Metadata-Version: 2.5
Name: murineshiftwork
Version: 2.16.2
Summary: Behaviour acquisition framework for standardised, scalable experiments.
Project-URL: Homepage, https://github.com/MurineShiftWork/murineshiftwork
Project-URL: Documentation, https://MurineShiftWork.github.io/murineshiftwork/
Project-URL: Issue Tracker, https://github.com/MurineShiftWork/murineshiftwork/issues
Author-email: "Lars B. Rollik" <lars@rollik.me>
License: BSD-3-Clause-NonCommercial
        
        Copyright (c) 2020-present, Lars B. Rollik.
        All rights reserved.
        
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        4. Any use of this software or its derivatives for COMMERCIAL purposes -
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License-File: LICENSE
Classifier: License :: Free for non-commercial use
Requires-Python: <3.14,>=3.12
Requires-Dist: ipython>=9.14.1
Requires-Dist: msw-core>=0.15.0
Requires-Dist: msw-io>=1.10.0
Requires-Dist: plotly>=5.0
Requires-Dist: pyarrow>=24.0.0
Requires-Dist: tqdm
Provides-Extra: agent
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Provides-Extra: calibration
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Requires-Dist: serial-scale-hx711>=2.1.4; extra == 'calibration'
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Requires-Dist: pypulsepal>=0.4.6; extra == 'dev'
Requires-Dist: pytest; extra == 'dev'
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Provides-Extra: flir
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Provides-Extra: full
Requires-Dist: msw-flir-bonsai>=0.4.1; extra == 'full'
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Provides-Extra: pulsepal
Requires-Dist: pypulsepal>=0.4.6; extra == 'pulsepal'
Provides-Extra: rce
Requires-Dist: rpi-camera-ensemble[conductor]>=0.6.2; extra == 'rce'
Provides-Extra: stage
Requires-Dist: one-axis-stage>=0.2.2; extra == 'stage'
Provides-Extra: tasks
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Description-Content-Type: text/markdown

# Murine Shift Work

Behaviour acquisition framework for standardised, scalable experiments.

```bash
msw run --setup rig-a --subject mouse001 --task sequence
```

---

## What it does

- **Behavioural tasks**: sequence learning, probabilistic switching, optotagging, calibration routines
- **Hardware abstraction**: interchangeable backends for behaviour controllers, cameras, stage, scale, stimulators
- **Config system**: layered YAML overrides (bundled defaults, rig overlay, task mode, subject, CLI)
- **Session files**: structured `.msw.session.yaml` + JSONL trial data; reader API for analysis
- **Live plot**: per-task online performance display during acquisition
- **TTL barcodes**: unique per-trial barcodes on BNC output for alignment with parallel recordings

---

## Installation

Requires Python ≥ 3.12 and [uv](https://docs.astral.sh/uv/).

```bash
pip install murineshiftwork
```

### First-time setup

```bash
msw init --config-dir /path/to/msw_configs
msw setup create rig-a
msw subject add -s mouse001
```

---

## Development

```bash
git clone https://github.com/MurineShiftWork/murineshiftwork.git
cd murineshiftwork
uv sync --group dev
uv run pytest tests/
```

Pre-commit hooks (ruff, mypy, secrets scan):

```bash
pre-commit install
```

---

## Docs

See `docs/` for CLI reference, config system, session files, and task guides.
Key architecture decisions are in `docs/MASTER_PLAN.md`.

---

## License

Copyright © 2021-2026 Lars B. Rollik.
See [LICENSE](LICENSE) for terms.
