Update pyproject.toml for uv and RTD

For uv we should use dependency-groups. This patch updates our scripts
to use the appropriate dependency-groups when running.

It also adds back project.optional-dependencies, which is only used for
ReadTheDocs due to its lack of native support for uv at the time.

Development directions are updated as we do not actually need to
manually build a uv virtual environment, now that the appropriate
commands are using dependency-groups.

Author: hinerm

.readthedocs.yaml

@@ -23,4 +23,4 @@ python:
    - method: pip
      path: .
      extra_requirements:
-     - dev
+     - docs

bin/lint.sh

@@ -4,10 +4,10 @@ dir=$(dirname "$0")
 cd "$dir/.."
 
 exitCode=0
-uv run ruff check --fix
+uv run --group dev ruff check --fix
 code=$?; test $code -eq 0 || exitCode=$code
-uv run ruff format
+uv run --group dev ruff format
 code=$?; test $code -eq 0 || exitCode=$code
-uv run validate-pyproject pyproject.toml
+uv run --group dev validate-pyproject pyproject.toml
 code=$?; test $code -eq 0 || exitCode=$code
 exit $exitCode

bin/test.sh

@@ -47,9 +47,9 @@ do
     echo "-------------------------------------"
     if [ $# -gt 0 ]
     then
-      uv run python -m pytest -p no:faulthandler $flag --java $java $@
+      uv run --group dev python -m pytest -p no:faulthandler $flag --java $java $@
     else
-      uv run python -m pytest -p no:faulthandler $flag --java $java tests
+      uv run --group dev python -m pytest -p no:faulthandler $flag --java $java tests
     fi
     code=$?
     if [ $code -eq 0 ]

doc/Development.md

@@ -29,13 +29,7 @@ If you are testing a project that *uses* `pyimagej` and need to see how changes
 
 PyImageJ documentation is built as a [Sphinx](https://www.sphinx-doc.org/en/master/)-built [ReadTheDocs](https://about.readthedocs.com/) site.
 
-To build the documentation, **you must create a `uv` virtual environment** with the additional development dependencies:
-
-```bash
-uv pip install -e ".[dev]"
-```
-
-Then, you can either use the documentation's own `Makefile` in the `/docs` directory:
+You can either use the documentation's own `Makefile` in the `/docs` directory:
 
 ```bash
 make html

doc/Makefile

@@ -4,7 +4,7 @@
 # You can set these variables from the command line, and also
 # from the environment for the first two.
 SPHINXOPTS    ?=
-SPHINXBUILD   ?= uv run sphinx-build
+SPHINXBUILD   ?= uv run --group docs sphinx-build
 SOURCEDIR     = .
 BUILDDIR      = _build
 

pyproject.toml

@@ -43,19 +43,23 @@ dependencies = [
     "xarray",
 ]
 
-[project.optional-dependencies]
+[dependency-groups]
 # Development tools
 dev = [
     "build",
-    "myst-nb",
     "pre-commit",
     "pytest",
     "ruff",
+    "validate-pyproject[all]",
+]
+# Local ReadTheDocs building
+# NOTE: duplicated in project.optional-dependencies
+docs = [
+    "myst-nb",
     "sphinx",
     "sphinx-copybutton",
     "sphinx_rtd_theme",
     "readthedocs-sphinx-search",
-    "validate-pyproject[all]",
 ]
 # Matplotlib display backend
 matplotlib = [
@@ -70,6 +74,17 @@ notebooks = [
     "scikit-image",
 ]
 
+# Remote ReadTheDocs building
+# NOTE: duplicated in dependency-groups
+[project.optional-dependencies]
+docs = [
+    "myst-nb",
+    "sphinx",
+    "sphinx-copybutton",
+    "sphinx_rtd_theme",
+    "readthedocs-sphinx-search",
+]
+
 [project.scripts]
 imagej = "imagej:imagej_main"