chore: Formatting and unsuported GitHub Actions runner Linux version

Author: jstlaurent

.github/workflows/test_ipu.yml

@@ -19,7 +19,7 @@ jobs:
         python-version: ["3.8"]
         pytorch-version: ["2.0"]
 
-    runs-on: "ubuntu-20.04"
+    runs-on: "ubuntu-22.04"
     timeout-minutes: 30
 
     defaults:
@@ -38,11 +38,11 @@ jobs:
       - name: Activate SDK + Install Requirements
         run: |
           python3 -m pip install --upgrade pip
-          wget -q -O 'poplar_sdk-ubuntu_20_04-3.3.0-208993bbb7.tar.gz' 'https://downloads.graphcore.ai/direct?package=poplar-poplar_sdk_ubuntu_20_04_3.3.0_208993bbb7-3.3.0&file=poplar_sdk-ubuntu_20_04-3.3.0-208993bbb7.tar.gz'
-          tar -xzf poplar_sdk-ubuntu_20_04-3.3.0-208993bbb7.tar.gz
-          python3 -m pip install poplar_sdk-ubuntu_20_04-3.3.0+1403-208993bbb7/poptorch-3.3.0+113432_960e9c294b_ubuntu_20_04-cp38-cp38-linux_x86_64.whl
+          wget -q -O 'poplar_sdk-ubuntu_22_04-3.3.0-208993bbb7.tar.gz' 'https://downloads.graphcore.ai/direct?package=poplar-poplar_sdk_ubuntu_22_04_3.3.0_208993bbb7-3.3.0&file=poplar_sdk-ubuntu_22_04-3.3.0-208993bbb7.tar.gz'
+          tar -xzf poplar_sdk-ubuntu_22_04-3.3.0-208993bbb7.tar.gz
+          python3 -m pip install poplar_sdk-ubuntu_22_04-3.3.0+1403-208993bbb7/poptorch-3.3.0+113432_960e9c294b_ubuntu_22_04-cp38-cp38-linux_x86_64.whl
           # Enable Poplar SDK (including Poplar and PopART)
-          source poplar_sdk-ubuntu_20_04-3.3.0+1403-208993bbb7/enable 
+          source poplar_sdk-ubuntu_22_04-3.3.0+1403-208993bbb7/enable 
           
           python -c "import poptorch"
 
@@ -51,7 +51,6 @@ jobs:
           wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/Tox21-7k-12-labels.csv.gz
           wget https://storage.valencelabs.com/graphium/datasets/neurips_2023/Small-dataset/qm9.csv.gz
 
-
           # Install the IPU specific and graphium requirements
           pip install -r requirements_ipu.txt
           # Install Graphium in dev mode

graphium/cli/fingerprints.py

@@ -2,5 +2,4 @@
 
 
 @app.command(name="fp")
-def get_fingerprints_from_model():
-    ...
+def get_fingerprints_from_model(): ...

graphium/config/_load.py

@@ -10,7 +10,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 import importlib.resources
 
 import omegaconf

graphium/config/_loader.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 # Misc
 import os
 from copy import deepcopy

graphium/config/config_convert.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 import omegaconf
 
 

graphium/data/collate.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from collections.abc import Mapping, Sequence
 
 # from pprint import pprint

graphium/data/datamodule.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 import tempfile
 from contextlib import redirect_stderr, redirect_stdout
 from typing import Type, List, Dict, Union, Any, Callable, Optional, Tuple, Iterable, Literal

graphium/data/dataset.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 import os
 from copy import deepcopy
 from functools import lru_cache

graphium/data/multilevel_utils.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 import pandas as pd
 import ast
 import numpy as np

graphium/data/normalization.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Optional
 from loguru import logger
 import numpy as np

graphium/data/sampler.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Dict, Optional
 from torch.utils.data.dataloader import Dataset
 

graphium/data/smiles_transform.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Type, List, Dict, Union, Any, Callable, Optional, Tuple, Iterable
 
 import os

graphium/data/utils.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Union, List, Callable, Dict, Tuple, Any, Optional
 
 import importlib.resources

graphium/features/commute.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Tuple, Union, Dict, Any
 
 import numpy as np

graphium/features/electrostatic.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Tuple, Union, Dict, Any
 
 import numpy as np

graphium/features/featurizer.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Union, List, Callable, Dict, Tuple, Any, Optional
 
 import inspect

graphium/features/graphormer.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Tuple, Union, Dict, Any
 
 import numpy as np

graphium/features/nmp.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Tuple, Optional, Dict, Union
 import importlib.resources
 from copy import deepcopy

graphium/features/positional_encoding.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Tuple, Union, Optional, Dict, Any, OrderedDict
 from copy import deepcopy
 import numpy as np

graphium/features/properties.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Union, List, Callable
 
 import numpy as np

graphium/features/rw.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Tuple, Union, Optional, List, Dict, Any, Iterable
 
 from scipy.sparse import issparse, spmatrix, coo_matrix

graphium/features/spectral.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Tuple, Union, Dict, Any
 from scipy.linalg import eig
 from scipy.sparse import csr_matrix, diags, issparse, spmatrix

graphium/features/transfer_pos_level.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Tuple, Union, List, Dict, Any, Optional
 
 import numpy as np

graphium/finetuning/finetuning.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Iterable, List, Dict, Tuple, Union, Callable, Any, Optional, Type
 
 from collections import OrderedDict

graphium/finetuning/finetuning_architecture.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Any, Dict, Optional, Union
 
 import torch

graphium/finetuning/fingerprinting.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 import torch
 
 from collections import defaultdict

graphium/finetuning/utils.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from copy import deepcopy
 from typing import Any, Dict, List, Union
 

graphium/hyper_param_search/results.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 _OBJECTIVE_KEY = "objective"
 
 

graphium/ipu/ipu_dataloader.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Callable, Iterable, Optional, List, Tuple, Dict, Any, Union
 from copy import deepcopy
 from dataclasses import dataclass

graphium/ipu/ipu_losses.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 import torch
 from torch import Tensor
 from torch.nn import BCELoss, BCEWithLogitsLoss, MSELoss, L1Loss

graphium/ipu/ipu_metrics.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Optional, Tuple, Sequence, Literal
 
 import torch

graphium/ipu/ipu_simple_lightning.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 import lightning
 from lightning_graphcore import IPUStrategy
 from lightning.pytorch.loggers import WandbLogger

graphium/ipu/ipu_utils.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 import os
 import tempfile
 from datetime import datetime

graphium/ipu/ipu_wrapper.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Dict, Any, Optional, Callable, Union, Type, Tuple, Iterable
 
 from torch_geometric.data import Batch

graphium/ipu/to_dense_batch.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Optional, Tuple
 
 import torch

graphium/nn/architectures/encoder_manager.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Iterable, Dict, Any, Optional
 from torch_geometric.data import Batch
 

graphium/nn/architectures/global_architectures.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Iterable, List, Dict, Literal, Tuple, Union, Callable, Any, Optional, Type
 from torch_geometric.data import Batch
 from graphium.ipu.to_dense_batch import to_dense_batch
@@ -923,9 +922,7 @@ def __init__(
         self.out_dim_edges = (
             out_dim_edges
             if out_dim_edges is not None
-            else self.hidden_dims_edges[-1]
-            if self.hidden_dims_edges
-            else 0
+            else self.hidden_dims_edges[-1] if self.hidden_dims_edges else 0
         )
         self.full_dims_edges = None
         if len(self.hidden_dims_edges) or self.out_dim_edges > 0:

graphium/nn/architectures/pyg_architectures.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from torch import Tensor
 from torch.nn import Module
 from typing import Tuple, Union, List, Optional

graphium/nn/base_graph_layer.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 import abc
 from typing import Union, Callable, List, Optional, Mapping
 from copy import deepcopy

graphium/nn/base_layers.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Union, Callable, Optional, Type, Tuple, Iterable
 from copy import deepcopy
 from loguru import logger

graphium/nn/encoders/signnet_pos_encoder.py

@@ -2,6 +2,7 @@
 SignNet https://arxiv.org/abs/2202.13013
 based on https://github.com/cptq/SignNet-BasisNet
 """
+
 from typing import Dict, Any, Optional, List
 
 import torch

graphium/nn/ensemble_layers.py

@@ -10,7 +10,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Union, Callable, Optional, Type, Tuple, Iterable
 from copy import deepcopy
 from loguru import logger

graphium/nn/pyg_layers/dimenet_pyg.py

@@ -11,7 +11,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Callable, Union, Optional, Tuple
 from functools import partial
 

graphium/nn/pyg_layers/gated_gcn_pyg.py

@@ -10,7 +10,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Union, Callable
 from functools import partial
 

graphium/nn/pyg_layers/gcn_pyg.py

@@ -10,7 +10,6 @@
 --------------------------------------------------------------------------------
 """
 
-
 from typing import Callable, Union
 from functools import partial