Merge remote-tracking branch 'origin/main' into test_against_nightly_deps

# Conflicts:
#	setup.py

Author: charavelg

.gitignore

@@ -112,6 +112,7 @@ docs/_build/
 docs/auto_examples/
 docs/examples/misc/ks_trained.hdf5
 docs/gen_modules/*/
+docs/**/sg_execution_times.rst
 
 # Local files
 private_info.md

CHANGELOG.md

@@ -15,6 +15,7 @@ Changelogs for this project are recorded in this file since v0.2.0.
 
 * Explicit exception when using Global Alignment Kernel with sigma close to zero ([#440](https://github.com/tslearn-team/tslearn/issues/440))
 * Fix shifting in K-shape shape extraction process ([#385](https://github.com/tslearn-team/tslearn/issues/385))
+* Support for `scikit-learn` up to 1.7 ([#549](https://github.com/tslearn-team/tslearn/issues/549))
 
 ### Removed
 

MANIFEST.in

@@ -1,12 +1,9 @@
-include *.rst
-recursive-include tslearn *.c *.h *.pyx
-include LICENSE
-include README.md
-include pyproject.toml
 include conftest.py
-include MANIFEST.in
 
 # exclude from sdist
 recursive-exclude .github *
+recursive-exclude tslearn.egg-info *
 exclude .readthedocs.yml
 exclude azure-pipelines.yml
+exclude sonar-project.properties
+exclude .gitignore

azure-pipelines.yml

@@ -43,7 +43,7 @@ jobs:
       set -xe
       python -m pip install pytest-azurepipelines
       pip list
-      python -m pytest -v tslearn/ -k "not test_all_estimators"
+      python -m pytest -v -k "not test_all_estimators"
     displayName: 'Test'
 
 - job: 'doctests_linux'
@@ -81,7 +81,7 @@ jobs:
       set -xe
       python -m pip install pytest-azurepipelines
       pip list
-      python -m pytest -v tslearn/ --doctest-modules -k "not test_ or test_all_estimators"
+      python -m pytest -v --doctest-modules -k "not test_ or test_all_estimators"
     displayName: 'Doctest'
 
 - job: 'tests_macOS'
@@ -119,7 +119,7 @@ jobs:
       set -xe
       python -m pip install pytest-azurepipelines
       pip list
-      python -m pytest -v tslearn/ -k "not test_all_estimators"
+      python -m pytest -v -k "not test_all_estimators"
     displayName: 'Test'
 
 - job: 'doctests_macOS'
@@ -157,7 +157,7 @@ jobs:
       set -xe
       python -m pip install pytest-azurepipelines
       pip list
-      python -m pytest -v tslearn/ --doctest-modules -k "not test_ or test_all_estimators"
+      python -m pytest -v --doctest-modules -k "not test_ or test_all_estimators"
     displayName: 'Doctest'
 
 - job: 'tests_windows'
@@ -192,7 +192,7 @@ jobs:
   - script: |
       python -m pip install pytest-azurepipelines
       pip list
-      python -m pytest -v tslearn/ -k "not test_all_estimators"
+      python -m pytest -v -k "not test_all_estimators"
     displayName: 'Test'
 
 - job: 'doctests_windows'
@@ -227,16 +227,12 @@ jobs:
   - script: |
       python -m pip install pytest-azurepipelines
       pip list
-      python -m pytest -v tslearn/ --doctest-modules -k "not test_ or test_all_estimators"
+      python -m pytest -v --doctest-modules -k "not test_ or test_all_estimators"
     displayName: 'Doctest'
 
-- job: 'tests_basic'
+- job: 'tests_doctests_basic'
   pool:
     vmImage: 'ubuntu-latest'
-  strategy:
-    matrix:
-      Python310:
-        python.version: '3.10'
   variables:
     OMP_NUM_THREADS: '2'
     NUMBA_NUM_THREADS: '2'
@@ -245,8 +241,8 @@ jobs:
   steps:
   - task: UsePythonVersion@0
     inputs:
-      versionSpec: '$(python.version)'
-    displayName: 'Use Python $(python.version)'
+      versionSpec: '3.10'
+    displayName: 'Use Python 3.10'
 
   - script: |
       set -xe
@@ -259,16 +255,20 @@ jobs:
       set -xe
       python -m pip install pytest-azurepipelines
       pip list
-      python -m pytest -v tslearn/ -k "not test_all_estimators"
+      python -m pytest -v --doctest-modules
     displayName: 'Test'
 
-- job: 'doctests_basic'
+- job: 'tests_sklearn_version'
   pool:
     vmImage: 'ubuntu-latest'
   strategy:
     matrix:
-      Python310:
-        python.version: '3.10'
+      sklearn1_4:
+        skLearnVersion: '1.4.0'
+      sklearn1_5:
+        skLearnVersion: '1.5.0'
+      sklearn1_6:
+        skLearnVersion: '1.6.0'
   variables:
     OMP_NUM_THREADS: '2'
     NUMBA_NUM_THREADS: '2'
@@ -277,30 +277,28 @@ jobs:
   steps:
   - task: UsePythonVersion@0
     inputs:
-      versionSpec: '$(python.version)'
-    displayName: 'Use Python $(python.version)'
+      versionSpec: '3.11'
+    displayName: 'Use Python 3.11'
 
   - script: |
       set -xe
       python --version
       python -m pip install --upgrade pip
-      python -m pip install .[tests]
-    displayName: 'Install tslearn and dependencies for tests'
+      python -m pip install 'scikit-learn~=$(skLearnVersion)'
+      python -m pip install .[tests,all_features]
+    displayName: 'Install tslearn all_features and dependencies for tests'
 
   - script: |
       set -xe
       python -m pip install pytest-azurepipelines
       pip list
-      python -m pytest -v tslearn/ --doctest-modules -k 'not test_ or test_all_estimators'
-    displayName: 'Doctest'
+      python -m pytest -v
+    displayName: 'Test sklearn versions'
+
 
 - job: 'codecov'  # must be a separate job to only disable Numbas's JIT here
   pool:
     vmImage: 'ubuntu-latest'
-  strategy:
-    matrix:
-      Python310:
-        python.version: '3.10'
   variables:
     OMP_NUM_THREADS: '2'
     NUMBA_DISABLE_JIT: '1'
@@ -310,22 +308,28 @@ jobs:
   steps:
   - task: UsePythonVersion@0
     inputs:
-      versionSpec: '$(python.version)'
-    displayName: 'Use Python $(python.version)'
+      versionSpec: '3.11'
+    displayName: 'Use Python 3.11'
 
   - script: |
       set -xe
       python --version
       python -m pip install --upgrade pip
-      python -m pip install .[tests,all_features]
+      python -m pip install .[tests]
     displayName: 'Install tslearn all_features and dependencies for tests'
 
   - script: |
       set -xe
       python -m pip install pytest-azurepipelines
       python -m pip install coverage pytest-cov
       pip list
-      python -m pytest -v tslearn/ --cov=tslearn
+      python -m pytest -v --cov=tests --cov=tslearn
+      python -m pip install .[all_features]
+      pip list
+      python -m pytest -v --cov=tests --cov=tslearn --cov-append
+      pip install scikit-learn~=1.4.0
+      pip list
+      python -m pytest -v --cov=tests --cov=tslearn --cov-append  -k "test_all_estimators or test_scaler_allow_variable_length"
     displayName: 'Test'
 
   # Upload coverage to codecov.io

docs/conf.py

@@ -15,8 +15,11 @@
 import os
 import subprocess
 import sys
+import tomllib
 import warnings
 
+from packaging.requirements import Requirement
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
@@ -242,15 +245,16 @@ def find_source():
 
 def get_dependencies():
     """ Retrieve required dependencies """
-    import distutils.core
-    from packaging.requirements import Requirement
-    setup_ = distutils.core.run_setup("../setup.py", stop_after='run')
-    return [Requirement(requirement) for requirement in setup_.install_requires]
+    with open("../pyproject.toml", "rb") as f:
+        pyproject = tomllib.load(f)
+        return [Requirement(requirement) for requirement in pyproject["project"]["dependencies"]]
+
 
 rst_templates= {
     "dependencies.rst": {"dependencies": get_dependencies()}
 }
 
+
 def setup(app):
     """ Setup our app """
     # Ensure pandoc is installed

docs/contributing.rst

@@ -117,7 +117,7 @@ Here is a description of useful tools to check your code locally:
   `pytest <https://docs.pytest.org/en/latest/>`_ and `pytest-cov <https://pytest-cov.readthedocs.io/en/latest/>`_ Python packages::
 
      $ pip install -e .[tests,all_features]
-     $ pytest --cov tslearn
+     $ pytest --cov
 
 - To build the documentation locally, install the following packages and run
   the ``make html`` command in the ``tslearn/docs`` folder::

docs/examples/autodiff/plot_soft_dtw_loss_for_pytorch_nn.py

@@ -115,11 +115,11 @@ def fit(self, X, y, max_epochs=10):
 ts_index = 50
 y_pred = model(X_test[:, :150, 0]).detach().numpy()
 
-plt.figure()
+plt.figure(1, layout="constrained")
 plt.title('Multi-step ahead forecasting using MSE')
 plt.plot(X_test[ts_index].ravel())
 plt.plot(np.arange(150, 275), y_pred[ts_index], 'r-')
-
+plt.show()
 
 ##############################################################################
 # Using Soft-DTW as a loss function
@@ -143,7 +143,8 @@ def fit(self, X, y, max_epochs=10):
 
 y_pred = model(X_test[:, :150, 0]).detach().numpy()
 
-plt.figure()
+plt.figure(2, layout="constrained")
 plt.title('Multi-step ahead forecasting using Soft-DTW loss')
 plt.plot(X_test[ts_index].ravel())
 plt.plot(np.arange(150, 275), y_pred[ts_index], 'r-')
+plt.show()

docs/examples/metrics/plot_dtw.py

@@ -67,7 +67,7 @@
 
 path, sim = metrics.dtw_path(s_y1, s_y2)
 
-plt.figure(1, figsize=(8, 8))
+plt.figure(layout="constrained", figsize=(8, 8))
 
 # definitions for the axes
 left, bottom = 0.01, 0.1
@@ -100,5 +100,4 @@
 ax_s_y.axis("off")
 ax_s_y.set_ylim((0, sz - 1))
 
-plt.tight_layout()
 plt.show()

docs/examples/metrics/plot_dtw_custom_metric.py

@@ -103,7 +103,7 @@ def arc_length(angle_1, angle_2, r=1.):
 rect_s_x = [left_h, bottom_h, width, h_ts]
 
 # Plot example 1
-plt.figure(1, figsize=(6, 6))
+plt.figure(1, layout="constrained", figsize=(6, 6))
 ax_dist = plt.axes(rect_dist)
 ax_s_x = plt.axes(rect_s_x)
 ax_s_y = plt.axes(rect_s_y)
@@ -133,7 +133,7 @@ def arc_length(angle_1, angle_2, r=1.):
                 horizontalalignment="center", verticalalignment="top")
 
 # Plot example 2
-plt.figure(2, figsize=(6, 6))
+plt.figure(2, layout="constrained", figsize=(6, 6))
 ax_dist = plt.axes(rect_dist)
 ax_s_x = plt.axes(rect_s_x)
 ax_s_y = plt.axes(rect_s_y)
@@ -153,5 +153,4 @@ def arc_length(angle_1, angle_2, r=1.):
 ax_s_y.imshow(np.flip(dataset_2[0], axis=1), aspect="auto", cmap=cm)
 ax_s_y.axis("off")
 
-plt.tight_layout()
 plt.show()

docs/examples/metrics/plot_lcss.py

@@ -62,5 +62,4 @@
 plt.legend()
 plt.title("Time series matching with DTW")
 
-plt.tight_layout()
 plt.show()