Moved all external tool executor classes (which use np) to a different directory.

openfold/features/data_pipeline.py

@@ -4,7 +4,7 @@ import numpy as np
 from typing import Mapping, Optional, Sequence
 
 from openfold.features import templates, parsers
-from openfold.features.tools import jackhmmer, hhblits, hhsearch
+from openfold.features.np import jackhmmer, hhblits, hhsearch
 from openfold.np import residue_constants
 
 FeatureDict = Mapping[str, np.ndarray]

openfold/features/tools/hhblits.py → openfold/features/np/hhblits.py

@@ -7,8 +7,8 @@ from typing import Any, Mapping, Optional, Sequence
 
 from absl import logging
 
-# Internal import (7716).
-from openfold.features.tools import utils
+
+from openfold.features.np import utils
 
 _HHBLITS_DEFAULT_P = 20
 _HHBLITS_DEFAULT_Z = 500

openfold/features/tools/hhsearch.py → openfold/features/np/hhsearch.py

@@ -8,8 +8,7 @@ from typing import Sequence
 from absl import logging
 
 
-# Internal import (7716).
-from openfold.features.tools import utils
+from openfold.features.np import utils
 
 
 class HHSearch:

openfold/features/tools/jackhmmer.py → openfold/features/np/jackhmmer.py

@@ -11,8 +11,7 @@ from urllib import request
 from absl import logging
 
 
-# Internal import (7716).
-from openfold.features.tools import utils
+from openfold.features.np import utils
 
 
 class Jackhmmer:

openfold/features/tools/kalign.py → openfold/features/np/kalign.py

@@ -6,7 +6,7 @@ from typing import Sequence
 
 from absl import logging
 
-from openfold.features.tools import utils
+from openfold.features.np import utils
 
 
 def _to_a3m(sequences: Sequence[str]) -> str: