added ruff linting; added github actions configuration

aimat-lab · Oct 7, 2024 · 8d1aed4 · 8d1aed4
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diff --git a/.github/workflows/run_test.yml b/.github/workflows/run_test.yml
@@ -0,0 +1,33 @@
+name: Run Unit Test
+
+on: [push]
+
+jobs:
+
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install uv
+        uv pip install -e .
+
+    - name: Lint with Ruff
+      run: |
+        pip install ruff
+        ruff check .
+
+    - name: Run tests
+      run: |
+        python -m unittest discover -s tests -p '*_test.py'
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -267,4 +267,18 @@ Additional changes:
 -------------------
 
 HOTFIX: The ``Megan.regression_reference`` running mean is now a ``nn.Parameter`` and therefore also included 
-when saving/loading the model from persistent files.
+when saving/loading the model from persistent files.
+
+0.18.2 - 08.08.2024
+-------------------
+
+HOTFIX: Removed batchnorm layers in the projection MLPs as this was causing significantly different results when 
+running the model in eval mode versus in 
+
+- modified the GraphAttentionLayerV2 to now use a "look ahead" aggregation of the neighbor nodes as well in the 
+  message update. significantly improves the explanations for the BA2Motifs dataset.
+
+0.18.3 - 01.10.2024
+-------------------
+
+- modified the augementations that are used for the contrastive learning now.
diff --git a/graph_attention_student/VERSION b/graph_attention_student/VERSION
@@ -1 +1 @@
-0.18.1
+0.18.2
diff --git a/graph_attention_student/assets/models/aqsoldb/process.py b/graph_attention_student/assets/models/aqsoldb/process.py
@@ -1,18 +1,7 @@
-import os
 import pathlib
-import typing as t
 
-import click
-import numpy as np
-import numpy.linalg as la
-import matplotlib as mpl
-import matplotlib.pyplot as plt
-import rdkit
-import rdkit.Chem.AllChem
 from rdkit import Chem
-from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
 
-import visual_graph_datasets.typing as tc
 # processing
 from visual_graph_datasets.processing.base import *
 from visual_graph_datasets.processing.colors import *

diff --git a/graph_attention_student/cli.py b/graph_attention_student/cli.py
@@ -1,12 +1,10 @@
 import os
-import sys
 import click
 
 from pycomex.experiment import run_experiment
 from pycomex.cli import ExperimentCLI
 
 from graph_attention_student.util import get_version
-from graph_attention_student.util import DATASETS_FOLDER
 from graph_attention_student.util import EXAMPLES_FOLDER
 from graph_attention_student.util import EXPERIMENTS_PATH
 

diff --git a/graph_attention_student/data.py b/graph_attention_student/data.py
@@ -1,36 +1,31 @@
 import os
 import sys
-import csv
 import time
 import json
 import random
 import orjson
 import logging
-import tempfile
 import typing as t
 from copy import copy
 from typing import List, Tuple, Optional, Dict, Callable
 from collections import defaultdict
 
-import cairosvg
 import numpy as np
 import networkx as nx
 import matplotlib.pyplot as plt
 import tensorflow as tf
 import visual_graph_datasets.typing as tv
-from rdkit import Chem
-from rdkit.Chem.Draw.rdMolDraw2D import MolDraw2DSVG
 from rdkit.Chem import rdDepictor
-rdDepictor.SetPreferCoordGen(True)
 
 import graph_attention_student.typing as tc
 from graph_attention_student.util import NULL_LOGGER
 from graph_attention_student.util import graph_dict_to_list_values
-from graph_attention_student.util import update_nested_dict
 from graph_attention_student.visualization import draw_extended_colors_graph
 from graph_attention_student.visualization import draw_edge_black
 from graph_attention_student.visualization import draw_node_color_scatter
 
+rdDepictor.SetPreferCoordGen(True)
+
 
 class NumericJsonEncoder(json.JSONEncoder):
 
@@ -96,7 +91,6 @@ def process_index_data_map(index_data_map: t.Dict[int, dict],
 
     :returns: A tuple of two lists.
     """
-    dataset_length = len(index_data_map)
     dataset_indices = []
     dataset = [None for _ in range(max(index_data_map.keys()) + 1)]
     for index, data in index_data_map.items():
@@ -270,7 +264,7 @@ def load_eye_tracking_dataset_dict(dataset_path: str,
     :param sanitize_dict:
     :return:
     """
-    logger.info(f'determining the file names...')
+    logger.info('determining the file names...')
     files = os.listdir(dataset_path)
     names = set()
     for file_name in files:
@@ -431,7 +425,7 @@ def graphs_locally_similar(primary_graph: dict,
                     primary_adjacency_mask[i][primary_index] = primary_ingoing
                     break
 
-                except StopIteration as e:
+                except StopIteration:
                     pass
 
         # If we have not found a similar node at the end of the iteration, then there is none within the
@@ -825,9 +819,9 @@ def insert_edge(self, i: int, j: int) -> None:
         else:
             edges = [[i, j], [j, i]]
 
-        for k, l in edges:
-            self.edge_indices[self.current_edge_index] = [k, l]
-            self.edge_attributes[self.current_edge_index] = self.create_single_edge_attributes(k, l)
+        for k, h in edges:
+            self.edge_indices[self.current_edge_index] = [k, h]
+            self.edge_attributes[self.current_edge_index] = self.create_single_edge_attributes(k, h)
             self.current_edge_index += 1
 
     def grow_nodes(self):

diff --git a/graph_attention_student/examples/README.rst b/graph_attention_student/examples/README.rst
@@ -0,0 +1,10 @@
+===========
+📌 Examples
+===========
+
+This folder defines a series of example scripts that demonstrate how to use various functionalities of the 
+``graph_attention_student`` package and the ``Megan`` graph neural network model.
+
+The examples are split into the following files:
+
+- ``00_quickstart.py``: A quickstart guide
diff --git a/graph_attention_student/examples/assets/aqsoldb_process.py b/graph_attention_student/examples/assets/aqsoldb_process.py
@@ -1,18 +1,7 @@
-import os
 import pathlib
-import typing as t
 
-import click
-import numpy as np
-import numpy.linalg as la
-import matplotlib as mpl
-import matplotlib.pyplot as plt
-import rdkit
-import rdkit.Chem.AllChem
 from rdkit import Chem
-from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
 
-import visual_graph_datasets.typing as tc
 # processing
 from visual_graph_datasets.processing.base import *
 from visual_graph_datasets.processing.colors import *

diff --git a/graph_attention_student/experiments/plot_explanations.py b/graph_attention_student/experiments/plot_explanations.py
@@ -5,8 +5,6 @@
 import typing as t
 
 import numpy as np
-import matplotlib.pyplot as plt
-import matplotlib.cm as cm
 from pycomex.functional.experiment import Experiment
 from pycomex.utils import file_namespace, folder_path
 from visual_graph_datasets.config import Config
@@ -15,7 +13,6 @@
 from visual_graph_datasets.data import VisualGraphDatasetWriter
 from visual_graph_datasets.processing.base import ProcessingBase
 from visual_graph_datasets.visualization.importances import create_importances_pdf
-from visual_graph_datasets.visualization.importances import create_combined_importances_pdf
 from visual_graph_datasets.visualization.importances import plot_node_importances_background
 from visual_graph_datasets.visualization.importances import plot_edge_importances_background
 

diff --git a/graph_attention_student/experiments/plot_explanations__megan.py b/graph_attention_student/experiments/plot_explanations__megan.py
@@ -1,9 +1,7 @@
 import os
-import pathlib
 import typing as t
 
 import numpy as np
-import matplotlib.pyplot as plt
 import matplotlib.cm as cm
 import matplotlib.colors as mcolors
 from graph_attention_student.visualization import truncate_colormap
@@ -13,7 +11,6 @@
 
 from graph_attention_student.torch.megan import Megan
 from graph_attention_student.utils import fidelity_from_deviation
-from graph_attention_student.visualization import truncate_colormap
 
 # == DATASET PARAMETERS ==
 # This section contains the parameters which determine the dataset and how to handle said dataset.

diff --git a/graph_attention_student/experiments/plot_explanations__megan__compas.py b/graph_attention_student/experiments/plot_explanations__megan__compas.py
@@ -1,13 +1,9 @@
 import os
-import json
 import pathlib
 import textwrap
 import typing as t
 
 import numpy as np
-import matplotlib.pyplot as plt
-import matplotlib.colors as mcolors
-import matplotlib.cm as cm
 from pycomex.functional.experiment import Experiment
 from pycomex.utils import file_namespace, folder_path
 

diff --git a/graph_attention_student/experiments/plot_explanations__megan__fia_49.py b/graph_attention_student/experiments/plot_explanations__megan__fia_49.py
@@ -1,13 +1,9 @@
 import os
-import json
 import pathlib
 import textwrap
 import typing as t
 
 import numpy as np
-import matplotlib.pyplot as plt
-import matplotlib.colors as mcolors
-import matplotlib.cm as cm
 from pycomex.functional.experiment import Experiment
 from pycomex.utils import file_namespace, folder_path
 

diff --git a/graph_attention_student/experiments/plot_explanations__megan__mutagenicity.py b/graph_attention_student/experiments/plot_explanations__megan__mutagenicity.py
@@ -1,13 +1,10 @@
 import os
-import json
 import pathlib
 import textwrap
 import typing as t
 
 import numpy as np
-import matplotlib.pyplot as plt
 import matplotlib.colors as mcolors
-import matplotlib.cm as cm
 from pycomex.functional.experiment import Experiment
 from pycomex.utils import file_namespace, folder_path
 

diff --git a/graph_attention_student/experiments/plot_explanations__megan__tadf.py b/graph_attention_student/experiments/plot_explanations__megan__tadf.py
@@ -1,13 +1,9 @@
 import os
-import json
 import pathlib
 import textwrap
 import typing as t
 
 import numpy as np
-import matplotlib.pyplot as plt
-import matplotlib.colors as mcolors
-import matplotlib.cm as cm
 from pycomex.functional.experiment import Experiment
 from pycomex.utils import file_namespace, folder_path
 

diff --git a/graph_attention_student/experiments/template_sub_experiment.py b/graph_attention_student/experiments/template_sub_experiment.py
@@ -7,7 +7,6 @@
 """
 import os
 import pathlib
-import typing as t
 
 from pycomex.util import Skippable
 from pycomex.experiment import SubExperiment

diff --git a/graph_attention_student/experiments/vgd_torch.py b/graph_attention_student/experiments/vgd_torch.py
@@ -21,10 +21,8 @@
 
 import pandas as pd
 import numpy as np
-import matplotlib as mpl
 import matplotlib.pyplot as plt
 import seaborn as sns
-import torch.nn as nn
 import pytorch_lightning as pl
 from matplotlib.backends.backend_pdf import PdfPages
 from sklearn.metrics import r2_score
@@ -42,7 +40,6 @@
 from visual_graph_datasets.web import ensure_dataset
 from visual_graph_datasets.data import VisualGraphDatasetReader
 from visual_graph_datasets.visualization.base import draw_image
-from torch_geometric.data import Data
 from torch_geometric.loader import DataLoader
 from lightning.pytorch.loggers import CSVLogger
 
@@ -618,8 +615,8 @@ def testing(e: Experiment):
         dataset_path = e.VISUAL_GRAPH_DATASET
 
     else:
-        e.log(f'dataset is not a local folder')
-        e.log(f'attempting to fetch dataset from remote file share...')
+        e.log('dataset is not a local folder')
+        e.log('attempting to fetch dataset from remote file share...')
         config = Config()
         config.load()
         dataset_path = ensure_dataset(e.VISUAL_GRAPH_DATASET, config)