Changes from code review

README.md

@@ -44,13 +44,13 @@ Below is a minimal example of using TopoModelX to load a simplicial complex data
 
 ```bash
 import numpy as np
+import toponetx as tnx
 import torch
-from topomodelx.datasets.graph import karate_club
 from topomodelx.nn.simplicial.san import SAN
 from topomodelx.utils.sparse import from_sparse
 
 # Step 1: Load the Karate Club dataset
-dataset = karate_club(complex_type="simplicial")
+dataset = tnx.karate_club(complex_type="simplicial")
 
 # Step 2: Prepare Laplacians and node/edge features
 laplacian_down = from_sparse(dataset.down_laplacian_matrix(rank=1))
@@ -79,16 +79,13 @@ y_hat_edge = model(x, laplacian_up=laplacian_up, laplacian_down=laplacian_down)
 
 ## 🤖 Installing TopoModelX
 
-`TopoModelX` is available on PyPI and can be installed using `pip`. 
-
-
-### Install with pip
-
-To install `TopoModelX` and its dependencies, run the following command:
+`TopoModelX` is available on PyPI and can be installed using `pip`.
+Run the following command:
 
 ```bash
 pip install topomodelx
 ```
+
 Then install torch, torch-scatter, torch-sparse with or without CUDA depending on your needs.
 
       ```bash

pyproject.toml

@@ -67,10 +67,9 @@ dev = ["TopoModelX[test, lint]"]
 all = ["TopoModelX[dev, doc]"]
 
 [project.urls]
-homepage = "https://github.com/pyt-team/TopoModelX"
-repository = "https://github.com/pyt-team/TopoModelX"
-documentation = "https://pyt-team.github.io/TopoModelX"
-issues = "https://github.com/pyt-team/TopoModelX/issues"
+documentation = "https://pyt-team.github.io/TopoModelX"  
+source = "https://github.com/pyt-team/TopoModelX"  
+issues = "https://github.com/pyt-team/TopoModelX/issues"  
 
 [tool.ruff]
 target-version = "py310"
@@ -95,7 +94,7 @@ select = [
     "PERF", # performance rules
     "RUF", # miscellaneous rules
 ]
-ignore = ["E501", "SIM115"] # line too long
+ignore = ["E501"] # line too long
 
 [tool.ruff.lint.pydocstyle]
 convention = "numpy"

test/tutorials/test_cell.py

@@ -9,20 +9,20 @@
 
 def _exec_tutorial(path):
     """Execute a tutorial notebook."""
-    file_name = tempfile.NamedTemporaryFile(suffix=".ipynb").name
-    args = [
-        "jupyter",
-        "nbconvert",
-        "--to",
-        "notebook",
-        "--execute",
-        "--ExecutePreprocessor.timeout=1000",
-        "--ExecutePreprocessor.kernel_name=python3",
-        "--output",
-        file_name,
-        path,
-    ]
-    subprocess.check_call(args)
+    with tempfile.NamedTemporaryFile(suffix=".ipynb") as tmp_file:
+        args = [
+            "jupyter",
+            "nbconvert",
+            "--to",
+            "notebook",
+            "--execute",
+            "--ExecutePreprocessor.timeout=1000",
+            "--ExecutePreprocessor.kernel_name=python3",
+            "--output",
+            tmp_file.name,
+            path,
+        ]
+        subprocess.check_call(args)
 
 
 paths = sorted(glob.glob("tutorials/cell/*.ipynb"))

test/tutorials/test_combinatorial.py

@@ -9,20 +9,20 @@
 
 def _exec_tutorial(path):
     """Execute a tutorial notebook."""
-    file_name = tempfile.NamedTemporaryFile(suffix=".ipynb").name
-    args = [
-        "jupyter",
-        "nbconvert",
-        "--to",
-        "notebook",
-        "--execute",
-        "--ExecutePreprocessor.timeout=1000",
-        "--ExecutePreprocessor.kernel_name=python3",
-        "--output",
-        file_name,
-        path,
-    ]
-    subprocess.check_call(args)
+    with tempfile.NamedTemporaryFile(suffix=".ipynb") as tmp_file:
+        args = [
+            "jupyter",
+            "nbconvert",
+            "--to",
+            "notebook",
+            "--execute",
+            "--ExecutePreprocessor.timeout=1000",
+            "--ExecutePreprocessor.kernel_name=python3",
+            "--output",
+            tmp_file.name,
+            path,
+        ]
+        subprocess.check_call(args)
 
 
 paths = sorted(glob.glob("tutorials/combinatorial/*.ipynb"))

test/tutorials/test_hypergraph.py

@@ -9,20 +9,20 @@
 
 def _exec_tutorial(path):
     """Execute a tutorial notebook."""
-    file_name = tempfile.NamedTemporaryFile(suffix=".ipynb").name
-    args = [
-        "jupyter",
-        "nbconvert",
-        "--to",
-        "notebook",
-        "--execute",
-        "--ExecutePreprocessor.timeout=1500",
-        "--ExecutePreprocessor.kernel_name=python3",
-        "--output",
-        file_name,
-        path,
-    ]
-    subprocess.check_call(args)
+    with tempfile.NamedTemporaryFile(suffix=".ipynb") as tmp_file:
+        args = [
+            "jupyter",
+            "nbconvert",
+            "--to",
+            "notebook",
+            "--execute",
+            "--ExecutePreprocessor.timeout=1500",
+            "--ExecutePreprocessor.kernel_name=python3",
+            "--output",
+            tmp_file.name,
+            path,
+        ]
+        subprocess.check_call(args)
 
 
 paths = sorted(glob.glob("tutorials/hypergraph/*.ipynb"))

test/tutorials/test_simplicial.py

@@ -9,20 +9,20 @@
 
 def _exec_tutorial(path):
     """Execute a tutorial notebook."""
-    file_name = tempfile.NamedTemporaryFile(suffix=".ipynb").name
-    args = [
-        "jupyter",
-        "nbconvert",
-        "--to",
-        "notebook",
-        "--execute",
-        "--ExecutePreprocessor.timeout=1000",
-        "--ExecutePreprocessor.kernel_name=python3",
-        "--output",
-        file_name,
-        path,
-    ]
-    subprocess.check_call(args)
+    with tempfile.NamedTemporaryFile(suffix=".ipynb") as tmp_file:
+        args = [
+            "jupyter",
+            "nbconvert",
+            "--to",
+            "notebook",
+            "--execute",
+            "--ExecutePreprocessor.timeout=1000",
+            "--ExecutePreprocessor.kernel_name=python3",
+            "--output",
+            tmp_file.name,
+            path,
+        ]
+        subprocess.check_call(args)
 
 
 paths = sorted(glob.glob("tutorials/simplicial/*.ipynb"))