🧰👌 Switch tooling to ruff (#197)

This PR updates the tooling to use [ruff](https://github.com/astral-sh/ruff) instead of multiple tools Have a look at the [ruff docs for an explanation of all the rules](https://beta.ruff.rs/docs/rules/) ### Change summary - 🧰✨ Added docformatter to pre-commit - 🧹 Formatted docstrings - 🧰👌 Replaced darglint with pydoclint - 🩹 Fixed docstring issues - 🧰✨ Added actionlint to pre-commit - 🧰👌 Replaced flake8 with ruff - 👌 Activated D ruff rule and fixed violations - 👌 Fix E741 (Ambiguous variable name: l) Error - 👌 Activated YTT, BLE, C4, T10, FA, ISC, INP, PIE, RSE, RET, ARG, PTH,… - 👌 Activated RUF ruff rule and fixed violations - 👌 Activated ERA ruff rule and fixed violations - 👌 Activated EM ruff rule and fixed violations - 👌 Activated PD ruff rule and fixed violations - 👌 Activated SIM ruff rule and fixed violations - 👌 Activated TCH ruff rule and fixed violations - 👌 Activated T20 ruff rule and fixed violations - 👌 Activated PT ruff rule and fixed violations - 👌 Activated PGH ruff rule and fixed violations - 👌 Activated N ruff rule and fixed violations - 👌 Activated B ruff rule and fixed violations - 👌 Activated UP ruff rule, fixed violations and removed pyupgrade hook - 🧹 Removed yesqa hook since this is handeled by RUF007 - 🧰 Pin and update pydoclint - 🧹 Updated pre-commit config and fixed issues - 🧰⬆️ Update pydoclint from 0.0.10 to 0.0.16 and fixed issues - 🩹🧪 Fix exception test to use new typing syntax - 🧹 Use modern typing after rebase - 🧰⬆️ Update pre-commit config to use latest versions - 📚👌 Added ruff and isort badges to readme - 🚇 Add py311 to CI unittest matrix ### Checklist - [x] ✔️ Passing the tests (mandatory for all PR's)
glotaran · Aug 9, 2023 · 60b74fe · 60b74fe
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -85,7 +85,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest, macOS-latest]
-        python-version: ["3.10"]
+        python-version: ["3.10", "3.11"]
 
     steps:
       - name: Check out repo

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -15,19 +15,25 @@ repos:
       - id: fix-encoding-pragma
         args: [--remove]
 
+  - repo: https://github.com/PyCQA/docformatter
+    rev: v1.7.5
+    hooks:
+      - id: docformatter
+        additional_dependencies: [tomli]
+        args: [--in-place, --config, ./pyproject.toml]
+
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: "0.13.0"
+    hooks:
+      - id: pyproject-fmt
+
   - repo: https://github.com/MarcoGorelli/absolufy-imports
     rev: v0.3.1
     hooks:
       - id: absolufy-imports
 
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.8.0
-    hooks:
-      - id: pyupgrade
-        args: [--py38-plus]
-
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 23.7.0
     hooks:
       - id: black
         language_version: python3
@@ -38,19 +44,13 @@ repos:
       - id: isort
         minimum_pre_commit_version: 2.9.0
 
-  - repo: https://github.com/asottile/yesqa
-    rev: v1.5.0
-    hooks:
-      - id: yesqa
-        additional_dependencies: [flake8-docstrings, darglint==1.8.0]
-
   - repo: https://github.com/asottile/setup-cfg-fmt
     rev: v2.4.0
     hooks:
       - id: setup-cfg-fmt
 
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0-alpha.9-for-vscode # Use the sha or tag you want to point at
+    rev: v3.0.1 # Use the sha or tag you want to point at
     hooks:
       - id: prettier
 
@@ -65,15 +65,15 @@ repos:
     rev: 1.7.0
     hooks:
       - id: nbqa-black
-        additional_dependencies: [black==22.6.0]
+        additional_dependencies: [black==23.7.0]
         args: [--nbqa-mutate]
       - id: nbqa-pyupgrade
         additional_dependencies: [pyupgrade==2.37.2]
         args: [--nbqa-mutate, --py38-plus]
       - id: nbqa-flake8
       - id: nbqa-check-ast
       - id: nbqa-isort
-        additional_dependencies: [isort==5.10.1]
+        additional_dependencies: [isort==5.12.0]
         args: [--nbqa-mutate]
 
   # Linters
@@ -93,23 +93,27 @@ repos:
         pass_filenames: false
         additional_dependencies: [click<8]
 
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.0.282
     hooks:
-      - id: flake8
-        args:
-          - "--max-line-length=99"
+      - id: ruff
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+    rev: 6.1.0
     hooks:
       - id: flake8
         alias: flake8-docs
         args:
-          - "--select=D,DAR"
+          - "--select=DOC"
+          - "--extend-ignore=DOC502"
+          - "--color=always"
+          - "--require-return-section-when-returning-none=False"
+          - "--allow-init-docstring=True"
+          - "--skip-checking-short-docstrings=False"
         name: "flake8 lint docstrings"
         exclude: "^(docs/|setup.py$|tests?/)"
-        additional_dependencies: [flake8-docstrings, darglint==1.8.0]
+        additional_dependencies: [pydoclint==0.1.4]
 
   - repo: https://github.com/rstcheck/rstcheck
     rev: "v6.1.2"
@@ -130,3 +134,8 @@ repos:
         types: [file]
         types_or: [python, pyi, markdown, rst, jupyter]
         args: ["--ignore-words-list=doas"]
+
+  - repo: https://github.com/rhysd/actionlint
+    rev: "v1.6.25"
+    hooks:
+      - id: actionlint
diff --git a/README.md b/README.md
@@ -6,8 +6,10 @@
 [![Documentation Status](https://readthedocs.org/projects/pyglotaran-extras/badge/?version=latest)](https://pyglotaran-extras.readthedocs.io/en/latest/?badge=latest)
 [![Binder](https://static.mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/glotaran/pyglotaran-extras.git/main?urlpath=lab%2Ftree%2Fdocs%2Fsource%2Fnotebooks)
 
-[![codecov](https://codecov.io/gh/glotaran/pyglotaran-extras/branch/main/graph/badge.svg?token=I6F412Y390)](https://codecov.io/gh/glotaran/pyglotaran-extras)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![Code style Python: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
+[![codecov](https://codecov.io/gh/glotaran/pyglotaran-extras/branch/main/graph/badge.svg?token=I6F412Y390)](https://codecov.io/gh/glotaran/pyglotaran-extras)
 [![Discord](https://img.shields.io/discord/883443835135475753.svg?label=&logo=discord&logoColor=ffffff&color=7389D8&labelColor=6A7EC2)](https://discord.gg/KfnEYRSTJx)
 
 Supplementary package for pyglotaran with (example) plotting code for use with the pyglotaran package.

diff --git a/pyglotaran_extras/deprecation/deprecation_utils.py b/pyglotaran_extras/deprecation/deprecation_utils.py
@@ -10,7 +10,7 @@
 )
 
 
-class OverDueDeprecation(Exception):
+class OverDueDeprecationError(Exception):
     """Error thrown when a deprecation should have been removed.
 
     See Also
@@ -104,11 +104,12 @@ def check_overdue(deprecated_qual_name_usage: str, to_be_removed_in_version: str
         parse_version(pyglotaran_extras_version()) >= parse_version(to_be_removed_in_version)
         and "dev" not in pyglotaran_extras_version()
     ):
-        raise OverDueDeprecation(
-            f"Support for {deprecated_qual_name_usage.partition('(')[0]!r} was "
-            f"supposed to be dropped in version: {to_be_removed_in_version!r}.\n"
+        msg = (
+            f"Support for {deprecated_qual_name_usage.partition('(')[0]!r} "
+            f"was supposed to be dropped in version: {to_be_removed_in_version!r}.\n"
             f"Current version is: {pyglotaran_extras_version()!r}"
         )
+        raise OverDueDeprecationError(msg)
 
 
 def warn_deprecated(
@@ -133,16 +134,13 @@ def warn_deprecated(
     to_be_removed_in_version : str
         Version the support for this usage will be removed.
 
-    stacklevel: int
+    stacklevel : int
         Stack at which the warning should be shown as raise. Default: 2
 
     Raises
     ------
     OverDueDeprecation
         If the current version is greater or equal to ``to_be_removed_in_version``.
-
-
-    -- noqa: DAR402
     """
     check_overdue(deprecated_qual_name_usage, to_be_removed_in_version)
     warn(

diff --git a/pyglotaran_extras/inspect/a_matrix.py b/pyglotaran_extras/inspect/a_matrix.py
@@ -2,16 +2,21 @@
 
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import numpy as np
-import xarray as xr
 from glotaran.utils.ipython import MarkdownStr
 from tabulate import tabulate
 
 from pyglotaran_extras.inspect.utils import pretty_format_numerical
 from pyglotaran_extras.inspect.utils import pretty_format_numerical_iterable
 from pyglotaran_extras.inspect.utils import wrap_in_details_tag
 from pyglotaran_extras.io.utils import result_dataset_mapping
-from pyglotaran_extras.types import ResultLike
+
+if TYPE_CHECKING:
+    import xarray as xr
+
+    from pyglotaran_extras.types import ResultLike
 
 
 def a_matrix_to_html_table(
@@ -25,26 +30,26 @@ def a_matrix_to_html_table(
 
     Parameters
     ----------
-    a_matrix: xr.DataArray
+    a_matrix : xr.DataArray
         DataArray containing the a-matrix values and coordinates.
-    megacomplex_suffix: str
+    megacomplex_suffix : str
         Megacomplex suffix used for the a-matrix data variable and coordinate names.
-    normalize_initial_concentration: bool
+    normalize_initial_concentration : bool
         Whether or not to normalize the initial concentration. Defaults to False.
-    decimal_places: int
+    decimal_places : int
         Decimal places to display. Defaults to 3.
 
     Returns
     -------
     str
         Multi header HTML table representing the a-matrix.
     """
-    species = a_matrix.coords[f"species_{megacomplex_suffix}"].values
+    species = a_matrix.coords[f"species_{megacomplex_suffix}"].to_numpy()
     # Crete a copy so normalization does not mutate the original values
     initial_concentration = np.array(
-        a_matrix.coords[f"initial_concentration_{megacomplex_suffix}"].values
+        a_matrix.coords[f"initial_concentration_{megacomplex_suffix}"].to_numpy()
     )
-    lifetime = a_matrix.coords[f"lifetime_{megacomplex_suffix}"].values
+    lifetime = a_matrix.coords[f"lifetime_{megacomplex_suffix}"].to_numpy()
 
     if normalize_initial_concentration is True:
         initial_concentration /= initial_concentration.sum()
@@ -53,7 +58,7 @@ def a_matrix_to_html_table(
         ["species<br>initial concentration<br>lifetime↓"]
         + [
             f"{sp}<br>{pretty_format_numerical(ic,decimal_places)}<br>&nbsp;"
-            for sp, ic in zip(species, initial_concentration)
+            for sp, ic in zip(species, initial_concentration, strict=True)
         ]
         + ["Sum"]
     )
@@ -62,11 +67,11 @@ def a_matrix_to_html_table(
         pretty_format_numerical_iterable(
             (lifetime, *amps, amps.sum()), decimal_places=decimal_places
         )
-        for lifetime, amps in zip(lifetime, a_matrix.values)
+        for lifetime, amps in zip(lifetime, a_matrix.values, strict=True)
     ]
     data.append(
         pretty_format_numerical_iterable(
-            ("Sum", *a_matrix.values.sum(axis=0), a_matrix.values.sum()),
+            ("Sum", *a_matrix.to_numpy().sum(axis=0), a_matrix.to_numpy().sum()),
             decimal_places=decimal_places,
         )
     )
@@ -96,18 +101,18 @@ def show_a_matrixes(
 
     Parameters
     ----------
-    result: ResultLike
+    result : ResultLike
         Result or result dataset.
-    normalize_initial_concentration: bool
+    normalize_initial_concentration : bool
         Whether or not to normalize the initial concentration. Defaults to False.
-    decimal_places: int
+    decimal_places : int
         Decimal places to display. Defaults to 3.
-    a_matrix_min_size: int
+    a_matrix_min_size : int | None
         Defaults to None.
-    expanded_datasets: tuple[str, ...]
+    expanded_datasets : tuple[str, ...]
         Names of dataset to expand the details view for. Defaults to empty tuple () which means no
         dataset is expanded.
-    heading_offset: int
+    heading_offset : int
         Number of heading level to offset the headings. Defaults to 2 which means that the
         first/top most heading is h3.
 

diff --git a/pyglotaran_extras/inspect/utils.py b/pyglotaran_extras/inspect/utils.py
@@ -2,11 +2,14 @@
 
 from __future__ import annotations
 
-from collections.abc import Generator
-from collections.abc import Iterable
+from typing import TYPE_CHECKING
 
 import numpy as np
 
+if TYPE_CHECKING:
+    from collections.abc import Generator
+    from collections.abc import Iterable
+
 
 def wrap_in_details_tag(
     details_content: str,
@@ -19,13 +22,13 @@ def wrap_in_details_tag(
 
     Parameters
     ----------
-    details_content: str
+    details_content : str
         Markdown string that should be displayed when the details are expanded.
-    summary_content: str | None
+    summary_content : str | None
         Summary test that should be displayed. Defaults to None so the summary is ``Details``.
-    summary_heading_level: int | None
+    summary_heading_level : int | None
         Level of the heading wrapping the ``summary`` if it is not None. Defaults to None.
-    is_open: bool
+    is_open : bool
         Whether or not the details tag should be initially opened. Defaults to False.
 
     Returns
@@ -55,14 +58,14 @@ def pretty_format_numerical(value: float | int, decimal_places: int = 1) -> str:
 
     Used to format values like the t-value.
 
-    TODO: remove after raise pyglotaran dependency to 0.7.0
+    TODO : remove after raise pyglotaran dependency to 0.7.0
     Forward port of https://github.com/glotaran/pyglotaran/pull/1192
 
     Parameters
     ----------
-    value: float | int
+    value : float | int
         Numerical value to format.
-    decimal_places: int
+    decimal_places : int
         Decimal places to display. Defaults to 1.
 
     Returns
@@ -93,9 +96,9 @@ def pretty_format_numerical_iterable(
 
     Parameters
     ----------
-    input_values: Iterable[str  |  float]
+    input_values : Iterable[str | float]
         Values that should be formatted.
-    decimal_places: int | None
+    decimal_places : int | None
         Number of decimal places a value should have, if None the original value will be used.
         Defaults to 3.
 

diff --git a/pyglotaran_extras/io/load_data.py b/pyglotaran_extras/io/load_data.py
@@ -20,10 +20,10 @@ def load_data(
     ----------
     result : DatasetConvertible | Result
         Result class instance, xarray Dataset or path to a dataset file.
-    dataset_name : str, optional
+    dataset_name : str | None
         Name of a specific dataset contained in ``result``, if not provided
         the first dataset will be extracted. Defaults to None.
-    _stacklevel: int
+    _stacklevel : int
         Stacklevel of the warning which is raised when ``result`` is of class ``Result``,
         contains multiple datasets and no ``dataset_name`` is provided. Changing this value is
         only required if you use this function inside of another function. Defaults to 2
@@ -56,6 +56,7 @@ def load_data(
                 stacklevel=_stacklevel,
             )
         return result.data[keys[0]]
-    if isinstance(result, (str, Path)):
+    if isinstance(result, str | Path):
         return load_data(load_dataset(result))
-    raise TypeError(f"Result needs to be of type {DatasetConvertible!r}, but was {result!r}.")
+    msg = f"Result needs to be of type {DatasetConvertible!r}, but was {result!r}."
+    raise TypeError(msg)