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17 changes: 17 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,23 @@ The fastest, easiest starting point for most Linux boxes, and now for Mac as wel

> If you pull updates into an existing clone and the `morphometrics` command seems out of date, re-run `pip install -e .` from the repo root inside the activated environment.

### Optional extras

Same pattern as the napari GUI — install into the morphometrics env to register extra `morphometrics` subcommands:

```bash
pip install -e ".[gui]" # adds: morphometrics gui
pip install -e ".[gpu]" # adds: morphometrics pycurv_gpu (needs CUDA torch)
```

Then use GPU curvature in place of the CPU step:

```bash
morphometrics pycurv_gpu config.yml mesh.surface.vtp
```

Existing morphometrics installs: `pip install -e ".[gpu]"` from a current clone (or `pip install "surface-morphometrics[gpu] @ git+https://github.com/grotjahnlab/surface_morphometrics.git"` if you are not developing from source).

### Option 2: Docker
Useful on Windows and other systems where graph-tool or pymeshlab do not play nicely with conda. The image ships with all dependencies pre-installed.
```bash
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5 changes: 5 additions & 0 deletions pyproject.toml
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Expand Up @@ -54,6 +54,11 @@ test = ["pytest"]
# PyPI, install it from git:
gui = ["surface-morphometrics-gui @ git+https://github.com/baradlab/surface-morphometrics-gui.git"]
# gui = ["surface-morphometrics-gui"] # use this once the GUI is on PyPI
# GPU curvature backend (pycurv-gpu). Adds `morphometrics pycurv_gpu` via the
# same entry-point group. Needs a CUDA-capable PyTorch build in this env
# (install torch first from https://pytorch.org if pip's default is wrong).
gpu = ["pycurv-gpu @ git+https://github.com/hemanthkapa/pycurv-gpu.git"]
# gpu = ["pycurv-gpu"] # use this once pycurv-gpu is on PyPI

[project.scripts]
morphometrics = "surface_morphometrics.cli:main"
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