Create installation script and documentation website

.gitignore

@@ -33,10 +33,16 @@ tmp_*
 *.core
 .DS_Store # for mac users
 **/.DS_Store
+**/.idea
 
 # test cache
 .pytest_cache
 pytestdebug.log
 
 # profiler
 *.prof
+
+# Documentation builds
+docs/build
+docs/source/pythonapi/generated/
+

.readthedocs.yaml

@@ -0,0 +1,32 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/source/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+   install:
+     - requirements: docs/requirements-rtd.txt

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/requirements-rtd.txt

@@ -0,0 +1,8 @@
+sphinx==7.2.6
+furo
+numpy
+numba
+matplotlib
+scipy
+h5py
+

docs/source/_templates/omcfunction.rst

@@ -0,0 +1,6 @@
+{{ fullname }}
+{{ underline }}
+
+.. currentmodule:: {{ module }}
+
+.. autofunction:: {{ objname }}

docs/source/conf.py

@@ -0,0 +1,66 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+
+import os, sys
+
+sys.path.insert(0, os.path.abspath("../.."))
+
+
+# On Read the Docs, need to mock any python packages that would require c
+from unittest.mock import MagicMock
+
+MOCK_MODULES = ["mpi4py"]
+sys.modules.update((mod_name, MagicMock()) for mod_name in MOCK_MODULES)
+
+
+# -- Project information -----------------------------------------------------
+
+project = "MC/DC"
+copyright = "2023, Center for Exascale Monte Carlo Neutron Transport (CEMeNT)"
+author = "Center for Exascale Monte Carlo Neutron Transport (CEMeNT)"
+
+# The full version, including alpha/beta/rc tags
+release = "0.1"
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+]
+autosummary_generate = True
+
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "furo"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]

docs/source/index.rst

@@ -0,0 +1,38 @@
+.. MC/DC documentation master file, created by
+   sphinx-quickstart on Fri Oct 27 14:14:47 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+
+=================================
+MC/DC: Monte Carlo Dynamic Code
+=================================
+
+MC/DC is a performant, scalable, and machine-portable Python-based 
+Monte Carlo neutron transport software in active development 
+by the `Center for Exascale Monte Carlo Neutron Transport <https://cement-psaap.github.io/>`_ (CEMeNT).
+
+.. note::
+   The project is in the early stages of *very* active development,
+   not even an alpha release! 
+
+
+.. only:: html
+
+   --------
+   Contents
+   --------
+
+.. toctree::
+   :maxdepth: 1
+
+   install
+   pythonapi/index
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/install.rst

@@ -0,0 +1,89 @@
+.. _install:
+
+===================
+Installation Guide
+===================
+
+This outlines the basic steps to install MC/DC on a local
+machine or on HPC machine.
+
+-----------------------------------
+Creating an MC/DC Conda environment
+-----------------------------------
+
+`Conda <https://conda.io/en/latest/>`_ is an open source package and environment management system 
+that runs on Windows, macOS, and Linux. It allows for easy installing and switching between multiple
+versions of software packages and their dependendencies. 
+We can't force you to use it, but we do *highly* recommend it, particularly
+if you plan on running MC/DC in `numba mode <https://numba.pydata.org/>`_.
+**The included installation script will fail if executed outside of a conda environment.**
+
+First, `conda` should be installed with `Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_
+or `Anaconda <https://www.anaconda.com/>`_. HPC instructions: 
+
+`Quartz <https://hpc.llnl.gov/hardware/compute-platforms/quartz>`_ (LLNL, x86_64), 
+
+.. code-block:: sh
+
+    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+    bash Miniconda3-latest-Linux-x86_64.sh
+
+
+`Lassen <https://hpc.llnl.gov/hardware/compute-platforms/lassen>`_ (LLNL, IBM Power9),
+
+.. code-block:: sh
+
+    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-ppc64le.sh
+    bash Miniconda3-latest-Linux-ppc64le.sh
+
+
+Then create and activate a new conda environment called `mcdc-env` in
+which to install MC/DC. This creates an environment with python3.11 
+installed.
+
+.. code-block:: sh
+
+    conda create -n mcdc-env python=3.11
+    conda activate mcdc-env
+
+-------------------------------------------
+Installing from Source on Linux or Mac OS X
+-------------------------------------------
+
+All MC/DC source code is hosted on `Github <https://github.com/CEMeNT-PSAAP/MCDC>`_.
+If you have `git <https://git-scm.com>`_, you can download MC/DC by entering the
+following commands in a terminal:
+
+.. code-block:: sh
+
+    git clone https://github.com/CEMeNT-PSAAP/MCDC.git
+    cd MCDC
+
+
+The MC/DC repository includes the script ``install.sh``, which will 
+build MC/DC and all of its dependencies and execute any necessary patches.
+This has been tested on Quartz, Lassen, and Apple M2 (as of 11/01/2023). 
+The ``install.sh`` script **will fail outside of a conda environment**.
+
+On HPC machines, the script will install mpi4py 
+`from source <https://mpi4py.readthedocs.io/en/stable/install.html#using-distutils>`_.
+This means that all appropriate modules must be loaded prior to executing.
+
+On Quartz, the default modules are sufficient (``intel-classic`` and ``mvapich2``). 
+On Lassen, ``module load gcc/8 cuda/11.3``. Then, 
+
+.. code-block:: sh
+
+    bash install.sh --hpc
+
+
+On local machines, mpi4py will be installed using conda,
+
+.. code-block:: sh
+
+    bash install.sh 
+
+
+To confirm that everything is properly installed, execute ``pytest`` from the MCDC directory. 
+
+

docs/source/pythonapi/index.rst

@@ -0,0 +1,74 @@
+.. _pythonapi:
+
+================
+Input Definition
+================
+
+Full API documentation.
+
+
+Defining materials
+------------------
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: omcfunction.rst
+
+   mcdc.material
+   mcdc.nuclide
+
+
+Defining geometry
+-----------------
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: omcfunction.rst
+
+   mcdc.surface
+   mcdc.cell
+   mcdc.universe
+   mcdc.lattice
+
+
+
+Defining simulation
+-------------------
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: omcfunction.rst
+
+   mcdc.source
+   mcdc.tally
+   mcdc.eigenmode
+   mcdc.setting
+
+
+
+Defining techniques
+-------------------
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: omcfunction.rst
+
+   mcdc.implicit_capture
+   mcdc.weighted_emission
+   mcdc.population_control
+   mcdc.branchless_collision
+   mcdc.time_census
+   mcdc.weight_window
+   mcdc.iQMC
+   mcdc.weight_roulette
+   mcdc.IC_generator
+   mcdc.dsm
+
+
+
+
+