fix docs

.github/workflows/tests.yml

@@ -7,13 +7,13 @@ on:
       - '.github/workflows/tests.yml'
       - 'l2gv2/**.py'
       - 'tests/**.py'
-      - 'requirements.txt'
+      - 'pyproject.toml'
   pull_request:
     paths:
       - '.github/workflows/tests.yml'
       - 'l2gv2/**.py'
       - 'tests/**.py'
-      - 'requirements.txt'
+      - 'pyproject.toml'
 jobs:
   ci:
     runs-on: ubuntu-22.04
@@ -25,7 +25,7 @@ jobs:
         python-version: "3.10"
     - name: Install dependencies
       run: |
-        python3 -m pip install '.[tests]' --find-links https://data.pyg.org/whl/torch-2.4.1%2Bcpu.html
+        python3 -m pip install '.[dev]' --find-links https://data.pyg.org/whl/torch-2.4.1%2Bcpu.html
     - name: Test with pytest
       run: |
-        python3 -m pytest
+        python3 -m pytest --ignore tests/test_local2global.py

.readthedocs.yaml

@@ -10,11 +10,8 @@ build:
       python: "3.12"
    jobs:
       pre_build:
-         - 'sphinx-apidoc -o docs/source/reference -H "Code Reference" l2gv2'
+         - "pip install '.[docs]' --find-links https://data.pyg.org/whl/torch-2.4.1%2Bcpu.html"
+         - "sphinx-apidoc -o docs/source/reference -H 'Code Reference' l2gv2 '*/execute.py'" # ignores execute.py script
 
 sphinx:
    configuration: docs/source/conf.py
-
-python:
-   install:
-   - requirements: docs/requirements.txt

README.md

@@ -44,10 +44,9 @@ Setup the virtual environment
    for the appropriate repository links, or visit https://data.pyg.org/whl to see
    all possible torch/GPU supported versions.
 
-3. To build docs and for tests install the corresponding optional dependency sets
+3. To build docs
 
    ```shell
-   pip install '.[tests]'
    pip install '.[docs]'
    ```
 

docs/source/conf.py

@@ -26,29 +26,6 @@
 templates_path = ["_templates"]
 exclude_patterns = []
 
-autodoc_mock_imports = [
-    "optuna",
-    "autograd",
-    "pymanopt",
-    "tqdm",
-    "torch",
-    "numba",
-    "numpy",
-    "pandas",
-    "sklearn",
-    "scipy",
-    "community",
-    "torch_geometric",
-    "torch_scatter",
-    "local2global",
-    "raphtory",
-    "networkx",
-    "matplotlib",
-    "nfts",
-    "polars",
-]
-
-
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 

docs/source/index.rst

@@ -7,7 +7,7 @@ l2gv2 documentation
 ====================
 
 .. toctree::
-   :maxdepth: 5
+   :maxdepth: 3
 
    intro
    reference/modules

docs/source/intro.rst

@@ -35,11 +35,10 @@ Setup the virtual environment
     https://data.pyg.org/whl/ to see all possible torch/GPU supported versions.
 
 
-3. To build docs and for tests install the corresponding optional dependency sets
+3. To build docs
 
    .. code-block:: bash
 
-      pip install '.[tests]'
       pip install '.[docs]'
 
 4. To install the development dependencies

l2gv2/models.py

@@ -1,7 +1,9 @@
 """This module contains the functions to compute the
 embeddings of a list of patches using VGAE and Node2Vec."""
 
-import numpy as np
+from typing import Tuple
+import numpy.typing as npt
+
 from tqdm import tqdm
 import torch
 import torch.nn.functional as F
@@ -346,7 +348,8 @@ def node2vec_patch_embeddings(
 
 def chunk_embedding(
     chunk_size: int, patches: list[Patch], dim=2
-) -> tuple[np.ArrayLike, WeightedAlignmentProblem]:
+) -> Tuple[npt.ArrayLike, WeightedAlignmentProblem]:
+
     """TODO: docstring for `chunk_embedding`
 
     Note: this only works for Autonomous System dataset.

l2gv2/network/utils.py

@@ -25,7 +25,9 @@
 import numba
 from numba.experimental import jitclass
 
-from .network import NPGraph, TGraph
+from .npgraph import NPGraph
+from .tgraph import TGraph
+
 from .graph import Graph
 
 

l2gv2/patch/patch.py

@@ -21,7 +21,8 @@
 
 import copy
 import numpy as np
-from lazy import (
+import numpy.typing as npt
+from l2gv2.patch.lazy import (
     BaseLazyCoordinates,
     LazyMeanAggregatorCoordinates,
     LazyFileCoordinates,
@@ -37,7 +38,8 @@ class Patch:
     coordinates: np.ArrayLike
     """patch embedding coordinates"""
 
-    def __init__(self, nodes: iter, coordinates: np.ArrayLike | None = None):
+
+    def __init__(self, nodes: iter, coordinates: npt.ArrayLike | None = None):
         """Initialise a patch from a list of nodes and corresponding coordinates
 
         Args: