Merge pull request #9 from AdamRJensen/sphinx

Setup sphinx and automatic documentation

.gitignore

@@ -1,5 +1,11 @@
 .ipynb_checkpoints
 .vscode
 */.ipynb_checkpoints/*
-__pycache__/*
-test_file.csv
+__pycache__/
+
+# Distribution / packaging
+*/build/
+*.egg-info/
+
+# generated documentation
+docs/source/generated

.readthedocs.yml

@@ -0,0 +1,18 @@
+version: 2
+
+conda:
+    environment: docs/environment.yml
+
+build:
+   image: latest
+
+# This part is necessary otherwise the project is not built
+python:
+   version: 3.7
+   install:
+      - method: pip
+        path: .
+
+# By default readthedocs does not checkout git submodules
+submodules:                                                                                                                          
+    include: all

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2021, Adam R. Jensen
+Copyright (c) 2021-2022, twoaxistracking Development Team
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.md

@@ -1,23 +1,28 @@
 # Open source code for calculating self-shading of two-axis tracking solar collectors
-This repository contains Python code for simulation self-shading in fields of two-axis solar trackers.
+"twoaxistracking" is a python package for simulating self-shading in fields of two-axis trackers.
 
-The two main functions are `generate_field_layout` and `two_axis_shading_fraction`. The function `generate_field_layout` calculates the collector locations for a user-defined regular field layout. For an introduction to regular field layouts and the defining parameters, please see the paper by [Cumpston and Pye (2014)](https://doi.org/10.1016/j.solener.2014.06.012).
+## Documentation
+The documentation can be found at [readthedocs](https://twoaxistracking.readthedocs.io/).
 
-The function `two_axis_shading_fraction` is used to calculate the shading fraction based on a specific field layout, aperture geometry, and solar position. Check out the [example tutorial](https://github.com/AdamRJensen/two_axis_tracker_shading/blob/main/notebooks/Example%20time%20series%20generation.ipynb) to get started! Alternatively, each function is documented according to the numpydoc style guide.
+## Installation and dependencies
+The package can be installed using pip:
 
+    pip install twoaxistracking
 
-## Dependencies
 The main non-standard dependency is `shapely`, which handles the geometric operations. It is recommended to install `shapely` using conda, which can be done by executing the following command in an Anaconda Prompt:
 
     conda install shapely
 
-The solar modeling library `pvlib` is recommended for calculating the solar position and can similarly be installed by the command:
+The solar modeling library `pvlib` is recommended for calculating the solar position and can be installed by the command:
 
-    conda install -c conda-forge pvlib-python
+## Citing
+If you use the package in published work, please cite:
+> Adam R. Jensen et al. 2022.
+> "Self-shading of two-axis tracking solar collectors: Impact of field layout, latitude, and aperture shape."
+> Accepted in Solar Energy.
 
 ## Contributing
 Contributions to the repository, e.g., bug fixes and improvements to speed up the code are more than welcome.
 
-
 ## License
 BSD 3-clause.

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/environment.yml

@@ -0,0 +1,15 @@
+name: readthedocs
+channels:
+    - defaults
+    - conda-forge
+dependencies:
+  - python=3.7
+  - pandas
+  - matplotlib
+  - numpy
+  - shapely # Should be installed with conda
+  - sphinx
+  - pip:
+        - pvlib
+        - myst-nb
+        - sphinx-book-theme

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
+
+if "%1" == "" goto help
+
+%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
+)
+
+%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 +1,75 @@
+# 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
+import sys
+sys.path.insert(0, os.path.abspath('../../'))
+
+# -- Project information -----------------------------------------------------
+
+project = 'Two-axis tracking'
+copyright = '2021-2022, twoaxistracking Development Team'
+author = 'twoaxistracking Development Team'
+
+
+# -- 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 = [
+    'myst_nb',  # markdown and jupyter-notebook parsing
+    'sphinx.ext.autodoc',  # generate documentation from docstrings
+    'sphinx.ext.autosummary',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.napoleon',  # parsing of Numpy docstrings
+]
+
+# 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 = 'sphinx_book_theme'
+html_title = 'Two-axis tracking'
+html_logo = "_static/twoaxistracking_logo.svg"
+html_favicon = "_static/twoaxistracking_logo.svg"
+
+# 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']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+html_show_copyright = False
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3/', None),
+    'numpy': ('https://numpy.org/doc/stable/', None),
+    'pandas': ('https://pandas.pydata.org/pandas-docs/stable', None),
+    'matplotlib': ('https://matplotlib.org/stable', None),
+    'shapely': ('https://shapely.readthedocs.io/en/stable', None),
+}
+
+# Number of seconds for a cell to execute before timeout (default=30)
+nbsphinx_timeout = 60

docs/source/documentation.rst

@@ -0,0 +1,11 @@
+.. currentmodule:: twoaxistracking
+
+
+Code documentation
+==================
+
+.. autosummary::
+   :toctree: generated/
+
+   shaded_fraction
+   generate_field_layout

docs/source/index.md

@@ -0,0 +1,35 @@
+# Simulating two-axis tracking solar collectors
+
+`twoaxistracking` is a python package for simulating two-axis tracking solar collectors, particularly self-shading.
+
+For a quick introduction to the package, check out the [intro tutorial](../notebooks/intro_tutorial) which demonstrates the main functionality. For further details, check out the [code documentation](../documentation).
+
+Note, in the photovoltaics community, two-axis trackers are also commonly referred to as dual-axis trackers (DAT).
+
+
+## Contributing
+Contributions to the repository, e.g., bug fixes, feature request are more than welcome!
+
+
+## License
+[BSD 3-clause](https://github.com/AdamRJensen/twoaxistracking/blob/main/LICENSE).
+
+
+## Citing
+If you use the package in published work, please cite:
+> Adam R. Jensen et al. 2022.
+> "Self-shading of two-axis tracking solar collectors: Impact of field layout, latitude, and aperture shape."
+> Solar Energy (2022). [https://doi.org/10.1016/j.solener.2022.02.023](https://doi.org/10.1016/j.solener.2022.02.023)
+
+
+```{toctree}
+:maxdepth: 1
+:hidden:
+
+notebooks/intro_tutorial
+installation
+documentation
+whatsnew
+notebooks/reference_dataset
+notebooks/field_layout_discretization
+```

docs/source/installation.md

@@ -0,0 +1,13 @@
+# Installation
+
+The package can be installed from [PyPi](https://pypi.org/) with the following command:
+
+    pip install twoaxistracking
+
+The main non-standard dependency is `shapely`, which handles the geometric operations (i.e., shading calculations). It is highly recommended to install `shapely` using conda, which can be done by executing the following command in an Anaconda Prompt:
+
+    conda install shapely
+
+The solar energy modeling library `pvlib` is recommended for calculating the solar position and can be installed by the command:
+
+    pip install pvlib

notebooks/numerical_simulations.ipynb → docs/source/notebooks/field_layout_discretization.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Numerical investigation of self-shading\n",
+    "# Field layout discretization\n",
     "\n",
     "This notebook demonstrates how to uniformly discretize the field layout parameters.\n",
     "\n",
@@ -56,7 +56,7 @@
        "<svg xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" width=\"100.0\" height=\"100.0\" viewBox=\"-0.54 -0.54 1.08 1.08\" preserveAspectRatio=\"xMinYMin meet\"><g transform=\"matrix(1,0,0,-1,0,0.0)\"><path fill-rule=\"evenodd\" fill=\"#66cc99\" stroke=\"#555555\" stroke-width=\"0.0216\" opacity=\"0.6\" d=\"M 0.5,-0.5 L 0.5,0.5 L -0.5,0.5 L -0.5,-0.5 L 0.5,-0.5 z\" /></g></svg>"
       ],
       "text/plain": [
-       "<shapely.geometry.polygon.Polygon at 0x28aed11d160>"
+       "<shapely.geometry.polygon.Polygon at 0x24f35d4cee0>"
       ]
      },
      "execution_count": 2,
@@ -242,14 +242,18 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Visualization of layout discretization\n",
-    "The following plots illustrate the discrete aspect ratios and offsets for GCR=0.2 and GCR=0.3. Note, each point shown is simulated for the all discrete rotations."
+    "## Visualization of layout discretization\n",
+    "The following plot illustrates the discrete aspect ratios and offsets for GCR=0.2 and GCR=0.3. Note, each point shown is simulated for the all discrete rotations."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 5,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-input"
+    ]
+   },
    "outputs": [
     {
      "data": {
@@ -292,7 +296,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -306,7 +310,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.7.11"
   }
  },
  "nbformat": 4,