From 676bc7c851f487cddc865fb16d7682bc4bb66cba Mon Sep 17 00:00:00 2001
From: pswain <peter.swain@ed.ac.uk>
Date: Thu, 1 Feb 2024 17:59:40 +0000
Subject: [PATCH] refactor(pipeline): cleaned multiprocessing in run
---
src/aliby/pipeline.py | 15 +++++----------
1 file changed, 5 insertions(+), 10 deletions(-)
diff --git a/src/aliby/pipeline.py b/src/aliby/pipeline.py
index b0cc310..5b78d34 100644
--- a/src/aliby/pipeline.py
+++ b/src/aliby/pipeline.py
@@ -293,17 +293,14 @@ class Pipeline(ProcessABC):
# multiple cores
with Pool(distributed) as p:
results = p.map(
- lambda x: self.run_one_position(*x),
- [
- (position_id, i)
- for i, position_id in enumerate(position_ids.items())
- ],
+ self.run_one_position,
+ [position_id for position_id in position_ids.items()],
)
else:
# single core
results = [
- self.run_one_position((position_id, position_id_path), 1)
- for position_id, position_id_path in tqdm(position_ids.items())
+ self.run_one_position(position_id)
+ for position_id in tqdm(position_ids.items())
]
# results is binary giving the success for each position
return results
@@ -323,9 +320,7 @@ class Pipeline(ProcessABC):
return out_file
def run_one_position(
- self,
- name_image_id: t.Tuple[str, str or Path or int],
- index: t.Optional[int] = None,
+ self, name_image_id: t.Tuple[str, str or Path or int]
):
"""Run a pipeline for one position."""
name, image_id = name_image_id
--
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