Initial Design documents (#6)

* initial design documents

docs/Makefile

@@ -0,0 +1,21 @@
+# Purpose: Convenience scripts to simplify some common Sphinx operations, such as rendering the content.
+
+# 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/conf.py

@@ -1,78 +1,70 @@
-"""Documentation Configuration"""
+"""Configuration file for the Sphinx documentation builder.
+
+For the full list of built-in configuration values, see the documentation:
+https://www.sphinx-doc.org/en/master/usage/configuration.html
+"""
 
-# Configuration file for the Sphinx documentation builder.
-#
-# For the full list of built-in configuration values, see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
 import os
 import sys
 
-import versioningit
+# import versioningit
 
 sys.path.insert(0, os.path.abspath("../src"))
 
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = "Project Name"
-copyright = "Copyright 2024"  # noqa A001
-author = "Author Name"
-
-# The short X.Y version
-# NOTE: need to specify the location of the pyproject.toml file instead of the
-#       location of the source tree
-version = versioningit.get_version("..")
-# The full version, including alpha/beta/rc tags
-release = ".".join(version.split(".")[:-1])
+project = "hyspecplanningtools"
+copyright = "2024, ORNL"  # noqa A001
+author = "ORNL"
+# version = versioningit.get_version("../../")
+# # The full version, including alpha/beta/rc tags
+# release = ".".join(version.split(".")[:-1])
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
 extensions = [
-    "sphinx.ext.autodoc",
-    "sphinx.ext.autosummary",
+    "sphinx.ext.duration",
     "sphinx.ext.doctest",
-    "sphinx.ext.todo",
-    "sphinx.ext.coverage",
-    "sphinx.ext.mathjax",
-    "sphinx.ext.ifconfig",
-    "sphinx.ext.viewcode",
-    "sphinx.ext.githubpages",
+    "sphinx.ext.autodoc",
     "sphinx.ext.intersphinx",
-    "sphinx.ext.napoleon",
-    "myst_parser",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.coverage",
+    "sphinxcontrib.mermaid",
 ]
-templates_path = ["_templates"]
 
-# The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-#
-source_suffix = [".rst", ".md"]
+autodoc_mock_imports = [
+    "qtpy",
+    "qtpy.uic",
+    "qtpy.QtWidgets",
+]
 
-# The master toctree document.
 master_doc = "index"
+source_suffix = [".rst", ".md"]
 
-# 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 = ["_build", "Thumbs.db", ".DS_Store"]
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3/", None),
+    "sphinx": ("https://www.sphinx-doc.org/en/master/", None),
+}
+intersphinx_disabled_domains = ["std"]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build"]
+pygments_style = "sphinx"
 
 
 # -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#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 = "sphinx_rtd_theme"  # please add corresponding package to environment.yml if you want to use it
-autosummary_generate = True
+html_theme = "sphinx_rtd_theme"  # pylint: disable=C0103
 
-# Napoleon settings
-napoleon_google_docstring = False
-napoleon_numpy_docstring = True
+html_theme_options = {"style_nav_header_background": "#472375"}
 
-# "Static" resources (like *.css *.js files, or images) to be included when generating the HTML documentation.
-if os.path.exists("_static"):
-    html_static_path = ["_static"]
+html_static_path = ["_static"]
+
+html_css_files = [
+    "css/custom.css",
+]
 
-# If true, `todo` and `todoList` produce output, else they produce nothing.
-todo_include_todos = True
+epub_show_urls = "footnote"  # pylint: disable=C0103

docs/make.bat

@@ -0,0 +1,37 @@
+REM Purpose: Convenience scripts to simplify some common Sphinx operations, such as rendering the content.
+
+@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/source/_static/css/custom.css

@@ -0,0 +1,11 @@
+/* makes the width expand the entire width*/
+.wy-nav-content {
+    min-width: 360px;
+    max-width: 100%;
+}
+
+/* allows table to be multi-line */
+table.docutils td {
+    word-wrap:break-word;
+    white-space:pre-wrap;
+}

docs/source/conf.py

@@ -0,0 +1,70 @@
+"""Configuration file for the Sphinx documentation builder.
+
+For the full list of built-in configuration values, see the documentation:
+https://www.sphinx-doc.org/en/master/usage/configuration.html
+"""
+
+import os
+import sys
+
+# import versioningit
+
+sys.path.insert(0, os.path.abspath("../../src"))
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "Hyspecplanningtools"
+copyright = "2024, ORNL"  # noqa A001
+author = "ORNL"
+# version = versioningit.get_version("../../")
+# # The full version, including alpha/beta/rc tags
+# release = ".".join(version.split(".")[:-1])
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.duration",
+    "sphinx.ext.doctest",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.coverage",
+    "sphinxcontrib.mermaid",
+]
+
+autodoc_mock_imports = [
+    "qtpy",
+    "qtpy.uic",
+    "qtpy.QtWidgets",
+]
+
+master_doc = "index"
+source_suffix = [".rst", ".md"]
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3/", None),
+    "sphinx": ("https://www.sphinx-doc.org/en/master/", None),
+}
+intersphinx_disabled_domains = ["std"]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build"]
+pygments_style = "sphinx"
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "sphinx_rtd_theme"  # pylint: disable=C0103
+
+html_theme_options = {"style_nav_header_background": "#472375"}
+
+html_static_path = ["_static"]
+
+html_css_files = [
+    "css/custom.css",
+]
+
+epub_show_urls = "footnote"  # pylint: disable=C0103

docs/source/design/index.rst

@@ -0,0 +1,19 @@
+.. _design__guidelines:
+
+=============================
+Hyspecplanningtools Design
+=============================
+
+Information, diagrams and flowcharts are included about the various components of the polarization tool.
+Please make sure to
+review and adhere to these guidelines when contributing to the project.
+
+
+Contents
+--------
+
+.. toctree::
+   :maxdepth: 2
+
+   polarizationmodel
+   polarizationflow