From 507d63567b596987b2b95e40ce6e777d03dfa78b Mon Sep 17 00:00:00 2001
From: Florian Frantzen <florian.frantzen@rwth-aachen.de>
Date: Mon, 31 Mar 2025 13:30:42 +0200
Subject: [PATCH 1/2] Rename `complex` variables to `domain`

The old name shadows the built-in `complex` class for complex numbers.
---
 topoembedx/classes/cell2vec.py                |  6 +++---
 topoembedx/classes/cell_diff2vec.py           |  6 +++---
 topoembedx/classes/deepcell.py                |  6 +++---
 .../higher_order_laplacian_eigenmaps.py       |  6 +++---
 topoembedx/classes/hoglee.py                  |  6 +++---
 topoembedx/classes/hope.py                    |  6 +++---
 topoembedx/neighborhood.py                    | 20 +++++++++----------
 7 files changed, 28 insertions(+), 28 deletions(-)

diff --git a/topoembedx/classes/cell2vec.py b/topoembedx/classes/cell2vec.py
index f0cc229..80e1aae 100644
--- a/topoembedx/classes/cell2vec.py
+++ b/topoembedx/classes/cell2vec.py
@@ -93,7 +93,7 @@ def __init__(
 
     def fit(
         self,
-        complex: tnx.Complex,
+        domain: tnx.Complex,
         neighborhood_type: Literal["adj", "coadj"] = "adj",
         neighborhood_dim=None,
     ) -> None:
@@ -101,7 +101,7 @@ def fit(
 
         Parameters
         ----------
-        complex : toponetx.classes.Complex
+        domain : toponetx.classes.Complex
             A complex object. The complex object can be one of the following:
             - CellComplex
             - CombinatorialComplex
@@ -128,7 +128,7 @@ def fit(
         colored hypergraph.
         """
         self.ind, self.A = neighborhood_from_complex(
-            complex, neighborhood_type, neighborhood_dim
+            domain, neighborhood_type, neighborhood_dim
         )
 
         g = nx.from_numpy_array(self.A)
diff --git a/topoembedx/classes/cell_diff2vec.py b/topoembedx/classes/cell_diff2vec.py
index 07e1fd8..4487205 100644
--- a/topoembedx/classes/cell_diff2vec.py
+++ b/topoembedx/classes/cell_diff2vec.py
@@ -73,7 +73,7 @@ def __init__(
 
     def fit(
         self,
-        complex: tnx.Complex,
+        domain: tnx.Complex,
         neighborhood_type: Literal["adj", "coadj"] = "adj",
         neighborhood_dim=None,
     ) -> None:
@@ -81,7 +81,7 @@ def fit(
 
         Parameters
         ----------
-        complex : toponetx.classes.Complex
+        domain : toponetx.classes.Complex
             A complex object. The complex object can be one of the following:
             - CellComplex
             - CombinatorialComplex
@@ -108,7 +108,7 @@ def fit(
         colored hypergraph.
         """
         self.ind, self.A = neighborhood_from_complex(
-            complex, neighborhood_type, neighborhood_dim
+            domain, neighborhood_type, neighborhood_dim
         )
 
         self.A.setdiag(1)
diff --git a/topoembedx/classes/deepcell.py b/topoembedx/classes/deepcell.py
index 2d3881b..b9cbbb2 100644
--- a/topoembedx/classes/deepcell.py
+++ b/topoembedx/classes/deepcell.py
@@ -73,7 +73,7 @@ def __init__(
 
     def fit(
         self,
-        complex: tnx.Complex,
+        domain: tnx.Complex,
         neighborhood_type: Literal["adj", "coadj"] = "adj",
         neighborhood_dim=None,
     ) -> None:
@@ -81,7 +81,7 @@ def fit(
 
         Parameters
         ----------
-        complex : toponetx.classes.Complex
+        domain : toponetx.classes.Complex
             A complex object. The complex object can be one of the following:
             - CellComplex
             - CombinatorialComplex
@@ -108,7 +108,7 @@ def fit(
         colored hypergraph.
         """
         self.ind, self.A = neighborhood_from_complex(
-            complex, neighborhood_type, neighborhood_dim
+            domain, neighborhood_type, neighborhood_dim
         )
 
         self.A.setdiag(1)
diff --git a/topoembedx/classes/higher_order_laplacian_eigenmaps.py b/topoembedx/classes/higher_order_laplacian_eigenmaps.py
index c724401..3be4211 100644
--- a/topoembedx/classes/higher_order_laplacian_eigenmaps.py
+++ b/topoembedx/classes/higher_order_laplacian_eigenmaps.py
@@ -38,7 +38,7 @@ def __init__(
 
     def fit(
         self,
-        complex: tnx.Complex,
+        domain: tnx.Complex,
         neighborhood_type: Literal["adj", "coadj"] = "adj",
         neighborhood_dim=None,
     ) -> None:
@@ -46,7 +46,7 @@ def fit(
 
         Parameters
         ----------
-        complex : toponetx.classes.Complex
+        domain : toponetx.classes.Complex
             A complex object. The complex object can be one of the following:
             - CellComplex
             - CombinatorialComplex
@@ -73,7 +73,7 @@ def fit(
         colored hypergraph.
         """
         self.ind, self.A = neighborhood_from_complex(
-            complex, neighborhood_type, neighborhood_dim
+            domain, neighborhood_type, neighborhood_dim
         )
 
         self.A.setdiag(1)
diff --git a/topoembedx/classes/hoglee.py b/topoembedx/classes/hoglee.py
index 5c70907..618498d 100644
--- a/topoembedx/classes/hoglee.py
+++ b/topoembedx/classes/hoglee.py
@@ -30,7 +30,7 @@ def __init__(self, dimensions: int = 128, seed: int = 42):
 
     def fit(
         self,
-        complex: tnx.Complex,
+        domain: tnx.Complex,
         neighborhood_type: Literal["adj", "coadj"] = "adj",
         neighborhood_dim=None,
     ) -> None:
@@ -38,7 +38,7 @@ def fit(
 
         Parameters
         ----------
-        complex : toponetx.classes.Complex
+        domain : toponetx.classes.Complex
             A complex object. The complex object can be one of the following:
             - CellComplex
             - CombinatorialComplex
@@ -65,7 +65,7 @@ def fit(
         colored hypergraph.
         """
         self.ind, self.A = neighborhood_from_complex(
-            complex, neighborhood_type, neighborhood_dim
+            domain, neighborhood_type, neighborhood_dim
         )
 
         self.A.setdiag(1)
diff --git a/topoembedx/classes/hope.py b/topoembedx/classes/hope.py
index 9c0e99a..93fbeb9 100644
--- a/topoembedx/classes/hope.py
+++ b/topoembedx/classes/hope.py
@@ -114,7 +114,7 @@ def _laplacian_pe(
 
     def fit(
         self,
-        complex: tnx.Complex,
+        domain: tnx.Complex,
         neighborhood_type: Literal["adj", "coadj"] = "adj",
         neighborhood_dim: dict | None = None,
     ) -> None:
@@ -122,7 +122,7 @@ def fit(
 
         Parameters
         ----------
-        complex : toponetx.classes.Complex
+        domain : toponetx.classes.Complex
             A complex object. The complex object can be one of the following:
             - CellComplex
             - CombinatorialComplex
@@ -165,7 +165,7 @@ def fit(
         >>> em = model.get_embedding(get_dict=True)
         """
         self.ind, self.A = neighborhood_from_complex(
-            complex, neighborhood_type, neighborhood_dim
+            domain, neighborhood_type, neighborhood_dim
         )
 
         self._embedding = self._laplacian_pe(self.A, self.dimensions)
diff --git a/topoembedx/neighborhood.py b/topoembedx/neighborhood.py
index 089291f..badc7e2 100644
--- a/topoembedx/neighborhood.py
+++ b/topoembedx/neighborhood.py
@@ -7,7 +7,7 @@
 
 
 def neighborhood_from_complex(
-    complex: tnx.Complex,
+    domain: tnx.Complex,
     neighborhood_type: Literal["adj", "coadj"] = "adj",
     neighborhood_dim=None,
 ) -> tuple[list, csr_matrix]:
@@ -15,11 +15,11 @@ def neighborhood_from_complex(
 
     This function returns the indices and matrix for the neighborhood specified
     by `neighborhood_type`
-    and `neighborhood_dim` for the input complex `complex`.
+    and `neighborhood_dim` for the input complex `domain`.
 
     Parameters
     ----------
-    complex : toponetx.classes.Complex
+    domain : toponetx.classes.Complex
         The complex to compute the neighborhood for.
     neighborhood_type : {"adj", "coadj"}, default="adj"
         The type of neighborhood to compute. "adj" for adjacency matrix, "coadj" for coadjacency matrix.
@@ -50,7 +50,7 @@ def neighborhood_from_complex(
     Raises
     ------
     TypeError
-        If `complex` is not a SimplicialComplex, CellComplex, PathComplex ColoredHyperGraph or CombinatorialComplex.
+        If `domain` is not a SimplicialComplex, CellComplex, PathComplex ColoredHyperGraph or CombinatorialComplex.
     TypeError
         If `neighborhood_type` is invalid.
     """
@@ -62,18 +62,18 @@ def neighborhood_from_complex(
             f"Input neighborhood_type must be `adj` or `coadj`, got {neighborhood_type}."
         )
 
-    if isinstance(complex, tnx.SimplicialComplex | tnx.CellComplex | tnx.PathComplex):
+    if isinstance(domain, tnx.SimplicialComplex | tnx.CellComplex | tnx.PathComplex):
         if neighborhood_type == "adj":
-            ind, A = complex.adjacency_matrix(neighborhood_dim["rank"], index=True)
+            ind, A = domain.adjacency_matrix(neighborhood_dim["rank"], index=True)
         else:
-            ind, A = complex.coadjacency_matrix(neighborhood_dim["rank"], index=True)
-    elif isinstance(complex, tnx.CombinatorialComplex | tnx.ColoredHyperGraph):
+            ind, A = domain.coadjacency_matrix(neighborhood_dim["rank"], index=True)
+    elif isinstance(domain, tnx.CombinatorialComplex | tnx.ColoredHyperGraph):
         if neighborhood_type == "adj":
-            ind, A = complex.adjacency_matrix(
+            ind, A = domain.adjacency_matrix(
                 neighborhood_dim["rank"], neighborhood_dim["via_rank"], index=True
             )
         else:
-            ind, A = complex.coadjacency_matrix(
+            ind, A = domain.coadjacency_matrix(
                 neighborhood_dim["rank"], neighborhood_dim["via_rank"], index=True
             )
     else:

From 851fee14f8366633d6646de68ec6959a70c43aa2 Mon Sep 17 00:00:00 2001
From: Florian Frantzen <florian.frantzen@rwth-aachen.de>
Date: Mon, 31 Mar 2025 14:40:37 +0200
Subject: [PATCH 2/2] Activate additional ruff rules

---
 conftest.py                                   | 30 +++++++++++++++++
 docs/conf.py                                  |  2 +-
 pyproject.toml                                | 33 +++++++++++++++++--
 test/test_neighborhood.py                     |  8 ++---
 test/test_tutorials.py                        | 21 +++++++++---
 topoembedx/__init__.py                        |  7 +---
 topoembedx/classes/__init__.py                |  8 +++++
 topoembedx/classes/cell2vec.py                |  2 +-
 topoembedx/classes/cell_diff2vec.py           |  2 +-
 topoembedx/classes/deepcell.py                |  2 +-
 .../higher_order_laplacian_eigenmaps.py       |  2 +-
 topoembedx/classes/hoglee.py                  |  2 +-
 topoembedx/classes/hope.py                    |  3 +-
 topoembedx/classes/random_walks.py            | 13 +++-----
 topoembedx/{exceptions.py => exception.py}    |  4 ++-
 topoembedx/neighborhood.py                    |  7 ++--
 16 files changed, 109 insertions(+), 37 deletions(-)
 create mode 100644 conftest.py
 rename topoembedx/{exceptions.py => exception.py} (69%)

diff --git a/conftest.py b/conftest.py
new file mode 100644
index 0000000..b70ad41
--- /dev/null
+++ b/conftest.py
@@ -0,0 +1,30 @@
+"""Configure our testing suite."""
+
+import networkx as nx
+import numpy as np
+import pytest
+import toponetx as tnx
+
+
+@pytest.fixture(autouse=True)
+def doctest_default_imports(doctest_namespace) -> None:
+    """Add default imports to the doctest namespace.
+
+    This fixture adds the following default imports to every doctest, so that their use
+    is consistent across all doctests without boilerplate imports polluting the
+    doctests themselves:
+
+    .. code-block:: python
+
+        import numpy as np
+        import networkx as nx
+        import toponetx as tnx
+
+    Parameters
+    ----------
+    doctest_namespace : dict
+        The namespace of the doctest.
+    """
+    doctest_namespace["np"] = np
+    doctest_namespace["nx"] = nx
+    doctest_namespace["tnx"] = tnx
diff --git a/docs/conf.py b/docs/conf.py
index 765b666..37490c2 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -3,7 +3,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "TopoEmbedX"
-copyright = "2022-2023, PyT-Team, Inc."
+copyright = "2022-2023, PyT-Team, Inc."  # noqa: A001
 author = "PyT-Team Authors"
 language = "en"
 
diff --git a/pyproject.toml b/pyproject.toml
index 1db4ffc..afdc483 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -113,20 +113,49 @@ select = [
     "E", # code style
     "W", # warnings
     "I", # import order
+    "D", # pydocstyle rules
     "UP", # pyupgrade rules
+    "YTT", # flake8-2020 rules
+    "S", # bandit rules
+    "BLE", # blind except
     "B", # bugbear rules
+    "A", # builtin shadowing
+    "COM", # comma rules
+    "C4", # comprehensions
+    "DTZ", # datetime rules
+    "T10", # debugger calls
+    "FA", # future annotations
+    "ISC", # implicit str concatenation
+    "ICN", # import conventions
+    "LOG", # logging rules
+    "G", # logging format rules
     "PIE", # pie rules
     "Q", # quote rules
+    "RSE", # raise rules
     "RET", # return rules
+    "SLOT", # slot rules
     "SIM", # code simplifications
+    "TID", # tidy imports
+    "TC", # type checking rules
+    "PTH", # use pathlib
+    "PD", # pandas rules
+    "PLC", # pylint conventions
+    "PLE", # pylint errors
+    "FLY", # flynt
     "NPY", # numpy rules
     "PERF", # performance rules
+    "FURB", # refurb
     "RUF", # miscellaneous rules
 ]
-ignore = ["E501"] # line too long
+ignore = [
+    "E501",    # line too long
+    "COM812",  # trailing commas; conflict with `ruff format`
+    "ISC001",  # implicitly single-line str concat; conflict with `ruff format`
+]
 
 [tool.ruff.lint.per-file-ignores]
-"__init__.py" = ["F401", "F403"]
+"__init__.py" = ["F403"]
+"test/**.py" = ["S101"]
 
 [tool.ruff.lint.pydocstyle]
 convention = "numpy"
diff --git a/test/test_neighborhood.py b/test/test_neighborhood.py
index 2302330..54c5141 100644
--- a/test/test_neighborhood.py
+++ b/test/test_neighborhood.py
@@ -29,21 +29,21 @@ def test_neighborhood_from_complex_matrix_dimension_cell_complex(self):
         cc2 = tnx.classes.CellComplex([[0, 1, 2], [1, 2, 3]])
 
         ind, A = tex.neighborhood.neighborhood_from_complex(cc1)
-        assert A.todense().shape == tuple([9, 9])
+        assert A.todense().shape == (9, 9)
         assert len(ind) == 9
 
         ind, A = tex.neighborhood.neighborhood_from_complex(cc2)
-        assert A.todense().shape == tuple([4, 4])
+        assert A.todense().shape == (4, 4)
         assert len(ind) == 4
 
         ind, A = tex.neighborhood.neighborhood_from_complex(
             cc1, neighborhood_type="coadj"
         )
-        assert A.todense().shape == tuple([9, 9])
+        assert A.todense().shape == (9, 9)
         assert len(ind) == 9
 
         ind, A = tex.neighborhood.neighborhood_from_complex(
             cc2, neighborhood_type="coadj"
         )
-        assert A.todense().shape == tuple([4, 4])
+        assert A.todense().shape == (4, 4)
         assert len(ind) == 4
diff --git a/test/test_tutorials.py b/test/test_tutorials.py
index d5ed160..aa6f53a 100644
--- a/test/test_tutorials.py
+++ b/test/test_tutorials.py
@@ -1,13 +1,20 @@
 """Unit tests for the tutorials."""
 
-import glob
 import subprocess
 import tempfile
+from pathlib import Path
 
 import pytest
 
 
 def _exec_tutorial(path):
+    """Execute the notebooks for testing in the given directory.
+
+    Parameters
+    ----------
+    path : str
+        Path to the tutorials directory.
+    """
     with tempfile.NamedTemporaryFile(suffix=".ipynb") as tmp_file:
         args = [
             "jupyter",
@@ -21,14 +28,20 @@ def _exec_tutorial(path):
             tmp_file.name,
             path,
         ]
-        subprocess.check_call(args)
+        subprocess.check_call(args)  # noqa: S603
 
 
 TUTORIALS_DIR = "tutorials"
-paths = sorted(glob.glob(f"{TUTORIALS_DIR}/*.ipynb"))
+paths = sorted(Path(TUTORIALS_DIR).glob("*.ipynb"))
 
 
 @pytest.mark.parametrize("path", paths)
 def test_tutorial(path):
-    """Test the tutorials."""
+    """Test the tutorials.
+
+    Parameters
+    ----------
+    path : str
+        Path to the tutorials directory.
+    """
     _exec_tutorial(path)
diff --git a/topoembedx/__init__.py b/topoembedx/__init__.py
index 8a56802..08392f5 100644
--- a/topoembedx/__init__.py
+++ b/topoembedx/__init__.py
@@ -1,8 +1,3 @@
 """Initialize the library with modules and other content."""
 
-from .classes.cell2vec import Cell2Vec
-from .classes.cell_diff2vec import CellDiff2Vec
-from .classes.deepcell import DeepCell
-from .classes.higher_order_laplacian_eigenmaps import HigherOrderLaplacianEigenmaps
-from .classes.hoglee import HOGLEE
-from .classes.hope import HOPE
+from .classes import *
diff --git a/topoembedx/classes/__init__.py b/topoembedx/classes/__init__.py
index fc63c89..9a6d7b9 100644
--- a/topoembedx/classes/__init__.py
+++ b/topoembedx/classes/__init__.py
@@ -1 +1,9 @@
 """Initialize the classes module of TopoEmbedX."""
+
+from .cell2vec import *
+from .cell_diff2vec import *
+from .deepcell import *
+from .higher_order_laplacian_eigenmaps import *
+from .hoglee import *
+from .hope import *
+from .random_walks import *
diff --git a/topoembedx/classes/cell2vec.py b/topoembedx/classes/cell2vec.py
index 80e1aae..36fff4d 100644
--- a/topoembedx/classes/cell2vec.py
+++ b/topoembedx/classes/cell2vec.py
@@ -111,7 +111,7 @@ def fit(
         neighborhood_type : {"adj", "coadj"}, default="adj"
             The type of neighborhood to compute. "adj" for adjacency matrix, "coadj" for coadjacency matrix.
         neighborhood_dim : dict
-            The integer parmaters needed to specify the neighborhood of the cells to generate the embedding.
+            The integer parameters needed to specify the neighborhood of the cells to generate the embedding.
             In TopoNetX  (co)adjacency neighborhood matrices are specified via one or two parameters.
             - For Cell/Simplicial/Path complexes (co)adjacency matrix is specified by a single parameter, this is precisely
             neighborhood_dim["rank"].
diff --git a/topoembedx/classes/cell_diff2vec.py b/topoembedx/classes/cell_diff2vec.py
index 4487205..0fd87cf 100644
--- a/topoembedx/classes/cell_diff2vec.py
+++ b/topoembedx/classes/cell_diff2vec.py
@@ -91,7 +91,7 @@ def fit(
         neighborhood_type : {"adj", "coadj"}, default="adj"
             The type of neighborhood to compute. "adj" for adjacency matrix, "coadj" for coadjacency matrix.
         neighborhood_dim : dict
-            The integer parmaters needed to specify the neighborhood of the cells to generate the embedding.
+            The integer parameters needed to specify the neighborhood of the cells to generate the embedding.
             In TopoNetX  (co)adjacency neighborhood matrices are specified via one or two parameters.
             - For Cell/Simplicial/Path complexes (co)adjacency matrix is specified by a single parameter, this is precisely
             neighborhood_dim["rank"].
diff --git a/topoembedx/classes/deepcell.py b/topoembedx/classes/deepcell.py
index b9cbbb2..f443179 100644
--- a/topoembedx/classes/deepcell.py
+++ b/topoembedx/classes/deepcell.py
@@ -91,7 +91,7 @@ def fit(
         neighborhood_type : {"adj", "coadj"}, default="adj"
             The type of neighborhood to compute. "adj" for adjacency matrix, "coadj" for coadjacency matrix.
         neighborhood_dim : dict
-            The integer parmaters needed to specify the neighborhood of the cells to generate the embedding.
+            The integer parameters needed to specify the neighborhood of the cells to generate the embedding.
             In TopoNetX  (co)adjacency neighborhood matrices are specified via one or two parameters.
             - For Cell/Simplicial/Path complexes (co)adjacency matrix is specified by a single parameter, this is precisely
             neighborhood_dim["rank"].
diff --git a/topoembedx/classes/higher_order_laplacian_eigenmaps.py b/topoembedx/classes/higher_order_laplacian_eigenmaps.py
index 3be4211..21742c9 100644
--- a/topoembedx/classes/higher_order_laplacian_eigenmaps.py
+++ b/topoembedx/classes/higher_order_laplacian_eigenmaps.py
@@ -56,7 +56,7 @@ def fit(
         neighborhood_type : {"adj", "coadj"}, default="adj"
             The type of neighborhood to compute. "adj" for adjacency matrix, "coadj" for coadjacency matrix.
         neighborhood_dim : dict
-            The integer parmaters needed to specify the neighborhood of the cells to generate the embedding.
+            The integer parameters needed to specify the neighborhood of the cells to generate the embedding.
             In TopoNetX  (co)adjacency neighborhood matrices are specified via one or two parameters.
             - For Cell/Simplicial/Path complexes (co)adjacency matrix is specified by a single parameter, this is precisely
             neighborhood_dim["rank"].
diff --git a/topoembedx/classes/hoglee.py b/topoembedx/classes/hoglee.py
index 618498d..3064ebe 100644
--- a/topoembedx/classes/hoglee.py
+++ b/topoembedx/classes/hoglee.py
@@ -48,7 +48,7 @@ def fit(
         neighborhood_type : {"adj", "coadj"}, default="adj"
             The type of neighborhood to compute. "adj" for adjacency matrix, "coadj" for coadjacency matrix.
         neighborhood_dim : dict
-            The integer parmaters needed to specify the neighborhood of the cells to generate the embedding.
+            The integer parameters needed to specify the neighborhood of the cells to generate the embedding.
             In TopoNetX  (co)adjacency neighborhood matrices are specified via one or two parameters.
             - For Cell/Simplicial/Path complexes (co)adjacency matrix is specified by a single parameter, this is precisely
             neighborhood_dim["rank"].
diff --git a/topoembedx/classes/hope.py b/topoembedx/classes/hope.py
index 93fbeb9..3184c97 100644
--- a/topoembedx/classes/hope.py
+++ b/topoembedx/classes/hope.py
@@ -146,9 +146,8 @@ def fit(
 
         Examples
         --------
-        >>> import toponetx as tnx
         >>> from topoembedx import HOPE
-        >>> ccc = tnx.classes.CombinatorialComplex()
+        >>> ccc = tnx.CombinatorialComplex()
         >>> ccc.add_cell([2, 5], rank=1)
         >>> ccc.add_cell([2, 4], rank=1)
         >>> ccc.add_cell([7, 8], rank=1)
diff --git a/topoembedx/classes/random_walks.py b/topoembedx/classes/random_walks.py
index 334e697..417e659 100644
--- a/topoembedx/classes/random_walks.py
+++ b/topoembedx/classes/random_walks.py
@@ -43,10 +43,10 @@ def transition_from_adjacency(
     This function generates a transition matrix from an adjacency matrix
     using the following steps:
 
-    1. Add self-loop to the adjaency matrix if self_loop is set to True
-    2. Compute the degree matrix
+    1. Add self-loop to the adjacency matrix if ``self_loop`` is set to ``True``.
+    2. Compute the degree matrix.
     3. Compute the transition matrix by taking the dot product of the inverse of
-       the degree matrix and the adjacency matrix
+       the degree matrix and the adjacency matrix.
 
     Parameters
     ----------
@@ -55,7 +55,7 @@ def transition_from_adjacency(
     sub_sampling : float, default=0.1
         The rate of subsampling.
     self_loop : bool, default=True
-        A flag indicating whether to add self-loop to the adjacency matrix.
+        Whether to add self-loops to the adjacency matrix.
 
     Returns
     -------
@@ -64,7 +64,6 @@ def transition_from_adjacency(
 
     Examples
     --------
-    >>> import numpy as np
     >>> A = np.array([[0, 1, 1, 0], [1, 0, 1, 0], [1, 1, 0, 1], [0, 0, 1, 0]])
     >>> transition_from_adjacency(A)
     array([[0.33333333, 0.33333333, 0.33333333, 0.        ],
@@ -165,7 +164,6 @@ def random_walk(
 
     Examples
     --------
-    >>> import numpy as np
     >>> transition_matrix = np.array(
     ...     [
     ...         [0.0, 1.0, 0.0, 0.0],
@@ -175,10 +173,9 @@ def random_walk(
     ...     ]
     ... )
     >>> states = ["A", "B", "C", "D"]
-    >>> walks = random_walk(
+    >>> random_walk(
     ...     length=3, num_walks=2, states=states, transition_matrix=transition_matrix
     ... )
-    >>> print(walks)
     [['B', 'C', 'D'], ['B', 'C', 'B']]
     """
     rw = RandomWalk(states, transition_matrix)
diff --git a/topoembedx/exceptions.py b/topoembedx/exception.py
similarity index 69%
rename from topoembedx/exceptions.py
rename to topoembedx/exception.py
index e8bb8f2..f64e434 100644
--- a/topoembedx/exceptions.py
+++ b/topoembedx/exception.py
@@ -1,4 +1,6 @@
-"""Base classes for TopoEmbedX exceptions."""
+"""Base errors and exceptions for TopoEmbedX."""
+
+__all__ = ["TopoEmbedXError", "TopoEmbedXException", "TopoEmbedXNotImplementedError"]
 
 
 class TopoEmbedXException(Exception):
diff --git a/topoembedx/neighborhood.py b/topoembedx/neighborhood.py
index badc7e2..0817f50 100644
--- a/topoembedx/neighborhood.py
+++ b/topoembedx/neighborhood.py
@@ -13,9 +13,8 @@ def neighborhood_from_complex(
 ) -> tuple[list, csr_matrix]:
     """Compute the neighborhood of a complex.
 
-    This function returns the indices and matrix for the neighborhood specified
-    by `neighborhood_type`
-    and `neighborhood_dim` for the input complex `domain`.
+    This function returns the indices and matrix for the neighborhood specified by
+    `neighborhood_type` and `neighborhood_dim` for the input complex `domain`.
 
     Parameters
     ----------
@@ -24,7 +23,7 @@ def neighborhood_from_complex(
     neighborhood_type : {"adj", "coadj"}, default="adj"
         The type of neighborhood to compute. "adj" for adjacency matrix, "coadj" for coadjacency matrix.
     neighborhood_dim : dict
-        The integer parmaters needed to specify the neighborhood of the cells to generate the embedding.
+        The integer parameters needed to specify the neighborhood of the cells to generate the embedding.
         In TopoNetX  (co)adjacency neighborhood matrices are specified via one or two parameters.
         - For Cell/Simplicial/Path complexes (co)adjacency matrix is specified by a single parameter, this is precisely
         neighborhood_dim["rank"].