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update MetricsEvaluator calls for cell-eval 0.7.0 #262

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Merged
abhinadduri merged 2 commits into from
Apr 9, 2026
Merged

update MetricsEvaluator calls for cell-eval 0.7.0 #262

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42cee4d
update MetricsEvaluator calls for cell-eval 0.7.0
LeonHafner Apr 1, 2026
e087a8c
Bump state version from 0.10.4 to 0.10.5
LeonHafner Apr 9, 2026
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4 changes: 2 additions & 2 deletions pyproject.toml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[project]
name = "arc-state"
version = "0.10.4"
version = "0.10.5"
description = "State is a machine learning model that predicts cellular perturbation response across diverse contexts."
readme = "README.md"
authors = [
Expand All @@ -27,7 +27,7 @@ dependencies = [
"geomloss>=0.2.6",
"transformers>=4.52.3",
"peft>=0.11.0",
"cell-eval>=0.6.8",
"cell-eval>=0.7.0",
"ipykernel>=6.30.1",
"scipy>=1.15.0",
]
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2 changes: 0 additions & 2 deletions src/state/_cli/_tx/_predict.py
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Expand Up @@ -578,7 +578,6 @@ def ensure_list(values, batch_size: int):
outdir=results_dir,
prefix=ct,
pdex_kwargs=pdex_kwargs,
batch_size=2048,
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@gemini-code-assist gemini-code-assist bot Apr 1, 2026

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high

The update for cell-eval 0.7.0 is incomplete. In this version, the outdir and prefix parameters have been moved from the MetricsEvaluator constructor to the compute() method. Currently, they are being passed to the constructor where they will be ignored, and the compute() call is missing them, which will prevent results from being saved to the correct directory. You should move these arguments to the evaluator.compute() call.

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@LeonHafner LeonHafner Apr 1, 2026

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outdir and prefix are still constructor parameters in 0.7.0. They were not moved to compute(). See here: https://github.com/ArcInstitute/cell-eval/blob/2db6b9c65498c2e801cc1cf96f2e42e65e7b5016/src/cell_eval/_evaluator.py#L64-L66

)
evaluator.compute(
profile=args.profile,
Expand Down Expand Up @@ -812,7 +811,6 @@ def ensure_list(values, batch_size: int):
outdir=results_dir,
prefix=ct,
pdex_kwargs=pdex_kwargs,
batch_size=2048,
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high

Similar to the pseudobulk evaluation above, the outdir and prefix parameters should be moved from the MetricsEvaluator constructor to the compute() method to ensure compatibility with the cell-eval 0.7.0 API and correct output handling.

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@LeonHafner LeonHafner Apr 1, 2026

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see above

)

evaluator.compute(
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