Merge pull request #171 from lucasimi/develop

Develop

Author: lucasimi

README.md

@@ -76,7 +76,7 @@ from sklearn.datasets import make_circles
 from sklearn.decomposition import PCA
 from sklearn.cluster import DBSCAN
 
-from tdamapper.core import MapperAlgorithm
+from tdamapper.learn import MapperAlgorithm
 from tdamapper.cover import CubicalCover
 from tdamapper.plot import MapperPlot
 

docs/source/notebooks/circles_online.ipynb

@@ -42,7 +42,7 @@
     "from sklearn.decomposition import PCA\n",
     "from sklearn.cluster import DBSCAN\n",
     "\n",
-    "from tdamapper.core import MapperAlgorithm\n",
+    "from tdamapper.learn import MapperAlgorithm\n",
     "from tdamapper.cover import CubicalCover\n",
     "from tdamapper.plot import MapperPlot\n",
     "\n",

docs/source/notebooks/digits_online.ipynb

@@ -10,7 +10,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 5,
    "id": "8cf55ffb",
    "metadata": {},
    "outputs": [],
@@ -21,7 +21,7 @@
     "from sklearn.cluster import AgglomerativeClustering\n",
     "from sklearn.decomposition import PCA\n",
     "\n",
-    "from tdamapper.core import MapperAlgorithm\n",
+    "from tdamapper.learn import MapperAlgorithm\n",
     "from tdamapper.cover import CubicalCover\n",
     "from tdamapper.clustering import FailSafeClustering\n",
     "from tdamapper.plot import MapperPlot\n",
@@ -41,7 +41,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 6,
    "id": "02d341cc",
    "metadata": {},
    "outputs": [],
@@ -68,7 +68,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 7,
    "id": "a20d99cf",
    "metadata": {},
    "outputs": [
@@ -163,7 +163,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 8,
    "id": "ee374256",
    "metadata": {},
    "outputs": [

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "tda-mapper"
-version = "0.7.3"
+version = "0.8.0"
 description = "A simple and efficient Python implementation of Mapper algorithm for Topological Data Analysis"
 readme = "README.md"
 authors = [{ name = "Luca Simi", email = "lucasimi90@gmail.com" }]

src/tdamapper/_common.py

@@ -6,13 +6,20 @@
 import numpy as np
 
 
-def warn_deprecated(deprecated, substitute):
-    msg = f'{deprecated} is deprecated and will be removed in a future version. Use {substitute} instead.'
-    warnings.warn(
-        msg,
-        DeprecationWarning,
-        stacklevel=2
-    )
+warnings.filterwarnings(
+    'default',
+    category=DeprecationWarning,
+    module=r'^tdamapper\.'
+)
+
+
+def deprecated(msg):
+    def deprecated_func(func):
+        def wrapper(*args, **kwargs):
+            warnings.warn(msg, DeprecationWarning, stacklevel=2)
+            return func(*args, **kwargs)
+        return wrapper
+    return deprecated_func
 
 
 def warn_user(msg):

src/tdamapper/clustering.py

@@ -8,7 +8,7 @@
     ParamsMixin,
     EstimatorMixin,
     clone,
-    warn_deprecated,
+    deprecated,
 )
 
 
@@ -17,25 +17,27 @@ class TrivialClustering(tdamapper.core.TrivialClustering):
     **DEPRECATED**: This class is deprecated and will be removed in a future
     release. Use :class:`tdamapper.core.TrivialClustering`.
     """
-    def __init__(self):
-        warn_deprecated(
-            TrivialClustering.__qualname__,
-            tdamapper.core.TrivialClustering.__qualname__,
-        )
-        super().__init__()
+
+    @deprecated(
+        'This class is deprecated and will be removed in a future release. '
+        'Use tdamapper.core.TrivialClustering.'
+    )
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
 
 
 class FailSafeClustering(tdamapper.core.FailSafeClustering):
     """
     **DEPRECATED**: This class is deprecated and will be removed in a future
     release. Use :class:`tdamapper.core.FailSafeClustering`.
     """
-    def __init__(self, clustering=None, verbose=True):
-        warn_deprecated(
-            FailSafeClustering.__qualname__,
-            tdamapper.core.FailSafeClustering.__qualname__,
-        )
-        super().__init__(clustering, verbose)
+
+    @deprecated(
+        'This class is deprecated and will be removed in a future release. '
+        'Use tdamapper.core.FailSafeClustering.'
+    )
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
 
 
 class _MapperClustering(EstimatorMixin, ParamsMixin):
@@ -73,13 +75,9 @@ class MapperClustering(_MapperClustering):
     release. Use :class:`tdamapper.learn.MapperClustering`.
     """
 
-    def __init__(self, cover=None, clustering=None, n_jobs=1):
-        warn_deprecated(
-            MapperClustering.__qualname__,
-            'tdamapper.learn.MapperClustering',
-        )
-        super().__init__(
-            cover=cover,
-            clustering=clustering,
-            n_jobs=n_jobs,
-        )
+    @deprecated(
+        'This class is deprecated and will be removed in a future release. '
+        'Use tdamapper.learn.MapperClustering.'
+    )
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)

src/tdamapper/core.py

@@ -35,7 +35,7 @@
 from tdamapper.utils.unionfind import UnionFind
 from tdamapper._common import (
     clone,
-    warn_deprecated,
+    deprecated,
     ParamsMixin,
     EstimatorMixin,
 )
@@ -424,25 +424,12 @@ class MapperAlgorithm(_MapperAlgorithm):
     release. Use :class:`tdamapper.learn.MapperAlgorithm`.
     """
 
-    def __init__(
-        self,
-        cover=None,
-        clustering=None,
-        failsafe=True,
-        verbose=True,
-        n_jobs=1,
-    ):
-        warn_deprecated(
-            MapperAlgorithm.__qualname__,
-            'tdamapper.learn.MapperAlgorithm',
-        )
-        super().__init__(
-            cover=cover,
-            clustering=clustering,
-            failsafe=failsafe,
-            verbose=verbose,
-            n_jobs=n_jobs,
-        )
+    @deprecated(
+        'This class is deprecated and will be removed in a future release. '
+        'Use tdamapper.learn.MapperAlgorithm.'
+    )
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
 
 
 class FailSafeClustering(ParamsMixin):

src/tdamapper/plot.py

@@ -9,7 +9,7 @@
 from tdamapper._plot_plotly import plot_plotly, plot_plotly_update
 from tdamapper._plot_pyvis import plot_pyvis
 
-from tdamapper._common import warn_deprecated
+from tdamapper._common import deprecated
 
 
 class MapperPlot:
@@ -289,6 +289,10 @@ class MapperLayoutInteractive:
     :type cmap: str, optional
     """
 
+    @deprecated(
+        'This class is deprecated and will be removed in a future release. '
+        'Use tdamapper.plot.MapperPlot.'
+    )
     def __init__(
         self,
         graph,
@@ -302,10 +306,6 @@ def __init__(
         height=512,
         cmap='jet',
     ):
-        warn_deprecated(
-            MapperLayoutInteractive.__qualname__,
-            MapperPlot.__qualname__,
-        )
         self.__graph = graph
         self.__dim = dim
         self.__iterations = iterations
@@ -450,6 +450,10 @@ class MapperLayoutStatic:
     :type cmap: str, optional
     """
 
+    @deprecated(
+        'This class is deprecated and will be removed in a future release. '
+        'Use tdamapper.plot.MapperPlot.'
+    )
     def __init__(
         self,
         graph,
@@ -463,10 +467,6 @@ def __init__(
         height=512,
         cmap='jet',
     ):
-        warn_deprecated(
-            MapperLayoutStatic.__qualname__,
-            MapperPlot.__qualname__,
-        )
         self.__colors = colors
         self.__agg = agg
         self.__title = title

tests/example.py

@@ -4,7 +4,7 @@
 from sklearn.decomposition import PCA
 from sklearn.cluster import DBSCAN
 
-from tdamapper.core import MapperAlgorithm
+from tdamapper.learn import MapperAlgorithm
 from tdamapper.cover import CubicalCover
 from tdamapper.plot import MapperPlot