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.gitignore

@@ -129,3 +129,4 @@ dmypy.json
 .pyre/
 
 src/shiver/_version.py
+.vscode/launch.json

README.md

@@ -47,6 +47,24 @@ To set the pre-commit hook before each git commit
 pre-commit install
 ```
 
+---
+**NOTE**
+
+When adding new views, presenters and methods. Please navigate to docs/source/repo_doc.rst. Add the new feature under the appropriate section following the given template:
+
+```bash
+.. automodule:: path.to.new.module
+   :members:
+```
+
+Once complete, rebuild the documentation:
+
+    cd SHIVER/docs/
+    make clean
+    make html
+
+---
+
 [![CI](https://github.com/neutrons/Shiver/actions/workflows/actions.yml/badge.svg?branch=next)](https://github.com/neutrons/Shiver/actions/workflows/actions.yml)
 [![codecov](https://codecov.io/gh/neutrons/shiver/branch/next/graph/badge.svg?token=J1ZNHXF6Ml)](https://codecov.io/gh/neutrons/shiver)
 [![OpenSSF Best Practices](https://bestpractices.coreinfrastructure.org/projects/7381/badge)](https://bestpractices.coreinfrastructure.org/projects/7381)

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/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/conf.py

@@ -0,0 +1,54 @@
+"""
+    Purpose: A Python script holding the configuration of the project. Contains the project
+    name and release information as well as some extra configuration keys.
+"""
+import os
+import sys
+import versioningit
+
+
+sys.path.insert(0, os.path.abspath("../../"))
+
+# 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
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "SHIVER"  # pylint: disable=C0103
+copyright = "2022, ORNL"  # pylint: disable=W0622, C0103
+author = "ORNL"  # pylint: disable=C0103
+version = versioningit.get_version("../../")
+release = ".".join(version.split(".")[:-1])  # pylint: disable=C0103
+
+# -- 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.autosummary",
+    "sphinx.ext.intersphinx",
+]
+
+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 = []
+
+
+# -- 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"}
+
+epub_show_urls = "footnote"  # pylint: disable=C0103

docs/source/getting_started.rst

@@ -0,0 +1,67 @@
+Getting Started
+===============
+
+.. _getting_started:
+
+
+
+Instructions for SHIVER development
+-----------------------------------
+
+Conda Configuration
+```````````````````
+Create and activate conda environment for ``SHIVER``.
+
+.. code-block:: sh
+
+    conda env create --file environment.yml
+    # or
+    mamba env create --file environment.yml
+
+    conda activate shiver
+
+Install ``SHIVER`` (in `editable mode <https://pip.pypa.io/en/stable/cli/pip_install/#cmdoption-e>`_) and start application
+
+.. code-block:: sh
+
+    python -m pip install -e .
+
+    shiver
+
+If it has been a while, once can update using
+
+.. code-block:: sh
+
+    conda activate shiver
+    conda env update --file environment.yml --prune
+
+To start ``SHIVER`` from within the Mantid workbench, start ``mantidworkbench`` then run the following in the
+``IPython`` console
+
+.. code-block:: sh
+
+    from shiver import Shiver
+    s = Shiver()
+    s.show()
+
+**For Developers**
+
+To run all tests for ``SHIVER``
+
+.. code-block:: sh
+
+    pytest
+    #or
+    python -m pytest
+
+To run ``pre-commit`` manually
+
+.. code-block:: sh
+
+    pre-commit run --all-files
+
+Or to set the ``pre-commit`` hook before each ``git`` commit
+
+.. code-block:: sh
+
+    pre-commit install

docs/source/index.rst

@@ -0,0 +1,35 @@
+.. Purpose: The root document of the project, which serves as welcome page and contains the root
+.. of the "table of contents tree" (or toctree).
+
+Welcome to SHIVER's documentation!
+==================================
+The Spectroscopy HIstogram Visualizer for Event Reduction **(SHIVER)** is a tool to
+allow examination of time of flight inelastic neutron data, from single crystal,
+direct geometry experiments. It is intended to perform the following tasks:
+
+* Transform time of flight data from multiple orientations into a single intermediate
+  structure in units of reciprocal space and energy transfer.
+
+
+* Allow slicing of the intermediate file and creation of histograms containing S(**Q**, ∆ *E*)
+  with various dimensionality
+
+
+* Visualize the histograms
+
+Check out the :doc:`usage` section for further information, including :ref:`installation`
+steps for this project.
+
+.. note::
+
+   This project is under active development.
+
+Contents
+--------
+
+.. toctree::
+   :maxdepth: 1
+
+   getting_started
+   usage
+   repo_doc

docs/source/repo_doc.rst

@@ -0,0 +1,97 @@
+Repository Documentation
+========================
+
+Shiver
+------
+.. automodule:: src.shiver.shiver
+   :members:
+
+Models
+------
+
+.. automodule:: src.shiver.models.sample
+   :members:
+
+.. automodule:: src.shiver.models.help
+   :members:
+
+.. automodule:: src.shiver.models.generate
+   :members:
+
+.. automodule:: src.shiver.models.convert_dgs_to_single_mde
+   :members:
+
+.. automodule:: src.shiver.models.makeslice
+   :members:
+
+.. automodule:: src.shiver.models.generate_dgs_mde
+   :members:
+
+.. automodule:: src.shiver.models.corrections
+   :members:
+
+.. automodule:: src.shiver.models.utils
+   :members:
+
+.. automodule:: src.shiver.models.histogram
+   :members:
+
+Presenters
+----------
+
+.. automodule:: src.shiver.presenters.sample
+   :members:
+
+.. automodule:: src.shiver.presenters.generate
+   :members:
+
+.. automodule::  src.shiver.presenters.histogram
+   :members:
+
+Views
+-----
+
+.. automodule:: src.shiver.views.histogram_parameters
+   :members:
+
+.. automodule:: src.shiver.views.sample
+   :members:
+
+.. automodule:: src.shiver.views.invalid_styles
+   :members:
+
+.. automodule:: src.shiver.views.oncat
+   :members:
+
+.. automodule:: src.shiver.views.generate
+   :members:
+
+.. automodule:: src.shiver.views.advanced_options
+   :members:
+
+.. automodule:: src.shiver.views.data
+   :members:
+
+.. automodule:: src.shiver.views.loading_buttons
+   :members:
+
+.. automodule:: src.shiver.views.workspace_tables
+   :members:
+
+.. automodule:: src.shiver.views.plots
+   :members:
+
+.. automodule:: src.shiver.views.mainwindow
+   :members:
+
+.. automodule:: src.shiver.views.reduction_parameters
+   :members:
+
+.. automodule:: src.shiver.views.corrections
+   :members:
+
+.. automodule:: src.shiver.views.polarized_options
+   :members:
+
+.. automodule:: src.shiver.views.histogram
+   :members:

docs/source/usage.rst

@@ -0,0 +1,38 @@
+Usage
+=====
+
+.. _installation:
+
+Installation
+------------
+
+
+Under Construction!
+
+Application Information
+-----------------------
+
+``SHIVER`` is a desktop application for generating histograms from direct
+geometry inelastic data related to spectroscopy event reduction. It is
+built as a python package and can be used either as a standalone application
+or as a package imported in Mantid workbench.
+
+.. note::
+    `Github Shiver Repository <https://github.com/neutrons/Shiver>`_
+
+Technologies
+------------
+
+The project is written in Python (>=3.8). It is highly dependent on `Manitd <https://www.mantidproject.org>`_.
+The Graphical User Interface (GUI) is based on `QtPy <https://github.com/spyder-ide/qtpy>`_ (version is defined by Mantid)
+
+
+Project Structure
+-----------------
+
+The main code of the project is at src/shiver and the tests are at ``tests/``
+folders. The project contains additional scripts at ``DGS_SC_scripts/`` folder,
+which are initial scripts that ``SHIVER`` was created around.
+
+The code follows the `MVP (Model-View-Presenter) <https://developer.mantidproject.org/MVPDesign.html>`_ Thus,
+all current and future changes will follow this pattern.

environment.yml

@@ -10,6 +10,8 @@ dependencies:
  - pytest=7.2.1
  - pytest-qt=4.2.0
  - pytest-cov=4.0.0
+ - sphinx
  - pip
  - pip:
    - https://oncat.ornl.gov/packages/pyoncat-1.4.1-py3-none-any.whl
+   - sphinx-rtd-theme