Fix imports.

.gitignore

@@ -1,4 +1,6 @@
 .DS_Store
 __pycache__/
+build/
+l2gv2.egg-info/
 .venv/
 docs/build/

docs/source/conf.py

@@ -1,10 +1,6 @@
-# Configuration file for the Sphinx documentation builder.
-#
-# For the full list of built-in configuration values, see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
-
-# -- Project information -----------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+# pylint: disable=invalid-name
+# pylint: disable=redefined-builtin
+import warnings
 
 project = "l2gv2"
 copyright = "2024"
@@ -23,9 +19,14 @@
     "show-inheritance": True,
 }
 
+# diable warnings
+warnings.filterwarnings("ignore", category=UserWarning)
+
 templates_path = ["_templates"]
 exclude_patterns = []
 
+# autodoc_mock_imports = ["torch", "torch.nn", "torch.optim", "torch_geometric"]
+
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 

l2gv2/clustering.py

@@ -10,7 +10,8 @@
 import numpy as np
 import numba
 
-from network import TGraph, NPGraph
+from .network.tgraph import TGraph
+from .network.npgraph import NPGraph
 from . import progress
 
 

l2gv2/embedding/eval.py

@@ -23,7 +23,7 @@
 from scipy.special import expit
 import torch
 from sklearn.metrics import roc_auc_score
-from .network import Graph
+from ..network.graph import Graph
 
 
 def reconstruction_auc(coordinates, graph: Graph, dist=False, max_samples=int(1e6)):

l2gv2/embedding/train.py

@@ -21,7 +21,7 @@
 
 import torch
 
-from .utils import EarlyStopping
+from ..utils import EarlyStopping
 
 
 def lr_grid_search(

l2gv2/models.py

@@ -2,7 +2,7 @@
 embeddings of a list of patches using VGAE and Node2Vec."""
 
 from typing import Tuple
-import numpy.typing as npt
+from numpy.typing import ArrayLike
 
 from tqdm import tqdm
 import torch
@@ -348,8 +348,7 @@ def node2vec_patch_embeddings(
 
 def chunk_embedding(
     chunk_size: int, patches: list[Patch], dim=2
-) -> Tuple[npt.ArrayLike, WeightedAlignmentProblem]:
-
+) -> Tuple[ArrayLike, WeightedAlignmentProblem]:
     """TODO: docstring for `chunk_embedding`
 
     Note: this only works for Autonomous System dataset.

l2gv2/patch/patch.py

@@ -21,7 +21,7 @@
 
 import copy
 import numpy as np
-import numpy.typing as npt
+from numpy.typing import ArrayLike
 from l2gv2.patch.lazy import (
     BaseLazyCoordinates,
     LazyMeanAggregatorCoordinates,
@@ -35,11 +35,10 @@ class Patch:
     index: dict[int, int]
     """mapping of node index to patch coordinate index"""
 
-    coordinates: np.ArrayLike
+    coordinates: ArrayLike
     """patch embedding coordinates"""
 
-
-    def __init__(self, nodes: iter, coordinates: npt.ArrayLike | None = None):
+    def __init__(self, nodes: iter, coordinates: ArrayLike | None = None):
         """Initialise a patch from a list of nodes and corresponding coordinates
 
         Args:

l2gv2/patch/patches.py

@@ -11,10 +11,10 @@
 
 import numba
 
-from .clustering import Partition
-from .network.tgraph import TGraph
-from .network.npgraph import JitGraph, NPGraph
-from .sparsify import (
+from ..clustering import Partition
+from ..network.tgraph import TGraph
+from ..network.npgraph import JitGraph, NPGraph
+from ..sparsify import (
     resistance_sparsify,
     relaxed_spanning_tree,
     edge_sampling_sparsify,

l2gv2/patch/utils.py

@@ -34,7 +34,7 @@
 import ilupp
 
 from tqdm.auto import tqdm
-from patch import Patch
+from .patch import Patch
 
 
 def random_gen(new_seed=None) -> np.random.Generator:

pyproject.toml

@@ -1,7 +1,12 @@
 [build-system]
-requires = ["pdm-backend"]
-build-backend = "pdm.backend"
+requires = ['setuptools>=40.8.0']
+build-backend = 'setuptools.build_meta'
 
+[tool.setuptools]
+
+  [tool.setuptools.packages.find]
+    where = ["."]
+    include = ["l2gv2", "l2gv2.patch", "l2gv2.network", "l2gv2.embedding", "l2gv2.embedding.dgi.layers", "l2gv2.embedding.dgi.models", "l2gv2.embedding.dgi.utils", "l2gv2.embedding.gae.layers", "l2gv2.embedding.gae.models", "l2gv2.embedding.gae.utils", "l2gv2.datasets"]
 
 # project
 # #######