Merge pull request #468 from Ensembl/jalvarez/minor_update

Remove old entry point left by mistake

pyproject.toml

@@ -141,7 +141,6 @@ schemas_json_validate = "ensembl.io.genomio.schemas.json.validate:main"
 # Sequence region
 seq_region_dump = "ensembl.io.genomio.seq_region.dump:main"
 seq_region_prepare = "ensembl.io.genomio.seq_region.prepare:main"
-seq_region_rename = "ensembl.io.genomio.seq_region.rename:main"
 
 [tool.setuptools]
 package-dir = {"" = "src/python"}

src/python/ensembl/io/genomio/__init__.py

@@ -14,4 +14,4 @@
 # limitations under the License.
 """Genome Input/Output (GenomIO) handling library."""
 
-__version__ = "1.6.0"
+__version__ = "1.6.1"

src/python/ensembl/io/genomio/database/meta_getter.py

@@ -12,8 +12,9 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-"""Connect to a core database and retrieve a meta_key:meta_value pair(s)  
-and dump meta_key/value pairs to stdout / JSON."""
+"""Connect to a core database and retrieve a meta_key:meta_value pair(s) and dump meta_key/value
+pairs to stdout / JSON.
+"""
 
 __all__ = ["get_meta_values"]
 

src/python/ensembl/io/genomio/fasta/chunk.py

@@ -14,7 +14,7 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-""""Split a set of nucleotide sequence(s) (.fasta, .gz) into smaller chunks."""
+"""Split a set of nucleotide sequence(s) (.fasta, .gz) into smaller chunks."""
 
 __all__ = [
     "check_chunk_size_and_tolerance",

src/python/ensembl/io/genomio/genbank/extract_data.py

@@ -420,7 +420,7 @@ def _format_write_seq_json(self) -> None:
                 "coord_system_level": "chromosome",
                 "circular": (seq.annotations["topology"] == "circular"),
                 "codon_table": codon_table,
-                "length": len(seq.seq),
+                "length": len(seq.seq),  # type: ignore[arg-type]
             }
             if "organelle" in seq.annotations:
                 seq_obj["location"] = self._prepare_location(str(seq.annotations["organelle"]))

src/python/ensembl/io/genomio/gff3/process.py

@@ -12,7 +12,8 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-"""Simplify and fix a GFF3 file and returns both a cleaned up GFF3 file and a functional annotation JSON file.
+"""Simplify and fix a GFF3 file and returns both a cleaned up GFF3 file and a functional annotation
+JSON file.
 """
 
 import logging

src/python/ensembl/io/genomio/gff3/restructure.py

@@ -12,8 +12,7 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-"""Restructure a gene model to a standard representation: `gene -> [ mRNAs -> [CDSs, exons] ]`
-"""
+"""Restructure a gene model to a standard representation: `gene -> [ mRNAs -> [CDSs, exons] ]`"""
 
 __all__ = [
     "restructure_gene",

src/python/ensembl/io/genomio/seq_region/collection.py

@@ -73,7 +73,7 @@ def _merge(self, source: SeqRegionDict, destination: SeqRegionDict) -> SeqRegion
     @staticmethod
     def make_seqregion_from_gbff(record_data: GBFFRecord) -> SeqRegionDict:
         """Returns a seq_region dict extracted from a GBFF record."""
-        seqr: SeqRegionDict = {"length": len(record_data.record.seq)}
+        seqr: SeqRegionDict = {"length": len(record_data.record.seq)}  # type: ignore[arg-type]
 
         if record_data.is_circular():
             seqr["circular"] = True

src/python/tests/database/test_dbconnection_lite.py

@@ -12,8 +12,7 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-"""Unit testing of `ensembl.io.genomio.database.dbconnection_lite` module.
-"""
+"""Unit testing of `ensembl.io.genomio.database.dbconnection_lite` module."""
 
 from typing import Callable, Optional
 

src/python/tests/genbank/test_extract_data_seq.py

@@ -218,7 +218,7 @@ def test_prepare_location_with_supported_organelle(
         result = formatted_files_generator._prepare_location(organelle)
         assert result == expected_location
 
-    @pytest.mark.parametrize("organelle", [("miton")])
+    @pytest.mark.parametrize("organelle", ["miton"])
     def test_prepare_location_with_unsupported_organelle(
         self,
         organelle: str,