ci: Switch from pydocstyle to ruff to check docstrings

.github/workflows/tests_local.yml

@@ -53,12 +53,15 @@ jobs:
 
           echo "::group::Run pylint..."
           pylint --rcfile=.pylintrc_ci queens tests
-          # pylint queens tests --rcfile=.pylintrc --output-format=json:pylint_warnings.json --fail-under 0
+          echo "::endgroup::"
+
+          echo "::group::Run ruff..."
+          ruff check
           echo "::endgroup::"
 
           # echo "::group::Create code quality report..."
+          # pylint queens tests --rcfile=.pylintrc --output-format=json:pylint_warnings.json --fail-under 0
           # python .gitlab/pipeline_utils/code_quality_creator.py pylint_warnings.json
-          # pydocstyle --match-dir='^(?!.*test).*$' queens
           # echo "::endgroup::"
 
           echo "::group::Check compatibility with licenses of dependencies..."

.gitlab/pipeline_utils/update_changelog.py

@@ -1,6 +1,6 @@
 #
 # SPDX-License-Identifier: LGPL-3.0-or-later
-# Copyright (c) 2024, QUEENS contributors.
+# Copyright (c) 2025, QUEENS contributors.
 #
 # This file is part of QUEENS.
 #
@@ -17,7 +17,7 @@
 import sys
 from pathlib import Path
 
-import gitlab
+import gitlab  # pylint: disable=import-error
 
 CHANGE_KEY = "change:"
 
@@ -28,6 +28,7 @@ def create_section(name, link, date, message, header_symbol, newline=True):
     Args:
         name (str): Name of the tag
         link (str): Link of the tag
+        date (obj): Date of the tag
         message (str): Tag message
         header_symbol (str): Symbol of the section
         newline (bool): Add newline after the section name

.pre-commit-config.yaml

@@ -1,5 +1,12 @@
 default_stages: [pre-commit, pre-merge-commit, pre-push, manual]
 repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.2 # Ruff version
+    hooks:
+      # Run the linter.
+      # Needs to placed before ruff formatter, black, isort and other formatters
+      - id: ruff
+        args: [ --fix ]
   - repo: local
     hooks:
       - id: trailing-whitespace
@@ -24,12 +31,6 @@ repos:
         language: python
         types: ["python"]
         pass_filenames: true
-      - id: pydocstyle
-        name: pydocstyle
-        entry: pydocstyle
-        language: python
-        types: ["python"]
-        additional_dependencies: ["toml"]
       - id: docformatter
         name: docformatter
         entry: docformatter

CONTRIBUTING.md

@@ -52,7 +52,7 @@ will lead to failing CI pipelines and will therefore not be merged.
 The code checks are conducted with [Pylint](https://pylint.org/),
 [isort](https://github.com/PyCQA/isort), and [Black](https://github.com/psf/black).
 Compliance with [Google style docstrings](https://github.com/google/styleguide/blob/gh-pages/pyguide.md#38-comments-and-docstrings)
-is checked with [pydocstyle](https://github.com/PyCQA/pydocstyle).
+is checked with [ruff](https://github.com/astral-sh/ruff).
 Complete and meaningful docstrings are required as they are used to generate the
 [documentation](#reading-and-writing-documentation).
 

dev-requirements.in

@@ -17,6 +17,6 @@ pydata-sphinx-theme
 pandoc
 pip-tools
 commitizen>=3.12.0
-pydocstyle>=6.3.0
 docformatter>=1.5.1
 yamllint>=1.19.0
+ruff

dev-requirements.txt

@@ -165,8 +165,6 @@ prompt-toolkit==3.0.36
     # via questionary
 pydata-sphinx-theme==0.16.0
     # via -r dev-requirements.in
-pydocstyle==6.3.0
-    # via -r dev-requirements.in
 pygments==2.18.0
     # via
     #   -c requirements.txt
@@ -214,6 +212,8 @@ ruamel-yaml==0.18.6
     # via pre-commit-hooks
 ruamel-yaml-clib==0.2.12
     # via ruamel-yaml
+ruff==0.9.2
+    # via -r dev-requirements.in
 semantic-version==2.10.0
     # via liccheck
 six==1.16.0
@@ -222,9 +222,7 @@ six==1.16.0
     #   bleach
     #   python-dateutil
 snowballstemmer==2.2.0
-    # via
-    #   pydocstyle
-    #   sphinx
+    # via sphinx
 soupsieve==2.6
     # via beautifulsoup4
 sphinx==8.1.3

pyproject.toml

@@ -58,10 +58,12 @@ force_grid_wrap = 0
 multi_line_output = 3
 include_trailing_comma = true
 
-[tool.pydocstyle]
+[tool.ruff.lint]
+select = ["D"] # pydocstyle rules
+ignore = ["D104"] # Missing docstring in public package
+
+[tool.ruff.lint.pydocstyle]
 convention = "google"
-match-dir = '(?!tests).*'
-match = '(?!__init__).*\.py'
 
 [tool.pytest.ini_options]
 addopts = '-m "not benchmark and not lnm_cluster and not imcs_cluster" --doctest-modules --doctest-continue-on-failure --doctest-ignore-import-errors'

queens/data_processor/data_processor_ensight.py

@@ -1,6 +1,6 @@
 #
 # SPDX-License-Identifier: LGPL-3.0-or-later
-# Copyright (c) 2024, QUEENS contributors.
+# Copyright (c) 2025, QUEENS contributors.
 #
 # This file is part of QUEENS.
 #
@@ -176,7 +176,11 @@ def _check_field_specification_dict(file_options_dict):
             file_options_dict (dict): Dictionary containing the field description for the
                                       physical fields of interest that should be read-in.
         """
-        required_keys_lst = ["target_time_lst", "physical_field_dict", "geometric_target"]
+        required_keys_lst = [
+            "target_time_lst",
+            "physical_field_dict",
+            "geometric_target",
+        ]
         if not set(required_keys_lst).issubset(set(file_options_dict.keys())):
             raise KeyError(
                 "The option 'file_options_dict' within the data_processor section must at least "
@@ -445,6 +449,7 @@ def _vtk_from_ensight(self, raw_data, target_time):
         """Load a vtk-object from the ensight file.
 
         Args:
+            raw_data (obj): Raw data from file
             target_time (float): Time the field should be evaluated on
 
         Returns:
@@ -488,7 +493,7 @@ def read_geometry_coordinates(external_geometry):
         This method uses the QUEENS external geometry module.
 
         Args:
-            external_geometry_obj (queens.fourc_dat_geometry)
+            external_geometry (queens.fourc_dat_geometry): QUEENS external geometry object
 
         Returns:
             dict: set with 4C topology

queens/data_processor/data_processor_ensight_interface.py

@@ -1,6 +1,6 @@
 #
 # SPDX-License-Identifier: LGPL-3.0-or-later
-# Copyright (c) 2024, QUEENS contributors.
+# Copyright (c) 2025, QUEENS contributors.
 #
 # This file is part of QUEENS.
 #
@@ -442,6 +442,7 @@ def deformed_grid(self, raw_data, time):
         such that the final result is the deformed grid at the specified time.
 
         Args:
+            raw_data (obj): Raw data from file
             time (float): Time value for data processing
 
         Returns:

queens/external_geometry/fourc_dat_geometry.py

@@ -1,6 +1,6 @@
 #
 # SPDX-License-Identifier: LGPL-3.0-or-later
-# Copyright (c) 2024, QUEENS contributors.
+# Copyright (c) 2025, QUEENS contributors.
 #
 # This file is part of QUEENS.
 #
@@ -477,7 +477,10 @@ def _sort_node_coordinates(self):
         self.node_coordinates["coordinates"] = [
             coord
             for _, coord in sorted(
-                zip(self.node_coordinates["node_mesh"], self.node_coordinates["coordinates"]),
+                zip(
+                    self.node_coordinates["node_mesh"],
+                    self.node_coordinates["coordinates"],
+                ),
                 key=lambda pair: pair[0],
             )
         ]
@@ -713,7 +716,9 @@ def _write_elementwise_materials(self, line, random_field_lst):
             material_fields[0]["name"] + "_" + str(i) for i in range(len(self.element_centers))
         ]
         self._write_coords_to_dict(
-            material_fields[0]["name"], material_field_placeholders, np.array(self.element_centers)
+            material_fields[0]["name"],
+            material_field_placeholders,
+            np.array(self.element_centers),
         )
 
         # check if the current material number is equal to base material and rewrite the base
@@ -899,7 +904,15 @@ def _write_design_point_dirichlet_conditions(self, random_field_lst, line):
                 )
 
                 # write the new fields to the dat file --------------------------------------------
-                for topo_node, random_field_1, random_field_2, random_field_3, f1, f2, f3 in zip(
+                for (
+                    topo_node,
+                    random_field_1,
+                    random_field_2,
+                    random_field_3,
+                    f1,
+                    f2,
+                    f3,
+                ) in zip(
                     node_set["topo_dnodes"],
                     realized_random_field_1,
                     realized_random_field_2,
@@ -1016,7 +1029,9 @@ def _assign_random_dirichlet_fields_per_geo_set(self, fields_dirich_on_geo_set):
                 fun_3 = dirich_field["funct_for_field"] * np.ones(set_shape)
 
             self._write_coords_to_dict(
-                dirich_field["name"], placeholders, np.array(self.node_coordinates["coordinates"])
+                dirich_field["name"],
+                placeholders,
+                np.array(self.node_coordinates["coordinates"]),
             )
 
         return (
@@ -1153,7 +1168,7 @@ def _get_my_topology(self, geo_set_name_type):
         I.e.e its node mappings, based on the type of the geometric set.
 
         Args:
-            geo_set_name_type:
+            geo_set_name_type (str): Name of the geometric set type.
 
         Returns:
             my_topology (lst): List with desired geometric topology
@@ -1203,7 +1218,11 @@ def _create_new_node_sets(self, random_fields_lst):
             my_topology_lst = self._get_my_topology(topology_type)
             nodes_mesh_lst.extend(
                 [
-                    {"node_mesh": topo["node_mesh"], "topo_dnodes": [], "name": topology_name}
+                    {
+                        "node_mesh": topo["node_mesh"],
+                        "topo_dnodes": [],
+                        "name": topology_name,
+                    }
                     for topo in my_topology_lst
                     if topo["topology_name"] == topology_name
                 ]

queens/interfaces/bmfmc_interface.py

@@ -1,6 +1,6 @@
 #
 # SPDX-License-Identifier: LGPL-3.0-or-later
-# Copyright (c) 2024, QUEENS contributors.
+# Copyright (c) 2025, QUEENS contributors.
 #
 # This file is part of QUEENS.
 #
@@ -61,6 +61,8 @@ def evaluate(self, samples, support="y", full_cov=False, gradient_bool=False):
                            *support=f*  the Gaussian process predicts w.r.t. the latent function
                            *f*. For the choice of *support=y* we predict w.r.t. the
                            simulation/experimental output *y*
+            full_cov (bool): Boolean that specifies whether the entire posterior covariance matrix
+                             should be returned or only the posterior variance
             gradient_bool (bool): Flag to determine whether the gradient of the function at
                                   the evaluation point is expected (*True*) or not (*False*)
 

queens/iterators/bmfia_iterator.py

@@ -1,6 +1,6 @@
 #
 # SPDX-License-Identifier: LGPL-3.0-or-later
-# Copyright (c) 2024, QUEENS contributors.
+# Copyright (c) 2025, QUEENS contributors.
 #
 # This file is part of QUEENS.
 #
@@ -218,7 +218,9 @@ def core_run(self):
 
         # ----- Set the feature strategy of the probabilistic mapping (select gammas)
         self.Z_train = self.set_feature_strategy(
-            self.Y_LF_train, self.X_train, self.coords_experimental_data[: self.Y_LF_train.shape[0]]
+            self.Y_LF_train,
+            self.X_train,
+            self.coords_experimental_data[: self.Y_LF_train.shape[0]],
         )
 
         return self.Z_train, self.Y_HF_train
@@ -257,7 +259,9 @@ def expand_training_data(self, additional_x_train, additional_y_lf_train=None):
         _logger.info("Training data was successfully expanded!")
 
         self.Z_train = self.set_feature_strategy(
-            self.Y_LF_train, self.X_train, self.coords_experimental_data[: self.Y_LF_train.shape[0]]
+            self.Y_LF_train,
+            self.X_train,
+            self.coords_experimental_data[: self.Y_LF_train.shape[0]],
         )
 
         return self.Z_train, self.Y_HF_train
@@ -397,6 +401,7 @@ def _get_coord_features(self, _, y_lf_mat, coords_mat):
                               and colum-wise variable dimensions.
             y_lf_mat (np.array): Low-fidelity output matrix with row-wise model realizations.
                                  Columns are different dimensions of the output.
+            coords_mat (np.array): Coordinates matrix.
 
         Returns:
             z_mat (np.array): Extended low-fidelity matrix containing
@@ -454,7 +459,7 @@ def _get_no_features(self, _x_mat, y_lf_mat, __):
     def _get_time_features(self, _, y_lf_mat, __):
         """Get the low-fidelity feature matrix with time features.
 
-         Args:
+        Args:
             y_lf_mat (np.array): Low-fidelity output matrix with row-wise model realizations.
                                  Columns are different dimensions of the output.
 

queens/iterators/hmc_iterator.py

@@ -1,6 +1,6 @@
 #
 # SPDX-License-Identifier: LGPL-3.0-or-later
-# Copyright (c) 2024, QUEENS contributors.
+# Copyright (c) 2025, QUEENS contributors.
 #
 # This file is part of QUEENS.
 #
@@ -131,8 +131,6 @@ def __init__(
     def init_mcmc_method(self):
         """Init the PyMC MCMC Model.
 
-        Args:
-
         Returns:
             step (obj): The MCMC Method within the PyMC Model
         """

queens/iterators/metropolis_hastings_pymc_iterator.py

@@ -1,6 +1,6 @@
 #
 # SPDX-License-Identifier: LGPL-3.0-or-later
-# Copyright (c) 2024, QUEENS contributors.
+# Copyright (c) 2025, QUEENS contributors.
 #
 # This file is part of QUEENS.
 #
@@ -168,8 +168,6 @@ def eval_log_likelihood_grad(self, samples):
     def init_mcmc_method(self):
         """Init the PyMC MCMC Model.
 
-        Args:
-
         Returns:
             step (obj): The MCMC Method within the PyMC Model
         """

queens/iterators/pymc_iterator.py

@@ -1,6 +1,6 @@
 #
 # SPDX-License-Identifier: LGPL-3.0-or-later
-# Copyright (c) 2024, QUEENS contributors.
+# Copyright (c) 2025, QUEENS contributors.
 #
 # This file is part of QUEENS.
 #
@@ -157,7 +157,7 @@ def __init__(
     def eval_log_prior(self, samples):
         """Evaluate natural logarithm of prior at samples of chains.
 
-         Args:
+        Args:
             samples (np.array): Samples to evaluate the prior at
 
         Returns:
@@ -328,7 +328,11 @@ def post_run(self):
         # process output takes a dict as input with key 'mean'
         results_dict = az.convert_to_inference_data(inference_data_dict)
         results = process_outputs(
-            {"sample_stats": sample_stats, "result": self.chains, "inference_data": results_dict},
+            {
+                "sample_stats": sample_stats,
+                "result": self.chains,
+                "inference_data": results_dict,
+            },
             self.result_description,
         )
         if self.result_description["write_results"]: