Reduce core dependencies, split in optional dependencies (#2265)

This PR introduces a more flexible dependency management system for Mesa, allowing users to choose which additional components they need while maintaining core functionality.

### Motivation
This change allows for more tailored installations, reducing unnecessary dependencies and potential conflicts, while ensuring core functionality remains intact.

### Key Changes
1. Updated `pyproject.toml` to define new optional dependency groups:
   - `[network]`: Network-related dependencies
   - `[viz]`: Visualization dependencies
   - `[rec]`: Recommended dependencies (includes network and viz)
   - `[all]`: All dependencies, including developer dependencies
   - Additional groups for development, examples, and documentation
2. Updated `README.md` with new installation instructions for optional dependencies.
3. Core dependencies now only include essential packages (numpy, pandas, tqdm).

### Installation Options
Users can now customize their Mesa installation:

```bash
# Basic installation with core dependencies
pip install -U --pre mesa

# Install with recommended dependencies
pip install -U --pre mesa[rec]

# Install with specific additional dependencies
pip install -U --pre mesa[network,viz]

# Install all dependencies (including dev dependencies)
pip install -U --pre mesa[all]
```

Author: EwoutH

README.md

@@ -39,6 +39,17 @@ To install our latest pre-release (3.0.0 alpha), run:
 ``` bash
 pip install -U --pre mesa
 ```
+With Mesa 3.0, we don't install all our dependencies anymore by default.
+```bash
+# You can customize the additional dependencies you need, if you want. Available are:
+pip install -U --pre mesa[network,viz]
+
+# This is equivalent to our recommended dependencies:
+pip install -U --pre mesa[rec]
+
+# To install all, including developer, dependencies:
+pip install -U --pre mesa[all]
+```
 
 You can also use `pip` to install the latest GitHub version:
 

pyproject.toml

@@ -36,36 +36,46 @@ classifiers = [
 ]
 readme = "README.md"
 dependencies = [
-  "click",
-  "cookiecutter",
-  "matplotlib",
-  "networkx",
   "numpy",
   "pandas",
-  "solara",
   "tqdm",
 ]
 dynamic = ["version"]
 
 [project.optional-dependencies]
+# User collections
+rec = ["mesa[network,viz]"]
+all = ["mesa[network,viz,dev,examples,docs]"]
+# Core dependencies
+network = [
+  "networkx",
+]
+viz = [
+  "matplotlib",
+  "solara",
+]
+# Dev and CI stuff
 dev = [
-  "ruff~=0.1.1",   # Update periodically
-  "pytest >= 4.6",
+  "mesa[rec]",
+  "ruff",
+  "pytest",
   "pytest-cov",
   "sphinx",
   "pytest-mock",
+  "cookiecutter",
 ]
 examples = [
-  "pytest >= 4.6",
-  "scipy"
+  "mesa[rec]",
+  "pytest",
+  "scipy",
 ]
 docs = [
   "sphinx",
   "ipython",
   "pydata_sphinx_theme",
   "seaborn",
   "myst-nb",
-  "myst-parser",         # Markdown in Sphinx
+  "myst-parser",  # Markdown in Sphinx
 ]
 
 [project.urls]