lint

Author: ncfrey

model_testing/inference.py

@@ -1,13 +1,13 @@
 # Lobster Model Inference
 
 import torch
-from lobster.model import LobsterPMLM, LobsterCBMPMLM
+from lobster.model import LobsterCBMPMLM, LobsterPMLM
 
 # Define the test protein sequence
 test_protein = "MGAGASAEEKHSRELEKKLKEDAEKDARTVKLLLLGAGESGKSTIVKQMKIIHQDGYSLEECLEFIAIIYGNTLQSILAIVRAMTTLNIQYGDSARQDDARKLMHMADTIEEGTMPKEMSDIIQRLWKDSGIQACFERASEYQLNDSAGYYLSDLERLVTPGYVPTEQDVLRSRVKTTGIIETQFSFKDLNFRMFDVGGQRSERKKWIHCFEGVTCIIFIAALSAYDMVLVEDDEVNRMHESLHLFNSICNHRYFATTSIVLFLNKKDVFFEKIKKAHLSICFPDYDGPNTYEDAGNYIKVQFLELNMRRDVKEIYSHMTCATDTQNVKFVFDAVTDIIIKENLKDCGLF"
 
 # Determine the device
-device = 'cuda' if torch.cuda.is_available() else 'cpu'
+device = "cuda" if torch.cuda.is_available() else "cpu"
 
 # Load the LobsterPMLM model
 lobster = LobsterPMLM("asalam91/lobster_24M").to(device)
@@ -29,7 +29,9 @@
 
 # Get protein concepts
 test_protein_concepts = cb_lobster.sequences_to_concepts([test_protein])[-1]
-test_protein_concepts_emb = cb_lobster.sequences_to_concepts_emb([test_protein])[-1][0]  # All of the known concepts are the same for all tokens...
+test_protein_concepts_emb = cb_lobster.sequences_to_concepts_emb([test_protein])[-1][
+    0
+]  # All of the known concepts are the same for all tokens...
 test_protein_concepts_unknown_emb = cb_lobster.sequences_to_concepts_emb([test_protein])[-1]
 
 # Print results

model_testing/intervene.py

@@ -1,19 +1,19 @@
+import Levenshtein
 import torch
 from lobster.model import LobsterCBMPMLM
-import Levenshtein
 
 device = "cuda" if torch.cuda.is_available() else "cpu"
 
 # Load the LobsterCBMPMLM model
 cb_lobster = LobsterCBMPMLM("asalam91/cb_lobster_24M").to(device)
 cb_lobster.eval()
-print (cb_lobster.list_supported_concept())
+print(cb_lobster.list_supported_concept())
 
-concept ="gravy"
-test_protein ="MGAGASAEEKHSRELEKKLKEDAEKDARTVKLLLLGAGESGKSTIVKQMKIIHQDGYSLEECLEFIAIIYGNTLQSILAIVRAMTTLNIQYGDSARQDDARKLMHMADTIEEGTMPKEMSDIIQRLWKDSGIQACFERASEYQLNDSAGYYLSDLERLVTPGYVPTEQDVLRSRVKTTGIIETQFSFKDLNFRMFDVGGQRSERKKWIHCFEGVTCIIFIAALSAYDMVLVEDDEVNRMHESLHLFNSICNHRYFATTSIVLFLNKKDVFFEKIKKAHLSICFPDYDGPNTYEDAGNYIKVQFLELNMRRDVKEIYSHMTCATDTQNVKFVFDAVTDIIIKENLKDCGLF"
+concept = "gravy"
+test_protein = "MGAGASAEEKHSRELEKKLKEDAEKDARTVKLLLLGAGESGKSTIVKQMKIIHQDGYSLEECLEFIAIIYGNTLQSILAIVRAMTTLNIQYGDSARQDDARKLMHMADTIEEGTMPKEMSDIIQRLWKDSGIQACFERASEYQLNDSAGYYLSDLERLVTPGYVPTEQDVLRSRVKTTGIIETQFSFKDLNFRMFDVGGQRSERKKWIHCFEGVTCIIFIAALSAYDMVLVEDDEVNRMHESLHLFNSICNHRYFATTSIVLFLNKKDVFFEKIKKAHLSICFPDYDGPNTYEDAGNYIKVQFLELNMRRDVKEIYSHMTCATDTQNVKFVFDAVTDIIIKENLKDCGLF"
 
-[new_protien] = cb_lobster.intervene_on_sequences([test_protein],concept,edits=5,intervention_type="negative")
+[new_protien] = cb_lobster.intervene_on_sequences([test_protein], concept, edits=5, intervention_type="negative")
 
 
 print(new_protien)
-print(Levenshtein.distance(test_protein, new_protien))
+print(Levenshtein.distance(test_protein, new_protien))

src/lobster/datasets/_ab_ag_sequence_ppi_dataset.py

@@ -1,7 +1,6 @@
 import logging
 
 import pytest
-from lobster.data import NegLogDataModule
 
 
 @pytest.fixture(autouse=True)
@@ -10,14 +9,3 @@ def configure_logging():
     logger.setLevel(logging.DEBUG)
     for handler in logger.handlers:
         handler.setLevel(logging.DEBUG)
-
-
-@pytest.fixture(scope="session")
-def ppi_datamodule(tmp_path_factory):
-    root = tmp_path_factory.mktemp("neglog")
-    return NegLogDataModule(
-        root=root,
-        download=False,
-        lengths=[0.7, 0.2, 0.1],
-        truncation_seq_length=50,
-    )