Adds pre-commit as the format and lint check in CI

Author: miguelgondu

pyproject.toml

@@ -65,7 +65,7 @@ rosetta_energy = [
     "biopython",
     "pyrosetta-installer",
 ]
-dev = ["black", "tox", "pytest", "bump-my-version"]
+dev = ["black", "tox", "pytest", "bump-my-version", "pre-commit", "pyright"]
 docs = ["sphinx", "furo"]
 
 [project.urls]
@@ -89,7 +89,7 @@ markers = [
 
 [tool.pyright]
 include = ["src/poli"]
-exclude = ["src/poli/core/util/proteins/rasp/inner_rasp", "src/poli/objective_repository/gfp_cbas"]
+exclude = ["src/poli/core/util/proteins/rasp/inner_rasp", "src/poli/objective_repository/gfp_cbas", "examples"]
 reportIncompatibleMethodOverride = "none"
 
 [tool.isort]

tox.ini

@@ -26,13 +26,9 @@ commands =
 [testenv:lint]
 description = check the code style with black
 deps =
-    black
-    isort
-    ruff
+    pre-commit
 commands =
-    black --check --diff .
-    isort --profile black --check-only src/
-    ruff check
+    pre-commit run --all-files
 
 [testenv:poli-base-py310]
 description = run the tests with pytest on the base environment for poli