set ruff as default linter

.github/workflows/linting.yml

@@ -45,5 +45,5 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
           extras-require: test
-      - name: Check style against standards using prospector
-        run: prospector --die-on-tool-error
+      - name: Check style against standards using ruff
+        run: ruff .

pyproject.toml

@@ -49,15 +49,14 @@ dependencies = [
     "tqdm >= 4.63.0",
     "freesasa >= 2.1.0",
     "tensorboard >= 0.9.0",
-    "protobuf >= 3.20.1"
+    "protobuf >= 3.20.1",
+    "ruff",
 ]
 
 [project.optional-dependencies]
 # development dependency groups
 test = [
     "pytest >= 7.4.0",
-    "pylint <= 2.17.5",
-    "prospector[with_pyroma] <= 1.10.2",
     "bump2version",
     "coverage",
     "pycodestyle",
@@ -88,5 +87,60 @@ exclude = ["tests*", "*tests.*", "*tests"]
 "*" = [
     "*.xlsx",
     "*.param",
-    "*.top", 
+    "*.top",
     "*residue-classes"]
+
+[tool.ruff]
+# Exclude a variety of commonly ignored directories.
+extend-exclude = [
+    "docs",
+    "reduce",
+]
+line-length = 159
+select = [
+    "F",  # Pyflakes
+    "E",  # pycodestyle (error)
+    "W",  # pycodestyle (warning)
+    "I",  # isort
+    "D",  # pydocstyle
+    "B",  # flake8-bugbear
+]
+ignore = [
+    "D100",  # Missing module docstring
+    "D101",  # Missing docstring in public class
+    "D102",  # Missing docstring in public method
+    "D103",  # Missing docstring in public function
+    "D104",  # Missing public package docstring
+    "D105",  # Missing docstring in magic method
+    "D107",  # Missing docstring in `__init__`
+    # The following list excludes rules irrelevant to the Google style
+    "D203",  # 1 blank line required before class docstring
+    "D204",
+    "D212",  # Multi-line docstring summary should start at the first line
+    "D213",  # Multi-line docstring summary should start at the second line
+    "D215",
+    "D400",
+    "D401",
+    "D404",  # First word of the docstring should not be This
+    "D406",
+    "D407",
+    "D408",
+    "D409",
+    "D413",
+    # flake8-bugbear
+    "B028",  # No explicit `stacklevel` keyword argument found
+]
+
+# Allow autofix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+unfixable = []
+
+[tool.ruff.lint]
+extend-safe-fixes = [
+    "D415",  # First line should end with a period, question mark, or exclamation point
+    "D300",  # Use triple double quotes `"""`
+    "D200",  # One-line docstring should fit on one line
+    ]
+
+[tool.ruff.isort]
+known-first-party = ["deeprank2"]