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Document local sibling-repo integration for XROMM workflows #3301

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Update local integration documentation 
Co-Authored-By: Oz <oz-agent@warp.dev>
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@homfunc @oz-agent
homfunc and oz-agent committed May 1, 2026
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9 changes: 9 additions & 0 deletions README.md
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Expand Up @@ -87,6 +87,15 @@ version with PyTorch and TensorFlow). We aim to depreciate the TF part in 2027.

We recommend using our conda file, see [here](https://github.com/DeepLabCut/DeepLabCut/blob/main/conda-environments/README.md) or the [`deeplabcut-docker` package](https://github.com/DeepLabCut/DeepLabCut/tree/main/docker).

## Local sibling-repo integration
This repository can also be used as a sibling checkout together with:
- `../XROMM_DLCTools`
- `../xmalab`

In that local layout, `XROMM_DLCTools` uses the optional `dlc` dependency group to import this checkout directly, and its baseline harness runs both a DeepLabCut smoke scenario and a broader end-to-end local workflow integration scenario.

See `instructions.md` in this repo for the local integration notes and exact commands.

# [Documentation: The DeepLabCut Process](https://deeplabcut.github.io/DeepLabCut/README.html)

Our docs walk you through using DeepLabCut, and key API points. For an overview of the toolbox and workflow for project management, see our step-by-step at [Nature Protocols paper](https://doi.org/10.1038/s41596-019-0176-0).
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39 changes: 39 additions & 0 deletions instructions.md
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# DeepLabCut Local Integration Instructions
These notes describe how this repository is used in the local 3-repo XROMM workflow together with `../XROMM_DLCTools` and `../xmalab`.
## 1) Expected local layout
Recommended sibling checkout layout:
- `XROMM_DLCTools/`
- `DeepLabCut/`
- `xmalab/`
`XROMM_DLCTools/pyproject.toml` maps its optional `dlc` dependency group to this repository through `tool.uv.sources`.
## 2) DeepLabCut’s role in the workflow
Within the integrated workflow, DeepLabCut provides:
- project creation / dataset generation support
- video analysis / prediction entrypoints
- the local import target used by `XROMM_DLCTools`
- synthetic smoke coverage through the baseline harness
The current local integration suite also uses this repo to verify that the newer workflow service in `XROMM_DLCTools` still interoperates with a sibling DeepLabCut checkout.
## 3) Local setup for this repo
Standard developer setup:
```bash
uv sync --group dev
```
When working from `../XROMM_DLCTools`, enable the sibling import path there with:
```bash
uv sync --group dlc
```
## 4) Integration validation from XROMM_DLCTools
Run these commands from `../XROMM_DLCTools`:
```bash
uv run python scripts/baseline_harness.py --scenario deeplabcut_repo_smoke --output-dir baseline_artifacts/deeplabcut_smoke --deeplabcut-repo ../DeepLabCut
```
Full multi-repo suite:
```bash
uv run python scripts/baseline_harness.py --scenario all --output-dir baseline_artifacts/integration_all --deeplabcut-repo ../DeepLabCut --xmalab-repo ../xmalab
```
True end-to-end local workflow scenario:
```bash
uv run python scripts/baseline_harness.py --scenario phase3_local_workflow_e2e --output-dir baseline_artifacts/e2e_local_workflow --deeplabcut-repo ../DeepLabCut --xmalab-repo ../xmalab
```
## 5) Compatibility notes
The local workflow integration path expects this repo to remain importable in “lite mode” when GUI dependencies are unavailable, and relies on the public `deeplabcut` import surface plus the synthetic project helpers under `examples/utils.py`.