Simplify development installation (#198)

* add all optional dependencies to dev requirements

* update contributing guide

* update PR test action

.github/workflows/pr.yml

@@ -33,6 +33,6 @@ jobs:
           python -m pip install --upgrade pip
           # Install cpu wheels only to speed up the build
           pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
-          pip install ".[metrics,dev]"
+          pip install ".[dev]"
       - name: Test with pytest
         run: pytest -v

CONTRIBUTING.md

@@ -3,11 +3,11 @@
 ## Development installation
 
 Clone or fork the repository,
-then make an editable installation with all the optional dependencies:
+then make an editable installation with all the development dependencies:
 
 ```sh
 # in project root directory (parent folder of pyproject.toml)
-pip install -e ".[dev,visual,metrics]"
+pip install -e ".[dev]"
 ```
 
 ## CI requirements

pyproject.toml

@@ -41,7 +41,6 @@ metrics = [
     "captum>=0.7.0",
 ]
 examples = ["napari", "jupyter", "jupytext"]
-
 visual = [
     "ipykernel",
     "graphviz",
@@ -51,8 +50,8 @@ visual = [
     "nbformat",
     "cmap",
 ]
-
 dev = [
+    "viscy[metrics,examples,visual]",
     "pytest",
     "pytest-cov",
     "hypothesis",