linting: change linter to ruff

.github/workflows/linting.yml

@@ -45,5 +45,6 @@ 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 .
+

.vscode/settings.json

@@ -1,14 +1,25 @@
 {
+    "editor.rulers": [
+        80,
+        100
+      ],
+    // python
     "[python]": {
+        "editor.formatOnSave": true,
+        "editor.defaultFormatter": "charliermarsh.ruff",
         "editor.codeActionsOnSave": {
-            "source.organizeImports": true
+            "source.fixAll.ruff": true,
+            "source.organizeImports.ruff": true,
         },
+        "linting.prospectorEnabled": false,
         "files.trimTrailingWhitespace": true,
+        "defaultInterpreterPath": "",
+        "python.languageServer": "Pylance",
     },
-
-    "python.linting.prospectorEnabled": true,
+    // python docstring
+    "autoDocstring.docstringFormat": "google",
     "notebook.lineNumbers": "on",
-
+    "notebook.diff.ignoreMetadata": true,
     "[*.yml]": {
         "files.trimTrailingWhitespace": true,
     },

README.dev.md

@@ -44,7 +44,7 @@ coverage report
 
 ## Linting
 
-We use [prospector](https://pypi.org/project/prospector/) with pyroma for linting. For running it locally, use `prospector` or `prospector <filepath_or_folderpath>` for specific files/folders.
+We use [ruff](https://docs.astral.sh/ruff/) for linting, sorting imports and formatting code. The configurations of `ruff` are set in [pyproject.toml](pyproject.toml) file.
 
 ## Versioning
 

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",
@@ -83,3 +82,51 @@ source = ["deeprank2"]
 [tool.setuptools.packages.find]
 include = ["deeprank2*"]
 exclude = ["tests*"]
+
+[tool.ruff]
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    "docs",
+    "reduce"
+]
+target-version = "py310"
+line-length = 159
+select = [
+    "F",    # Pyflakes
+    "E",    # pycodestyle (error)
+    "W",    # pycodestyle (warning)
+    "I",    # isort
+    "D",    # pydocstyle
+]
+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",
+]
+
+# Allow autofix for all enabled rules (when `--fix`) is provided.
+fixable = ["A", "B", "C", "D", "E", "F", "I"]
+
+[tool.ruff.isort]
+known-first-party = ["deeprank2"]
+force-single-line = true
+lines-after-imports = 2
+no-lines-before = ["future","standard-library","third-party","first-party","local-folder"]