Initial commit documentation

.github/workflows/docs.yml

@@ -0,0 +1,36 @@
+name: docs
+
+on:
+  push:
+    branches: [ "docs" ]
+  pull_request:
+    branches: [ "docs" ]
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Install packages
+      run: sudo apt update && sudo apt install -y git build-essential curl wget python3 python3-pip texlive texlive-pictures texlive-latex-extra pdf2svg poppler-utils netpbm imagemagick ghostscript
+    - name: Install Python packages
+      run: sudo pip install sphinx sphinx-rtd-theme sphinxcontrib-tikz
+    - name: Build documentation
+      run: cd docs && make html
+    - name: Upload math result for job 1
+      uses: actions/upload-artifact@v3
+      with:
+        name: html-docs
+        path: ./docs/_build/html
+
+  deploy:
+    runs-on: [self-hosted, linux, x64]
+    needs: build-docs
+    steps:
+    - name: Download docs
+      uses: actions/download-artifact@v3
+      with:
+        name: html-docs
+        path: html-docs
+    - name: Deploy
+      run: touch ${{ secrets.DEPLOY_PATH }}/html && rm -r ${{ secrets.DEPLOY_PATH }}/html/* && cp -rv html-docs/* ${{ secrets.DEPLOY_PATH }}/html

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     = .
+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/_static/css/custom.css

@@ -0,0 +1,11 @@
+.tight-table td {
+    white-space: normal !important;
+}
+
+.wy-side-nav-search {
+    background: #ccc0ce;
+}
+
+.icon.icon-home {
+    color: #5a0089;
+}

docs/_templates/breadcrumbs.html

@@ -0,0 +1,4 @@
+<div style="text-align: right;">
+<a href="https://github.com/ifilot/pyqint" target="_blank"><i class="fa-brands fa-github"></i> Github</a>
+</div>
+<hr>

docs/community_guidelines.rst

@@ -0,0 +1,14 @@
+.. _community_guidelines:
+.. index:: Community Guidelines
+
+Community guidelines
+********************
+
+* Contributions to :program:`PyQInt` are always welcome and appreciated. Before doing
+  so, please first read the `CONTRIBUTING <https://github.com/ifilot/pyqint/blob/master/CONTRIBUTING.md>`_
+  guide.
+* For reporting issues or problems with the software, you are kindly invited to
+  `to open a new issue on Github with the bug tag <https://github.com/ifilot/pyqint/issues/new?labels=bug>`_.
+* If you seek support in using :program:`PyQInt`, please
+  `open an issue with the question tag <https://github.com/ifilot/pyqint/issues/new?labels=question>`_.
+* If you wish to contact the developers, please send an e-mail to i.a.w.filot@tue.nl.

docs/conf.py

@@ -0,0 +1,71 @@
+# 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('.'))
+import sphinx_rtd_theme
+
+# -- Project information -----------------------------------------------------
+
+project = 'PyTessel'
+copyright = '2023, Inorganic Materials and Catalysis'
+author = 'Ivo Filot'
+
+
+# -- 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.mathjax',
+    'sphinx.ext.autosectionlabel',
+    'sphinx_rtd_theme'
+]
+
+# 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 = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- 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'
+
+# 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".
+master_doc = 'index'
+html_static_path = ['_static']
+# html_theme_options = {
+#     'display_version': True,
+#     'analytics_id': 'G-H71EPP6GVB'
+# }
+html_logo = "_static/img/pytessel_logo_128.png"
+html_favicon = "_static/img/favicon.ico"
+html_css_files = [
+    "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.1.1/css/all.min.css"
+]
+
+# other options
+html_show_sourcelink = False
+
+def setup(app):
+   app.add_css_file('css/custom.css')

docs/index.rst

@@ -0,0 +1,32 @@
+PyTessel: isosurface generation tool
+====================================
+
+.. image:: https://img.shields.io/github/v/tag/ifilot/pytessel?label=version
+   :alt: GitHub tag (latest SemVer)
+.. image:: https://github.com/ifilot/pytessel/actions/workflows/build.yml/badge.svg
+   :target: https://github.com/ifilot/pytessel/actions/workflows/build.yml
+.. image:: https://img.shields.io/badge/License-GPLv3-blue.svg
+   :target: https://www.gnu.org/licenses/gpl-3.0
+
+:program:`PyTessel` is a Python package for building isosurfaces from 3D scalar
+ fields.
+
+:program:`PyTessel` has been developed at the Eindhoven University of Technology,
+Netherlands. :program:`PyTessel` and its development are hosted on `github
+<https://github.com/ifilot/pytessel>`_.  Bugs and feature
+requests are ideally submitted via the `github issue tracker
+<https://github.com/ifilot/pytessel/issues>`_.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   installation
+   user_interface
+   community_guidelines
+
+Indices and tables
+------------------
+
+* :ref:`genindex`
+* :ref:`search`

docs/installation.rst

@@ -0,0 +1,65 @@
+.. _installation:
+.. index:: Installation
+
+Installation
+============
+
+.. tip::
+    For Windows users with relatively little experience with Python, we warmly
+    recommend to use the `Anaconda distribution <https://www.anaconda.com/products/distribution>`_.
+    Anaconda is an all-in-one package containing the Python compiler,
+    an integrated desktop environment (Spyder) and plenty of useful Python
+    packages such as numpy and matplotlib.
+
+:program:`PyTessel` is distributed via both Anaconda package as well as PyPI. For
+Windows, it is recommended to install :program:`PyTessel` via Anaconda, while
+for Linux, we recommend to use PyPI.
+
+Windows / Anaconda
+------------------
+
+To install :program:`PyTessel` under Windows, open an Anaconda Prompt window
+and run::
+
+    conda install -c ifilot pytessel
+
+.. note::
+    Sometimes Anaconda is unable to resolve the package dependencies. This can
+    be caused by a broken environment. An easy solution is to create a new
+    environment. See the "Troubleshooting" section at the end of this page
+    for more information.
+
+Linux / PyPI
+------------
+
+To install :program:`PyTessel` systemwide, run::
+
+    sudo pip install pytessel
+
+or to install :program:`PyTessel` only for the current user, run::
+
+    pip install pytessel
+
+Troubleshooting
+---------------
+
+The Anaconda packaging system can sometimes be quite finicky and sometimes
+packages conflict with each other. A way to work around this issue is to create
+a separate environment and only use that environment for the electronic
+resources associated with this project.
+
+To create the new environment (called eoesc-env), run::
+
+    conda create -n eoesc-env python=3.9
+
+Next, open the environment with::
+
+    conda activate eoesc-env
+
+and install the required packages::
+
+    conda install -c ifilot pyqint pytessel
+
+Finally, you can install the IDE Spyder using::
+
+    conda install spyder matplotlib scipy pandas openpyxl

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=.
+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.http://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/user_interface.rst

@@ -0,0 +1,5 @@
+.. _user-interface:
+.. index:: userinterface
+
+User Interface
+==============