Update and apply Pre-Commit hooks (#134)

Author: btschwertfeger

.pre-commit-config.yaml

@@ -1,17 +1,20 @@
+# -*- coding: utf-8 -*-
+# Copyright (C) 2023 Benjamin Thomas Schwertfeger
+# GitHub: https://github.com/btschwertfeger
+#
+
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.9
+    rev: v0.7.0
     hooks:
       - id: ruff
-        args: [--fix]
+        args:
+          - --fix
+          - --preview
+          - --exit-non-zero-on-fix
       - id: ruff-format
-  - repo: https://github.com/pycqa/flake8
-    rev: 7.1.0
-    hooks:
-      - id: flake8
-        args: ["--select=E9,F63,F7,F82", "--show-source", "--statistics"]
   # - repo: https://github.com/pre-commit/mirrors-mypy # FIXME
-  #   rev: v1.8.0
+  #   rev: v1.13.0
   #   hooks:
   #     - id: mypy
   #       name: mypy
@@ -23,14 +26,14 @@ repos:
     rev: v2.3.0
     hooks:
       - id: codespell
-        additional_dependencies:
-          - tomli
+        additional_dependencies: [tomli]
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0
     hooks:
       # all available hooks can be found here: https://github.com/pre-commit/pre-commit-hooks/blob/main/.pre-commit-hooks.yaml
       - id: check-yaml
       - id: check-ast
+      - id: check-json
       - id: check-toml
       - id: check-docstring-first
       - id: check-case-conflict
@@ -53,26 +56,32 @@ repos:
     rev: v1.10.0
     hooks:
       - id: python-use-type-annotations
+      - id: python-check-blanket-noqa
+      - id: python-check-blanket-type-ignore
+      - id: python-check-mock-methods
+      - id: rst-backticks
+      - id: python-no-eval
+      - id: python-no-log-warn
       - id: rst-backticks
-      # - id: rst-inline-touching-normal
+      - id: rst-inline-touching-normal
       - id: rst-directive-colons
       - id: text-unicode-replacement-char
-  # - repo: https://github.com/psf/black
-  #   rev: 24.2.0
-  #   hooks:
-  #     - id: black
-  # - repo: https://github.com/adamchainz/blacken-docs
-  #   rev: 1.16.0
-  #   hooks:
-  #     - id: blacken-docs
-  #       additional_dependencies: [black==23.12.0]
   - repo: https://github.com/PyCQA/isort # TODO: remove as soon as ruff is stable
     rev: 5.13.2
     hooks:
       - id: isort
-        args: ["--profile=black"] # solves conflicts between black and isort
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.2
+        args: [--profile=black]
+  - repo: https://github.com/PyCQA/bandit
+    rev: 1.7.10
+    hooks:
+      - id: bandit
+        exclude: "^tests/.*|examples/.*"
+  - repo: https://github.com/yunojuno/pre-commit-xenon
+    rev: v0.1
     hooks:
-      - id: prettier
+      - id: xenon
+        args:
+          - --max-average=B
+          - --max-modules=B
+          - --max-absolute=C
 exclude: '\.nc$|^tests/fixture/|\.ipynb$'

README.md

@@ -293,11 +293,13 @@ Notes:
 
 - First check if there is an existing issue or PR that addresses your
   problem/solution. If not - create one first - before creating a PR.
-- Typo fixes, project configuration, CI, documentation or style/formatting PRs will be
-  rejected. Please create an issue for that.
+- Typo fixes, project configuration, CI, documentation or style/formatting PRs
+  will be rejected. Please create an issue for that.
 - PRs must provide a reasonable, easy to understand and maintain solution for an
   existing problem. You may want to propose a solution when creating the issue
   to discuss the approach before creating a PR.
+- There is currently no need for the implementation of further bias correction
+  methods.
 
 <a name="references"></a>
 

cmethods/__init__.py

@@ -53,7 +53,7 @@ def print_version(
     """Prints the version of the package"""
     if not value or ctx.resilient_parsing:
         return
-    from importlib.metadata import version
+    from importlib.metadata import version  # noqa: PLC0415
 
     echo(version("python-cmethods"))
     ctx.exit()

cmethods/core.py

@@ -144,7 +144,7 @@ def adjust(
     #       to unrealistic monthly transitions. If such behavior is wanted,
     #       mock this function or apply ``CMethods.__apply_ufunc` directly
     #       on your data sets.
-    if kwargs.get("group", None) is None:
+    if kwargs.get("group") is None:
         return apply_ufunc(method, obs, simh, simp, **kwargs).to_dataset()
 
     if method not in SCALING_METHODS:

cmethods/distribution.py

@@ -42,7 +42,7 @@ def quantile_mapping(
     """
     check_adjust_called(
         function_name="quantile_mapping",
-        adjust_called=kwargs.get("adjust_called", None),
+        adjust_called=kwargs.get("adjust_called"),
     )
     check_np_types(obs=obs, simh=simh, simp=simp)
 
@@ -73,7 +73,7 @@ def quantile_mapping(
             xbins,
             cdf_simh,
             left=kwargs.get("val_min", 0.0),
-            right=kwargs.get("val_max", None),
+            right=kwargs.get("val_max"),
         )
         return get_inverse_of_cdf(cdf_obs, epsilon, xbins)  # Eq. 2
 
@@ -157,7 +157,7 @@ def detrended_quantile_mapping(
                 xbins,
                 cdf_simh,
                 left=kwargs.get("val_min", 0.0),
-                right=kwargs.get("val_max", None),
+                right=kwargs.get("val_max"),
             )
             X = np.interp(epsilon, cdf_obs, xbins) * ensure_dividable(
                 m_simp_mean,
@@ -205,7 +205,7 @@ def quantile_delta_mapping(
     """
     check_adjust_called(
         function_name="quantile_delta_mapping",
-        adjust_called=kwargs.get("adjust_called", None),
+        adjust_called=kwargs.get("adjust_called"),
     )
     check_np_types(obs=obs, simh=simh, simp=simp)
 

cmethods/scaling.py

@@ -43,7 +43,7 @@ def linear_scaling(
     """
     check_adjust_called(
         function_name="linear_scaling",
-        adjust_called=kwargs.get("adjust_called", None),
+        adjust_called=kwargs.get("adjust_called"),
     )
     check_np_types(obs=obs, simh=simh, simp=simp)
 
@@ -85,7 +85,7 @@ def variance_scaling(
     """
     check_adjust_called(
         function_name="variance_scaling",
-        adjust_called=kwargs.get("adjust_called", None),
+        adjust_called=kwargs.get("adjust_called"),
     )
     check_np_types(obs=obs, simh=simp, simp=simp)
 
@@ -130,7 +130,7 @@ def delta_method(
     """
     check_adjust_called(
         function_name="delta_method",
-        adjust_called=kwargs.get("adjust_called", None),
+        adjust_called=kwargs.get("adjust_called"),
     )
     check_np_types(obs=obs, simh=simh, simp=simp)
 

cmethods/utils.py

@@ -32,7 +32,7 @@ def __init__(self: UnknownMethodError, method: str, available_methods: list):
 
 def check_adjust_called(
     function_name: str,
-    adjust_called: Optional[bool] = None,
+    adjust_called: Optional[bool] = None,  # noqa: FBT001
 ) -> None:
     """
     Displays a user warning in case a correction function was not called via

doc/conf.py

@@ -11,7 +11,9 @@
 """This module is the configuration for the Sphinx documentation building process"""
 
 import sys
+from os.path import join
 from pathlib import Path
+from shutil import copyfile
 
 project = "python-cmethods"
 copyright = "2023, Benjamin Thomas Schwertfeger"  # pylint: disable=redefined-builtin
@@ -29,9 +31,6 @@
 
 
 def setup(app) -> None:  # noqa: ARG001
-    from os.path import join
-    from shutil import copyfile
-
     copyfile(join("..", "examples", "examples.ipynb"), "examples.ipynb")
 
 

doc/methods.rst

@@ -92,7 +92,7 @@ where:
     >>> variable = "tas" # temperatures
     >>> result = adjust(
     ...     method="linear_scaling",
-    ...     obs=obs[variable],
+    ...     obs=obsh[variable],
     ...     simh=simh[variable],
     ...     simp=simp[variable],
     ...     kind="+",
@@ -173,7 +173,7 @@ enables the adjustment of the standard deviation in the following step.
     >>> variable = "tas" # temperatures
     >>> result = adjust(
     ...     method="variance_scaling",
-    ...     obs=obs[variable],
+    ...     obs=obsh[variable],
     ...     simh=simh[variable],
     ...     simp=simp[variable],
     ...     kind="+",
@@ -257,7 +257,7 @@ where:
     >>> variable = "tas" # temperatures
     >>> result = adjust(
     ...     method="delta_method",
-    ...     obs=obs[variable],
+    ...     obs=obsh[variable],
     ...     simh=simh[variable],
     ...     simp=simp[variable],
     ...     kind="+",
@@ -340,7 +340,7 @@ In the following the equations of Alex J. Cannon (2015) are shown and explained:
     >>> variable = "tas" # temperatures
     >>> qm_adjusted = adjust(
     ...     method="quantile_mapping",
-    ...     obs=obs[variable],
+    ...     obs=obsh[variable],
     ...     simh=simh[variable],
     ...     simp=simp[variable],
     ...     n_quantiles=250,
@@ -417,7 +417,7 @@ where:
     >>> simp = xr.open_dataset("path/to/the_dataset_to_adjust-scenario_period.nc")
     >>> variable = "tas" # temperatures
     >>> qm_adjusted = detrended_quantile_mapping(
-    ...     obs=obs[variable],
+    ...     obs=obsh[variable],
     ...     simh=simh[variable],
     ...     simp=simp[variable],
     ...     n_quantiles=250
@@ -520,7 +520,7 @@ following the additive and multiplicative variant are shown.
     >>> variable = "tas" # temperatures
     >>> qdm_adjusted = adjust(
     ...     method="quantile_delta_mapping",
-    ...     obs=obs[variable],
+    ...     obs=obsh[variable],
     ...     simh=simh[variable],
     ...     simp=simp[variable],
     ...     n_quantiles=250,

pyproject.toml

@@ -250,8 +250,11 @@ cache-dir = ".cache/ruff"
 lint.task-tags = ["todo", "TODO"]
 
 [tool.ruff.lint.per-file-ignores]
+"cmethods/types.py" = [
+  "A005", # Shadowing builtin
+]
 "doc/*.py" = [
-  "CPY001",  # Missing copyright notice at top of file
+  # "CPY001",  # Missing copyright notice at top of file
   "PTH118",  # `os.path.join()` should be replaced by `Path` with `/` operator,
   "PTH123",  # `open()` should be replaced by `Path.open()`
   "PTH100",  # `os.path.abspath()` should be replaced by `Path.resolve()`

tests/conftest.py

@@ -22,7 +22,7 @@
 FIXTURE_DIR: str = os.path.join(os.path.dirname(__file__), "fixture")
 
 
-@pytest.fixture()
+@pytest.fixture
 def cli_runner() -> CliRunner:
     """Provide a cli-runner for testing the CLI"""
     return CliRunner()
@@ -43,7 +43,7 @@ def dask_cluster() -> Any:
     client.close()
 
 
-@pytest.fixture()
+@pytest.fixture
 def datasets() -> dict:
     obsh_add, obsp_add, simh_add, simp_add = get_datasets(kind="+")
     obsh_mult, obsp_mult, simh_mult, simp_mult = get_datasets(kind="*")
@@ -65,7 +65,7 @@ def datasets() -> dict:
 
 
 @lru_cache(maxsize=None)
-@pytest.fixture()
+@pytest.fixture
 def datasets_from_zarr() -> dict:
     return {
         "+": {