Fileglancer support - #81
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March 13, 2026 17:36
NVIDIA re-uploaded cuda-version-13.1-hd92462c_3.conda with different bytes, so the pinned sha256 no longer matched and installs failed with a hash mismatch. Refreshed the entry via `pixi update cuda-version`, which also upgraded the lock file format from v6 to v7. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
# Conflicts: # cellmap_flow/utils/ds.py # pyproject.toml
# Conflicts: # cellmap_flow/utils/ds.py
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🟡 Changes recommended
There are concrete metadata/config inconsistencies (versions and runnable labeling) and a dependency declaration issue that can break installs/solves or confuse users.
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Pull request overview
Adds Fileglancer-oriented launch/config support by introducing Pixi environment metadata plus a runnable definition, and adjusts the viewer/server launch flow to better integrate with service-style execution.
Changes:
- Added
pixi.tomlandrunnables.yamlto define a Pixi-based environment and a Fileglancer runnable command. - Updated server/job-launch plumbing to invoke the server via
pixi run ...and adjusted the dashboard launch to bind to an ephemeral port and print/write a service URL. - Minor viewer-related tweaks (e.g., project/charge-group selection) and small cleanup/doc updates.
File summaries
| File | Description |
|---|---|
| runnables.yaml | New runnable/service definition for launching the tool via Pixi. |
| pyproject.toml | Adds a new dependency entry. |
| pixi.toml | New Pixi workspace/environment definition and tasks. |
| cellmap_flow/utils/neuroglancer_utils.py | Adjusts viewer URL flow (no longer calls show(url)). |
| cellmap_flow/utils/ds.py | Refines compressor-metadata cleaning doc/logic for tensorstore compatibility. |
| cellmap_flow/utils/bsub_utils.py | Updates how the server command is constructed for job submission. |
| cellmap_flow/server.py | Minor formatting-only change. |
| cellmap_flow/models/models_config.py | Minor formatting-only change. |
| cellmap_flow/dashboard/app.py | Reworks dashboard startup using a Werkzeug server and publishes the service URL. |
| cellmap_flow/cli/viewer_cli.py | Adds project/charge-group handling for viewer launches. |
Review details
Suppressed comments (1)
cellmap_flow/cli/viewer_cli.py:39
- The docstring example uses
cellmap_flow_viewer, but the actual script entry point iscellmap_flow_view(see pyproject.toml [project.scripts]). This will cause copy/paste failures for users.
def main(dataset, project, log_level):
"""
Start CellMap Flow viewer with a dataset.
Example:
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- Comments generated: 6
- Review effort level: Lite
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| except Exception as e: | ||
| logger.warning(f"Failed to write service URL to {service_url_path}: {e}") |
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| dependencies = [ | ||
| "cellpose", | ||
| "pymorton", | ||
| "numpy", |
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| from cellmap_flow.utils import zarr_v3 | ||
| from cellmap_flow.globals import g | ||
| import os | ||
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| from cellmap_flow.utils.web_utils import ( |
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| [workspace] | ||
| name = "cellmap-flow" | ||
| version = "0.1.7" | ||
| description = "Realtime prediction using neuroglancer" |
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| name: CellMap Flow | ||
| description: Real-time neural network inference on EM microscopy data. | ||
| version: "0.1.7" |
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| name: Run Inference | ||
| description: Run model inference from a YAML configuration file using cellmap_flow_yaml. | ||
| # conda_env: cellmap-flow | ||
| command: pixi run cellmap_flow_view |
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