From 0197811315d8dfbd38671cdd79f24b2cf1ade180 Mon Sep 17 00:00:00 2001
From: Jorge Alvarez Jarreta <jalvarez@ebi.ac.uk>
Date: Mon, 24 Jun 2024 09:06:16 +0100
Subject: [PATCH] update GenomIO to use ensembl-utils v0.3.0

---
 conftest.py                                                 | 2 +-
 pyproject.toml                                              | 2 +-
 src/python/ensembl/io/genomio/annotation/load.py            | 2 +-
 src/python/ensembl/io/genomio/database/dbconnection_lite.py | 2 +-
 src/python/ensembl/io/genomio/genome_stats/dump.py          | 4 ++--
 src/python/ensembl/io/genomio/seq_region/rename.py          | 2 +-
 6 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/conftest.py b/conftest.py
index ad4af6ee5..b1831e1e3 100644
--- a/conftest.py
+++ b/conftest.py
@@ -14,4 +14,4 @@
 # limitations under the License.
 """Global pytest configuration for Ensembl GenomIO tests."""
 
-pytest_plugins = ("ensembl.plugins.pytest_unittest",)
+pytest_plugins = ("ensembl.utils.plugin",)
diff --git a/pyproject.toml b/pyproject.toml
index 4023b3d58..48a3c2466 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -53,7 +53,7 @@ dependencies = [
     "biopython == 1.81",
     "ensembl-hive @ git+https://github.com/Ensembl/ensembl-hive.git",
     "ensembl-py @ git+https://github.com/Ensembl/ensembl-py.git",  # minimum v2.0.0
-    "ensembl-utils >= 0.2.0",
+    "ensembl-utils >= 0.3.0",
     "jsonschema >= 4.6.0",
     "intervaltree >= 3.1.0",
     "mysql-connector-python >= 8.0.29",
diff --git a/src/python/ensembl/io/genomio/annotation/load.py b/src/python/ensembl/io/genomio/annotation/load.py
index 461e844b9..9bf09643f 100644
--- a/src/python/ensembl/io/genomio/annotation/load.py
+++ b/src/python/ensembl/io/genomio/annotation/load.py
@@ -22,9 +22,9 @@
 from sqlalchemy import and_
 
 from ensembl.core.models import Gene, Transcript, ObjectXref, Xref
-from ensembl.database import DBConnection
 from ensembl.io.genomio.utils import get_json
 from ensembl.utils.argparse import ArgumentParser
+from ensembl.utils.database import DBConnection
 from ensembl.utils.logging import init_logging_with_args
 
 
diff --git a/src/python/ensembl/io/genomio/database/dbconnection_lite.py b/src/python/ensembl/io/genomio/database/dbconnection_lite.py
index 1fd719214..c317145f8 100644
--- a/src/python/ensembl/io/genomio/database/dbconnection_lite.py
+++ b/src/python/ensembl/io/genomio/database/dbconnection_lite.py
@@ -23,8 +23,8 @@
 from sqlalchemy import create_engine, select
 from sqlalchemy.orm import Session
 
-from ensembl.database import DBConnection
 from ensembl.core.models import Meta
+from ensembl.utils.database import DBConnection
 
 
 _DB_PATTERN_RELEASE = re.compile(r".+_(?:core|otherfeatures|variation)_(?P<release>\d+)_\d+_\d+")
diff --git a/src/python/ensembl/io/genomio/genome_stats/dump.py b/src/python/ensembl/io/genomio/genome_stats/dump.py
index 1ae8ab23a..28a14b936 100644
--- a/src/python/ensembl/io/genomio/genome_stats/dump.py
+++ b/src/python/ensembl/io/genomio/genome_stats/dump.py
@@ -24,9 +24,9 @@
 from sqlalchemy.orm import Session
 
 from ensembl.core.models import SeqRegionAttrib, AttribType, Gene, Transcript
-from ensembl.database import URL
 from ensembl.io.genomio.database import DBConnectionLite
 from ensembl.utils.argparse import ArgumentParser
+from ensembl.utils.database import StrURL
 from ensembl.utils.logging import init_logging_with_args
 
 
@@ -129,7 +129,7 @@ def get_genome_stats(self) -> Dict[str, Any]:
         return genome_stats
 
 
-def dump_genome_stats(url: URL) -> Dict[str, Any]:
+def dump_genome_stats(url: StrURL) -> Dict[str, Any]:
     """Returns JSON object containing the genome stats (assembly and annotation) of the given core database.
 
     Args:
diff --git a/src/python/ensembl/io/genomio/seq_region/rename.py b/src/python/ensembl/io/genomio/seq_region/rename.py
index 916fbdb2e..94647916c 100644
--- a/src/python/ensembl/io/genomio/seq_region/rename.py
+++ b/src/python/ensembl/io/genomio/seq_region/rename.py
@@ -24,8 +24,8 @@
 from sqlalchemy.orm import Session
 
 from ensembl.core.models import SeqRegion, SeqRegionSynonym, SeqRegionAttrib
-from ensembl.database import DBConnection
 from ensembl.utils.argparse import ArgumentParser
+from ensembl.utils.database import DBConnection
 from ensembl.utils.logging import init_logging_with_args