docs: removed builder classes

Author: BitterB0NG0

docs/source/conf.py

@@ -20,4 +20,4 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
 extensions = ['sphinx.ext.napoleon', 'myst_parser']
-autodoc_member_order = 'bysource'
+autodoc_member_order = 'groupwise'

docs/source/index.md

@@ -9,7 +9,7 @@ visualizes simulation geometries, and runs MCNP simulations in parallel.
 ```{eval-rst}
 .. toctree::
    :maxdepth: 1
-
+   
    cli
    pymcnp
    installation

docs/source/pymcnp.md

@@ -1,14 +1,14 @@
 # PyMCNP Package
 
+> [!WARNING]
+> Warning: PyMCNP is in active development! Please, double check eveything works. Reports error on [GitHub](https://github.com/FSIBT/PyMCNP).
+
 PyMCNP provides the backend for the CLI and useful tools for programatically interfacing with
 MCNP. This package supports INP, PTRAC, and MESHTAL parsing and the CLI backend using subpackages:
 
 * [inp subpackage](/pymcnp/inp): INP parsing.
-
 * [meshtal subpackage](/pymcnp/meshtal): MESHTAL parsing.
-
 * [ptrac subpackage](/pymcnp/ptrac): PTRAC parsing. 
-
 * [cli subpackage](/pymcnp/cli): CLI backend.
 
 ## Table of Contents
@@ -30,55 +30,49 @@ PyMCNP represents MCNP files using the ``Inp``, ``Meshtal``, and ``Ptrac`` AST c
 ``inp``, ``meshtal``, and ``ptrac`` subpackages. These classes have important methods for translating PyMCNP and MCNP:
 
 * ``from_mcnp``. Parses MCNP source, checking for syntax and semantic errors.
-
 * ``to_mcnp``. Generates MCNP source from PyMCNP objects, reformatting.
-
 * ``from_file``. Parses MCNP file.
-
 * ``to_file``. Generates MCNP file from PyMCNP objects.
 
 ### ``Inp`` Class
 
 ```{eval-rst}
 .. autoclass:: pymcnp.Inp
    :members:
+   :inherited-members:
 ```
 
 [inp subpackage](pymcnp/inp)
 
-### ``Meshtal`` Class
+### ``Outp`` Class
 
 ```{eval-rst}
-.. autoclass:: pymcnp.Meshtal
+.. autoclass:: pymcnp.Outp
    :members:
+   :inherited-members:
 ```
 
-[meshtal subpackage](pymcnp/meshtal)
+[meshtal subpackage](pymcnp/outp)
 
 ### ``Ptrac`` Class
 
 ```{eval-rst}
 .. autoclass:: pymcnp.Ptrac
    :members:
+   :inherited-members:
 ```
 
 [ptrac subpackage](pymcnp/ptrac)
 
-## Builder Classes
-
-AST classes are immutable, but ``Inp`` has a builder class. ``InpBuilder`` is a mutable wrapper without input
-validation, and it has a method for constructing ``Inp``:
-
-* ``build``. Attempts to build ``Inp`` using ``InpBuilder``'s fields.
-
-### ``InpBuilder`` Class
+### ``Meshtal`` Class
 
 ```{eval-rst}
-.. autoclass:: pymcnp.InpBuilder
+.. autoclass:: pymcnp.Meshtal
    :members:
+   :inherited-members:
 ```
 
-[inp subpackage](pymcnp/inp)
+[meshtal subpackage](pymcnp/meshtal)
 
 ## Filter & Processor Classes
 
@@ -87,35 +81,37 @@ The ``*Filtered`` and ``*Processed`` classes help handle large ``Meshtal`` and `
 and ``MeshtalProcessed`` have overridable methods for processing data, and all can be run:
 
 * ``check_*``. Returns ``True``/``False`` if data should be kept/removed.
-
 * ``process_*``. Operates with side effects on data.
-
 * ``run``. Runs the filter or processor.
 
 ### ``MeshtalFiltered`` Class
 
 ```{eval-rst}
 .. autoclass:: pymcnp.MeshtalFiltered
    :members:
+   :inherited-members:
 ```
 
 ### ``PtracFiltered`` Class
 
 ```{eval-rst}
 .. autoclass:: pymcnp.PtracFiltered
    :members:
+   :inherited-members:
 ```
 
 ### ``MeshtalProcessed`` Class
 
 ```{eval-rst}
 .. autoclass:: pymcnp.MeshtalProcessed
    :members:
+   :inherited-members:
 ```
 
 ### ``PtracProcessed`` Class
 
 ```{eval-rst}
 .. autoclass:: pymcnp.PtracProcessed
    :members:
+   :inherited-members:
 ```

docs/source/pymcnp/cli.md

@@ -8,51 +8,54 @@
 * ``pymcnp run``
 * ``pymcnp visualize``
 
-## Modules
+## CLI Classes
 
-Each module contains corresponding classes which enapsulate the subcommands' functionality,
-enabiling programmatic access to the CLI:
+### ``Check`` Class
 
-* ``Check``
-* ``Convert``
-* ``Plot``
-* ``Run``
+``Check`` compares and fixes MCNP files, using ``difflib``,
 
-### ``check.Check`` Class
+```{eval-rst}
+.. autoclass:: pymcnp.cli.Check
+   :members:
+   :inherited-members:
+```
+
+### ``Convert`` Class
 
-``check`` contains the ``Check`` class which compares MCNP files using ``difflib`` and
-formats them.
+``Convert`` converts OUTP files to csv or parquet files, using ``pandas``.
 
 ```{eval-rst}
-.. autoclass:: pymcnp.cli.check.Check
+.. autoclass:: pymcnp.cli.Convert
    :members:
+   :inherited-members:
 ```
 
-### ``convert.Convert`` Class
+### ``Plot`` Class
 
-``convert`` contains the ``Convert`` class which converts OUTP files, using ``pandas``, to
-CSV or parquet files.
+``Plot`` plots OUTP files, using ``matplotlib``.
 
 ```{eval-rst}
-.. autoclass:: pymcnp.cli.convert.Convert
+.. autoclass:: pymcnp.cli.Plot
    :members:
+   :inherited-members:
 ```
 
-### ``plot.Plot`` Class
+### ``Run`` Class
 
-``plot`` contains the ``Plot`` class which plots OUTP files, using ``matplotlib``.
+``Run`` runs MCNP simulations in parallel, using ``subprocess``.
 
 ```{eval-rst}
-.. autoclass:: pymcnp.cli.plot.Plot
+.. autoclass:: pymcnp.cli.Run
    :members:
+   :inherited-members:
 ```
 
-### ``run.Run`` Class
+### ``Visualize`` Class
 
-``run`` contains the ``Run`` class which runs MCNP simulations, in series or parallel,
-on given INP.
+``Visualize`` visualizes INP surfaces and cell geometries, using ``pyvista``.
 
 ```{eval-rst}
-.. autoclass:: pymcnp.cli.run.Run
+.. autoclass:: pymcnp.cli.Visualize
    :members:
+   :inherited-members:
 ```

docs/source/pymcnp/inp.md

@@ -1,6 +1,6 @@
 # ``pymcnp.inp`` Subpackage
 
-> [!CAUTION]
+> [!WARNING]
 > The following non-terminals are not currently supported:
 > * data.Field (3.3.3.12)
 > * data.Mplot (3.3.7.2.5)
@@ -12,11 +12,8 @@
 > * data.Fm (3.3.5.7)
 > * data.Ft (3.3.5.18)
 
-> [!WARNING]
-> Warning: PyMCNP is in active development! Please, double check eveything works. Reports error on [GitHub](https://github.com/FSIBT/PyMCNP).
-
 ``pymcnp.inp`` contains the INP parser. PyMCNP implements an object-oriented recursive
-descent parser, modeling INP as the following context-free-grammar described in modified Bakus-Naur form:
+descent parser, approximates INP as the following context-free-grammar described in modified Bakus-Naur form:
 
 ```
 <CellOption> = ...;
@@ -33,7 +30,10 @@ descent parser, modeling INP as the following context-free-grammar described in
 
 ```{eval-rst}
 .. toctree::
+   :maxdepth: 1
+
    inp/cell
+   inp/like
    inp/surface
    inp/data
 ```
@@ -44,80 +44,52 @@ PyMCNP represents INP non-terminals with AST classes and stores them in nested s
 These AST class have methods for translating PyMCNP and INP:
 
 * ``from_mcnp``. Parses INP source, checking for syntax and semantic errors.
-
 * ``to_mcnp``. Generates INP source from PyMCNP objects, reformatting.
 
 ### ``Comment`` Class
 
 ```{eval-rst}
 .. autoclass:: pymcnp.inp.Comment
    :members:
+   :inherited-members:
 ```
 
 ### ``Cell`` Class
 
 ```{eval-rst}
 .. autoclass:: pymcnp.inp.Cell
    :members:
+   :inherited-members:
 ```
 
 [cell subpackage](inp/cell)
 
-### ``Surface`` Class
-
-```{eval-rst}
-.. autoclass:: pymcnp.inp.Surface
-   :members:
-```
-
-[surface subpackage](inp/surface)
-
-### ``Data`` Class
-
-```{eval-rst}
-.. autoclass:: pymcnp.inp.Data
-   :members:
-```
-
-[data subpackage](inp/data)
-
-## Builder Classes
-
-AST classes are immutable, but they have corresponding builder classes. These builder classes are mutable
-wrappers without input validation, and they have a method for constructing AST classes:
-
-* ``build``. Attempts to build corresponding AST class using the builder classes' fields.
-
-### ``CommentBuilder`` Class
-
-```{eval-rst}
-.. autoclass:: pymcnp.inp.CommentBuilder
-   :members:
-```
-
-### ``CellBuilder`` Class
+### ``Like`` Class
 
 ```{eval-rst}
-.. autoclass:: pymcnp.inp.CellBuilder
+.. autoclass:: pymcnp.inp.Like
    :members:
+   :inherited-members:
 ```
 
-[cell subpackage](inp/cell)
+[like subpackage](inp/like)
 
-### ``SurfaceBuilder`` Class
+### ``Surface`` Class
 
 ```{eval-rst}
-.. autoclass:: pymcnp.inp.SurfaceBuilder
+.. autoclass:: pymcnp.inp.Surface
    :members:
+   :inherited-members:
 ```
 
 [surface subpackage](inp/surface)
 
-### ``DataBuilder`` Class
+### ``Data`` Class
 
 ```{eval-rst}
-.. autoclass:: pymcnp.inp.DataBuilder
+.. autoclass:: pymcnp.inp.Data
    :members:
+   :inherited-members:
 ```
 
 [data subpackage](inp/data)