Update to latest versions of sklearn and scipy (#239)

* Fixed `_ndim_coords_from_arrays` import

* Adding `validate_data` calls and tags for CUR, FPS, PCovCUR, and PCovFPS

* Adding `validate_data` calls and updated tags to Ridge2FoldCV

* Added `validate_data` calls to PCovR

* Added `validate_data` calls to KPCovR

* Fixing linting

* Fix rendering issues and depencies

* update pyproject.toml

* fix some tests

* update runners

* fix docs

* lint plus warnings as errors

* update infra

* Updates to fix sklearn branch (#241)

* replacing `self._validate_data` with `validate_data`

* Additional fixes

* Fixing scikit-learn warnings

* Fixing PCovR to work with 1D column vectors

* Fixing examples

* Changing shape of y in pcovr tests

* Fixing PCovR to not mess with data shape

---------

Co-authored-by: Christian Jorgensen <[email protected]>

* Update pyproject.toml

Co-authored-by: Rose K. Cersonsky <[email protected]>

* Removing print statement in tests/test_kernel_pcovr.py

Co-authored-by: Rose K. Cersonsky <[email protected]>

* Fixing artifact in WHO example

* Adding test for incorrect score threshold type

* Updating test

* Fixing validation checks in CUR + FPS

* Fix linting

* Update coverage collection

* Update changelog

---------

Co-authored-by: cajchristian <[email protected]>
Co-authored-by: Christian Jorgensen <[email protected]>
Co-authored-by: Rose K. Cersonsky <[email protected]>

Author: 4 people

.github/workflows/build.yml

@@ -15,7 +15,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: "3.12"
+        python-version: "3.13"
 
     - name: install tests dependencies
       run: python -m pip install tox

.github/workflows/docs.yml

@@ -16,7 +16,7 @@ jobs:
       - name: setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: install tests dependencies
         run: python -m pip install tox

.github/workflows/lint.yml

@@ -14,7 +14,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: "3.12"
+        python-version: "3.13"
 
     - name: install tests dependencies
       run: python -m pip install tox

.github/workflows/tests.yml

@@ -11,8 +11,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-22.04, macos-14, windows-2022]
-        python-version: ["3.9", "3.12"]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.10", "3.13"]
 
     steps:
     - uses: actions/checkout@v4
@@ -23,10 +23,12 @@ jobs:
         python-version: ${{ matrix.python-version }}
 
     - name: install tests dependencies
-      run: python -m pip install tox
+      run: python -m pip install tox coverage[toml]
 
     - name: run Python tests
-      run: tox -e tests
+      run: |
+        tox -e tests
+        coverage xml
 
     - name: upload to codecov.io
       uses: codecov/codecov-action@v5

.gitignore

@@ -1,3 +1,4 @@
+*.coverage*
 *.pyc
 *.ipynb_checkpoints*
 __pycache__

.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: "3.12"
+    python: "3.13"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

CHANGELOG

@@ -13,6 +13,8 @@ The rules for CHANGELOG file:
 
 0.3.0 (XXXX/XX/XX)
 ------------------
+- 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.

examples/pcovr/PCovR-WHODataset.py

@@ -109,7 +109,7 @@
 r_pcovr = Ridge(alpha=1e-4, fit_intercept=False, random_state=0).fit(
     T_train_pcovr, y_train
 )
-yp_pcovr = r_pcovr.predict(T_test_pcovr)
+yp_pcovr = r_pcovr.predict(T_test_pcovr).reshape(-1, 1)
 
 plt.scatter(y_scaler.inverse_transform(y_test), y_scaler.inverse_transform(yp_pcovr))
 r_pcovr.score(T_test_pcovr, y_test)
@@ -128,7 +128,7 @@
 T_pca = pca.transform(X)
 
 r_pca = Ridge(alpha=1e-4, fit_intercept=False, random_state=0).fit(T_train_pca, y_train)
-yp_pca = r_pca.predict(T_test_pca)
+yp_pca = r_pca.predict(T_test_pca).reshape(-1, 1)
 
 plt.scatter(y_scaler.inverse_transform(y_test), y_scaler.inverse_transform(yp_pca))
 r_pca.score(T_test_pca, y_test)

examples/pcovr/PCovR.py

@@ -50,7 +50,7 @@
 )
 pcovr.fit(X_scaled, y_scaled)
 T = pcovr.transform(X_scaled)
-yp = y_scaler.inverse_transform(pcovr.predict(X_scaled))
+yp = y_scaler.inverse_transform(pcovr.predict(X_scaled).reshape(-1, 1))
 
 fig, ((axT, axy), (caxT, caxy)) = plt.subplots(
     2, 2, figsize=(8, 5), gridspec_kw=dict(height_ratios=(1, 0.1))
@@ -90,7 +90,7 @@
     )
     pcovr.fit(X_scaled, y_scaled)
     T = pcovr.transform(X_scaled)
-    yp = y_scaler.inverse_transform(pcovr.predict(X_scaled))
+    yp = y_scaler.inverse_transform(pcovr.predict(X_scaled).reshape(-1, 1))
 
     axes[0, i].scatter(
         T[:, 0], T[:, 1], s=50, alpha=0.8, c=y, cmap=cmapX, edgecolor="k"
@@ -136,7 +136,7 @@
 )
 kpcovr.fit(X_scaled, y_scaled)
 T = kpcovr.transform(X_scaled)
-yp = y_scaler.inverse_transform(kpcovr.predict(X_scaled))
+yp = y_scaler.inverse_transform(kpcovr.predict(X_scaled).reshape(-1, 1))
 
 fig, ((axT, axy), (caxT, caxy)) = plt.subplots(
     2, 2, figsize=(8, 5), gridspec_kw=dict(height_ratios=(1, 0.1))

examples/pcovr/PCovR_Regressors.py

@@ -24,13 +24,12 @@
 mixing = 0.5
 
 X, y = load_diabetes(return_X_y=True)
-y = y.reshape(X.shape[0], -1)
 
 X_scaler = StandardScaler()
 X_scaled = X_scaler.fit_transform(X)
 
 y_scaler = StandardScaler()
-y_scaled = y_scaler.fit_transform(y)
+y_scaled = y_scaler.fit_transform(y.reshape(-1, 1))
 
 
 # %%