Merge branch 'main' into main

Author: ceriottm

.codecov.yml

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

.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: monthly
+    open-pull-requests-limit: 1
+    groups:
+      action-dependencies:
+        patterns:
+          - "*" # A wildcard to create one PR for all dependencies in the ecosystem

.github/workflows/build.yml

@@ -10,12 +10,15 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
-    - run: pip install tox
+        python-version: "3.13"
+
+    - name: install tests dependencies
+      run: python -m pip install tox
 
     - name: Test build integrity
       run: tox -e build

.github/workflows/docs.yml

@@ -11,13 +11,15 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+
       - name: setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
-      - name: install dependencies
-        run: |
-          python -m pip install tox
+          python-version: "3.13"
+
+      - name: install tests dependencies
+        run: python -m pip install tox
+
       - name: build documentation
         run: tox -e docs

.github/workflows/lint.yml

@@ -9,12 +9,15 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
-    - run: pip install tox
+        python-version: "3.13"
+
+    - name: install tests dependencies
+      run: python -m pip install tox
 
     - name: Lint the code
       run: tox -e lint

.github/workflows/release.yml

@@ -0,0 +1,41 @@
+name: Release
+
+on:
+  push:
+    tags: ["*"]
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/skmatter
+    permissions:
+      id-token: write
+      contents: write
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: setup Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.13"
+    - run: python -m pip install tox
+    - name: Build package
+      run: tox -e build
+    - name: Publish distribution to PyPI
+      if: startsWith(github.ref, 'refs/tags/v')
+      uses: pypa/gh-action-pypi-publish@release/v1
+    - name: Publish to GitHub release
+      if: startsWith(github.ref, 'refs/tags/v')
+      uses: softprops/action-gh-release@v2
+      with:
+        files: |
+          dist/*.tar.gz
+          dist/*.whl
+        prerelease: ${{ contains(github.ref, '-rc') }}
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/tests.yml

@@ -11,31 +11,28 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        include:
-          - os: ubuntu-22.04
-            python-version: "3.8"
-          - os: ubuntu-22.04
-            python-version: "3.11"
-          - os: macos-11
-            python-version: "3.8"
-          - os: macos-11
-            python-version: "3.11"
-          - os: windows-2019
-            python-version: "3.8"
-          - os: windows-2019
-            python-version: "3.11"
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.10", "3.13"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - run: pip install tox
+
+    - name: install tests dependencies
+      run: python -m pip install tox coverage[toml]
 
     - name: run Python tests
-      run: tox -e tests
-    - uses: codecov/codecov-action@v3
+      run: |
+        tox -e tests
+        coverage xml
+
+    - name: upload to codecov.io
+      uses: codecov/codecov-action@v5
       with:
+        fail_ci_if_error: true
         files: ./tests/coverage.xml
+        token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -1,3 +1,4 @@
+*.coverage*
 *.pyc
 *.ipynb_checkpoints*
 __pycache__
@@ -10,3 +11,4 @@ __pycache__
 build/
 dist/
 docs/src/examples
+sg_execution_times.rst

.readthedocs.yaml

@@ -7,9 +7,9 @@ version: 2
 
 # Set the version of Python and other tools we need
 build:
-  os: ubuntu-22.04
+  os: ubuntu-lts-latest
   tools:
-    python: "3.10"
+    python: "3.13"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

CHANGELOG

@@ -13,10 +13,26 @@ The rules for CHANGELOG file:
 
 0.3.0 (XXXX/XX/XX)
 ------------------
+- 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)
+- 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.
+- Updating ``skmatter.datasets`` submodule to support sklearn 1.5.0 (#229)
+- Add `SparseKDE` class (#222)
+- Add `QuickShift` class (#222)
+- Add an example on how to conduct PAMM algorithm with `SparseKDE` and `QuickShift`
+  (#222)
+- Add H2O-BLYP-Piglet dataset (#222)
+- Add two distance metrics that support the periodic boundry condition, 
+  `periodic_pairwise_euclidean_distances` and `pairwise_mahalanobis_distances` (#222)
 
 0.2.0 (2023/08/24)
 ------------------
-
 - Add this ``CHANGELOG`` file (#198)
 - Update example of WHO feature selection (#212)
 - Rename ``RidgeRegression2FoldCV`` -> ``Ridge2FoldCV`` (#211)
@@ -40,14 +56,12 @@ The rules for CHANGELOG file:
 
 0.1.4 (2023/03/14)
 ------------------
-
 - documentation formatting fixes for math and datasets (#161, #163)
 - changing the way the distance to the convex hull is computed in the
   ``DirectionalConvexHull`` due to numerical issues with the old method (#165)
 
 0.1.3 (2023/03/02)
 ------------------
-
 - Refactor ``scikit-cosmo`` to ``scikit-matter`` (#157, #151)
 - Deprecation warning was added to link to renamed package (#154)
 - dropped Python `<3.8` support, because we are now using ``scikit-learn`` version
@@ -62,7 +76,6 @@ The rules for CHANGELOG file:
 
 0.1.2 (2022/07/04)
 ------------------
-
 - fixed a bug in the orthonormalization step of ``PCov-CUR`` (#118)
 - users can now initialize ``FPS`` selecting using a list of selected points, allowing
   to restart the selection in the middle (#116)
@@ -71,15 +84,13 @@ The rules for CHANGELOG file:
 
 0.1.1 (2021/11/30)
 ------------------
-
 - fixed a bug in the ``orthonormalization`` step of ``PCov-CUR`` (#118)
 - users can now initialize ``FPS`` selecting using a list of selected points, allowing to
   restart the selection in the middle (#116)
 - KPCovR is now able to use pre-fitted regressor in the same way that ``PCovR`` can (#113)
 
 0.1.0 (2021/05/12)
 ------------------
-
 - first release out of the lab
 
 .. inclusion-marker-changelog-end