From 93c2545b0cff7d45b6e6ea4bc320696e01c5f0c0 Mon Sep 17 00:00:00 2001
From: esteinig <eike.steinig@unimelb.edu.au>
Date: Sat, 10 Feb 2024 11:14:12 +1100
Subject: [PATCH] chore(brick): fix generator annotation

---
 brick/api/client.py      | 2 +-
 brick/api/core/config.py | 6 ++++--
 brick/api/main.py        | 4 ++--
 brick/api/tasks.py       | 2 +-
 brick/rings.py           | 4 ++--
 5 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/brick/api/client.py b/brick/api/client.py
index 00379d5..a4c1a1e 100644
--- a/brick/api/client.py
+++ b/brick/api/client.py
@@ -59,7 +59,7 @@ async def close(self):
 
 async def fetch_sessions_generator(
     api_client: ApiClient, logger: logging.Logger | None = None
-) -> AsyncGenerator[Session]:
+) -> AsyncGenerator[Session, None, None]:
     if logger:
         logger.info(f"Requesting session identifiers from API")
 
diff --git a/brick/api/core/config.py b/brick/api/core/config.py
index ac23910..6afc7af 100644
--- a/brick/api/core/config.py
+++ b/brick/api/core/config.py
@@ -82,8 +82,10 @@ def get_mongodb_secret_pwd(cls, v: str):
     @field_validator("GENOMAD_DATABASE", mode="after")
     def check_genomad_database(cls, v: Path):
         if v and not v.exists():
-            logging.warn(f"geNomad database directory not found! ({v})")
-            logging.warn(
+            logging.warning(
+                f"geNomad database directory not found! ({v})"
+            )  # tests run on action runner must avoid pulling database
+            logging.warning(
                 f"Attempts to execute `genomad` will fail in the `process_genomad_ring` worker!"
             )
         return v
diff --git a/brick/api/main.py b/brick/api/main.py
index 20a4556..4a583be 100644
--- a/brick/api/main.py
+++ b/brick/api/main.py
@@ -29,8 +29,8 @@ def init_working_directory(settings: Settings):
 
     # Create working directory
     if not settings.WORK_DIRECTORY.exists():
-        logging.warn(f"Working directory does not exist: {settings.WORK_DIRECTORY}")
-        logging.warn(
+        logging.warning(f"Working directory does not exist: {settings.WORK_DIRECTORY}")
+        logging.warning(
             f"Attempting to create working directory path for server operations..."
         )
 
diff --git a/brick/api/tasks.py b/brick/api/tasks.py
index 19785a8..f005d39 100644
--- a/brick/api/tasks.py
+++ b/brick/api/tasks.py
@@ -843,6 +843,6 @@ def check_or_update_label_ring(
 
 
 @contextlib.contextmanager
-def create_tmp_directory(root_dir: str = None) -> Generator[Path]:
+def create_tmp_directory(root_dir: str = None) -> Generator[Path, None, None]:
     with tempfile.TemporaryDirectory(dir=root_dir) as temp_dir:
         yield Path(temp_dir)
diff --git a/brick/rings.py b/brick/rings.py
index f612407..caade2d 100644
--- a/brick/rings.py
+++ b/brick/rings.py
@@ -279,7 +279,7 @@ def parse_blastn_output(
 
 
 # Generator function
-def parse_aggregated_genomad_output(file: Path) -> Generator[GenomadEntry]:
+def parse_aggregated_genomad_output(file: Path) -> Generator[GenomadEntry, None, None]:
     """
     Parses the aggregated_classification output from a sliced genome file
     """
@@ -306,7 +306,7 @@ def extract_genomad_contiguous_segments(
     min_segment_length: int,  # should be a multiple of slice length
     prediction_classes: List[GenomadPredictionClass],
     segment_type: RingSegmentType,
-) -> Generator[RingSegment] | Generator[LabelSegment]:
+) -> Generator[RingSegment, None, None] | Generator[LabelSegment, None, None]:
     """Extracts segments of high probabilty for each prediction class with a minimum total length for label or annotation rings"""
 
     segments = []