Cleanup

Author: ddomingof

src/diffupy/__init__.py

@@ -1,31 +1,3 @@
 # -*- coding: utf-8 -*-
 
-"""
-The goal of this package is to re-implement the Diffusion algorithm described in ... in Python.
-
-Installation
-------------
-1. ``diffupy`` can be installed with the following commmands:
-
-.. code-block:: sh
-
-    python3 -m pip install ...
-
-2. or in editable mode with:
-
-.. code-block:: sh
-
-    git clone ..
-
-.. code-block:: sh
-
-    cd diffupy
-
-.. code-block:: sh
-
-    python3 -m pip install -e .
-
-How to use
-----------
-
-"""
+"""DiffuPy."""

src/diffupy/constants.py

@@ -1,3 +1,5 @@
+# -*- coding: utf-8 -*-
+
 """Constants of diffupy."""
 
 import os

src/diffupy/diffuse.py

@@ -10,13 +10,16 @@
 import numpy as np
 
 from .diffuse_raw import diffuse_raw
+from .matrix import Matrix
 from .utils import get_label_list_graph
 from .validate_input import _validate_scores
 
-from .matrix import Matrix
-
 log = logging.getLogger(__name__)
 
+__all__ = [
+    'diffuse',
+]
+
 
 def diffuse(
         input_scores: Matrix,

src/diffupy/diffuse_raw.py

@@ -13,6 +13,11 @@
 
 logger = logging.getLogger()
 
+__all__ = [
+    'calculate_scores',
+    'diffuse_raw',
+]
+
 
 def calculate_scores(
         col_ind: int,

src/diffupy/kernels.py

@@ -17,6 +17,14 @@
 log = logging.getLogger(__name__)
 
 
+__all__ = [
+    'diffusion_kernel',
+    'commute_time_kernel',
+    'inverse_cosine_kernel',
+    'regularised_laplacian_kernel',
+    'p_step_kernel',
+]
+
 def commute_time_kernel(graph: nx.Graph, normalized: bool = False) -> Matrix:
     """Compute the commute-time kernel, which is the expected time of going back and forth between a couple of nodes.
     If the network is connected, then the commuted time kernel will be totally dense, therefore reflecting global

src/diffupy/matrix.py

@@ -12,6 +12,10 @@
 
 log = logging.getLogger(__name__)
 
+__all__ = [
+    'Matrix',
+    'LaplacianMatrix',
+]
 
 class Matrix:
     """Matrix class."""