Merge pull request #711 from hakonanes/licenseheaders-in-pre-commit

Update tooling

.github/dependabot.yml

@@ -0,0 +1,29 @@
+##
+## Copyright 2019-2025 the kikuchipy developers
+##
+## This file is part of kikuchipy.
+##
+## kikuchipy is free software: you can redistribute it and/or modify
+## it under the terms of the GNU General Public License as published by
+## the Free Software Foundation, either version 3 of the License, or
+## (at your option) any later version.
+##
+## kikuchipy is distributed in the hope that it will be useful,
+## but WITHOUT ANY WARRANTY; without even the implied warranty of
+## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+## GNU General Public License for more details.
+##
+## You should have received a copy of the GNU General Public License
+## along with kikuchipy.  If not, see <http://www.gnu.org/licenses/>.##
+
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/perhaps_make_tagged_release_draft.py

@@ -1,4 +1,5 @@
-# Copyright 2019-2024 The kikuchipy developers
+#
+# Copyright 2019-2025 the kikuchipy developers
 #
 # This file is part of kikuchipy.
 #
@@ -13,7 +14,7 @@
 # GNU General Public License for more details.
 #
 # You should have received a copy of the GNU General Public License
-# along with kikuchipy. If not, see <http://www.gnu.org/licenses/>.
+# along with kikuchipy. If not, see <http://www.gnu.org/licenses/>.#
 
 import re
 
@@ -45,10 +46,12 @@
             elif line.startswith(pypi_version):
                 changelog_end = i - 1
     with open("release_part_in_changelog.rst", mode="w") as f:
+        # fmt: off
         f.write(
             "kikuchipy is an open-source Python library for processing, simulating and indexing of electron backscatter diffraction (EBSD) patterns.\n\n"
             f"See below, the `changelog <https://kikuchipy.org/en/stable/changelog.html>`_ or the `GitHub changelog <https://github.com/pyxem/kikuchipy/compare/v{pypi_version}...v{branch_version}>`_ for all updates from the previous release.\n\n"
         )
+        # fmt: on
         for line in content[changelog_start:changelog_end]:
             f.write(line)
 

.github/workflows/tests.yml

@@ -1,3 +1,21 @@
+##
+## Copyright 2019-2025 the kikuchipy developers
+##
+## This file is part of kikuchipy.
+##
+## kikuchipy is free software: you can redistribute it and/or modify
+## it under the terms of the GNU General Public License as published by
+## the Free Software Foundation, either version 3 of the License, or
+## (at your option) any later version.
+##
+## kikuchipy is distributed in the hope that it will be useful,
+## but WITHOUT ANY WARRANTY; without even the implied warranty of
+## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+## GNU General Public License for more details.
+##
+## You should have received a copy of the GNU General Public License
+## along with kikuchipy. If not, see <http://www.gnu.org/licenses/>.
+##
 name: Tests
 
 on:
@@ -10,37 +28,13 @@ on:
   workflow_dispatch:
 
 jobs:
-  code:
-    name: code style
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: psf/black@stable
-
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.12'
-
-      - uses: isort/isort-action@master
-        with:
-          configuration: --profile black --filter-files --force-sort-within-sections --check-only --diff
-
-      - name: Install Black with Jupyter extension
-        run: |
-          pip install black[jupyter]
-
-      - name: Check code style of Jupyter notebooks
-        run: |
-          black --diff --line-length 77 doc/tutorials/*.ipynb
-
   tests:
     name: ${{ matrix.os }}-py${{ matrix.python-version }}${{ matrix.LABEL }}
     runs-on: ${{ matrix.os }}
     timeout-minutes: 15
     env:
       MPLBACKEND: agg
-      PYTEST_ARGS: --reruns 2 -n 2 --cov=kikuchipy
+      PYTEST_ARGS: --cov-branch --cov-report=xml --reruns 2 -n 2 --cov=kikuchipy
     strategy:
       fail-fast: false
       matrix:
@@ -126,17 +120,8 @@ jobs:
         run: |
           coverage report --show-missing
 
-      - name: Upload coverage to Coveralls
-        if: ${{ matrix.os == 'ubuntu-latest' }}
-        uses: AndreMiras/coveralls-python-action@develop
+      - name: Upload coverage reports to Codecov
+        if: ${{ github.repository_owner == 'pyxem' }}
+        uses: codecov/codecov-action@v5
         with:
-          parallel: true
-
-  coveralls-finish:
-    needs: tests
-    runs-on: ubuntu-latest
-    steps:
-    - name: Coveralls finished
-      uses: AndreMiras/coveralls-python-action@develop
-      with:
-        parallel-finished: true
+          token: ${{ secrets.CODECOV_TOKEN }}

.license.tmpl

@@ -0,0 +1,16 @@
+Copyright 2019-${years} the ${projectname} developers
+
+This file is part of ${projectname}.
+
+${projectname} is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+${projectname} is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with ${projectname}. If not, see <http://www.gnu.org/licenses/>.

.pre-commit-config.yaml

@@ -1,17 +1,43 @@
+##
+## Copyright 2019-2025 the kikuchipy developers
+##
+## This file is part of kikuchipy.
+##
+## kikuchipy is free software: you can redistribute it and/or modify
+## it under the terms of the GNU General Public License as published by
+## the Free Software Foundation, either version 3 of the License, or
+## (at your option) any later version.
+##
+## kikuchipy is distributed in the hope that it will be useful,
+## but WITHOUT ANY WARRANTY; without even the implied warranty of
+## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+## GNU General Public License for more details.
+##
+## You should have received a copy of the GNU General Public License
+## along with kikuchipy. If not, see <http://www.gnu.org/licenses/>.
+##
 repos:
-    # https://black.readthedocs.io/en/stable/index.html
-    - repo: https://github.com/psf/black-pre-commit-mirror
-      rev: 24.8.0
-      hooks:
-      - id: black
+  # https://docs.astral.sh/ruff/configuration
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.8
+    hooks:
+      - id: ruff
+      - id: ruff-format
+  # https://black.readthedocs.io/en/stable/index.html
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 24.10.0
+    hooks:
       - id: black-jupyter
         files: \.ipynb
         args: [--line-length=77]
-    # https://pycqa.github.io/isort/
-    - repo: https://github.com/pycqa/isort
-      rev: 5.13.2
-      hooks:
-        - id: isort
-          name: isort (python)
-          args:
-            [--profile=black, --filter-files, --force-sort-within-sections]
+  - repo: https://github.com/johann-petrak/licenseheaders.git
+    rev: v0.8.8
+    hooks:
+      - id: licenseheaders
+        args: ["-t", ".license.tmpl", "-cy", "-n", "kikuchipy", "-f"]
+
+# https://pre-commit.ci/#configuration
+ci:
+  autofix_prs: false
+  # TODO: Remove skip once (nearly) all files are formatted with the license template
+  skip: [licenseheaders]

README.rst

@@ -22,8 +22,8 @@ library.
 .. |python| image:: https://img.shields.io/badge/python-3.10+-blue.svg
    :target: https://www.python.org/downloads/
 
-.. |Coveralls| image:: https://coveralls.io/repos/github/pyxem/kikuchipy/badge.svg?branch=develop
-   :target: https://coveralls.io/github/pyxem/kikuchipy?branch=develop
+.. |coverage| image:: https://codecov.io/github/hakonanes/kikuchipy/graph/badge.svg?token=tyF8x9nJKC
+   :target: https://codecov.io/github/pyxem/kikuchipy
 
 .. |pypi_downloads| image:: https://img.shields.io/pypi/dm/kikuchipy.svg?label=pypi%20downloads
    :target: https://pypi.org/project/kikuchipy
@@ -54,7 +54,7 @@ library.
 +----------------------+------------------------------------------------+
 | Build status         | |tests_status| |docs| |python|                 |
 +----------------------+------------------------------------------------+
-| Metrics              | |Coveralls|                                    |
+| Metrics              | |coverage|                                     |
 +----------------------+------------------------------------------------+
 | Activity             | |pypi_downloads| |conda_downloads|             |
 +----------------------+------------------------------------------------+

conftest.py

@@ -1,4 +1,5 @@
-# Copyright 2019-2024 The kikuchipy developers
+#
+# Copyright 2019-2025 the kikuchipy developers
 #
 # This file is part of kikuchipy.
 #
@@ -9,11 +10,11 @@
 #
 # kikuchipy is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
 #
 # You should have received a copy of the GNU General Public License
-# along with kikuchipy. If not, see <http://www.gnu.org/licenses/>.
+# along with kikuchipy.  If not, see <http://www.gnu.org/licenses/>.#
 
 # Why is this file located in the top directory and not in tests/?
 # Because if it was, running "pytest --doctest-modules src" wouldn't
@@ -153,11 +154,13 @@ def dummy_signal(
     s.xmap = CrystalMap(
         rotations=Rotation.identity((nav_size,)),
         # fmt: off
-        phase_id=np.array([
-            [0, 0, 1],
-            [1, 1, 0],
-            [0, 1, 0],
-        ]).ravel(),
+        phase_id=np.array(
+            [
+                [0, 0, 1],
+                [1, 1, 0],
+                [0, 1, 0],
+            ]
+        ).ravel(),
         # fmt: on
         phase_list=phase_list,
         x=x.ravel(),

doc/conf.py

@@ -1,3 +1,21 @@
+#
+# Copyright 2019-2025 the kikuchipy developers
+#
+# This file is part of kikuchipy.
+#
+# kikuchipy is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# kikuchipy is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with kikuchipy.  If not, see <http://www.gnu.org/licenses/>.#
+
 # Configuration file for the Sphinx documentation app.
 # See the documentation for a full list of configuration options:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
@@ -6,7 +24,6 @@
 import inspect
 import os
 from os.path import dirname, relpath
-from pathlib import Path
 import re
 import sys
 import warnings
@@ -269,7 +286,7 @@ def linkcode_resolve(domain, info):
 pv.set_jupyter_backend("static")
 try:
     pv.start_xvfb()
-except:
+except Exception:
     pass
 
 # -- Copy button customization (taken from PyVista)

doc/dev/code_style.rst

@@ -6,20 +6,12 @@ Code style
 The code making up kikuchipy is formatted closely following the `Style Guide for Python
 Code <https://peps.python.org/pep-0008/>`__ with
 :doc:`The Black Code style <black:the_black_code_style/current_style>`.
-We use `pre-commit <https://pre-commit.com>`__ to run ``black`` automatically prior to
-each local commit.
+We use `pre-commit <https://pre-commit.com>`__ to run ``black`` (via
+`ruff <https://docs.astral.sh/ruff/>`__) automatically prior to each local commit.
 Please install it in your environment::
 
     pre-commit install
 
-Next time you commit some code, your code will be formatted inplace according to
-``black``.
-
-``black`` can format Jupyter notebooks as well. Code lines in tutorial notebooks should
-be limited to 77 characters to display nicely in the documentation::
-
-    black -l 77 <your_nice_notebook>.ipynb
-
 Note that ``black`` won't format `docstrings <https://peps.python.org/pep-0257/>`__.
 We follow the :doc:`numpydoc <numpydoc:format>` standard (with some exceptions), and the
 docstrings are checked against this standard when building the documentation.

doc/dev/continuous_integration.rst

@@ -2,8 +2,9 @@ Continuous integration (CI)
 ===========================
 
 We use `GitHub Actions <https://github.com/pyxem/kikuchipy/actions>`__ to ensure that
-kikuchipy can be installed on Windows, macOS and Linux (Ubuntu). After a successful
-installation of the package, the CI server runs the tests. After the tests return no
-errors, code coverage is reported to `Coveralls
-<https://coveralls.io/github/pyxem/kikuchipy?branch=develop>`__. Add ``"[skip ci]"``
-to a commit message to skip this workflow on any commit to a pull request.
+kikuchipy can be installed on Windows, macOS, and Linux (Ubuntu).
+After a successful installation of the package, the CI server runs the tests.
+After the tests return no errors, code coverage is reported to `Codecov
+<https://app.codecov.io/github/pyxem/kikuchipy>`__.
+Add ``"[skip ci]"`` to a commit message to skip this workflow on any commit to a pull
+request.