74,5 +73,11 @@ zip-safe = true
 [tool.setuptools.package-data]
 "streamflow.plugins.unito.postgresql" = ["schemas/*.json", "schemas/*.sql"]
 
-[tool.isort]
-profile = "black"
+[tool.ruff]
+exclude = ["streamflow/cwl/antlr"]
+line-length = 88
+target-version = "py310"
+
+[tool.ruff.lint]
+select = ["E", "W", "F", "B", "I"]
+ignore = ["E203", "E501", "B904"]

tests/conftest.py

@@ -64,7 +64,7 @@ def are_equals(elem1, elem2, obj_compared=None):
     if isinstance(elem1, Collection) and not isinstance(elem1, dict):
         if len(elem1) != len(elem2):
             return False
-        for e1, e2 in zip(elem1, elem2):
+        for e1, e2 in zip(elem1, elem2, strict=True):
             if not are_equals(e1, e2, obj_compared):
                 return False
         return True

tox.ini

@@ -35,6 +35,6 @@ passenv =
 
 [testenv:lint]
 allowlist_externals = make
-commands = make flake8 format-check codespell-check pyupgrade
+commands = make format-check codespell-check pyupgrade
 dependency_groups = lint
 description = Lint the Python code