diff --git a/README.md b/README.md index 29fb6cd..43b22c4 100755 --- a/README.md +++ b/README.md @@ -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 If you pull updates into an existing clone and the `morphometrics` command seems out of date, re-run `pip install -e .` from the repo root inside the activated environment.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 diff --git a/pyproject.toml b/pyproject.toml index 5c4bbc6..ed4ce59 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -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"