ci: improve tests_local workflow (#103)

* ci: improve tests_local workflow

* ci: switch license checking framework

* ci: Switch from pydocstyle to ruff to check docstrings

* ci: change name of coverage report artifact

.github/workflows/tests_local.yml

@@ -2,6 +2,8 @@
 name: tests_local
 
 on:
+  schedule:
+    - cron: '0 1 * * *'
   pull_request:
   push:
     branches:
@@ -37,19 +39,50 @@ jobs:
         uses: ./.github/actions/create_python_environment
       - name: Get Python package manager
         run: echo "PYTHON_PACKAGE_MANAGER=${{steps.environment.outputs.ppm}}" >> $GITHUB_ENV
-      - name: Codechecks
+      - name: Code checks
         run: |
           $PYTHON_PACKAGE_MANAGER activate queens
-          isort --check-only queens tests > track_isort.txt 2>&1
-          black --check queens tests > track_black.txt 2>&1
-          pylint --rcfile=.pylintrc_ci queens tests | tee track_pylint.txt 2>&1
-          pylint queens tests --rcfile=.pylintrc --output-format=json:pylint_warnings.json --fail-under 0
-          python .gitlab/pipeline_utils/code_quality_creator.py pylint_warnings.json
-          pydocstyle --match-dir='^(?!.*test).*$' queens > track_pydocstyle.txt 2>&1
+
+          echo "::group::Run isort..."
+          isort --check-only queens tests
+          echo "::endgroup::"
+
+          echo "::group::Run black..."
+          black --check queens tests
+          echo "::endgroup::"
+
+          echo "::group::Run pylint..."
+          pylint --rcfile=.pylintrc_ci queens tests
+          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
+          # echo "::endgroup::"
+
+          echo "::group::Check compatibility with licenses of dependencies..."
+          liccheck -r requirements.txt
+          echo "::endgroup::"
+
+          echo "::group::Create an rc file for the license header check..."
+          python .gitlab/pipeline_utils/create_licenserc.py --template_file ".gitlab/pipeline_utils/.licenserc_template.yaml" --text_file "license_header.tmpl" --output_file ".licenserc.yaml" --placeholder "license_header"
+          echo "::endgroup::"
+      - name: Check License headers
+        uses: apache/skywalking-eyes/[email protected]
       - name: Run pytest
         run: |
           $PYTHON_PACKAGE_MANAGER activate queens
           pytest -v -m "unit_tests or integration_tests or integration_tests_fourc" --cov --cov-report=term --cov-report=html:html_coverage_report --cov-report=xml:xml_coverage_report.xml $TEST_TIMING_OPTION --color=yes -o junit_logging=all --junitxml=test_junit.xml
+      - name: Upload coverage report
+        uses: actions/upload-pages-artifact@v3
+        with:
+          name: html-coverage-report
+          path: html_coverage_report/
+          retention-days: 7
       - name: Publish junit pytest report
         uses: mikepenz/action-junit-report@v5
         if: success() || failure() # always run even if the previous step fails

.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 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'
@@ -92,3 +94,57 @@ show_missing = false
 
 [tool.coverage.html]
 directory = "html_coverage_report"
+
+[tool.liccheck]
+authorized_licenses = [
+        "apache",
+        "apache 2.0",
+        "Apache-2.0",
+        "apache software license",
+        "apache license, version 2.0",
+        "apache license version 2.0",
+        "apache license 2.0",
+        "apache software",
+        "bsd",
+        "new bsd",
+        "bsd license",
+        "new bsd license",
+        "3-clause bsd",
+        "BSD 3-Clause",
+        "BSD-3-Clause",
+        "simplified bsd",
+        "CMU License (MIT-CMU)",
+        "gnu lgpl",
+        "GNU Library or Lesser General Public License (LGPL)",
+        "lgpl",
+        "historical permission notice and disclaimer (hpnd)",
+        "isc",
+        "isc license",
+        "isc license (iscl)",
+        "mit",
+        "mit license",
+        "mozilla public license 2.0",
+        "mozilla public license 2.0 (mpl 2.0)",
+        "python software foundation",
+        "python software foundation license",
+        "University of Illinois/NCSA Open Source",
+        "zlib/libpng",
+]
+unauthorized_licenses = [
+        "gpl v3",
+        "gpl v2",
+        "gpl",
+        "GNU general public license (gpl)",
+        "IBM Public License",
+        "RPL",
+        "Reciprocal Public License",
+        "Sleepycat License",
+]
+[tool.liccheck.authorized_packages]
+# filelock has public domain license without restrictions
+# see https://github.com/tox-dev/py-filelock
+filelock = ">=3"
+# cons is under LGPL-3
+cons = ">=0.4.5"
+# namex is under Apache 2.0 see https://github.com/fchollet/namex?tab=License-1-ov-file
+namex = "==0.0.8"

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.
 #
@@ -445,6 +445,7 @@ 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 +489,7 @@ 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.
 #
@@ -1153,7 +1153,7 @@ 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

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.
 #
@@ -397,6 +397,7 @@ 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 +455,7 @@ 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.