ruff all

Author: Jhsmit

docs/gen_ref_pages.py

@@ -1,5 +1,4 @@
 """Generate the code reference pages."""
-from functools import partial
 from pathlib import Path
 
 import mkdocs_gen_files

pyhdx/batch_processing.py

@@ -13,7 +13,7 @@
 from pyhdx.config import cfg
 from pyhdx.fileIO import read_dynamx
 from pyhdx.models import HDXMeasurement, HDXMeasurementSet
-from pyhdx.process import correct_d_uptake, apply_control, filter_peptides
+from pyhdx.process import correct_d_uptake, apply_control
 
 
 time_factors = {"s": 1, "m": 60.0, "min": 60.0, "h": 3600, "d": 86400}

pyhdx/cli.py

@@ -86,9 +86,9 @@ def fetch(num: int = typer.Option(10, min=1, help="Maximum number of datasets to
         print("All datasets already downloaded")
 
     if failed:
-        print(f"Failed to download: {' ,'.join(failed)}")
+        print(f"Failed to download: {', '.join(failed)}")
     if success:
-        print(f"Downloaded: {' ,'.join(success)}")
+        print(f"Downloaded: {', '.join(success)}")
 
 
 @datasets_app.command()

pyhdx/fitting.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from collections import namedtuple
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 from functools import partial
 from typing import Union, Optional, Any, Literal
 

pyhdx/fitting_torch.py

@@ -7,7 +7,6 @@
 from scipy import constants, linalg
 
 from pyhdx.fileIO import dataframe_to_file
-from pyhdx.config import cfg
 
 
 # TORCH_DTYPE = t.double

pyhdx/local_cluster.py

@@ -105,7 +105,7 @@ def blocking_cluster():
         n_workers = cfg.cluster.n_workers
         local_cluster = LocalCluster(scheduler_port=port, n_workers=n_workers)
         print(f"Started local cluster at {local_cluster.scheduler_address}")
-    except OSError as e:
+    except OSError:
         print(f"Could not start local cluster with at port: {port}")
         raise
     try:

pyhdx/models.py

@@ -3,7 +3,6 @@
 import os
 import textwrap
 import warnings
-from functools import partial
 from numbers import Number
 from typing import Optional, Any, Union, TYPE_CHECKING
 
@@ -19,7 +18,7 @@
 from pyhdx.alignment import align_dataframes
 from pyhdx.fileIO import dataframe_to_file
 from pyhdx.process import verify_sequence, parse_temperature, correct_d_uptake, apply_control
-from pyhdx.support import reduce_inter, dataframe_intersection, array_intersection
+from pyhdx.support import reduce_inter, dataframe_intersection
 from pyhdx.config import cfg
 
 if TYPE_CHECKING:

pyhdx/output.py

@@ -51,7 +51,7 @@ class FitReport(FitResultPlotBase):
 
     def __init__(self, fit_result, title=None, doc=None, add_date=True, temp_dir=None, **kwargs):
         super().__init__(fit_result)
-        self.title = title or f"Fit report"
+        self.title = title or "Fit report"
         self.doc = doc or self._init_doc(add_date=add_date)
         self._temp_dir = temp_dir or self.make_temp_dir()
         self._temp_dir = Path(self._temp_dir)

pyhdx/process.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-from functools import reduce
 import warnings
 from typing import Optional, Literal, Union
 

pyhdx/support.py

@@ -666,7 +666,7 @@ def make_monomer(input_file, output_file):
                 if line.startswith("COMPND") and "CHAIN" in line:
                     res = re.findall(":(.*);", line)[0]
                     line = line.replace(res + ";", " A;" + " " * (len(res) - 2))
-                if line.startswith("ATOM") and not " A " in line:
+                if line.startswith("ATOM") and " A " not in line:
                     continue
                 elif line.startswith("HETATM") and "HOH" in line:
                     continue