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Multiple fixes related to sumner2 config and docker image #97

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Merged
bergsalex merged 1 commit into from
Oct 9, 2025
Merged

Multiple fixes related to sumner2 config and docker image #97

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1 change: 0 additions & 1 deletion .dockerignore
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,6 @@ docs/
.nf-test
mouse-tracking-runtime
nextflow
support_code
vm
*.h5
*.sh
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4 changes: 3 additions & 1 deletion Dockerfile
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Expand Up @@ -8,7 +8,7 @@ ENV UV_SYSTEM_PYTHON=1 \
PYTHONUNBUFFERED=1

# Copy metadata first for layer caching
COPY pyproject.toml uv.lock* README.md ./
COPY pyproject.toml uv.lock* README.md support_code ./

# Only install runtime dependencies
RUN uv sync --frozen --no-group dev --no-group test --no-group lint --no-install-project
Expand All @@ -18,4 +18,6 @@ COPY src ./src

RUN uv pip install --system .

COPY support_code ./support_code

CMD ["mouse-tracking-runtime", "--help"]
4 changes: 2 additions & 2 deletions nextflow/configs/profiles/sumner2.config
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Expand Up @@ -29,8 +29,8 @@ params {
tracking_code_dir = "/kumar_lab_models/mouse-tracking-runtime/"
gait_code_dir = "/gait-analysis/"
vfi_code_dir = "/vfi/Code/"
support_code_dir = "/mouse-tracking-runtime/support_code/"
heuristic_classifier_folder = "/JABS-postprocess/heuristic_classifiers/"
support_code_dir = "/workspace/support_code/"
heuristic_classifier_folder = "/opt/JABS-postprocess/src/jabs_postprocess/heuristic_classifiers/"
filter_processed = false
Comment on lines 31 to 34

@keithshep keithshep Oct 9, 2025

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I assume this is fixing paths that were broken before?

@SkepticRaven SkepticRaven Oct 9, 2025

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These were the paths before the docker/container changes. This should correct those paths.


jabs_version = "v0.37.0"
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2 changes: 1 addition & 1 deletion pyproject.toml
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@@ -1,6 +1,6 @@
[project]
name = "mouse-tracking"
version = "0.1.2"
version = "0.1.3"
description = "Runtime environment for mouse tracking experiments"
requires-python = ">=3.10,<3.11"
packages = ["src/mouse_tracking"]
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2 changes: 1 addition & 1 deletion uv.lock
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