Merge pull request #763 from padix-key/ruff

Update ruff version

Author: padix-key

.github/workflows/test_and_deploy.yml

@@ -46,7 +46,7 @@ jobs:
         python-version: "3.12"
     - name: Install ruff
       # Keep in sync with the corresponding versions in pyproject.toml
-      run: pip install ruff==0.6.9 numpydoc==1.8.0
+      run: pip install ruff==0.9.7 numpydoc==1.8.0
     - name: Check code formatting
       run: ruff format --diff
     - name: Lint code base

doc/apidoc.py

@@ -119,7 +119,7 @@ def _create_package_page(doc_path, package_name, classes, functions, subpackages
         string = dedent(f"""
 
             {category}
-            {"-"*len(category)}
+            {"-" * len(category)}
 
             .. autosummary::
                 :nosignatures:

doc/examples/scripts/sequence/annotation/sigma_domains.py

@@ -111,7 +111,7 @@
             ax.text(
                 x=(last + first) / 2,
                 y=i,
-                s=rf"$\sigma_{j+1}$",
+                s=rf"$\sigma_{j + 1}$",
                 ha="center",
                 va="center",
             )

doc/examples/scripts/structure/modeling/docking.py

@@ -107,7 +107,7 @@
 correlation, p_value = spearmanr(energies, rmsd)
 
 figure, ax = plt.subplots(figsize=(8.0, 6.0))
-ax.set_title(f"$r_s$ = {correlation:.2f} ($p$ = {p_value*100:.1f}%)")
+ax.set_title(f"$r_s$ = {correlation:.2f} ($p$ = {p_value * 100:.1f}%)")
 ax.scatter(energies, rmsd, marker="+", color="black")
 ax.set_xlabel("Energy (kcal/mol)")
 ax.set_ylabel("RMSD (Å)")

environment.yml

@@ -28,7 +28,7 @@ dependencies:
   - pytest >=7.0
   - pytest-codspeed >=2.0
   # Code style, keep in sync with the versions in pyproject.toml
-  - ruff =0.6.9
+  - ruff =0.9.7
   - numpydoc =1.8.0
   # Interfaced software in biotite.application (can also be installed separately)
   - autodock-vina

pyproject.toml

@@ -37,7 +37,7 @@ test = [
   "pytest-codspeed",
 ]
 lint = [
-  "ruff == 0.6.9",
+  "ruff == 0.9.7",
   "numpydoc == 1.8.0",
 ]
 

src/biotite/application/application.py

@@ -157,7 +157,7 @@ def join(self, timeout=None):
             if timeout is not None and time.time() - self._start_time > timeout:
                 self.cancel()
                 raise TimeoutError(
-                    f"The application expired its timeout " f"({timeout:.1f} s)"
+                    f"The application expired its timeout ({timeout:.1f} s)"
                 )
             else:
                 time.sleep(self.wait_interval())

src/biotite/application/clustalo/app.py

@@ -172,7 +172,7 @@ def get_distance_matrix(self):
         """
         if self._mbed:
             raise ValueError(
-                "Getting the distance matrix requires " "'full_matrix_calculation()'"
+                "Getting the distance matrix requires 'full_matrix_calculation()'"
             )
         return self._dist_matrix
 

src/biotite/application/localapp.py

@@ -279,7 +279,7 @@ def evaluate(self):
         if exit_code != 0:
             err_msg = self.get_stderr().replace("\n", " ")
             raise SubprocessError(
-                f"'{self._bin_path}' returned with exit code {exit_code}: " f"{err_msg}"
+                f"'{self._bin_path}' returned with exit code {exit_code}: {err_msg}"
             )
 
     def clean_up(self):

src/biotite/application/msaapp.py

@@ -68,7 +68,7 @@ def __init__(self, sequences, bin_path, matrix=None):
         # Check matrix symmetry
         if matrix is not None and not matrix.is_symmetric():
             raise ValueError(
-                "A symmetric matrix is required for " "multiple sequence alignments"
+                "A symmetric matrix is required for multiple sequence alignments"
             )
 
         # Check whether the program supports the alignment for the given

src/biotite/application/util.py

@@ -63,7 +63,7 @@ def map_matrix(matrix):
     """
     if matrix is None:
         raise TypeError(
-            "A substitution matrix must be provided for custom " "sequence types"
+            "A substitution matrix must be provided for custom sequence types"
         )
     # Create a protein substitution matrix with the values taken
     # from the original matrix

src/biotite/database/entrez/download.py

@@ -110,7 +110,7 @@ def fetch(
     for i, id in enumerate(uids):
         # Verbose output
         if verbose:
-            print(f"Fetching file {i+1:d} / {len(uids):d} ({id})...", end="\r")
+            print(f"Fetching file {i + 1:d} / {len(uids):d} ({id})...", end="\r")
         # Fetch file from database
         if target_path is not None:
             file = join(target_path, id + "." + suffix)

src/biotite/database/entrez/query.py

@@ -173,7 +173,8 @@ class SimpleQuery(Query):
         "SUBS",
         "WORD",
         "TI",
-        "TITL" "VOL",
+        "TITL",
+        "VOL",
     ]
 
     def __init__(self, term, field=None):

src/biotite/database/pubchem/download.py

@@ -114,7 +114,7 @@ def fetch(
             raise TypeError("CIDs must be given as integers, not as string")
         # Verbose output
         if verbose:
-            print(f"Fetching file {i+1:d} / {len(cids):d} ({cid})...", end="\r")
+            print(f"Fetching file {i + 1:d} / {len(cids):d} ({cid})...", end="\r")
 
         # Fetch file from database
         if target_path is not None:

src/biotite/database/pubchem/query.py

@@ -332,7 +332,7 @@ def __init__(self, **kwargs):
                     )
         if not query_key_found:
             raise TypeError(
-                "Expected exactly one of 'smiles', 'smarts', 'inchi', 'sdf' " "or 'cid'"
+                "Expected exactly one of 'smiles', 'smarts', 'inchi', 'sdf' or 'cid'"
             )
         if "number" in kwargs:
             self._number = kwargs["number"]

src/biotite/database/rcsb/download.py

@@ -91,7 +91,7 @@ def fetch(pdb_ids, format, target_path=None, overwrite=False, verbose=False):
     for i, id in enumerate(pdb_ids):
         # Verbose output
         if verbose:
-            print(f"Fetching file {i+1:d} / {len(pdb_ids):d} ({id})...", end="\r")
+            print(f"Fetching file {i + 1:d} / {len(pdb_ids):d} ({id})...", end="\r")
 
         # Fetch file from database
         if target_path is not None:

src/biotite/database/rcsb/query.py

@@ -257,7 +257,7 @@ def __init__(
             "exists",
         ]:
             raise TypeError(
-                f"Constructor got an unexpected keyword argument " f"'{self._operator}'"
+                f"Constructor got an unexpected keyword argument '{self._operator}'"
             )
 
         # Convert dates into ISO 8601
@@ -944,8 +944,7 @@ def _initialize_query_dict(query, return_type, group_by, content_types):
     if group_by is not None:
         if not group_by.is_compatible_return_type(return_type):
             raise ValueError(
-                f"Return type '{return_type}' is not compatible "
-                f"with the given Grouping"
+                f"Return type '{return_type}' is not compatible with the given Grouping"
             )
         request_options["group_by"] = group_by.get_content()
 

src/biotite/interface/pymol/cgo.py

@@ -304,7 +304,7 @@ def get_multiline_cgo(start, end, color, width=1.0):
 
     if len(start) != len(end):
         raise IndexError(
-            f"{len(start)} start positions are given, " f"but {len(end)} end positions"
+            f"{len(start)} start positions are given, but {len(end)} end positions"
         )
     for p in start:
         _expect_length(p, "start", 3)

src/biotite/interface/pymol/object.py

@@ -303,7 +303,7 @@ def exists(self):
     def _check_existence(self):
         if not self.exists():
             raise NonexistentObjectError(
-                f"A PyMOL object with the name {self._name} " f"does not exist anymore"
+                f"A PyMOL object with the name {self._name} does not exist anymore"
             )
 
     @validate
@@ -371,7 +371,7 @@ def where(self, index):
             # - PyMOLs indexing starts at 1-> 'start+1'
             # - Stop in 'intervals' is exclusive -> 'stop+1-1' -> 'stop'
             index_selection = " or ".join(
-                [f"index {start+1}-{stop}" for start, stop in intervals]
+                [f"index {start + 1}-{stop}" for start, stop in intervals]
             )
             # Constrain the selection to given object name
             return f"%{self._name} and ({index_selection})"

src/biotite/interface/pymol/shapes.py

@@ -71,8 +71,7 @@ def draw_arrows(
         raise IndexError("Expected 2D array for start and end positions")
     if len(start) != len(end):
         raise IndexError(
-            f"Got {len(start)} start positions, "
-            f"but expected {len(end)} end positions"
+            f"Got {len(start)} start positions, but expected {len(end)} end positions"
         )
     expected_length = len(start)
     radius = _arrayfy(radius, expected_length, 1)

src/biotite/sequence/align/matrix.py

@@ -173,7 +173,7 @@ def __init__(self, alphabet1, alphabet2, score_matrix):
             self._fill_with_matrix_dict(matrix_dict)
         else:
             raise TypeError(
-                "Matrix must be either a dictionary, " "an 2-D ndarray or a string"
+                "Matrix must be either a dictionary, an 2-D ndarray or a string"
             )
         # This class is immutable and has a getter function for the
         # score matrix -> make the score matrix read-only
@@ -442,7 +442,7 @@ def __str__(self):
         for i, symbol in enumerate(self._alph1):
             string += f"{str(symbol):>1}"
             for j in range(len(self._alph2)):
-                string += f" {int(self._matrix[i,j]):>3d}"
+                string += f" {int(self._matrix[i, j]):>3d}"
             string += "\n"
         # Remove terminal line break
         string = string[:-1]

src/biotite/sequence/align/statistics.py

@@ -168,7 +168,7 @@ def from_samples(
             raise ValueError("A symmetric substitution matrix is required")
         if not matrix.get_alphabet1().extends(alphabet):
             raise ValueError(
-                "The substitution matrix is not compatible " "with the given alphabet"
+                "The substitution matrix is not compatible with the given alphabet"
             )
         score_matrix = matrix.score_matrix()[: len(alphabet), : len(alphabet)]
         if (

src/biotite/sequence/annotation.py

@@ -97,8 +97,8 @@ def __init__(self, first, last, strand=Strand.FORWARD, defect=Defect.NONE):
     def __repr__(self):
         """Represent Location as a string for debugging."""
         return (
-            f'Location({self._first}, {self._last}, strand={"Location." + str(self._strand)}, '
-            f'defect={"Location." + str(self._defect)})'
+            f"Location({self._first}, {self._last}, strand={'Location.' + str(self._strand)}, "
+            f"defect={'Location.' + str(self._defect)})"
         )
 
     @property
@@ -361,7 +361,7 @@ def __init__(self, features=None):
     def __repr__(self):
         """Represent Annotation as a string for debugging."""
         return (
-            f'Annotation([{", ".join([feat.__repr__() for feat in self._features])}])'
+            f"Annotation([{', '.join([feat.__repr__() for feat in self._features])}])"
         )
 
     def __copy_create__(self):
@@ -389,8 +389,7 @@ def add_feature(self, feature):
         """
         if not isinstance(feature, Feature):
             raise TypeError(
-                f"Only 'Feature' objects are supported, "
-                f"not {type(feature).__name__}"
+                f"Only 'Feature' objects are supported, not {type(feature).__name__}"
             )
         self._features.add(feature)
 
@@ -503,7 +502,7 @@ def __getitem__(self, index):
     def __delitem__(self, item):
         if not isinstance(item, Feature):
             raise TypeError(
-                f"Only 'Feature' objects are supported, " f"not {type(item).__name__}"
+                f"Only 'Feature' objects are supported, not {type(item).__name__}"
             )
         self.del_feature(item)
 

src/biotite/sequence/io/fasta/convert.py

@@ -275,8 +275,7 @@ def _process_nucleotide_sequence(x):
 def _convert_to_string(sequence, as_rna):
     if not isinstance(sequence.get_alphabet(), LetterAlphabet):
         raise ValueError(
-            "Only sequences using single letter alphabets "
-            "can be stored in a FASTA file"
+            "Only sequences using single letter alphabets can be stored in a FASTA file"
         )
     if isinstance(sequence, NucleotideSequence) and as_rna:
         return str(sequence).replace("T", "U")

src/biotite/sequence/io/fasta/file.py

@@ -102,7 +102,7 @@ def __setitem__(self, header, seq_str):
         if not isinstance(header, str):
             raise IndexError("'FastaFile' only supports header strings as keys")
         if not isinstance(seq_str, str):
-            raise TypeError("'FastaFile' only supports sequence strings " "as values")
+            raise TypeError("'FastaFile' only supports sequence strings as values")
         # Create lines for new header and sequence (with line breaks)
         new_lines = [">" + header.replace("\n", "").strip()] + wrap_string(
             seq_str, width=self._chars_per_line

src/biotite/sequence/io/fastq/file.py

@@ -302,10 +302,10 @@ def _find_entries(self):
                 else:  # score_len > seq_len
                     raise InvalidFileError(
                         f"The amount of scores is not equal to the sequence "
-                        f"length for the sequence in line {seq_start_i+1} "
+                        f"length for the sequence in line {seq_start_i + 1} "
                     )
             else:
-                raise InvalidFileError(f"Line {i+1} in FASTQ file is invalid")
+                raise InvalidFileError(f"Line {i + 1} in FASTQ file is invalid")
         # At the end of the file, the last sequence or score block
         # must have properly ended
         if in_sequence or in_scores:
@@ -392,7 +392,7 @@ def read_iter(file, offset):
                     yield identifier, ("".join(seq_str_list), scores)
                 else:  # score_len > seq_len
                     raise InvalidFileError(
-                        "The amount of scores is not equal to the sequence " "length"
+                        "The amount of scores is not equal to the sequence length"
                     )
 
             else:

src/biotite/sequence/io/gff/convert.py

@@ -84,7 +84,7 @@ def set_annotation(gff_file, annotation, seqid=None, source=None, is_stranded=Tr
     for feature in sorted(annotation):
         if len(feature.locs) > 1 and "ID" not in feature.qual:
             raise ValueError(
-                "The 'Id' qualifier is required " "for features with multiple locations"
+                "The 'Id' qualifier is required for features with multiple locations"
             )
         ## seqid ##
         if seqid is not None and " " in seqid:

src/biotite/sequence/io/gff/file.py

@@ -303,8 +303,7 @@ def __setitem__(self, index, item):
     def __getitem__(self, index):
         if (index >= 0 and index >= len(self)) or (index < 0 and -index > len(self)):
             raise IndexError(
-                f"Index {index} is out of range for GFFFile with "
-                f"{len(self)} entries"
+                f"Index {index} is out of range for GFFFile with {len(self)} entries"
             )
 
         line_index = self._entries[index]

src/biotite/sequence/seqtypes.py

@@ -601,7 +601,7 @@ def get_molecular_weight(self, monoisotopic=False):
 
         if np.isnan(weight):
             raise ValueError(
-                "Sequence contains ambiguous amino acids, " "cannot calculate weight"
+                "Sequence contains ambiguous amino acids, cannot calculate weight"
             )
         return weight
 

src/biotite/structure/alphabet/unkerasify.py

@@ -71,7 +71,7 @@ def read(self):
             (w1,) = self._get("I")
             (b0,) = self._get("I")
             weights = (
-                np.frombuffer(self._read(f"={w0*w1}f"), dtype="f4")
+                np.frombuffer(self._read(f"={w0 * w1}f"), dtype="f4")
                 .reshape(w0, w1)
                 .copy()
             )