Add documentation

doc/Makefile

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+# 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      = output
+
+# 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)

doc/_static/custom.css

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+/* override table width restrictions as found on https://github.com/getpelican/pelican/issues/1311 */
+.wy-table-responsive table td, .wy-table-responsive table th {
+    /* !important prevents the common CSS stylesheets from
+       overriding this as on RTD they are loaded after this stylesheet */
+    white-space: normal !important;
+}
+
+.wy-table-responsive {
+    overflow: visible !important;
+}

doc/conf.py

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+# 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('.'))
+
+# Django autodoc
+sys.path.insert(0, os.path.abspath('../polyclinic_scheduling'))
+os.environ['DJANGO_SETTINGS_MODULE'] = 'polyclinic_scheduling.settings'
+import django
+django.setup()
+
+# -- Project information -----------------------------------------------------
+
+project = 'Poliklinieken Planning Tool'
+copyright = '2020, Joshua Rubingh'
+author = 'Joshua Rubingh'
+
+# The full version, including alpha/beta/rc tags
+release = '1.0'
+
+# The master toctree document.
+master_doc = 'index'
+
+# -- 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.napoleon',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.coverage',
+    'sphinx_markdown_builder',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = 'en'
+
+# 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','build/*']
+
+# -- 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 = 'alabaster'
+
+# 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']
+
+html_theme_options = {
+    'logo': 'RUG_Logo.jpg',
+    'logo_name' : True
+}
+
+# -- Options for LaTeX output ---------------------------------------------
+# Install Ubuntu/Debian package(s): texlive-latex-recommended, texlive-fonts-recommended, texlive-latex-extra, netpbm
+latex_engine = 'pdflatex'
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    'papersize': 'a4paper',
+    'releasename':" ",
+    # Sonny, Lenny, Glenn, Conny, Rejne, Bjarne and Bjornstrup
+    # 'fncychap': '\\usepackage[Lenny]{fncychap}',
+    'fncychap': '\\usepackage{fncychap}',
+    'fontpkg': '\\usepackage{amsmath,amsfonts,amssymb,amsthm}',
+
+    'figure_align':'htbp',
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    'preamble': r'''
+        %%%%%%%%%%%%%%%%%%%% Meher %%%%%%%%%%%%%%%%%%
+        %%%add number to subsubsection 2=subsection, 3=subsubsection
+        %%% below subsubsection is not good idea.
+        \setcounter{secnumdepth}{3}
+        %
+        %%%% Table of content upto 2=subsection, 3=subsubsection
+        \setcounter{tocdepth}{1}
+
+        \usepackage{amsmath,amsfonts,amssymb,amsthm}
+        \usepackage{graphicx}
+
+        %%% reduce spaces for Table of contents, figures and tables
+        %%% it is used "\addtocontents{toc}{\vskip -1.2cm}" etc. in the document
+        \usepackage[notlot,nottoc,notlof]{}
+
+        \usepackage{color}
+        \usepackage{transparent}
+        \usepackage{eso-pic}
+        \usepackage{lipsum}
+
+        \usepackage{footnotebackref} %%link at the footnote to go to the place of footnote in the text
+
+        %% spacing between line
+        \usepackage{setspace}
+        %%%%\onehalfspacing
+        %%%%\doublespacing
+        \singlespacing
+
+
+        %%%%%%%%%%% datetime
+        \usepackage{datetime}
+
+        \newdateformat{MonthYearFormat}{%
+            \monthname[\THEMONTH], \THEYEAR}
+
+
+        %% RO, LE will not work for 'oneside' layout.
+        %% Change oneside to twoside in document class
+        \usepackage{fancyhdr}
+        \pagestyle{fancy}
+        \fancyhf{}
+
+        %%% Alternating Header for oneside
+        \fancyhead[L]{\ifthenelse{\isodd{\value{page}}}{ \small \nouppercase{\leftmark} }{}}
+        \fancyhead[R]{\ifthenelse{\isodd{\value{page}}}{}{ \small \nouppercase{\rightmark} }}
+
+        %%% Alternating Header for two side
+        %\fancyhead[RO]{\small \nouppercase{\rightmark}}
+        %\fancyhead[LE]{\small \nouppercase{\leftmark}}
+
+        %% for oneside: change footer at right side. If you want to use Left and right then use same as header defined above.
+        %% \fancyfoot[R]{\ifthenelse{\isodd{\value{page}}}{{\tiny Meher Krishna Patel} }{\href{http://pythondsp.readthedocs.io/en/latest/pythondsp/toc.html}{\tiny PythonDSP}}}
+
+        %%% Alternating Footer for two side
+        %% %\fancyfoot[RO, RE]{\scriptsize Meher Krishna Patel (mekrip@gmail.com)}
+
+        %%% page number
+        \fancyfoot[CO, CE]{\thepage}
+
+        \renewcommand{\headrulewidth}{0.5pt}
+        \renewcommand{\footrulewidth}{0.5pt}
+
+        \RequirePackage{tocbibind} %%% comment this to remove page number for following
+        \addto\captionsenglish{\renewcommand{\contentsname}{Table of contents}}
+        %% \addto\captionsenglish{\renewcommand{\listfigurename}{List of figures}}
+        %% \addto\captionsenglish{\renewcommand{\listtablename}{List of tables}}
+        %% % \addto\captionsenglish{\renewcommand{\chaptername}{Chapter}}
+
+
+        %%reduce spacing for itemize
+        \usepackage{enumitem}
+        \setlist{nosep}
+
+        %%%%%%%%%%% Quote Styles at the top of chapter
+        %% \usepackage{epigraph}
+        %% \setlength{\epigraphwidth}{0.8\columnwidth}
+        %% \newcommand{\chapterquote}[2]{\epigraphhead[60]{\epigraph{\textit{#1}}{\textbf {\textit{--#2}}}}}
+        %%%%%%%%%%% Quote for all places except Chapter
+        %% \newcommand{\sectionquote}[2]{{\quote{\textit{``#1''}}{\textbf {\textit{--#2}}}}}
+    ''',
+
+
+    'maketitle': r'''
+        \pagenumbering{Roman} %%% to avoid page 1 conflict with actual page 1
+
+        \begin{titlepage}
+
+            \begingroup % for PDF information dictionary
+                \def\endgraf{ }\def\and{\& }%
+                \pdfstringdefDisableCommands{\def\\{, }}% overwrite hyperref setup
+                \hypersetup{pdfauthor={\@author}, pdftitle={\@title}}%
+            \endgroup
+
+            \centering
+
+            \vspace*{40mm} %%% * is used to give space from top
+            \textbf{\Huge {RUG Poliklinieken Planning Tool} }
+
+            \vspace{0mm}
+            \begin{figure}[!h]
+                \centering
+                \includegraphics[scale=0.4]{RUG_Logo.jpg}
+            \end{figure}
+
+            \vspace{100mm}
+            \Large \textbf{{Joshua Rubingh}}
+
+
+            \small Created on : May, 2020
+
+            \vspace*{0mm}
+            \small  Last updated : \MonthYearFormat\today
+
+
+            %% \vfill adds at the bottom
+            \vfill
+            %% \small \textit{More documents are freely available at }{\href{http://pythondsp.readthedocs.io/en/latest/pythondsp/toc.html}{PythonDSP}}
+        \end{titlepage}
+
+        \clearpage
+        \pagenumbering{roman}
+        \tableofcontents
+        \listoffigures
+        \listoftables
+        \clearpage
+        \pagenumbering{arabic}
+        ''',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+    'sphinxsetup': \
+        'hmargin={0.7in,0.7in}, vmargin={1in,1in}, \
+        verbatimwithframe=true, \
+        TitleColor={rgb}{0,0,0}, \
+        HeaderFamily=\\rmfamily\\bfseries, \
+        InnerLinkColor={rgb}{0,0,1}, \
+        OuterLinkColor={rgb}{0,0,1}',
+
+        'tableofcontents':' ',
+}
+
+latex_logo = '_static/RUG_Logo.jpg'
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'documentation.tex', project,
+     author, 'report')
+]

doc/index.rst

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+.. Poliklinieken Planning documentation master file, created by
+   sphinx-quickstart on Mon May 18 13:21:06 2020.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+=====================================================
+Welcome to Poliklinieken Planning Tool documentation!
+=====================================================
+
+Here you can read more information about the Poliklinieken Planning Tool.
+
+.. toctree::
+   :caption: Table of Contents
+   :maxdepth: 2
+
+   install
+   models
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

doc/install.rst

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+============
+Installation
+============
+
+In order to install this Polyclinic Schedule Tool, we use the following packages / software.
+
+* NGINX
+* MySQL
+* Django
+
+First we need to checkout the code.
+
+.. code-block:: bash
+
+    git clone https://git.web.rug.nl/P300021/poli_planning.git /opt/poli_planning
+
+-----
+NGINX
+-----
+Install NGINX. For Ubuntu this would be
+
+.. code-block:: console
+
+    sudo apt install nginx
+
+Also configure SSL (https://letsencrypt.org/) to make the connections secure. This is outside this installation scope.
+
+Setup
+-----
+After installation of the packages, create a symbolic link in the `/etc/nginx/sites-enabled` so that a new VHost is created.
+
+.. code-block:: console
+
+    ln -s /opt/poli_planning/nginx/vhost.conf /etc/nginx/sites-enabled/poli_planning
+
+Important parts of the VHost configuration:
+
+.. literalinclude:: ../nginx/vhost.conf
+    :language: bash
+
+In order to test if NGINX is configured correctly run `nginx -t` and it should give an OK message:
+
+.. code-block:: bash
+
+    nginx: the configuration file /etc/nginx/nginx.conf syntax is ok
+    nginx: configuration file /etc/nginx/nginx.conf test is successful
+
+------
+Django
+------
+We install Django with standard settings. We could run it in Aync way, but then you need some more steps: https://docs.djangoproject.com/en/3.0/howto/deployment/asgi/ So for now, we keep it simple.
+
+Install
+=======
+Create a python virtual environment
+
+.. code-block:: bash
+
+    cd /opt/poli_planning
+    python3 -m venv python3_env
+    source python3_env/bin/activate
+
+Finally we install the required Python modules
+
+.. code-block:: python
+
+    pip install -r requirements
+
+This will install all the needed Python modules we need to run this Django project.
+
+Settings
+--------
+The settings for Django are set in an `.env` file so that you can easily change the environment from production to testing. There is an `.env.example` file that could be used as a template.
+
+.. literalinclude:: ../polyclinic_scheduling/polyclinic_scheduling/.env.example
+    :language: jproperties
+
+Next we have to make the database structure. If you are using SQLite3 as a backend, make sure the database file **DOES** exist on disk.
+
+.. code-block:: console
+
+    touch /opt/poli_planning/polyclinic_scheduling/db.sqlite3
+
+Then in the Python virtual environment we run the following commands:
+
+.. code-block:: console
+
+    ./manage.py migrate
+    ./manage.py compilemessages
+    ./manage.py collectstatic
+
+And finally you should be able to start the Django application
+
+.. code-block:: console
+
+    ./manage.py runserver

doc/make.bat

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+@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.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

doc/models.rst

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+======
+Models
+======
+
+.. automodule:: lib.models.base
+   :members:
+
+.. automodule:: apps.employee.models
+   :members:
+
+.. automodule:: apps.hospital.models
+   :members:
+
+.. automodule:: apps.polyclinic.models
+   :members:
+
+.. automodule:: apps.schedule.models
+   :members:

doc/requirements.txt

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+Sphinx==3.0.0
+sphinx-markdown-builder==0.5.4