actions

Author: ncfrey

.github/workflows/push.yml

@@ -42,7 +42,7 @@ jobs:
     runs-on: "ubuntu-latest"
     steps:
       - uses: "actions/checkout@v4"
-      - uses: "chartboost/ruff-action@v1"
+      - uses: "astral-sh/ruff-action@v1"
         with:
           args: "format --check"
   # pypi:

src/lobster/data/__init__.py

@@ -3,7 +3,6 @@
 from ._constants import (  # nopycln: import
     ESM_MODEL_NAMES,
 )
-from ._cyno_pk_datamodule import CynoPKClearanceLightningDataModule
 from ._dataframe_dataset_in_memory import (  # nopycln: import
     DataFrameDatasetInMemory,
     DataFrameLightningDataModule,
@@ -16,15 +15,12 @@
 )
 from ._minhasher import LobsterMinHasher
 from ._mmseqs import MMSeqsRunner
-from ._neglog_datamodule import NegLogDataModule
 from ._structure_datamodule import PDBDataModule
 from ._utils import (  # nopycln: import
     load_pickle,
 )
 
 __all__ = [
-    "ContactMapDataModule",
-    "NegLogDataModule",
     "PDBDataModule",
     "DataFrameDatasetInMemory",
 ]

src/lobster/datasets/__init__.py

@@ -1,2 +1 @@
-from ._ab_ag_sequence_ppi_dataset import AbAgSequencePPIDataset
 from ._calm_dataset import CalmDataset

src/lobster/extern/openfold_utils/_rigids.py

@@ -372,7 +372,7 @@ def __getitem__(self, index: Any) -> Rotation:
             The indexed rotation
 
         """
-        if type(index) != tuple:
+        if not isinstance(index, tuple):
             index = (index,)
 
         if self._rot_mats is not None:
@@ -947,7 +947,7 @@ def __getitem__(
             The indexed tensor
 
         """
-        if type(index) != tuple:
+        if not isinstance(index, tuple):
             index = (index,)
 
         return Rigid(

src/lobster/tokenization/_pmlm_tokenizer_transform.py

@@ -33,7 +33,6 @@ def __init__(
         verbose: bool = True,
         tokenizer_dir: Optional[str] = "pmlm_tokenizer",
         mlm: bool = True,
-        reversal_augmentation: bool = False,
     ):
         super().__init__()