docs: updated documentation

Author: BitterB0NG0

docs/source/cli.md

@@ -0,0 +1,70 @@
+# PyMCNP CLI
+
+PyMCNP provides tools for formatting MCNP files, visualizing MCNP geometries, and running
+MCNP simulations using the ``pymcnp`` CLI.
+
+## Manual Pages
+
+The manual page for ``pymcnp``:
+
+```{eval-rst}
+.. literalinclude:: ../../src/pymcnp/main.py
+   :language: python
+   :start-after: """
+   :end-before: """
+```
+
+### Check
+
+The manual page for ``pymcnp check``:
+
+```{eval-rst}
+.. literalinclude:: ../../src/pymcnp/cli/check.py
+   :language: python
+   :start-after: """
+   :end-before: """
+```
+
+### Convert
+
+The manual page for ``pymcnp convert``:
+
+```{eval-rst}
+.. literalinclude:: ../../src/pymcnp/cli/convert.py
+   :language: python
+   :start-after: """
+   :end-before: """
+```
+
+### Plot
+
+The manual page for ``pymcnp plot``:
+
+```{eval-rst}
+.. literalinclude:: ../../src/pymcnp/cli/plot.py
+   :language: python
+   :start-after: """
+   :end-before: """
+```
+
+### Run
+
+The manual page for ``pymcnp run``:
+
+```{eval-rst}
+.. literalinclude:: ../../src/pymcnp/cli/run.py
+   :language: python
+   :start-after: """
+   :end-before: """
+```
+
+### Visualize
+
+The manual page for ``pymcnp visualize``:
+
+```{eval-rst}
+.. literalinclude:: ../../src/pymcnp/cli/visualize.py
+   :language: python
+   :start-after: """
+   :end-before: """
+```

docs/source/cli.rst

@@ -20,13 +20,4 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
 extensions = ['sphinx.ext.napoleon', 'myst_parser']
-
-templates_path = ['_templates']
-exclude_patterns = []
 autodoc_member_order = 'bysource'
-
-# -- Options for HTML output -------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
-
-html_theme = 'sphinx_rtd_theme'
-html_static_path = []

docs/source/conf.py

@@ -1,7 +1,5 @@
 # Examples
 
-For examples using the command line, see the [Comand Line Interface](cli.rst).
-
 ## Loading a file
 
     import pymcnp
@@ -19,11 +17,10 @@ use the universal `modify` function.
 	filename = "/path/to/data/input.i'
 	data = pymcnp.read_input(filename)
 
-	pymcnp.modify(x.data.card_s['nps'], npp=100_000)
+	pymcnp.modify(x.data._cards['nps'], npp=100_000)
 
 	data.to_mcnp_file('/path/to/data/new_file_name.i')
 
-
 However, dor common operations, we have specific helper functions, so
 the above can also be done using:
 
@@ -127,10 +124,8 @@ the data of a specific one and easily plot it.
 Creates the following image:
 ![F1F8 Tally plot](./images/Example-F1F8-tally.png)
 
-
 ### Energy and time
 
-
     file = "data/output_files/png_e.o"
     out = pymcnp.outp.ReadOutput(file)
 

docs/source/examples.md

@@ -0,0 +1,36 @@
+# PyMCNP Documentation
+
+PyMCNP is a Python package and CLI for interfacing
+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
+   installation
+   examples
+   contributing
+```
+
+## Components
+
+PyMCNP has two main components:
+
+* [pymcnp CLI](cli)
+
+* [pymcnp Library](pymcnp)
+
+## Guides
+
+PyMCNP has guides:
+
+* [Installation](installation)
+
+* [Examples](examples)
+
+* [Contributing](contributing)