update for JOSS

JOSS Intro Tutorial Fix

- update line lengths (to 79) in tutorials
- edit intro tutorial per JOSS requests
- edit visualization tutorial per JOSS request
- update pyproject.toml to autofix code cell lengths
- remove pyprojoect.toml spurious assumption about it being taken care of black formatting
- add .virtual documents to .gitignore
- test_agent was reformatted due to pyproject.toml changes
- remove upper left version switcher
- update email in pyproject.toml

Author: tpike3

.gitignore

@@ -69,6 +69,7 @@ target/
 
 # Jupyter and iPython notebook checkpoints
 *.ipynb_checkpoints
+*.virtual_documents
 
 # Spyder app workspace config file
 .spyderworkspace

docs/conf.py

@@ -1,4 +1,3 @@
-# noqa: D100
 #!/usr/bin/env python3
 #
 # Mesa documentation build configuration file, created by
@@ -16,8 +15,8 @@
 import os
 import os.path as osp
 import pathlib
-import sys
 import string
+import sys
 from datetime import date
 
 # If extensions (or modules to document with autodoc) are in another directory,
@@ -47,7 +46,7 @@
     "sphinx.ext.viewcode",
     "sphinx.ext.napoleon",  # for google style docstrings
     "myst_nb",  # For Markdown and Jupyter notebooks
-    "sphinx_copybutton" # For copying the code in the documentation
+    "sphinx_copybutton",  # For copying the code in the documentation
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -131,11 +130,7 @@
 # further.  For a list of options available for each theme, see the
 # documentation.
 html_theme_options = {
-    "navbar_start": ["navbar-logo", "version-switcher"],  # Show switcher in navbar
-    "switcher": {
-        "json_url": "https://mesa.readthedocs.io/latest/_static/switcher.json",  # URL of your switcher.json file
-        "version_match": version  # Automatically matches the current version
-    }
+    "navbar_start": ["navbar-logo"],
 }
 
 # Add any paths that contain custom themes here, relative to this directory.
@@ -177,7 +172,7 @@
 
 # Custom sidebar templates, maps document names to template names.
 html_sidebars = {
-    'migration_guide': [],  # No sidebar migration
+    "migration_guide": [],  # No sidebar migration
 }
 
 # Additional templates that should be rendered to pages, maps page names to
@@ -297,8 +292,9 @@
 intersphinx_mapping = {"python": ("https://docs.python.org/3", None)}
 
 
-
-def write_example_md_file(agent_filename, model_filename, readme_filename, app_filename, md_filepath, template):
+def write_example_md_file(
+    agent_filename, model_filename, readme_filename, app_filename, md_filepath, template
+):
     with open(agent_filename) as content_file:
         agent_file = content_file.read()
     with open(model_filename) as content_file:
@@ -310,17 +306,30 @@ def write_example_md_file(agent_filename, model_filename, readme_filename, app_f
 
     with open(md_filepath, "w") as fh:
         content = template.substitute(
-            dict(agent_file=agent_file, model_file=model_file,
-                 readme_file=readme_file, app_file=app_file)
+            dict(
+                agent_file=agent_file,
+                model_file=model_file,
+                readme_file=readme_file,
+                app_file=app_file,
+            )
         )
         fh.write(content)
 
+
 def setup_examples_pages():
     # create md files for all examples
     # check what examples exist
     examples_folder = osp.abspath(osp.join(HERE, "..", "mesa", "examples"))
-    basic_examples = [("basic", f.path) for f in os.scandir(osp.join(examples_folder, "basic")) if f.is_dir() and not f.name.startswith("__") ]
-    advanced_examples = [("advanced", f.path) for f in os.scandir(osp.join(examples_folder, "advanced")) if f.is_dir() and not f.name.startswith("__")]
+    basic_examples = [
+        ("basic", f.path)
+        for f in os.scandir(osp.join(examples_folder, "basic"))
+        if f.is_dir() and not f.name.startswith("__")
+    ]
+    advanced_examples = [
+        ("advanced", f.path)
+        for f in os.scandir(osp.join(examples_folder, "advanced"))
+        if f.is_dir() and not f.name.startswith("__")
+    ]
     examples = basic_examples + advanced_examples
 
     with open(os.path.join(HERE, "example_template.txt")) as fh:
@@ -329,7 +338,9 @@ def setup_examples_pages():
     root_folder = pathlib.Path(os.path.join(HERE, "examples"))
     root_folder.mkdir(parents=True, exist_ok=True)
     pathlib.Path(os.path.join(root_folder, "basic")).mkdir(parents=True, exist_ok=True)
-    pathlib.Path(os.path.join(root_folder, "advanced")).mkdir(parents=True, exist_ok=True)
+    pathlib.Path(os.path.join(root_folder, "advanced")).mkdir(
+        parents=True, exist_ok=True
+    )
 
     examples_md = []
     for kind, example in examples:
@@ -344,7 +355,14 @@ def setup_examples_pages():
         examples_md.append((base_name, f"{kind}/{base_name}"))
 
         md_filepath = os.path.join(HERE, "examples", kind, md_filename)
-        write_example_md_file(agent_filename, model_filename, readme_filename, app_filename, md_filepath, template)
+        write_example_md_file(
+            agent_filename,
+            model_filename,
+            readme_filename,
+            app_filename,
+            md_filepath,
+            template,
+        )
 
     # create overview of examples.md
     with open(os.path.join(HERE, "examples_overview_template.txt")) as fh:
@@ -357,14 +375,21 @@ def setup_examples_pages():
         content = template.substitute(
             dict(
                 readme=readme_md,
-                example_paths="\n".join([f"{' '.join(a.split('_'))} </examples/{b}>" for a, b in examples_md]),
+                example_paths="\n".join(
+                    [
+                        f"{' '.join(a.split('_'))} </examples/{b}>"
+                        for a, b in examples_md
+                    ]
+                ),
             )
         )
         fh.write(content)
 
+
 def setup(app):
     setup_examples_pages()
 
+
 #
 if __name__ == "__main__":
-    setup_examples_pages()
+    setup_examples_pages()