flake8

.flake8

@@ -6,4 +6,4 @@ select = B,C,E,F,W,T4,B9
 exclude =
     tests,
     scripts,
-    docs*
+    docs

.pre-commit-config.yaml

@@ -17,16 +17,16 @@ repos:
   - id: mixed-line-ending
 # Code formatting
 - repo: https://github.com/ambv/black
-  rev: 24.2.0
+  rev: 24.10.0
   hooks:
   - id: black
+    exclude: tests
 # Further linting (e.g. module imported but not used)
 - repo: https://github.com/PyCQA/flake8
   rev: 7.1.1
   hooks:
   - id: flake8
-    args:
-      - --exclude=tests,scripts,docs
+    exclude: ^(tests/|scripts/|docs/)
 # Verify that requirements.txt is up to date with poetry dependencies every commit
 - repo: https://github.com/python-poetry/poetry
   rev: 1.8.3

scripts/guess_alphabet.py

@@ -32,7 +32,9 @@ def guess_alphabet(sequence):
     else:
         if not isinstance(sequence, str):
             warnings.warn(
-                ("Input is {}, expected string, " "unicode string, Seq or SeqRecord " "objects!").format(type(sequence))
+                ("Input is {}, expected string, " "unicode string, Seq or SeqRecord " "objects!").format(
+                    type(sequence)
+                )
             )
         sequence = str(sequence)
 

src/pydna/amplicon.py

@@ -123,12 +123,12 @@ def figure(self):
         fzc = tp.seq.crick[::-1][fp.position - fp._fp : fp.position]
         rzc = tp.seq.crick[::-1][rp.position : rp.position + rp._fp]
         f = f"""
-            {" " *ft}5{faz}...{raz}3
+            {" " * ft}5{faz}...{raz}3
              {sp3}{"|" * rp._fp}
             {sp3}3{rp.seq[::-1]}5
             5{fp.seq}3
-             {"|" *fp._fp:>{len(fp)}}
-            {" " *ft}3{fzc}...{rzc}5
+             {"|" * fp._fp:>{len(fp)}}
+            {" " * ft}3{fzc}...{rzc}5
             """
         # breakpoint()
         return _pretty_str(_textwrap.dedent(f).strip("\n"))

src/pydna/amplify.py

@@ -17,7 +17,7 @@
 from pydna.utils import flatten as _flatten
 
 from pydna.utils import iupac_compl_regex as _iupac_compl_regex
-from pydna.utils import rc as _rc, shift_feature as _shift_feature
+from pydna.utils import shift_feature as _shift_feature
 from pydna.utils import anneal_from_left as _anneal_from_left
 from pydna.amplicon import Amplicon as _Amplicon
 from pydna.primer import Primer as _Primer
@@ -27,7 +27,8 @@
 from Bio.SeqFeature import SimpleLocation as _SimpleLocation
 from Bio.SeqFeature import CompoundLocation as _CompoundLocation
 from pydna.seq import Seq as _Seq
-import itertools as _itertools
+
+# import itertools as _itertools
 import re as _re
 import copy as _copy
 import operator as _operator

src/pydna/dseq.py

@@ -47,6 +47,15 @@
 from Bio.Restriction import RestrictionBatch as _RestrictionBatch
 from Bio.Restriction import CommOnly
 
+from typing import (
+    TYPE_CHECKING,
+    List as _List,
+    Tuple as _Tuple,
+    Union as _Union,
+    TypeVar as _TypeVar,
+    Iterable as _Iterable,
+)
+
 try:
     from itertools import pairwise as _pairwise
 except ImportError:
@@ -59,16 +68,8 @@ def _pairwise(iterable):
             yield a, b
             a = b
 
-pos_w_enz = _namedtuple("enzpos", "position enzyme recsite")
 
-from typing import (
-    TYPE_CHECKING,
-    List as _List,
-    Tuple as _Tuple,
-    Union as _Union,
-    TypeVar as _TypeVar,
-    Iterable as _Iterable,
-)
+pos_w_enz = _namedtuple("enzpos", "position enzyme recsite")
 
 
 if TYPE_CHECKING:
@@ -1413,7 +1414,6 @@ def __repr__(self):
         if overlaps := _cuts_overlap(cutsites):
             raise ValueError(f"Enzyme pairs with cut overlap: {overlaps}")
 
-
         if not cutsites:
             return tuple(), tuple(), None, None
 

src/pydna/dseqrecord.py

@@ -17,15 +17,17 @@
 from pydna._pretty import pretty_str as _pretty_str
 from pydna.utils import flatten as _flatten, location_boundaries as _location_boundaries
 from pydna.utils import unfold_feature as _unfold_feature
-from pydna.utils import rc as _rc
+
+# from pydna.utils import rc as _rc
 from pydna.utils import shift_location as _shift_location
 from pydna.utils import shift_feature as _shift_feature
 from pydna.common_sub_strings import common_sub_strings as _common_sub_strings
 from Bio import SeqIO
 from Bio.SeqFeature import SeqFeature as _SeqFeature
 from Bio.SeqFeature import CompoundLocation as _CompoundLocation
 from Bio.SeqFeature import SimpleLocation as _SimpleLocation
-from Bio.SeqFeature import ExactPosition as _ExactPosition
+
+# from Bio.SeqFeature import ExactPosition as _ExactPosition
 from pydna.seqrecord import SeqRecord as _SeqRecord
 from Bio.Seq import translate as _translate
 from pydna.utils import identifier_from_string as _identifier_from_string
@@ -517,6 +519,7 @@ def write(self, filename=None, f="gb"):
             # The filename alread exists in current directory
             # We assume it contains a sequence
             from pydna.readers import read
+
             old = read(filename)
             if self == old:
                 # The sequence object to be saved is identical to the on disk.

src/pydna/seqrecord.py

@@ -29,7 +29,8 @@
 from pydna._pretty import PrettyTable as _PrettyTable
 
 import re as _re
-import pickle as _pickle
+
+# import pickle as _pickle
 from copy import copy as _copy
 
 from pydna import _PydnaWarning
@@ -627,7 +628,7 @@ def removeprefix(text, prefix):
 
         if format == "pydnafasta":
             return _pretty_str(
-                f">{self.id} {len(self)} bp {dict(((True,'circular'),(False,'linear')))[self.seq.circular]}\n{str(self.seq)}\n"
+                f">{self.id} {len(self)} bp {dict(((True, 'circular'), (False, 'linear')))[self.seq.circular]}\n{str(self.seq)}\n"
             )
         if format == "primer":
             return _pretty_str(

src/pydna/utils.py

@@ -46,6 +46,7 @@ def _pairwise(iterable):
             yield a, b
             a = b
 
+
 # For functions that take str or bytes as input and return str or bytes as output, matching the input type
 StrOrBytes = _TypeVar("StrOrBytes", str, bytes)
 
@@ -1511,11 +1512,15 @@ def eq(*args, **kwargs):
 #     y = sorted([right_watson, right_crick])
 #     return (x[1] > y[0]) != (y[1] < x[0])
 
+
 def cuts_overlap(cutsites):
 
     srt_pos = [(tuple(sorted((ep.position, ep.position - ep.enzyme.ovhg))), ep) for ep in cutsites]
 
-    combs = {(ep1.enzyme, x, ep2.enzyme, y): (x[1] > y[0]) != (y[1] < x[0]) for ((x, ep1), (y, ep2)) in _itertools.combinations(srt_pos, 2)}
+    combs = {
+        (ep1.enzyme, x, ep2.enzyme, y): (x[1] > y[0]) != (y[1] < x[0])
+        for ((x, ep1), (y, ep2)) in _itertools.combinations(srt_pos, 2)
+    }
 
     return [comb for comb, val in combs.items() if val]