Fix issues to improve code quality (#555)

- Use list in slots instead of string
   - Add self argument
   - Remove unused module 're'

Also add DeepSource configuration

Signed-off-by: Jai <jai@deepsource.io>

.deepsource.toml

@@ -0,0 +1,10 @@
+version = 1
+
+test_patterns = [
+  "tests/"
+]
+
+[[analyzers]]
+name = "python"
+enabled = true
+runtime_version = "3.x.x"

hgvs/dataproviders/interface.py

@@ -125,7 +125,7 @@ def schema_version(self):
         pass
 
     @abc.abstractmethod
-    def get_acs_for_protein_seq(seq):
+    def get_acs_for_protein_seq(self, seq):
         pass
 
     @abc.abstractmethod

hgvs/dataproviders/seqfetcher.py

@@ -7,7 +7,6 @@
 
 import logging
 import os
-import re
 
 import bioutils.seqfetcher
 

hgvs/decorators/lru_cache.py

@@ -23,7 +23,7 @@
 
 
 class _HashedSeq(list):
-    __slots__ = 'hashvalue'
+    __slots__ = ['hashvalue']
 
     def __init__(self, tup, hash=hash):
         self[:] = tup
@@ -95,7 +95,7 @@ def lru_cache(maxsize=100, typed=False, mode=None, cache=None):
 
     :param mode: cache run mode
         None:   the default lru cache behaver
-        LEARN:  queries are executed against persistent cache from file "filename"; 
+        LEARN:  queries are executed against persistent cache from file "filename";
                 in the event of a miss, the novel query and results would be written to cache, then returned.
         RUN:    queries are executed against caches; misses result in DataNotLocallyAvailableError
         VERIFY: always execute the function; if persistent cache value and returned value are different, raise VerifyFailedError

hgvs/location.py

@@ -5,7 +5,7 @@
 
   * integers and integer intervals (e.g., NC_012345.6:g.3403243_3403248A>C)
   * CDS positions and intervals (e.g., NM_01234.5:c.56+12_56+14delAC)
-  * CDS stop coordinates (e.g., NM_01234.5:c.*13A>C)  
+  * CDS stop coordinates (e.g., NM_01234.5:c.*13A>C)
 
 Classes:
 
@@ -48,7 +48,7 @@ def __repr__(self):
     @property
     def is_uncertain(self):
         """return True if the position is marked uncertain or undefined"""
-        return self.uncertain or self.base in None
+        return self.uncertain or self.base is None
 
     def _set_uncertain(self):
         "mark this location as uncertain and return reference to self; this is called during parsing (see hgvs.ometa)"

hgvs/normalizer.py

@@ -202,12 +202,12 @@ def _get_boundary(self, var):
                 right = float("inf")
 
                 # TODO: #242: implement methods to find tx regions
-                for i in range(0, len(exon_starts)):
+                for i, _ in enumerate(exon_starts):
                     if (var.posedit.pos.start.base - 1 >= exon_starts[i]
                             and var.posedit.pos.start.base - 1 < exon_ends[i]):
                         break
 
-                for j in range(0, len(exon_starts)):
+                for j, _ in enumerate(exon_starts):
                     if (var.posedit.pos.end.base - 1 >= exon_starts[j] and var.posedit.pos.end.base - 1 < exon_ends[j]):
                         break