Add ruff and mypy to pre-commit. Configure ruff as linter and formatter.

Co-authored-by: Virginia Morales <vmorales@arfima.com>
Co-authored-by: Arfima Dev <dev@arfima.com>

Signed-off-by: Xavier Barrachina Civera <xbarrachina@arfima.com>

Author: xbarra

.pre-commit-config.yaml

@@ -3,7 +3,6 @@ repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0
     hooks:
-      - id: trailing-whitespace
       - id: check-merge-conflict
       - id: end-of-file-fixer
       - id: name-tests-test
@@ -15,28 +14,32 @@ repos:
       - id: check-yaml
       - id: check-symlinks
       - id: detect-private-key
-      - id: check-ast
-      - id: debug-statements
 
   - repo: https://github.com/Lucas-C/pre-commit-hooks
     rev: v1.5.5
     hooks:
       - id: remove-tabs
 
-  - repo: https://github.com/psf/black
-    rev: '24.4.2'
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.6
     hooks:
-      - id: black
-      - id: black-jupyter
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix, --config=pyproject.toml]
+      - id: ruff-format
 
-  - repo: https://github.com/s-weigand/flake8-nb
-    rev: v0.5.3
+  - repo: local
     hooks:
-      - id: flake8-nb
-        additional_dependencies:
-          - pep8-naming
-        # Ignore all format-related checks as Black takes care of those.
-        args:
-          - --ignore=E2, W5, F401, E401, E704
-          - --select=E, W, F, N
-          - --max-line-length=120
+      - id: mypy-cache
+        name: "create mypy cache"
+        language: system
+        pass_filenames: false
+        entry: bash -c 'if [ ! -d .mypy_cache ];
+          then /bin/mkdir .mypy_cache; fi; exit 0'
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.10.1"
+    hooks:
+      - id: mypy
+        verbose: true
+        args: ["--show-error-codes", "--install-types", "--non-interactive"]
+        additional_dependencies: ["pytest", "types-requests"]

docs/conf.py

@@ -60,7 +60,11 @@
 autosummary_generate = True
 
 # Docstrings of private methods
-autodoc_default_options = {"members": True, "undoc-members": True, "private-members": False}
+autodoc_default_options = {
+    "members": True,
+    "undoc-members": True,
+    "private-members": False,
+}
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output

pyproject.toml

@@ -78,21 +78,11 @@ test = [
   "pytest-cov",
   "sphinx-pyproject"
 ]
-lint = [
-  "isort",
-  "black",
-  "pyproject-flake8",
-  "flake8",
-  "flake8-nb",
-  "mypy",
-  "pre-commit",
-  "tox"
-]
-"black[jupyter]" = []
-pandas = []
 dev = [
-    "pandas>=2.0.3",
-    "geopandas>=0.13.2"
+    "mypy",
+    "pre-commit",
+    "ruff",
+    "tox",
 ]
 
 [tool.pdm.scripts]
@@ -113,40 +103,83 @@ addopts = "-v"
 warn_unreachable = true
 ignore_missing_imports = true
 
-[tool.isort]
-profile = "black"
-multi_line_output = 3
-include_trailing_comma = true
-force_grid_wrap = 0
-use_parentheses = true
-ensure_newline_before_comments = true
-line_length = 120
-
 [tool.coverage.run]
 source = "src"
 omit = "tests/*"
 relative_files = true
 
-[tool.yapf]
-blank_line_before_nested_class_or_def = true
-column_limit = 88
-
-[tool.black]
-line-length = 120
-exclude = '''
-/(
-    \.git
-  | \.tox
-  | \venv
-  | \.venv
-  | \*.env
-  | \build
-  | \dist
-)/
-'''
-
-[tool.flake8]
-max-line-length = "120"
-extend-ignore = [
-  "E501",
+[tool.ruff]
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".git-rewrite",
+    ".hg",
+    ".ipynb_checkpoints",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".pyenv",
+    ".pytest_cache",
+    ".pytype",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    ".vscode",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "site-packages",
+    "venv",
+]
+
+[tool.ruff.lint]
+extend-fixable = [
+    # Instead of trailing-whitespace
+    "W291", "W293"
+    ]
+
+extend-select = [
+    # Instead of pydocstyle
+    "D",
+    #Instead of flake8
+    "E", "F","B",
+    # Instead of pep8-naming
+    "N",
+    # Instead of flake8-debugger or debug-statements
+    "T10",
 ]
+
+ignore = [
+    "E203",
+    "E501",
+    # Avoid incompatible rules
+    "D203",
+    "D213",
+
+    # Ignore this rules so that precommit passes. Uncomment to start fixing them
+    "B006", "B008", "B904", "B012", "B024",
+    "D",
+    "F401",
+]
+
+[tool.ruff.lint.extend-per-file-ignores]
+# Ignore `D` rules everywhere except for the `src/` directory.
+"!src/**.py" = ["D"]
+
+[tool.ruff.lint.pycodestyle]
+max-line-length = 120
+
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
+skip-magic-trailing-comma = false
+line-ending = "auto"
+#docstring-code-format = false
+docstring-code-line-length = "dynamic"

src/physrisk/api/v1/common.py

@@ -35,13 +35,17 @@ class Asset(BaseModel, extra="allow"):
     )
     latitude: float = Field(description="Latitude in degrees")
     longitude: float = Field(description="Longitude in degrees")
-    type: Optional[str] = Field(None, description="Type of the asset <level_1>/<level_2>/<level_3>")
+    type: Optional[str] = Field(
+        None, description="Type of the asset <level_1>/<level_2>/<level_3>"
+    )
     location: Optional[str] = Field(
-        None, description="Location (e.g. Africa, Asia, Europe, Global, Oceania, North America, South America)"
+        None,
+        description="Location (e.g. Africa, Asia, Europe, Global, Oceania, North America, South America)",
     )
     capacity: Optional[float] = Field(None, description="Power generation capacity")
     attributes: Optional[Dict[str, str]] = Field(
-        None, description="Bespoke attributes (e.g. number of storeys, structure type, occupancy type)"
+        None,
+        description="Bespoke attributes (e.g. number of storeys, structure type, occupancy type)",
     )
 
 
@@ -81,7 +85,8 @@ class IntensityCurve(BaseModel):
 
     intensities: List[float] = Field([], description="Hazard indicator intensities.")
     return_periods: Optional[List[float]] = Field(
-        [], description="[Deprecated] Return period in years in the case of an acute hazard."
+        [],
+        description="[Deprecated] Return period in years in the case of an acute hazard.",
     )
     index_values: Optional[Union[List[float], List[str]]] = Field(
         [],
@@ -100,7 +105,9 @@ class ExceedanceCurve(BaseModel):
     """General exceedance curve (e.g. hazazrd, impact)."""
 
     values: np.ndarray = Field(default_factory=lambda: np.zeros(10), description="")
-    exceed_probabilities: np.ndarray = Field(default_factory=lambda: np.zeros(10), description="")
+    exceed_probabilities: np.ndarray = Field(
+        default_factory=lambda: np.zeros(10), description=""
+    )
 
     class Config:
         arbitrary_types_allowed = True
@@ -110,7 +117,9 @@ class Distribution(BaseModel):
     """General exceedance curve (e.g. hazazrd, impact)."""
 
     bin_edges: np.ndarray = Field(default_factory=lambda: np.zeros(11), description="")
-    probabilities: np.ndarray = Field(default_factory=lambda: np.zeros(10), description="")
+    probabilities: np.ndarray = Field(
+        default_factory=lambda: np.zeros(10), description=""
+    )
 
     class Config:
         arbitrary_types_allowed = True
@@ -119,8 +128,12 @@ class Config:
 class HazardEventDistrib(BaseModel):
     """Intensity curve of an acute hazard."""
 
-    intensity_bin_edges: np.ndarray = Field(default_factory=lambda: np.zeros(10), description="")
-    probabilities: np.ndarray = Field(default_factory=lambda: np.zeros(10), description="")
+    intensity_bin_edges: np.ndarray = Field(
+        default_factory=lambda: np.zeros(10), description=""
+    )
+    probabilities: np.ndarray = Field(
+        default_factory=lambda: np.zeros(10), description=""
+    )
     path: List[str] = Field([], description="Path to the hazard indicator data source.")
 
     class Config:
@@ -139,7 +152,9 @@ class VulnerabilityCurve(BaseModel):
     intensity: List[float] = Field(...)
     intensity_units: str = Field(description="units of the intensity")
     impact_mean: List[float] = Field(description="mean impact (damage or disruption)")
-    impact_std: List[float] = Field(description="standard deviation of impact (damage or disruption)")
+    impact_std: List[float] = Field(
+        description="standard deviation of impact (damage or disruption)"
+    )
 
     class Config:
         arbitrary_types_allowed = True
@@ -154,9 +169,15 @@ class VulnerabilityCurves(BaseModel):
 class VulnerabilityDistrib(BaseModel):
     """Defines a vulnerability matrix."""
 
-    intensity_bin_edges: np.ndarray = Field(default_factory=lambda: np.zeros(10), description="")
-    impact_bin_edges: np.ndarray = Field(default_factory=lambda: np.zeros(10), description="")
-    prob_matrix: np.ndarray = Field(default_factory=lambda: np.zeros(10), description="")
+    intensity_bin_edges: np.ndarray = Field(
+        default_factory=lambda: np.zeros(10), description=""
+    )
+    impact_bin_edges: np.ndarray = Field(
+        default_factory=lambda: np.zeros(10), description=""
+    )
+    prob_matrix: np.ndarray = Field(
+        default_factory=lambda: np.zeros(10), description=""
+    )
 
     class Config:
         arbitrary_types_allowed = True

src/physrisk/api/v1/exposure_req_resp.py

@@ -11,7 +11,8 @@ class AssetExposureRequest(BaseModel):
 
     assets: Assets
     calc_settings: CalcSettings = Field(
-        default_factory=CalcSettings, description="Interpolation method."  # type:ignore
+        default_factory=CalcSettings,
+        description="Interpolation method.",  # type:ignore
     )
     scenario: str = Field("rcp8p5", description="Name of scenario ('rcp8p5')")
     year: int = Field(
@@ -29,7 +30,9 @@ class AssetExposureRequest(BaseModel):
 class Exposure(BaseModel):
     category: str
     value: Optional[float]
-    path: str = Field("unknown", description="Path to the hazard indicator data source.")
+    path: str = Field(
+        "unknown", description="Path to the hazard indicator data source."
+    )
 
 
 class AssetExposure(BaseModel):
@@ -40,7 +43,9 @@ class AssetExposure(BaseModel):
         description="""Asset identifier; will appear if provided in the request
         otherwise order of assets in response is identical to order of assets in request.""",
     )
-    exposures: Dict[str, Exposure] = Field({}, description="Category (value) for each hazard type (key).")
+    exposures: Dict[str, Exposure] = Field(
+        {}, description="Category (value) for each hazard type (key)."
+    )
 
 
 class AssetExposureResponse(BaseModel):