Merge pull request #7 from cclauss/patch-1

GitHub Action to find undefined names in Python code

.github/workflows/undefined_names.yml

+name: undefined_names
+on: [pull_request, push]
+jobs:
+  undefined_names:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - run: pip install --upgrade pip
+      - run: pip install flake8
+      - run: flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics

openfold/data/mmcif_parsing.py

@@ -26,6 +26,7 @@ from Bio import PDB
 from Bio.Data import SCOPData
 import numpy as np
 
+from openfold.data.templates import MultipleChainsError
 import openfold.np.residue_constants as residue_constants
 
 

openfold/utils/feats.py

@@ -13,11 +13,14 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import math
+
 import numpy as np
 import torch
 import torch.nn as nn
 from typing import Dict
 
+from openfold.np import protein
 import openfold.np.residue_constants as rc
 from openfold.utils.affine_utils import T
 from openfold.utils.tensor_utils import (

openfold/utils/loss.py

@@ -14,6 +14,7 @@
 # limitations under the License.
 
 from functools import partial
+import logging
 import ml_collections
 import numpy as np
 import torch