Update for scikit-learn 1.2 (#267)

Author: clonker

deeptime/base.py

@@ -2,8 +2,7 @@
 from collections import defaultdict
 from inspect import signature
 from typing import Optional, List
-
-from sklearn.base import _pprint as pprint_sklearn
+from pprint import PrettyPrinter
 
 
 class _BaseMethodsMixin(abc.ABC):
@@ -12,10 +11,12 @@ class _BaseMethodsMixin(abc.ABC):
     """
 
     def __repr__(self):
+        pp = PrettyPrinter(indent=1, depth=2)
         name = '{cls}-{id}:'.format(id=id(self), cls=self.__class__.__name__)
-        return '{name}{params}]'.format(
-            name=name, params=pprint_sklearn(self.get_params(), offset=len(name), )
-        )
+        offset = "".join([' '] * len(name))
+        params = pp.pformat(self.get_params())
+        params = params.replace('\n', '\n' + offset)
+        return '{name}[{params}]'.format(name=name, params=params)
 
     def get_params(self, deep=False):
         r"""Get the parameters.

deeptime/sindy/_sindy.py

@@ -409,7 +409,7 @@ class STLSQ(LinearRegression):
 
     def __init__(self, threshold=0.1, alpha=0.05, max_iter=20, ridge_kw=None, normalize=False, fit_intercept=False,
                  copy_X=True):
-        super().__init__(fit_intercept=fit_intercept, normalize=normalize, copy_X=copy_X)
+        super().__init__(fit_intercept=fit_intercept, copy_X=copy_X)
         self.threshold = threshold
         self.alpha = alpha
         self.max_iter = max_iter

pyproject.toml

@@ -49,6 +49,8 @@ tests = [
     'tqdm==4.64.0',
     "cython>=0.29.30",
     "pybind11>=2.10.1",
+    "networkx",
+    "matplotlib",
     "cmake>=3.24",
     "ninja; platform_system!='Windows'"
 ]

tests/base/test_base_interface.py

@@ -57,3 +57,10 @@ def test_mock_model():
 
     with assert_raises(ValueError):
         m.set_params(nope=33)
+
+    representation = repr(m)
+    things_that_should_be_represented = [
+        "MockModel", "A", "a", "55", "p1", "1.0", "p2", "2.0", "p3", "3.0", "p4", "55"
+    ]
+    for s in things_that_should_be_represented:
+        assert_(s in representation)

tests/markov/hmm/test_integration.py

@@ -97,7 +97,6 @@ def test_observation_probabilities(hmm_scenario):
     assert_almost_equal(minerr, 0, decimal=2)
 
 
-@flaky(max_runs=3)
 def test_stationary_distribution(hmm_scenario):
     model = hmm_scenario.hmm
     minerr = 1e6