Merge pull request #26 from cthoyt/add-black-isort

Re-enable flake8 check

Author: benedekrozemberczki

.github/workflows/main.yaml

@@ -23,6 +23,12 @@ jobs:
           python-version: 3.7
       - run: conda --version
       - run: which python
+      - name: Install general requirements
+        run: |
+          pip install tox
+      - name: Run flake8
+        run: |
+          tox -e flake8
       - name: Run installation.
         run: |
          conda install -y scipy

chemicalx/__init__.py

@@ -1,5 +1,9 @@
-from chemicalx.data import contextfeatureset, drugfeatureset, labeledtriples, datasetloader  # noqa:F401,F403
-
+from chemicalx.data import (  # noqa:F401,F403
+    contextfeatureset,
+    datasetloader,
+    drugfeatureset,
+    labeledtriples,
+)
 from chemicalx.models import (  # noqa:F401,F403
     audnnsynergy,
     caster,
@@ -16,5 +20,4 @@
     mrgnn,
     ssiddi,
 )
-
 from chemicalx.version import __version__

chemicalx/data/__init__.py

@@ -1,10 +1,10 @@
 from class_resolver import Resolver
 
+from .batchgenerator import *  # noqa:F401,F403
 from .contextfeatureset import *  # noqa:F401,F403
-from .drugfeatureset import *  # noqa:F401,F403
-from .labeledtriples import *  # noqa:F401,F403
 from .datasetloader import *  # noqa:F401,F403
+from .drugfeatureset import *  # noqa:F401,F403
 from .drugpairbatch import *  # noqa:F401,F403
-from .batchgenerator import *  # noqa:F401,F403
+from .labeledtriples import *  # noqa:F401,F403
 
 dataset_resolver = Resolver.from_subclasses(base=DatasetLoader)

chemicalx/data/batchgenerator.py

@@ -1,10 +1,17 @@
 import math
-import torch
-import pandas as pd
-import numpy as np
 from typing import List
+
+import numpy as np
+import pandas as pd
+import torch
 from torchdrug.data import PackedGraph
-from chemicalx.data import LabeledTriples, DrugFeatureSet, ContextFeatureSet, DrugPairBatch
+
+from chemicalx.data import (
+    ContextFeatureSet,
+    DrugFeatureSet,
+    DrugPairBatch,
+    LabeledTriples,
+)
 
 
 class BatchGenerator:

chemicalx/data/contextfeatureset.py

@@ -1,7 +1,8 @@
-import torch
-import numpy as np
 from typing import Dict, List
 
+import numpy as np
+import torch
+
 
 class ContextFeatureSet(dict):
     """

chemicalx/data/datasetloader.py

@@ -1,10 +1,12 @@
 import io
 import json
-import numpy as np
-import pandas as pd
 import urllib.request
 from typing import Dict
-from chemicalx.data import DrugFeatureSet, ContextFeatureSet, LabeledTriples
+
+import numpy as np
+import pandas as pd
+
+from chemicalx.data import ContextFeatureSet, DrugFeatureSet, LabeledTriples
 
 __all__ = [
     "DatasetLoader",

chemicalx/data/drugfeatureset.py

@@ -1,8 +1,9 @@
+from typing import Dict, List, Union
+
+import numpy as np
 import torch
 import torchdrug
-import numpy as np
-from typing import List, Dict, Union
-from torchdrug.data import Molecule, Graph, PackedGraph
+from torchdrug.data import Graph, Molecule, PackedGraph
 
 
 class DrugFeatureSet(dict):

chemicalx/data/labeledtriples.py

@@ -1,5 +1,6 @@
-import pandas as pd
 from typing import List, Tuple
+
+import pandas as pd
 from sklearn.model_selection import train_test_split
 
 

chemicalx/models/deepsynergy.py

@@ -4,7 +4,8 @@
 
 class DeepSynergy(torch.nn.Module):
     r"""The DeepSynergy model from the `"DeepSynergy: Predicting
-    Anti-Cancer Drug Synergy with Deep Learning" <https://academic.oup.com/bioinformatics/article/34/9/1538/4747884>`_ paper.
+    Anti-Cancer Drug Synergy with Deep Learning"
+    <https://academic.oup.com/bioinformatics/article/34/9/1538/4747884>`_ paper.
 
     Args:
         context_channels (int): The number of context features.

chemicalx/models/epgcnds.py

@@ -7,7 +7,8 @@
 
 class EPGCNDS(torch.nn.Module):
     r"""The EPGCN-DS model from the `"Structure-Based Drug-Drug Interaction Detection
-    via Expressive Graph Convolutional Networks and Deep Sets " <https://ojs.aaai.org/index.php/AAAI/article/view/7236>`_ paper.
+    via Expressive Graph Convolutional Networks and Deep Sets"
+    <https://ojs.aaai.org/index.php/AAAI/article/view/7236>`_ paper.
 
     Args:
         in_channels (int): The number of molecular features.

examples/deepsynergy_examples.py

@@ -1,9 +1,10 @@
-import torch
 import pandas as pd
-from tqdm import tqdm
+import torch
 from sklearn.metrics import roc_auc_score
+from tqdm import tqdm
+
+from chemicalx.data import BatchGenerator, DatasetLoader
 from chemicalx.models import DeepSynergy
-from chemicalx.data import DatasetLoader, BatchGenerator
 
 loader = DatasetLoader("drugcombdb")
 

examples/epgcnds_examples.py

@@ -1,8 +1,9 @@
-import torch
 import pandas as pd
-from tqdm import tqdm
+import torch
 from sklearn.metrics import roc_auc_score
-from chemicalx.data import DatasetLoader, BatchGenerator
+from tqdm import tqdm
+
+from chemicalx.data import BatchGenerator, DatasetLoader
 from chemicalx.models import EPGCNDS
 
 loader = DatasetLoader("drugcombdb")

tests/unit/test_batching.py

@@ -1,5 +1,6 @@
 import unittest
-from chemicalx.data import DatasetLoader, BatchGenerator
+
+from chemicalx.data import BatchGenerator, DatasetLoader
 
 
 class TestGeneratorDrugCombDB(unittest.TestCase):

tests/unit/test_dataset.py

@@ -1,4 +1,5 @@
 import unittest
+
 from chemicalx.data import DatasetLoader
 
 

tests/unit/test_datastructures.py

@@ -1,6 +1,8 @@
 import unittest
+
 import numpy as np
 import pandas as pd
+
 from chemicalx.data import ContextFeatureSet, DrugFeatureSet, LabeledTriples
 
 
@@ -16,8 +18,8 @@ def setUp(self):
 
     def test_get(self):
         assert self.context_feature_set["context_2"].shape == (1, 3)
-        assert ("context_2" in self.context_feature_set) == True
-        assert self.context_feature_set.has_context("context_2") == True
+        assert "context_2" in self.context_feature_set
+        assert self.context_feature_set.has_context("context_2")
 
     def test_delete(self):
         self.another_context_feature_set = self.context_feature_set
@@ -63,8 +65,8 @@ def setUp(self):
 
     def test_get(self):
         assert self.drug_feature_set["drug_1"]["features"].shape == (1, 3)
-        assert ("drug_2" in self.drug_feature_set) == True
-        assert self.drug_feature_set.has_drug("drug_2") == True
+        assert "drug_2" in self.drug_feature_set
+        assert self.drug_feature_set.has_drug("drug_2")
 
     def test_delete(self):
         self.another_drug_feature_set = self.drug_feature_set

tests/unit/test_models.py

@@ -1,7 +1,8 @@
 import unittest
+
 import torch
-from chemicalx.data import DatasetLoader, BatchGenerator
 
+from chemicalx.data import BatchGenerator, DatasetLoader
 from chemicalx.models import (
     CASTER,
     DPDDI,

tox.ini

@@ -15,21 +15,22 @@ deps =
     isort
 skip_install = true
 commands =
-    black ./chemicalx/ ./tests/ setup.py
-    isort ./chemicalx/ ./tests/ setup.py
+    black chemicalx/ tests/ examples/ setup.py
+    isort chemicalx/ tests/ examples/ setup.py
 description = Run linters.
 
 [testenv:flake8]
 deps =
     flake8
     flake8-black
     flake8-isort
+skip_install = true
 commands =
-    flake8 --ignore=F401,F403 --max-line-length 120 ./chemicalx/ ./tests/ setup.py
+    flake8 --ignore=F401,F403,F405,E203 --max-line-length 120 chemicalx/ tests/ examples/ setup.py
 
 [testenv:mypy]
 deps = mypy
 skip_install = true
 commands =
-    mypy --install-types --non-interactive --ignore-missing-imports ./chemicalx/ ./tests/
-description = Run the mypy tool to check static typing on the project.
+    mypy --install-types --non-interactive --ignore-missing-imports chemicalx/ tests/ examples/ setup.py
+description = Run the mypy tool to check static typing on the project.