style: update ruff

Author: jsstevenson

pyproject.toml

@@ -93,6 +93,7 @@ src = ["src"]
 exclude = ["docs/source/conf.py"]
 
 [tool.ruff.lint]
+select = ["ALL"]
 ignore = [
     # unused
     "AIR",
@@ -152,14 +153,16 @@ ignore = [
 # INP001 - implicit-namespace-package
 # SLF001 - private-member-access
 # ARG001 - unused-function-argument
+# PLR2004 - magic-value-comparison
 "tests/*" = [
     "ANN001",
     "ANN2",
     "D",
     "S101",
     "INP001",
     "SLF001",
-    "ARG001"
+    "ARG001",
+    "PLR2004",
 ]
 "*__init__.py" = ["F401"]
 "src/cool_seq_tool/schemas.py" = ["ANN201", "N805", "ANN001"]

src/cool_seq_tool/handlers/seqrepo_access.py

@@ -58,9 +58,8 @@ def get_reference_sequence(
             start, end = get_inter_residue_pos(start, end, coordinate_type)
             if start == end:
                 end += 1
-        else:
-            if start is not None and coordinate_type == CoordinateType.RESIDUE:
-                start -= 1
+        elif start is not None and coordinate_type == CoordinateType.RESIDUE:
+            start -= 1
 
         try:
             sequence = self.sr.fetch(ac, start=start, end=end)

src/cool_seq_tool/mappers/alignment.py

@@ -68,11 +68,10 @@ async def p_to_c(
         # codon. We want to return inter-residue (0-based), so we subtract 1 from this.
         if coordinate_type == CoordinateType.RESIDUE:
             c_pos = (p_start_pos * 3) - 3, p_end_pos * 3
+        elif p_start_pos == p_end_pos:
+            c_pos = ((p_start_pos + 1) * 3) - 3, (p_end_pos + 1) * 3
         else:
-            if p_start_pos == p_end_pos:
-                c_pos = ((p_start_pos + 1) * 3) - 3, (p_end_pos + 1) * 3
-            else:
-                c_pos = ((p_start_pos + 1) * 3) - 3, p_end_pos * 3
+            c_pos = ((p_start_pos + 1) * 3) - 3, p_end_pos * 3
 
         return {
             "c_ac": c_ac,

src/cool_seq_tool/mappers/exon_genomic_coords.py

@@ -723,11 +723,10 @@ def _get_tx_segment(
                 seg_genomic_pos = offset + genomic_ac_data.alt_start_i
             else:
                 seg_genomic_pos = genomic_ac_data.alt_end_i - offset
+        elif strand == Strand.POSITIVE:
+            seg_genomic_pos = offset + genomic_ac_data.alt_end_i
         else:
-            if strand == Strand.POSITIVE:
-                seg_genomic_pos = offset + genomic_ac_data.alt_end_i
-            else:
-                seg_genomic_pos = genomic_ac_data.alt_start_i - offset
+            seg_genomic_pos = genomic_ac_data.alt_start_i - offset
 
         genomic_loc, err_msg = self._get_vrs_seq_loc(
             genomic_ac,

src/cool_seq_tool/mappers/feature_overlap.py

@@ -158,14 +158,13 @@ def get_grch38_mane_gene_cds_overlap(
             if not re.match(f"^{CHR_PATTERN}$", chromosome):
                 error_msg = "`chromosome` must be 1, ..., 22, X, or Y"
                 raise FeatureOverlapError(error_msg)
+        elif identifier:
+            chromosome = self._get_chr_from_alt_ac(identifier)
+            if identifier.startswith("ga4gh:SQ."):
+                ga4gh_seq_id = identifier
         else:
-            if identifier:
-                chromosome = self._get_chr_from_alt_ac(identifier)
-                if identifier.startswith("ga4gh:SQ."):
-                    ga4gh_seq_id = identifier
-            else:
-                error_msg = "Must provide either `chromosome` or `identifier`"
-                raise FeatureOverlapError(error_msg)
+            error_msg = "Must provide either `chromosome` or `identifier`"
+            raise FeatureOverlapError(error_msg)
 
         # Convert residue to inter-residue
         if coordinate_type == CoordinateType.RESIDUE:
@@ -234,8 +233,8 @@ def _get_seq_loc(
 
         resp = {}
         refget_ac = ga4gh_seq_id.split("ga4gh:")[-1]
-        for gene, group in feature_df.group_by("gene"):
-            gene = gene[0]
+        for gene_l, group in feature_df.group_by("gene"):
+            gene = gene_l[0]
             _gene_overlap_data = [
                 CdsOverlap(
                     cds=_get_seq_loc(

src/cool_seq_tool/mappers/mane_transcript.py

@@ -545,10 +545,9 @@ def _validate_reading_frames(
                         new_rf,
                     )
                     return False
-            else:
-                if pos_index == 0:
-                    _logger.warning("%s must having start position", ac)
-                    return False
+            elif pos_index == 0:
+                _logger.warning("%s must having start position", ac)
+                return False
         return True
 
     def _validate_references(

src/cool_seq_tool/sources/uta_database.py

@@ -664,11 +664,10 @@ async def get_genomic_tx_data(
                     genomic_tx_data.alt_pos_range[0] + pos_change[0],
                     genomic_tx_data.alt_pos_range[1] - pos_change[1],
                 )
+        elif genomic_tx_data.strand == Strand.NEGATIVE:
+            alt_pos_change_range = (pos[1], pos[0])
         else:
-            if genomic_tx_data.strand == Strand.NEGATIVE:
-                alt_pos_change_range = (pos[1], pos[0])
-            else:
-                alt_pos_change_range = pos
+            alt_pos_change_range = pos
 
         return GenomicTxMetadata(
             **genomic_tx_data.model_dump(),
@@ -953,7 +952,7 @@ def database(self) -> str | None:
     def schema(self) -> str | None:
         """Create schema property."""
         path_elems = self.path.split("/")
-        return path_elems[2] if len(path_elems) > 2 else None
+        return path_elems[2] if len(path_elems) > 2 else None  # noqa: PLR2004
 
     @property
     def sanitized_url(self) -> str: