fix line lengths and modify test

Noble-Lab · May 7, 2024 · 0ecbd80 · 0ecbd80
1 parent 81aa073
commit 0ecbd80
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Showing 2 changed files with 21 additions and 11 deletions.
diff --git a/casanovo/denovo/model.py b/casanovo/denovo/model.py
@@ -993,8 +993,10 @@ class DBSpec2Pep(Spec2Pep):
     """
     Inherits Spec2Pep
 
-    Hijacks teacher-forcing implemented in Spec2Pep and uses it to predict scores between a spectra and associated peptide.
-    Input format is .mgf, with comma-separated targets and decoys in the SEQ field. Decoys should have a prefix of "decoy_".
+    Hijacks teacher-forcing implemented in Spec2Pep and
+    uses it to predict scores between a spectra and associated peptide.
+    Input format is .mgf, with comma-separated targets
+    and decoys in the SEQ field. Decoys should have a prefix of "decoy_".
     """
 
     num_pairs = None  # Modified to be predict_batch_size from config
@@ -1120,22 +1122,29 @@ def _calc_match_score(
     batch_all_aa_scores: torch.Tensor, truth_aa_indicies: torch.Tensor
 ) -> List[float]:
     """
-    Take in teacher-forced scoring of amino acids of the peptides (in a batch) and use the truth labels
-    to calculate a score between the input spectra and associated peptide. The score is the geometric
+    Take in teacher-forced scoring of amino acids
+    of the peptides (in a batch) and use the truth labels
+    to calculate a score between the input spectra and
+    associated peptide. The score is the geometric
     mean of the AA probabilities
 
         Parameters
         ----------
         batch_all_aa_scores : torch.Tensor
-            Amino acid scores for all amino acids in the vocabulary for every prediction made to generate the associated peptide (for an entire batch)
+            Amino acid scores for all amino acids in
+            the vocabulary for every prediction made to generate
+            the associated peptide (for an entire batch)
         truth_aa_indicies : torch.Tensor
-            Indicies of the score for each actual amino acid in the peptide (for an entire batch)
+            Indicies of the score for each actual amino acid
+            in the peptide (for an entire batch)
 
         Returns
         -------
         score : list[float], list[list[float]]
-            The score between the input spectra and associated peptide (for an entire batch)
-            a list of lists of per amino acid scores (for an entire batch)
+            The score between the input spectra and associated peptide
+            (for an entire batch)
+            a list of lists of per amino acid scores
+            (for an entire batch)
     """
     # Remove trailing tokens from predictions,
     batch_all_aa_scores = batch_all_aa_scores[:, :-1]

diff --git a/tests/test_integration.py b/tests/test_integration.py
@@ -47,16 +47,17 @@ def test_annotate(
         == "SEQ=LESLIEK,PEPTIDEK,decoy_KEILSEL,decoy_KEDITEPP"
     )
     assert (
-        seq_lines[2].strip()
-        == "SEQ=+42.011LEM+15.995SLIM+15.995EK,+43.006PEN+0.984PTIQ+0.984DEK,decoy_-17.027KM+15.995EILSEL,decoy_+43.006-17.027KEDITEPP,decoy_KEDIQ+0.984TEPPQ+0.984"
+        seq_lines[2].strip() == "SEQ=+42.011LEM+15.995SLIM+15.995EK,"
+        "+43.006PEN+0.984PTIQ+0.984DEK,decoy_-17.027KM+15.995EILSEL,"
+        "decoy_+43.006-17.027KEDITEPP,decoy_KEDIQ+0.984TEPPQ+0.984"
     )
 
 
 def test_db_search(
     mgf_small_unannotated, tide_dir_small, tiny_config, tmp_path, monkeypatch
 ):
     # Run a command:
-    monkeypatch.setattr(casanovo, "__version__", "4.1.1")
+    monkeypatch.setattr(casanovo, "__version__", "4.1.0")
     run = functools.partial(
         CliRunner().invoke, casanovo.main, catch_exceptions=False
     )