chore: change linter to Ruff (#216)

* chore: add ruff linter; remove flake8, isort, pydocstyle

* docs: edit changelog

* chore: add rules to ruff

* fix: missing import

* chore: remove unnecessary exclude

.gitignore

@@ -146,3 +146,6 @@ lightning_logs/
 
 # files_cache
 files/
+
+# ruff
+.ruff_cache

.pre-commit-config.yaml

@@ -7,39 +7,28 @@ repos:
     hooks:
       - id: conventional-pre-commit
         stages: [commit-msg]
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: 'v0.0.259'
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
   - repo: https://github.com/psf/black
     rev: 23.1.0
     hooks:
       - id: black-jupyter
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-        name: isort (python)
   - repo: https://github.com/PyCQA/docformatter
     rev: v1.5.1
     hooks:
       - id: docformatter
         additional_dependencies: [tomli]
         args: ["--in-place", "--config", "./pyproject.toml"]
-  - repo: https://github.com/pycqa/pydocstyle
-    rev: 6.3.0
-    hooks:
-      - id: pydocstyle
-        additional_dependencies: ["toml", "tomli"]
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
-    hooks:
-      - id: flake8
-        additional_dependencies:
-          - flake8-bugbear
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.0.1
+    rev: v1.1.1
     hooks:
       - id: mypy
         additional_dependencies: ["types-requests"]
   - repo: https://github.com/pdm-project/pdm
-    rev: 2.4.7
+    rev: 2.4.9
     hooks:
       - id: pdm-lock-check
       - id: pdm-export
@@ -61,7 +50,7 @@ repos:
       - id: check-added-large-files
       - id: detect-private-key
   - repo: https://github.com/dosisod/refurb
-    rev: v1.13.0
+    rev: v1.15.0
     hooks:
       - id: refurb
         language: python

.vscode/extensions.json

@@ -1,3 +1,3 @@
 {
-  "recommendations": ["njpwerner.autodocstring"]
+  "recommendations": ["njpwerner.autodocstring", "charliermarsh.ruff"]
 }

.vscode/settings.json.default

@@ -1,13 +1,19 @@
 {
-  "editor.formatOnSave": true,
-  "python.formatting.provider": "black",
-  "python.linting.flake8Enabled": true,
   "python.linting.enabled": true,
   "python.linting.mypyEnabled": true,
+  "[python]": {
+    "editor.formatOnSave": true,
+    "editor.codeActionsOnSave": {
+      "source.fixAll": true,
+      "source.organizeImports": true
+    }
+  },
+  "python.formatting.provider": "black",
   "autoDocstring.docstringFormat": "google",
   "python.testing.pytestArgs": [
     "tests"
   ],
   "python.testing.unittestEnabled": false,
   "python.testing.pytestEnabled": true,
+  "python.analysis.typeCheckingMode": "off",
 }

CHANGELOG.md

@@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - Change embedders and joiners interface to have `.transform` method
+- Change linter to Ruff and removed flake8, isort, pydocstyle
 
 ### Deprecated
 

examples/regionizers/h3_regionizer.ipynb

@@ -149,7 +149,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.14"
+   "version": "3.11.1"
   },
   "vscode": {
    "interpreter": {

pyproject.toml

@@ -67,12 +67,9 @@ dev = ["bumpver>=2022.1118"]
 lint = [
     "pre-commit~=2.20",
     "black[jupyter]>=22.10.0",
-    "flake8~=5.0",
-    "pydocstyle[toml]>=6.1.1",
-    "flake8-docstrings>=1.6.0",
-    "isort~=5.10",
     "mypy~=0.982",
     "docformatter[tomli]>=1.5.0",
+    "ruff>=0.0.259",
 ]
 # pdm add -dG test <library>
 test = [
@@ -112,19 +109,37 @@ line-length = 100
 target-version = ["py38", "py39", "py310", "py311"]
 preview = true
 
-[tool.isort]
-profile = "black"
+[tool.ruff]
+line-length = 100
+target-version = "py38"
+select = [
+    "E", "W",       # pycodestyle
+    "F",            # pyflakes
+    "UP",           # pyupgrade
+    "D",            # pydocstyle
+    "I",            # isort
+    "B",            # flake8-bugbear
+    "NPY",          # NumPy
+    "YTT",          # flake8-2020
+    "Q",            # flake8-quotes
+    "PLE", "PLW",   # pylint (add "PLR" in the future)
+    "PIE",          # misc lints
+    "TID",          # tidy imports
+    "ISC",          # implicit string concatenation
+    "TCH",          # type-checking imports
+    # "N",            # pep8-naming
+    # "ANN",          # flake8-annotations
+]
+ignore = ["D212"]
+extend-exclude = [
+    "old",
+]
 
-[tool.bumpver]
-current_version = "0.0.1"
-version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
-commit_message = "chore: bump version {old_version} -> {new_version}"
-commit = true
-tag = true
-push = false
+[tool.ruff.pydocstyle]
+convention = "google"
 
-[tool.bumpver.file_patterns]
-"pyproject.toml" = ['current_version = "{version}"', 'version = "{version}"']
+[tool.ruff.pycodestyle]
+max-doc-length = 100
 
 [tool.mypy]
 strict = true
@@ -134,11 +149,6 @@ no_implicit_optional = true
 check_untyped_defs = true
 warn_return_any = true
 
-[tool.pydocstyle]
-convention = "google"
-add-select = ["D213"]
-add-ignore = ["D202", "D212"]
-
 [tool.docformatter]
 syntax = 'google'
 black = true
@@ -152,6 +162,17 @@ pre-summary-newline = true
 close-quotes-on-newline = true
 wrap-one-line = true
 
+[tool.bumpver]
+current_version = "0.0.1"
+version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
+commit_message = "chore: bump version {old_version} -> {new_version}"
+commit = true
+tag = true
+push = false
+
+[tool.bumpver.file_patterns]
+"pyproject.toml" = ['current_version = "{version}"', 'version = "{version}"']
+
 [tool.pytest.ini_options]
 addopts = ["--import-mode=importlib"]
 markers = ["slow: marks tests as slow (deselect with '-m \"not slow\"')"]

srai/exceptions.py

@@ -4,14 +4,10 @@
 class SRAIException(Exception):
     """Base class for all SRAI exceptions."""
 
-    pass
-
 
 class ModelNotFitException(SRAIException):
     """Exception raised when a model is not fit."""
 
-    pass
-
 
 class LoadedDataIsEmptyException(SRAIException):
     """Exception when the loaded data returned by the loader is empty."""

srai/loaders/gtfs_loader.py

@@ -154,7 +154,7 @@ def _validate_feed(self, feed: "Feed", fail: bool = True) -> None:
         if (validation_result["type"] == "error").sum() > 0:
             import warnings
 
-            warnings.warn(f"Invalid GTFS feed: \n{validation_result}", RuntimeWarning)
+            warnings.warn(f"Invalid GTFS feed: \n{validation_result}", RuntimeWarning, stacklevel=2)
             if fail:
                 raise ValueError("Invalid GTFS feed.")
 

srai/loaders/osm_loaders/filters/popular.py

@@ -27,6 +27,7 @@ def get_popular_tags(
     This is a wrapper around the `popular` taginfo api endpoint [1].
     It queries the API, and optionally filters the results
     according to argument values.
+
     Args:
         in_wiki_only (bool, optional): If True, only return results tags
             that have at least one wiki page. Defaults to False.

srai/loaders/osm_loaders/pbf_file_downloader.py

@@ -159,7 +159,7 @@ def download_pbf_file_for_polygon(self, polygon: Polygon) -> Path:
                 extraction_uuid = start_extract_result["uuid"]
                 status_check_url = start_extract_result["url"]
             except KeyError:
-                warnings.warn(json.dumps(start_extract_result))
+                warnings.warn(json.dumps(start_extract_result), stacklevel=2)
                 raise
 
             with tqdm() as pbar:

srai/loaders/osm_loaders/pbf_file_handler.py

@@ -3,9 +3,8 @@
 
 This module contains a handler capable of parsing a PBF file into a GeoDataFrame.
 """
-import os
 import warnings
-from typing import Any, Callable, Dict, Optional, Sequence, Union
+from typing import TYPE_CHECKING, Any, Callable, Dict, Optional, Sequence, Union
 
 import geopandas as gpd
 import osmium
@@ -20,6 +19,9 @@
 from srai.loaders.osm_loaders.filters.hex2vec import HEX2VEC_FILTER
 from srai.loaders.osm_loaders.filters.osm_tags_type import osm_tags_type
 
+if TYPE_CHECKING:
+    import os
+
 
 class PbfFileHandler(osmium.SimpleHandler):  # type: ignore
     """
@@ -66,7 +68,7 @@ def __init__(
             region_geometry (BaseGeometry, optional): Region which can be used to filter only
                 intersecting OSM objects. Defaults to None.
         """
-        super(PbfFileHandler, self).__init__()
+        super().__init__()
         self.filter_tags = tags
         if self.filter_tags:
             self.filter_tags_keys = set(self.filter_tags.keys())
@@ -234,7 +236,7 @@ def _get_osm_geometry(
             geometry = wkblib.loads(wkb, hex=True)
         except RuntimeError as ex:
             message = str(ex)
-            warnings.warn(message, RuntimeWarning)
+            warnings.warn(message, RuntimeWarning, stacklevel=2)
 
         return geometry
 

srai/loaders/osm_way_loader/osm_way_loader.py

@@ -143,7 +143,7 @@ def _graph_from_gdf(self, gdf: gpd.GeoDataFrame) -> Tuple[gpd.GeoDataFrame, gpd.
         Obtain the raw road infrastructure data from OSM.
 
         Args:
-            gss (gpd.GeoDataFrame): (Multi)Polygons for which to download road infrastructure data.
+            gdf (gpd.GeoDataFrame): (Multi)Polygons for which to download road infrastructure data.
 
         Returns:
             Tuple[gpd.GeoDataFrame, gpd.GeoDataFrame]: Road infrastructure as (intersections, roads)
@@ -324,7 +324,7 @@ def _sanitize(self, x: Any, column_name: str) -> Any:
                     x = x * constants.MPH_TO_KMH
                 x = float(x)
             elif column_name == "width":
-                if x.endswith("m") or x.endswith("meter"):
+                if x.endswith(("m", "meter")):
                     x = x.split("m")[0].strip()
                 elif "'" in x:
                     x = float(x.split("'")[0].strip())

srai/neighbourhoods/_base.py

@@ -37,7 +37,6 @@ def get_neighbours(self, index: IndexType) -> Set[IndexType]:
         Returns:
             Set[IndexType]: Indexes of the neighbours.
         """
-        pass  # pragma: no cover
 
     def get_neighbours_up_to_distance(self, index: IndexType, distance: int) -> Set[IndexType]:
         """

srai/regionizers/_spherical_voronoi.py

@@ -25,7 +25,7 @@
 
 
 def _generate_sphere_parts() -> None:
-    global SPHERE_PARTS, SPHERE_PARTS_BOUNDING_BOXES
+    global SPHERE_PARTS, SPHERE_PARTS_BOUNDING_BOXES  # noqa: PLW0603
 
     if not SPHERE_PARTS:
         # LON: 0; LAT: 0
@@ -85,6 +85,7 @@ def map_to_geocentric(lon: float, lat: float, ell: Ellipsoid) -> Tuple[float, fl
     Args:
         lon (float): longitude of a point in a wgs84 crs.
         lat (float): latitude of a point in a wgs84 crs.
+        ell (Ellipsoid): an ellipsoid.
 
     Returns:
         Tuple[float, float, float]: (x, y, z) coordinates tuple.
@@ -101,6 +102,7 @@ def map_from_geocentric(x: float, y: float, z: float, ell: Ellipsoid) -> Tuple[f
         x (float): X cartesian coordinate.
         y (float): Y cartesian coordinate.
         z (float): Z cartesian coordinate.
+        ell (Ellipsoid): an ellipsoid.
 
     Returns:
         Tuple[float, float]: longitude and latitude coordinates in a wgs84 crs.

srai/utils/_optional.py

@@ -45,17 +45,17 @@ def import_optional_dependency(
     try:
         imported_module = importlib.import_module(module)
         return imported_module if name is None else getattr(imported_module, name)
-    except ImportError:
+    except ImportError as exc:
         error_msg = (
             f'Missing optional dependency "{module}". Please install required packages using '
             f"`pip install srai[{dependency_group}]`."
         )
         if error == ImportErrorHandle.RAISE:
-            raise ImportError(error_msg)
+            raise ImportError(error_msg) from exc
         if error == ImportErrorHandle.WARN:
             import warnings
 
-            warnings.warn(f"{error_msg} Skipping import.", ImportWarning)
+            warnings.warn(f"{error_msg} Skipping import.", ImportWarning, stacklevel=2)
     return None
 
 
@@ -71,6 +71,5 @@ def import_optional_dependencies(
         error (ErrorHandle, {'raise', 'warn', 'ignore'}): Information what to do when any of
             the modules hasn't been found. Defaults to ErrorHandle.RAISE.
     """
-
     for module in modules:
         import_optional_dependency(dependency_group=dependency_group, module=module, error=error)

tests/embedders/test_gtfs2vec_embedder.py

@@ -180,7 +180,7 @@ def test_transform_with_mismatched_features_count(
     """Test GTFS2VecEmbedder transform with mismatched features count."""
     embedder = GTFS2VecEmbedder(skip_autoencoder=False)
     mock_model = mocker.MagicMock()
-    mock_model.configure_mock(**{"n_fetures": 42})
+    mock_model.configure_mock(n_features=42)
     embedder._model = mock_model
 
     with pytest.raises(ValueError):