fix: doc index, docstring typos

dPys · Dec 7, 2024 · 8958a32 · 8958a32
1 parent 19105a1
commit 8958a32
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Showing 6 changed files with 19 additions and 25 deletions.
diff --git a/README.md b/README.md
@@ -26,15 +26,13 @@
 ## Installation
 
 ```bash
-git clone https://github.com/dpys/nxbench.git
-cd nxbench
-pip install -e .[cuda]  # CUDA support is needed for CuGraph benchmarking
+pip install nxbench
 ```
 
 For benchmarking using CUDA-based tools like [CuGraph](https://github.com/rapidsai/cugraph):
 
 ```bash
-pip install -e .[cuda]
+pip install nxbench[cuda]  # CUDA support is needed for CuGraph benchmarking
 ```
 
 ## Quick Start

diff --git a/doc/api/index.rst b/doc/api/index.rst
@@ -5,8 +5,10 @@ API Documentation
    :maxdepth: 2
    :caption: Contents:
 
-   nxbench.core
+   nxbench
    nxbench.benchmarks
    nxbench.data
+   nxbench.data.scripts
    nxbench.validation
+   nxbench.validation.scripts
    nxbench.viz
diff --git a/doc/api/nxbench.rst b/doc/api/nxbench.rst
@@ -30,11 +30,3 @@ nxbench.log module
    :members:
    :undoc-members:
    :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: nxbench
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/doc/conf.py b/doc/conf.py
@@ -195,12 +195,16 @@
     ("py:class", "Path"),
     ("py:class", "Document"),
     ("py:class", "function"),
+    ("py:class", "click.ClickException"),
+    ("py:class", "pd.DataFrame"),
+    ("py:class", "bs4.BeautifulSoup"),
 ]
 
 autodoc_inherit_docstrings = False
 
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
     "networkx": ("https://networkx.org/documentation/stable/", None),
     "pydantic": ("https://docs.pydantic.dev/latest/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),

diff --git a/doc/installation.md b/doc/installation.md
@@ -1,25 +1,23 @@
 # Installation
 
-Clone the repository and install the package:
+PyPi:
 
 ```bash
-git clone https://github.com/dpys/nxbench.git
-cd nxbench
-pip install -e .
+pip install nxbench
 ```
 
 For benchmarking using CUDA-based tools like [CuGraph](https://github.com/rapidsai/cugraph):
 
 ```bash
-pip install -e .[cuda]  # CUDA support is needed for CuGraph benchmarking
+pip install nxbench[cuda]
 ```
 
 ## Development Setup
 
-Install development dependencies:
+Install development dependencies (testing and documentation):
 
 ```bash
-pip install -e .[test,doc]  # For testing and documentation
+pip install -e .[test,doc]
 ```
 
 Run tests to ensure everything is set up correctly:

diff --git a/nxbench/validation/base.py b/nxbench/validation/base.py
@@ -64,7 +64,7 @@ def validate_node_scores(
     ----------
     result : dict
         Dictionary mapping nodes to scores
-    graph : networkx.nx.Graph or networkx.nx.DiGraph
+    graph : nx.Graph or nx.DiGraph
         Original graph
     score_range : tuple of float, default=(0.0, 1.0)
         Expected range for scores (min, max)
@@ -162,7 +162,7 @@ def validate_communities(
     ----------
     result : list of sets
         List of node sets representing communities
-    graph : networkx.nx.Graph or networkx.nx.DiGraph
+    graph : nx.Graph or nx.DiGraph
         Original graph
     allow_overlap : bool, default=False
         Whether communities can overlap
@@ -230,7 +230,7 @@ def validate_path_lengths(
     result : dict of dict
         Dictionary mapping source nodes to dictionaries mapping target nodes to
         distances
-    graph : networkx.nx.Graph or networkx.nx.DiGraph
+    graph : nx.Graph or nx.DiGraph
         Original graph
     check_symmetry : bool, default=False
         Whether to verify that distances are symmetric (for undirected graphs)
@@ -296,7 +296,7 @@ def validate_flow(
     ----------
     result : tuple
         (flow_value, flow_dict) tuple from max flow algorithm
-    graph : networkx.nx.Graph or networkx.nx.DiGraph
+    graph : nx.Graph or nx.DiGraph
         Original graph
     check_conservation : bool, default=True
         Whether to verify flow conservation at all nodes
@@ -407,7 +407,7 @@ def validate_similarity_scores(
     ----------
     result : iterable of tuples
         (node_u, node_v, score) tuples from similarity measure
-    graph : networkx.nx.Graph or networkx.nx.DiGraph
+    graph : nx.Graph or nx.DiGraph
         Original graph
     score_range : tuple of float, default=(0.0, 1.0)
         Expected range for similarity scores