Fixes #214, Fixing module import structure to conform to python best …

…practices.

test/classes/test_reportviews.py

@@ -2,9 +2,7 @@
 
 import pytest
 
-from toponetx import CombinatorialComplex, HyperEdge
-from toponetx.classes.cell import Cell
-from toponetx.classes.cell_complex import CellComplex
+from toponetx.classes import Cell, CellComplex, CombinatorialComplex, HyperEdge
 from toponetx.classes.reportviews import CellView, HyperEdgeView, NodeView, SimplexView
 from toponetx.exception import TopoNetXError
 

toponetx/__init__.py

@@ -1,30 +1,4 @@
 __version__ = "0.0.2"
 
-from toponetx.exception import (
-    TopoNetXError,
-    TopoNetXException,
-    TopoNetXNotImplementedError,
-)
 
-from .classes.cell import Cell
-from .classes.cell_complex import CellComplex
-from .classes.combinatorial_complex import CombinatorialComplex
-from .classes.complex import Complex
-from .classes.hyperedge import HyperEdge
-from .classes.reportviews import CellView, HyperEdgeView, NodeView, SimplexView
-from .classes.simplex import Simplex
-from .classes.simplicial_complex import SimplicialComplex
-from .datasets.graph import karate_club
-from .datasets.mesh import coseg, shrec_16, stanford_bunny
-from .transform.graph_to_cell_complex import homology_cycle_cell_complex
-from .transform.graph_to_simplicial_complex import (
-    graph_2_clique_complex,
-    graph_2_neighbor_complex,
-    graph_to_clique_complex,
-    graph_to_neighbor_complex,
-)
-from .utils.structure import (
-    neighborhood_list_to_neighborhood_dict,
-    sparse_array_to_neighborhood_dict,
-    sparse_array_to_neighborhood_list,
-)
+__all__ = ["algorithms", "classes", "datasets", "transform", "utils"]

toponetx/algorithms/__init__.py

@@ -1 +1 @@
-from toponetx.algorithms.spectrum import *
+from .spectrum import *

toponetx/classes/__init__.py

@@ -1,8 +1,23 @@
-from .cell import *
-from .cell_complex import *
-from .combinatorial_complex import *
-from .complex import *
-from .hyperedge import *
-from .reportviews import *
-from .simplex import *
-from .simplicial_complex import *
+from .cell import Cell
+from .cell_complex import CellComplex
+from .combinatorial_complex import CombinatorialComplex
+from .complex import Atom, Complex
+from .hyperedge import HyperEdge
+from .reportviews import CellView, HyperEdgeView, NodeView, SimplexView
+from .simplex import Simplex
+from .simplicial_complex import SimplicialComplex
+
+__all__ = [
+    "CellComplex",
+    "Cell",
+    "CombinatorialComplex",
+    "Atom",
+    "Complex",
+    "HyperEdge",
+    "HyperEdgeView",
+    "CellView",
+    "SimplexView",
+    "NodeView",
+    "Simplex",
+    "SimplicialComplex",
+]

toponetx/utils/structure.py

@@ -27,6 +27,13 @@
 
 from scipy.sparse import csr_matrix
 
+__all__ = [
+    "sparse_array_to_neighborhood_list",
+    "neighborhood_list_to_neighborhood_dict",
+    "sparse_array_to_neighborhood_dict",
+    "incidence_to_adjacency",
+]
+
 
 def sparse_array_to_neighborhood_list(
     sparse_array, src_dict=None, dst_dict=None

tutorials/01_simplicial_complexes.ipynb

@@ -73,7 +73,7 @@
    "source": [
     "import numpy as np\n",
     "\n",
-    "from toponetx import SimplicialComplex as sc"
+    "from toponetx.classes import SimplicialComplex as sc"
    ]
   },
   {
@@ -1274,7 +1274,7 @@
  "metadata": {
   "celltoolbar": "Tags",
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3.10.11 ('TopoNetX')",
    "language": "python",
    "name": "python3"
   },
@@ -1289,6 +1289,11 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.10.11"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "451a7a2cf09dfa0c0cb86ffbef03c452948bc098596cedd81cbba4e03b20199b"
+   }
   }
  },
  "nbformat": 4,

tutorials/02_cell_complexes.ipynb

@@ -57,7 +57,7 @@
    "source": [
     "import numpy as np\n",
     "\n",
-    "from toponetx import CellComplex as Cc"
+    "from toponetx.classes import CellComplex as Cc"
    ]
   },
   {

tutorials/03_combinatorial_complexes.ipynb

@@ -55,7 +55,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from toponetx import CombinatorialComplex as cc"
+    "from toponetx.classes import CombinatorialComplex as cc"
    ]
   },
   {