pip install: move extra libraries into pyproject.toml, fix documentation

Author: Arun Persaud

docs/source/contributing.md

@@ -1,47 +1,55 @@
 # Contributing
 
-We welcome contributions to code, documentation, tests, and files, just create a [GitHub issue](https://github.com/FSIBT/PyMCNP/issues).
+We welcome contributions to code, documentation, tests, and files,
+just create a [GitHub issue](https://github.com/FSIBT/PyMCNP/issues).
 
 ## Contributing
 
-PyMCNP source code is accessable for contributions, suggestions, and bug reports on [GitHub](https://github.com/FSIBT/PyMCNP):
+PyMCNP source code is accessable for contributions, suggestions, and
+bug reports on [GitHub](https://github.com/FSIBT/PyMCNP):
 
     # Installing
     git clone https://github.com/FSIBT/PyMCNP
     cd PyMCNP
-    pip install -e .
+    pip install -e .[dev]
 
     # Running
     pymcnp
 
-To contribute, use [pre-commit](https://pre-commit.com) and [ruff](https://docs.astral.sh/ruff/):
+To contribute, use [pre-commit](https://pre-commit.com) and
+[ruff](https://docs.astral.sh/ruff/). These will be automatically
+included when using the optional _dev_ dependency.
 
     # Installing
-    pip install pre-commit ruff
     cd PyMCNP
     pre-commit install
 
-    # Running
-    pre-commit
-
 ## Testing
 
-To run the PyMCNP test suite, after cloning the PyMCNP GitHub repository, use the following commands to install [pytest](https://docs.pytest.org/en/stable/) with [pytest-cov](https://pytest-cov.readthedocs.io/en/latest/) inside the PyMCNP directory:
+To run the PyMCNP test suite, after cloning the PyMCNP GitHub
+repository, use the following commands to install
+[pytest](https://docs.pytest.org/en/stable/) with
+[pytest-cov](https://pytest-cov.readthedocs.io/en/latest/) inside the
+PyMCNP directory. This can be done automatically using the _test_
+dependency. By default coverage and testmon will be used with pytest.
 
     # Installing
-    pip install pytest-cov
     cd PyMCNP
+    pip install -e .[test]
     python -m pytest
 
     # Running
     pytest --cov --cov-report term-missing:skip-covered
 
 ## Documenting
 
-To rebuild the documentation using [Sphinx](https://www.sphinx-doc.org/en/master/) and [Napolean](https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html):
+To rebuild the documentation using
+[Sphinx](https://www.sphinx-doc.org/en/master/) and
+[Napolean](https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html). This
+can be done automatically using the _doc_ dependency. 
 
     # Installing
-    pip install sphinx
+    pip install -e .[doc]
 
     # Running
     cd docs

docs/source/index.md

@@ -1,15 +1,15 @@
 # PyMCNP Documentation
 
 PyMCNP is a Python package and CLI for interfacing
-with [MCNP](https://mcnp.lanl.gov). PyMCNP parsers MCNP files, 
+with [MCNP](https://mcnp.lanl.gov). PyMCNP parsers MCNP files,
 visualizes simulation geometries, and runs MCNP simulations in parallel.
 
 ## Table of Contents
 
 ```{eval-rst}
 .. toctree::
    :maxdepth: 1
-   
+
    cli
    pymcnp
 

pyproject.toml

@@ -33,10 +33,9 @@ dependencies = [
     "molmass",
     "numpy",
     "pandas",
-    "pytest",
+    "pyvista",
     "rich",
     "scipy",
-    "pyvista",
 ]
 
 [project.optional-dependencies]
@@ -46,6 +45,19 @@ docs = [
     "sphinx_rtd_theme",
 ]
 
+dev = [
+    "pre-commit",
+    "ruff",
+]
+
+test = [
+    "pytest",
+    "pytest-cov",
+    "pytest-testmon",
+    "PyQt5",
+]
+
+
 [project.urls]
 Documentation = "https://pymcnp.readthedocs.io/en/latest/"
 Homepage = "https://github.com/FSIBT/PyMCNP"
@@ -61,6 +73,12 @@ where = ["./src"]
 [tool.setuptools_scm]
 write_to = "./src/version.py"
 
+[tool.pytest.ini_options]
+addopts = "--testmon --cov --cov-report=term-missing:skip-covered"
+testpaths = [
+    "tests"
+]
+
 [tool.ruff]
 line-length = 200
 lint.ignore = ["E741", "E742"]