Removed deprecated imports

Author: lucasimi

benchmarks/benchmark.py

@@ -9,7 +9,7 @@
 from sklearn.decomposition import PCA
 
 import tdamapper as tm
-from tdamapper.clustering import TrivialClustering
+from tdamapper.core import TrivialClustering
 
 
 def _segment(cardinality, dimension, noise=0.1, start=None, end=None):
@@ -81,7 +81,7 @@ def run_gm(X, n, p):
 
 def run_tm(X, n, p):
     t0 = time.time()
-    tm.core.MapperAlgorithm(
+    tm.learn.MapperAlgorithm(
         cover=tm.cover.CubicalCover(
             n_intervals=n,
             overlap_frac=p,

src/tdamapper/clustering.py

@@ -46,7 +46,11 @@ def fit(self, X, y=None):
         X, y = self._validate_X_y(X, y)
         cover = TrivialCover() if self.cover is None else self.cover
         cover = clone(cover)
-        clustering = TrivialClustering() if self.clustering is None else self.clustering
+        clustering = (
+            tdamapper.core.TrivialClustering()
+            if self.clustering is None
+            else self.clustering
+        )
         clustering = clone(clustering)
         n_jobs = self.n_jobs
         y = X if y is None else y

tests/example.py

@@ -25,4 +25,4 @@
 
 # Visualize the Mapper graph
 fig = MapperPlot(graph, dim=2, seed=42, iterations=60).plot_plotly(colors=labels)
-fig.show(config={"scrollZoom": True})
+# fig.show(config={"scrollZoom": True})

tests/test_unit_core.py

@@ -4,9 +4,8 @@
 import numpy as np
 from sklearn.cluster import DBSCAN
 
-from tdamapper.clustering import TrivialClustering
 from tdamapper.core import (
-    MapperAlgorithm,
+    TrivialClustering,
     TrivialCover,
     mapper_connected_components,
     mapper_labels,
@@ -17,6 +16,7 @@
     ProximityCubicalCover,
     StandardCubicalCover,
 )
+from tdamapper.learn import MapperAlgorithm
 
 dist = "euclidean"
 

tests/test_unit_params.py

@@ -3,9 +3,8 @@
 from sklearn.cluster import DBSCAN
 
 from tdamapper._common import clone
-from tdamapper.clustering import MapperClustering
-from tdamapper.core import MapperAlgorithm
 from tdamapper.cover import BallCover, CubicalCover
+from tdamapper.learn import MapperAlgorithm, MapperClustering
 
 
 class TestParams(unittest.TestCase):

tests/test_unit_plot.py

@@ -3,10 +3,10 @@
 import networkx as nx
 import numpy as np
 
-from tdamapper.clustering import TrivialClustering
-from tdamapper.core import MapperAlgorithm
+from tdamapper.core import TrivialClustering
 from tdamapper.cover import BallCover
-from tdamapper.plot import MapperLayoutInteractive, MapperLayoutStatic, MapperPlot
+from tdamapper.learn import MapperAlgorithm
+from tdamapper.plot import MapperPlot
 
 
 class TestMapperPlot(unittest.TestCase):
@@ -72,46 +72,48 @@ def test_two_connected_clusters_deprecated(self):
             np.array([0.0, 0.0]),
             np.array([1.0, 1.0]),
         ]
-        mp = MapperAlgorithm(
+        mapper_algo = MapperAlgorithm(
             cover=BallCover(1.1, metric="euclidean"), clustering=TrivialClustering()
         )
-        g = mp.fit_transform(data, data)
-        mp_plot1 = MapperLayoutInteractive(
+        g = mapper_algo.fit_transform(data, data)
+        mapper_plot_1 = MapperPlot(
             g,
             dim=2,
-            colors=data,
             seed=123,
             iterations=10,
+        )
+        mapper_plot_1.plot_plotly(
+            colors=data,
             agg=np.nanmax,
             width=200,
             height=200,
             title="example",
             cmap="jet",
         )
-        mp_plot1.plot()
-        mp_plot2 = MapperLayoutInteractive(
+        mapper_plot_2 = MapperPlot(
             g,
             dim=3,
-            colors=data,
             seed=123,
             iterations=10,
+        )
+        fig = mapper_plot_2.plot_plotly(
+            colors=data,
             agg=np.nanmax,
             width=200,
             height=200,
             title="example",
             cmap="jet",
         )
-        mp_plot2.plot()
-        mp_plot2.update(
+        mapper_plot_2.plot_plotly_update(
+            fig,
             colors=data,
-            seed=124,
-            iterations=15,
             agg=np.nanmin,
             width=300,
             height=300,
             title="example-updated",
             cmap="viridis",
         )
-        mp_plot2.plot()
-        mp_plot3 = MapperLayoutStatic(g, colors=data, dim=2)
-        mp_plot3.plot()
+        mapper_plot_3 = MapperPlot(g, dim=2)
+        mapper_plot_3.plot_matplotlib(
+            colors=data,
+        )

tests/test_unit_sklearn.py

@@ -4,9 +4,8 @@
 import numpy as np
 from sklearn.utils.estimator_checks import check_estimator
 
-from tdamapper.clustering import MapperClustering
-from tdamapper.core import MapperAlgorithm
 from tdamapper.cover import BallCover, CubicalCover, KNNCover
+from tdamapper.learn import MapperAlgorithm, MapperClustering
 from tests.setup_logging import setup_logging