Refactor optional dependencies in pyproject.toml to retain old pip behaviour

This sadly introduces some duplication for [all].

Author: jbcoe

pyproject.toml

@@ -39,7 +39,7 @@ nle-ttyplay = "nle.scripts.ttyplay:main"
 nle-ttyplay2 = "nle.scripts.ttyplay2:main"
 nle-read-tty = "nle.scripts.read_tty:main"
 
-[dependency-groups]
+[project.optional-dependencies]
 dev = [
   "pre-commit>=2.0.1",
   "isort>=5.13.2",
@@ -54,8 +54,21 @@ dev = [
 ]
 agent = ["torch>=1.3.1"]
 all = [
-  {include-group = "agent"},
-  {include-group = "dev"},
+  "pre-commit>=2.0.1",
+  "isort>=5.13.2",
+  "cmake_format>=0.6.10",
+  "memory-profiler>=0.60.0",
+  "pytest>=6.2.5",
+  "pytest-benchmark>=3.4.1",
+  "sphinx>=2.4.4",
+  "sphinx-rtd-theme>=0.4.3",
+  "setuptools>=69.5.1",
+  "ruff>=0.4.3","torch>=1.3.1"
+]
+
+[dependency-groups]
+dev = [
+  "nle[dev]"
 ]
 
 [tool.black]