Merge branch 'main' into main

Author: ceriottm

.codecov.yml

@@ -4,9 +4,9 @@ coverage:
   status:
     project:
       default:
-        target: 95%
+        target: 90%
     patch:
       default:
-        target: 95%
+        target: 90%
 
 comment: false

.github/workflows/tests-dev.yml

@@ -0,0 +1,27 @@
+name: Tests dev
+
+on:
+  schedule:
+    # check once a week on mondays
+    - cron: '0 10 * * 1'
+
+jobs:
+  tests-dev:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install tests dependencies
+        run: python -m pip install tox
+
+      - name: Run tests against scikit-learn dev version
+        run: tox -e tests-dev

.github/workflows/tests.yml

@@ -22,10 +22,10 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: install tests dependencies
+    - name: Install tests dependencies
       run: python -m pip install tox coverage[toml]
 
-    - name: run Python tests
+    - name: Run Python tests
       run: |
         tox -e tests
         coverage xml

.gitignore

@@ -6,6 +6,7 @@ __pycache__
 *.swp
 *.swo
 *DS_Store
+_version.py
 
 .tox/
 build/

CHANGELOG

@@ -11,17 +11,23 @@ The rules for CHANGELOG file:
 
 .. inclusion-marker-changelog-start
 
-0.3.0 (XXXX/XX/XX)
+0.3.1 (2025/06/30)
+------------------
+- Fix typos and make minor edits to ``PCovC`` and ``KPCovR`` docs (#254)
+- Fix ``assertTrue`` typos in ``KPCovR`` testing suite (#254)
+- Add ``KernelPCovC`` class and examples (#254)
+
+0.3.0 (2025/06/12)
 ------------------
 - Add ``_BasePCov`` class (#248)
 - Add ``PCovC`` class that inherits shared functionality from ``_BasePCov`` (#248)
 - Add ``PCovC`` testing suite and examples (#248)
-- Modify ``PCovR`` to inherit shared functionality from ``_BasePCov_`` (#248)
-- Update to sklearn >= 1.6.0 and scipy >= 1.15.0 (#239)
+- Modify ``PCovR`` to inherit shared functionality from ``_BasePCov`` (#248)
+- Update to sklearn >= 1.7.0 and scipy >= 1.15.0 (#239, #257)
 - Fixed moved function import from scipy and bump scipy dependency to 1.15.0 (#236)
 - Fix rendering issues for `SparseKDE` and `QuickShift` (#236)
 - Updating ``FPS`` to allow a numpy array of ints as an initialize parameter (#145)
-- Supported Python versions are now ranging from 3.9 - 3.12.
+- Supported Python versions are now ranging from 3.9 - 3.13.
 - Updating ``skmatter.datasets`` submodule to support sklearn 1.5.0 (#229)
 - Add `SparseKDE` class (#222)
 - Add `QuickShift` class (#222)

CITATION.cff

@@ -0,0 +1,28 @@
+cff-version: 1.2.0
+message: "If you use scikit-matter for your work, please read and cite it as below."
+title: >-
+  scikit-matter : a suite of generalisable machine learning methods born out of chemistry and materials science [version 2; peer review: 3 approved, 1 approved with reservations]
+type: journalArticle
+issue: 81
+volume: 3
+authors: 
+  - family-names: Goscinski
+    given-names: Alexander
+  - family-names: Principe
+    given-names: Victor P.
+  - family-names: Fraux
+    given-names: Guillaume
+  - family-names: Kliavinek
+    given-names: Sergei
+  - family-names: Helfrecht
+    given-names: Benjamin A.
+  - family-names: Loche
+    given-names: Philip
+  - family-names: Ceriotti
+    given-names: Michele
+  - family-names: Cersonsky
+    given-names: Rose K.
+date-published: 2023
+identifiers: 
+  - type: doi
+    value: 10.12688/openreseurope.15789.2

MANIFEST.in

@@ -1,6 +1,7 @@
 graft src
 
 include LICENSE
+include CITATION.cff
 include README.rst
 
 prune docs

README.rst

@@ -1,13 +1,16 @@
 scikit-matter
 =============
-|tests| |codecov| |pypi| |conda| |docs| |doi|
+
+|tests| |codecov| |pypi| |conda| |docs-stable| |docs-latest| |doi|
 
 A collection of ``scikit-learn`` compatible utilities that implement methods born out of
 the materials science and chemistry communities.
 
-For details, tutorials, and examples, please have a look at our `documentation`_.
+For details, tutorials, and examples, please have a look at our documentation_. We also
+provide a `latest documentation`_ from the current unreleased development version.
 
-.. _`documentation`: https://scikit-matter.readthedocs.io
+.. _`documentation`: https://scikit-matter.readthedocs.io/en/v0.3.1/
+.. _`latest documentation`: https://scikit-matter.readthedocs.io/en/latest
 
 .. marker-installation
 
@@ -98,9 +101,13 @@ Thanks goes to all people that make scikit-matter possible:
    :alt: Code coverage
    :target: https://codecov.io/gh/scikit-learn-contrib/scikit-matter/
 
-.. |docs| image:: https://img.shields.io/badge/documentation-latest-sucess
-   :alt: Python
-   :target: documentation_
+.. |docs-stable| image:: https://img.shields.io/badge/📚_Documentation-stable-sucess
+   :alt: Documentation of stable released version
+   :target: `documentation`_
+
+.. |docs-latest| image:: https://img.shields.io/badge/📒_Documentation-latest-yellow.svg
+   :alt: Documentation of latest unreleased version
+   :target: `latest documentation`_
 
 .. |pypi| image:: https://img.shields.io/pypi/v/skmatter.svg
    :alt: Latest PYPI version

docs/src/contributing.rst

@@ -212,3 +212,49 @@ properly. It should look something like this:
 
 You're good to go! Time to submit a `pull request.
 <https://github.com/lab-cosmo/scikit-matter/pulls>`_
+
+How to Perform a Release
+-------------------------
+
+1. **Prepare a Release Pull Request**
+
+   - Based on the main branch create branch ``release-x.y.z`` and a PR.
+   - Ensure that all `CI tests
+     <https://github.com/scikit-learn-contrib/scikit-matter/actions>`_ pass.
+   - Optionally, run the tests locally to double-check.
+
+2. **Update the Changelog**
+
+   - Edit the changelog located in ``CHANGELOG``:
+      - Add a new section for the new version, summarizing the changes based on the
+        PRs merged since the last release.
+      - Leave a placeholder section titled *Unreleased* for future updates.
+
+3. **Merge the PR and Create a Tag**
+
+   - Merge the release PR.
+   - Update the ``main`` branch and check that the latest commit is the release PR with
+     ``git log``
+   - Create a tag on directly the ``main`` branch.
+   - Push the tag to GitHub. For example for a release of version ``x.y.z``:
+
+     .. code-block:: bash
+
+        git checkout main
+        git pull
+        git tag -a vx.y.z -m "Release vx.y.z"
+        git push --tags
+
+4. **Finalize the GitHub Release**
+
+   - Once the PR is merged, the CI will automatically:
+      - Publish the package to PyPI.
+      - Create a draft release on GitHub.
+   - Update the GitHub release notes by pasting the changelog for the version.
+
+5. **Merge Conda Recipe Changes**
+
+   - May resolve and then merge an automatically created PR on the `conda recipe
+     <https://github.com/conda-forge/skmatter-feedstock>`_.
+   - Once thus PR is merged and the new version will be published automatically on the
+     `conda-forge <https://anaconda.org/conda-forge/skmatter>`_ channel.

docs/src/index.rst

@@ -1,5 +1,21 @@
 .. automodule:: skmatter
 
+.. raw:: html
+
+     <style>
+        /* Overriding bootstrap font color so that text appears white
+           in dark theme */
+        html[data-theme="dark"] .card-text {
+            color: var(--pst-color-text-base);
+        }
+
+        /* Overriding bootstrap border color so that border appears white
+           in dark theme */
+        html[data-theme="dark"] .card {
+            --bs-card-border-color: var(--pst-color-border);
+        }
+    </style>
+
 .. raw:: html
 
     <div class="container">