Group dependencies #10

This introduces sets of optional-dependencies to `pyproject.toml` that allow for reduced dependency installation. The `openlifu-test-app` project, for example, can package only the hardware-communication required dependencies by using the `[io]` option. The base application as used in Slicer should now be installed with the `[app]` option.

Author: peterhollender

pyproject.toml

@@ -31,31 +31,52 @@ dynamic = ["version"]
 dependencies = [
   "xarray[io]",
   "numpy<2",
-  "matplotlib",
   "pandas",
   "scipy",
+  "watchdog"
+]
+
+[project.optional-dependencies]
+jupyter = [
+  "ipykernel",
+  "matplotlib",
+]
+mesh = [
+  "embreex; platform_machine=='x86_64' or platform_machine=='AMD64'",
+  "trimesh",
+  "scikit-image",
   "vtk",
-  "h5py",
-  "opencv-contrib-python",
-  "crc",
+  "Pillow",
+  "OpenEXR"
+]
+db = [
   "nibabel",
-  "sphinx",
-  "ipykernel",
-  "pyserial",
+  "pydicom"
+]
+io = [
+  "crc",
   "crcmod",
+  "pyserial"
+]
+sim = [
   "k-wave-python==0.4.0",
-  "nvidia-ml-py",
-  "OpenEXR",
-  "scikit-image",
-  "trimesh",
-  "embreex; platform_machine=='x86_64' or platform_machine=='AMD64'",
-  "onnxruntime==1.18.0",
-  "pydicom",
+  "nvidia-ml-py"
+]
+cloud = [
+  "requests",
   "watchdog",
   "python-socketio[client]"
 ]
-
-[project.optional-dependencies]
+photogrammetry = [
+  "embreex; platform_machine=='x86_64' or platform_machine=='AMD64'",
+  "opencv-contrib-python",
+  "onnxruntime==1.18.0",
+  "trimesh",
+  "scikit-image",
+  "vtk",
+  "Pillow",
+  "OpenEXR"
+]
 test = [
   "pytest >=6",
   "pytest-cov >=3",
@@ -74,6 +95,12 @@ docs = [
   "sphinx_autodoc_typehints",
   "furo>=2023.08.17",
 ]
+all = [
+  "openlifu[jupyter, mesh, db, io, sim, cloud, photogrammetry, test, dev, docs]",
+]
+app = [
+  "openlifu[mesh, db, io, sim, cloud, photogrammetry]",
+]
 
 [project.urls]
 Homepage = "https://github.com/OpenwaterHealth/OpenLIFU-python"
@@ -86,6 +113,9 @@ Changelog = "https://github.com/OpenwaterHealth/OpenLIFU-python/releases"
 version.source = "vcs"
 build.hooks.vcs.version-file = "src/openlifu/_version.py"
 
+[tool.hatch.metadata]
+allow-direct-references = true
+
 [tool.hatch.envs.default]
 features = ["test"]
 scripts.test = "pytest {args}"