API change: predict -> transform

scikit-learn-contrib · Apr 21, 2021 · ef35289 · ef35289
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diff --git a/doc/basics.ipynb b/doc/basics.ipynb
@@ -95,8 +95,8 @@
     "\n",
     "This can be done with any of these calls: \n",
     "- .fit(data).dimension_\n",
-    "- .fit(data).predict() \n",
-    "- .fit_predict(data)"
+    "- .fit(data).transform() \n",
+    "- .fit_transform(data)"
    ],
    "cell_type": "markdown",
    "metadata": {}
@@ -130,15 +130,15 @@
     "\n",
     "To compute local ID call either: \n",
     "- .fit\\_pw(data).dimension\\_pw_\n",
-    "- .fit_pw(data).predict_pw()\n",
-    "- .fit_predict_pw(data)\n",
+    "- .fit_pw(data).transform_pw()\n",
+    "- .fit_transform_pw(data)\n",
     "\n",
     "Several estimators also naturally compute the distribution of local ID to derive the global ID estimates. \n",
     "\n",
     "These estimators do not have a .fit\\_pw() method since .fit() already computes local estimates and you can simply call : \n",
     "- .fit(data).dimension\\_pw_\n",
-    "- .fit(data).predict_pw()\n",
-    "- .fit_predict_pw(data)\n"
+    "- .fit(data).transform_pw()\n",
+    "- .fit_transform_pw(data)\n"
    ],
    "cell_type": "markdown",
    "metadata": {}

diff --git a/doc/skdim.datasets.BenchmarkManifolds.generate.rst b/doc/skdim.datasets.BenchmarkManifolds.generate.rst
@@ -1,4 +1,4 @@
-:github_url: https://github.com/theislab/scvelo/tree/master/scikit-dimension/skdim/datasets.py#L383-L436
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/datasets.py#L374-L427
 
 
 

diff --git a/doc/skdim.datasets.BenchmarkManifolds.rst b/doc/skdim.datasets.BenchmarkManifolds.rst
@@ -20,8 +20,4 @@ skdim.datasets.BenchmarkManifolds
 
       ~skdim.datasets.BenchmarkManifolds.generate
 
-
-
-
-
 
diff --git a/doc/skdim.datasets.hyperBall.rst b/doc/skdim.datasets.hyperBall.rst
@@ -1,4 +1,4 @@
-:github_url: https://github.com/theislab/scvelo/tree/master/scikit-dimension/skdim/datasets.py#L38-L69
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/datasets.py#L38-L69
 
 
 

diff --git a/doc/skdim.datasets.hyperSphere.rst b/doc/skdim.datasets.hyperSphere.rst
@@ -1,4 +1,4 @@
-:github_url: https://github.com/theislab/scvelo/tree/master/scikit-dimension/skdim/datasets.py#L72-L95
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/datasets.py#L72-L95
 
 
 

diff --git a/doc/skdim.datasets.hyperTwinPeaks.rst b/doc/skdim.datasets.hyperTwinPeaks.rst
@@ -1,4 +1,4 @@
-:github_url: https://github.com/theislab/scvelo/tree/master/scikit-dimension/skdim/datasets.py#L98-L122
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/datasets.py#L98-L122
 
 
 

diff --git a/doc/skdim.datasets.lineDiskBall.rst b/doc/skdim.datasets.lineDiskBall.rst
@@ -1,4 +1,4 @@
-:github_url: https://github.com/theislab/scvelo/tree/master/scikit-dimension/skdim/datasets.py#L125-L187
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/datasets.py#L125-L187
 
 
 

diff --git a/doc/skdim.datasets.swissRoll3Sph.rst b/doc/skdim.datasets.swissRoll3Sph.rst
@@ -1,4 +1,4 @@
-:github_url: https://github.com/theislab/scvelo/tree/master/scikit-dimension/skdim/datasets.py#L190-L245
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/datasets.py#L190-L245
 
 
 

diff --git a/doc/skdim.id.CorrInt.fit.rst b/doc/skdim.id.CorrInt.fit.rst
@@ -1,4 +1,4 @@
-:github_url: https://github.com/theislab/scvelo/tree/master/scikit-dimension/skdim/id/_CorrInt.py#L61-L87
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_CorrInt.py#L57-L83
 
 
 

diff --git a/doc/skdim.id.CorrInt.fit_pw.rst b/doc/skdim.id.CorrInt.fit_pw.rst
@@ -1,4 +1,4 @@
-:github_url: https://github.com/theislab/scvelo/tree/master/scikit-dimension/skdim/id/_CorrInt.py#L155-L201
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_CorrInt.py#L207-L253
 
 
 

diff --git a/doc/skdim.id.CorrInt.fit_transform.rst b/doc/skdim.id.CorrInt.fit_transform.rst
@@ -0,0 +1,10 @@
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_CorrInt.py#L192-L205
+
+
+
+skdim.id.CorrInt.fit\_transform
+===============================
+
+.. currentmodule:: skdim.id
+
+.. automethod:: CorrInt.fit_transform
diff --git a/doc/skdim.id.CorrInt.fit_transform_pw.rst b/doc/skdim.id.CorrInt.fit_transform_pw.rst
@@ -0,0 +1,10 @@
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_CorrInt.py#L284-L335
+
+
+
+skdim.id.CorrInt.fit\_transform\_pw
+===================================
+
+.. currentmodule:: skdim.id
+
+.. automethod:: CorrInt.fit_transform_pw
diff --git a/doc/skdim.id.CorrInt.get_params.rst b/doc/skdim.id.CorrInt.get_params.rst
@@ -1,4 +1,4 @@
-:github_url: https://github.com/theislab/scvelo/tree/master/scikit-dimension/skdim/id/_CorrInt.py#L189-L219
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_CorrInt.py#L178-L200
 
 
 

diff --git a/doc/skdim.id.CorrInt.rst b/doc/skdim.id.CorrInt.rst
@@ -19,16 +19,12 @@ skdim.id.CorrInt
       :toctree: .
 
       ~skdim.id.CorrInt.fit
-      ~skdim.id.CorrInt.fit_predict
-      ~skdim.id.CorrInt.fit_predict_pw
       ~skdim.id.CorrInt.fit_pw
+      ~skdim.id.CorrInt.fit_transform
+      ~skdim.id.CorrInt.fit_transform_pw
       ~skdim.id.CorrInt.get_params
-      ~skdim.id.CorrInt.predict
-      ~skdim.id.CorrInt.predict_pw
       ~skdim.id.CorrInt.set_params
-
-
-
-
+      ~skdim.id.CorrInt.transform
+      ~skdim.id.CorrInt.transform_pw
 
 
diff --git a/doc/skdim.id.CorrInt.set_params.rst b/doc/skdim.id.CorrInt.set_params.rst
@@ -1,4 +1,4 @@
-:github_url: https://github.com/theislab/scvelo/tree/master/scikit-dimension/skdim/id/_CorrInt.py#L221-L263
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_CorrInt.py#L202-L244
 
 
 

diff --git a/doc/skdim.id.CorrInt.transform.rst b/doc/skdim.id.CorrInt.transform.rst
@@ -0,0 +1,10 @@
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_CorrInt.py#L177-L190
+
+
+
+skdim.id.CorrInt.transform
+==========================
+
+.. currentmodule:: skdim.id
+
+.. automethod:: CorrInt.transform
diff --git a/doc/skdim.id.CorrInt.transform_pw.rst b/doc/skdim.id.CorrInt.transform_pw.rst
@@ -0,0 +1,10 @@
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_CorrInt.py#L255-L282
+
+
+
+skdim.id.CorrInt.transform\_pw
+==============================
+
+.. currentmodule:: skdim.id
+
+.. automethod:: CorrInt.transform_pw
diff --git a/doc/skdim.id.DANCo.fit.rst b/doc/skdim.id.DANCo.fit.rst
@@ -1,4 +1,4 @@
-:github_url: https://github.com/theislab/scvelo/tree/master/scikit-dimension/skdim/id/_DANCo.py#L92-L134
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_DANCo.py#L89-L132
 
 
 

diff --git a/doc/skdim.id.DANCo.fit_pw.rst b/doc/skdim.id.DANCo.fit_pw.rst
@@ -1,4 +1,4 @@
-:github_url: https://github.com/theislab/scvelo/tree/master/scikit-dimension/skdim/id/_DANCo.py#L155-L201
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_DANCo.py#L207-L253
 
 
 

diff --git a/doc/skdim.id.DANCo.fit_transform.rst b/doc/skdim.id.DANCo.fit_transform.rst
@@ -0,0 +1,10 @@
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_DANCo.py#L192-L205
+
+
+
+skdim.id.DANCo.fit\_transform
+=============================
+
+.. currentmodule:: skdim.id
+
+.. automethod:: DANCo.fit_transform
diff --git a/doc/skdim.id.DANCo.fit_transform_pw.rst b/doc/skdim.id.DANCo.fit_transform_pw.rst
@@ -0,0 +1,10 @@
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_DANCo.py#L284-L335
+
+
+
+skdim.id.DANCo.fit\_transform\_pw
+=================================
+
+.. currentmodule:: skdim.id
+
+.. automethod:: DANCo.fit_transform_pw
diff --git a/doc/skdim.id.DANCo.get_params.rst b/doc/skdim.id.DANCo.get_params.rst
@@ -1,4 +1,4 @@
-:github_url: https://github.com/theislab/scvelo/tree/master/scikit-dimension/skdim/id/_DANCo.py#L189-L219
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_DANCo.py#L178-L200
 
 
 

diff --git a/doc/skdim.id.DANCo.rst b/doc/skdim.id.DANCo.rst
@@ -19,16 +19,12 @@ skdim.id.DANCo
       :toctree: .
 
       ~skdim.id.DANCo.fit
-      ~skdim.id.DANCo.fit_predict
-      ~skdim.id.DANCo.fit_predict_pw
       ~skdim.id.DANCo.fit_pw
+      ~skdim.id.DANCo.fit_transform
+      ~skdim.id.DANCo.fit_transform_pw
       ~skdim.id.DANCo.get_params
-      ~skdim.id.DANCo.predict
-      ~skdim.id.DANCo.predict_pw
       ~skdim.id.DANCo.set_params
-
-
-
-
+      ~skdim.id.DANCo.transform
+      ~skdim.id.DANCo.transform_pw
 
 
diff --git a/doc/skdim.id.DANCo.set_params.rst b/doc/skdim.id.DANCo.set_params.rst
@@ -1,4 +1,4 @@
-:github_url: https://github.com/theislab/scvelo/tree/master/scikit-dimension/skdim/id/_DANCo.py#L221-L263
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_DANCo.py#L202-L244
 
 
 

diff --git a/doc/skdim.id.DANCo.transform.rst b/doc/skdim.id.DANCo.transform.rst
@@ -0,0 +1,10 @@
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_DANCo.py#L177-L190
+
+
+
+skdim.id.DANCo.transform
+========================
+
+.. currentmodule:: skdim.id
+
+.. automethod:: DANCo.transform
diff --git a/doc/skdim.id.DANCo.transform_pw.rst b/doc/skdim.id.DANCo.transform_pw.rst
@@ -0,0 +1,10 @@
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_DANCo.py#L255-L282
+
+
+
+skdim.id.DANCo.transform\_pw
+============================
+
+.. currentmodule:: skdim.id
+
+.. automethod:: DANCo.transform_pw
diff --git a/doc/skdim.id.ESS.fit.rst b/doc/skdim.id.ESS.fit.rst
@@ -1,4 +1,4 @@
-:github_url: https://github.com/theislab/scvelo/tree/master/scikit-dimension/skdim/id/_ESS.py#L301-L372
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_ESS.py#L362-L434
 
 
 

diff --git a/doc/skdim.id.ESS.fit_once.rst b/doc/skdim.id.ESS.fit_once.rst
@@ -1,4 +1,4 @@
-:github_url: https://github.com/theislab/scvelo/tree/master/scikit-dimension/skdim/id/_ESS.py#L85-L105
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_ESS.py#L80-L100
 
 
 

diff --git a/doc/skdim.id.ESS.fit_transform.rst b/doc/skdim.id.ESS.fit_transform.rst
@@ -0,0 +1,10 @@
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_ESS.py#L451-L492
+
+
+
+skdim.id.ESS.fit\_transform
+===========================
+
+.. currentmodule:: skdim.id
+
+.. automethod:: ESS.fit_transform
diff --git a/doc/skdim.id.ESS.fit_transform_pw.rst b/doc/skdim.id.ESS.fit_transform_pw.rst
@@ -0,0 +1,10 @@
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_ESS.py#L523-L563
+
+
+
+skdim.id.ESS.fit\_transform\_pw
+===============================
+
+.. currentmodule:: skdim.id
+
+.. automethod:: ESS.fit_transform_pw
diff --git a/doc/skdim.id.ESS.get_params.rst b/doc/skdim.id.ESS.get_params.rst
@@ -1,4 +1,4 @@
-:github_url: https://github.com/theislab/scvelo/tree/master/scikit-dimension/skdim/id/_ESS.py#L189-L219
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_ESS.py#L178-L200
 
 
 

diff --git a/doc/skdim.id.ESS.rst b/doc/skdim.id.ESS.rst
@@ -20,15 +20,11 @@ skdim.id.ESS
 
       ~skdim.id.ESS.fit
       ~skdim.id.ESS.fit_once
-      ~skdim.id.ESS.fit_predict
-      ~skdim.id.ESS.fit_predict_pw
+      ~skdim.id.ESS.fit_transform
+      ~skdim.id.ESS.fit_transform_pw
       ~skdim.id.ESS.get_params
-      ~skdim.id.ESS.predict
-      ~skdim.id.ESS.predict_pw
       ~skdim.id.ESS.set_params
-
-
-
-
+      ~skdim.id.ESS.transform
+      ~skdim.id.ESS.transform_pw
 
 
diff --git a/doc/skdim.id.ESS.set_params.rst b/doc/skdim.id.ESS.set_params.rst
@@ -1,4 +1,4 @@
-:github_url: https://github.com/theislab/scvelo/tree/master/scikit-dimension/skdim/id/_ESS.py#L221-L263
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_ESS.py#L202-L244
 
 
 

diff --git a/doc/skdim.id.ESS.transform.rst b/doc/skdim.id.ESS.transform.rst
@@ -0,0 +1,10 @@
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_ESS.py#L436-L449
+
+
+
+skdim.id.ESS.transform
+======================
+
+.. currentmodule:: skdim.id
+
+.. automethod:: ESS.transform
diff --git a/doc/skdim.id.ESS.transform_pw.rst b/doc/skdim.id.ESS.transform_pw.rst
@@ -0,0 +1,10 @@
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_ESS.py#L494-L521
+
+
+
+skdim.id.ESS.transform\_pw
+==========================
+
+.. currentmodule:: skdim.id
+
+.. automethod:: ESS.transform_pw
diff --git a/doc/skdim.id.FisherS.buildSeparabilityGraph.rst b/doc/skdim.id.FisherS.buildSeparabilityGraph.rst
@@ -1,4 +1,4 @@
-:github_url: https://github.com/theislab/scvelo/tree/master/scikit-dimension/skdim/id/_FisherS.py#L494-L581
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_FisherS.py#L491-L578
 
 
 

diff --git a/doc/skdim.id.FisherS.check_symmetric.rst b/doc/skdim.id.FisherS.check_symmetric.rst
@@ -1,4 +1,4 @@
-:github_url: https://github.com/theislab/scvelo/tree/master/scikit-dimension/skdim/id/_FisherS.py#L583-L585
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_FisherS.py#L580-L582
 
 
 

diff --git a/doc/skdim.id.FisherS.fit.rst b/doc/skdim.id.FisherS.fit.rst
@@ -1,4 +1,4 @@
-:github_url: https://github.com/theislab/scvelo/tree/master/scikit-dimension/skdim/id/_FisherS.py#L87-L130
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_FisherS.py#L82-L127
 
 
 

diff --git a/doc/skdim.id.FisherS.fit_pw.rst b/doc/skdim.id.FisherS.fit_pw.rst
@@ -1,4 +1,4 @@
-:github_url: https://github.com/theislab/scvelo/tree/master/scikit-dimension/skdim/id/_FisherS.py#L155-L201
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_FisherS.py#L207-L253
 
 
 

diff --git a/doc/skdim.id.FisherS.fit_transform.rst b/doc/skdim.id.FisherS.fit_transform.rst
@@ -0,0 +1,10 @@
+:github_url: https://github.com/j-bac/scikit-dimension/tree/master/scikit-dimension/skdim/id/_FisherS.py#L192-L205
+
+
+
+skdim.id.FisherS.fit\_transform
+===============================
+
+.. currentmodule:: skdim.id
+
+.. automethod:: FisherS.fit_transform