first version of documentation

.gitignore

@@ -14,3 +14,6 @@ __pycache__
 .ipynb_checkpoints/
 .pytest_cache
 
+# documentation
+docs/_build/
+

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/README.md

@@ -0,0 +1,11 @@
+# Documentation
+
+To create the documentation use
+```
+(sbmlsim) pip install -r requirements-docs.txt
+(sbmlsim) cd docs
+(sbmlsim) ./make_docs.sh
+```
+
+The documentation is build using `sphinx` with the 
+[sphinx-rtd-theme](https://sphinx-rtd-theme.readthedocs.io/en/latest/configuring.html) 

docs/conf.py

@@ -0,0 +1,54 @@
+# 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 = 'sbmlsim'
+copyright = '2019, Matthias König'
+author = 'Matthias König'
+
+
+# -- 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 = [
+    'recommonmark',
+    '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".
+html_static_path = ['_static']

docs/index.rst

@@ -0,0 +1,23 @@
+.. sbmlsim documentation master file, created by
+   sphinx-quickstart on Tue Oct 22 08:52:36 2019.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to sbmlsim's documentation!
+===================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   overview
+   notebooks/simjson.rst
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

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/make_docs.sh

@@ -0,0 +1,53 @@
+#!/bin/bash
+###############################################################
+# Build script for tellurium documentation from rst files and 
+# python docstrings in the tellurium package
+#
+# execute this script in the docs folder i.e., after
+# 	cd tellurium/docs
+#
+# Usage: 
+#	./make_docs.sh 2>&1 | tee ./make_docs.log
+#
+# The documentation is written in docs/_build
+###############################################################
+DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+
+date
+echo "--------------------------------------"
+echo "remove old documentation"
+echo "--------------------------------------"
+rm -rf _built
+rm -rf _static
+rm -rf _templates
+rm -rf _notebooks
+
+echo "--------------------------------------"
+echo "convert notebooks to rst"
+echo "--------------------------------------"
+NBDIR=$DIR/notebooks
+
+# convert the notebooks to rst after running headlessly
+# if errors should abort, remove the --allow-errors option
+jupyter nbconvert --ExecutePreprocessor.timeout=600 --to=rst --allow-errors --execute $NBDIR/*.ipynb
+
+echo "--------------------------------------"
+echo "postprocessing notebooks rst"
+echo "--------------------------------------"
+# remove the following lines from the documentation
+# sed -i '/%matplotlib inline/d' ./*.rst
+
+# change the image locations (FIXME)
+sed -i -- 's/.. image:: /.. image:: notebooks\/docs\//g' ./*.rst
+
+
+echo "--------------------------------------"
+echo "create html docs"
+echo "--------------------------------------"
+cd $DIR
+# make html
+sphinx-build -b html . _build/html
+
+# open documentation
+firefox _build/html/index.html
+

docs/notebooks/simjson.ipynb

@@ -0,0 +1,69 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# JSON simulation language\n",
+    "For simple exchange of simulation descriptions a JSON format for the simulation was\n",
+    "developed."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "0.0.6\n"
+     ]
+    }
+   ],
+   "source": [
+    "import sbmlsim\n",
+    "print(sbmlsim.__version__)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "sbmlsim",
+   "language": "python",
+   "name": "sbmlsim"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.9"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

docs/notebooks/simjson.rst

@@ -0,0 +1,22 @@
+.. code:: ipython3
+
+    %load_ext autoreload
+    %autoreload 2
+
+JSON simulation language
+========================
+
+For simple exchange of simulation descriptions a JSON format for the
+simulation was developed.
+
+.. code:: ipython3
+
+    import sbmlsim
+    print(sbmlsim.__version__)
+
+
+.. parsed-literal::
+
+    0.0.6
+
+

docs/overview.md

@@ -0,0 +1,28 @@
+# Overview
+
+**Mission**: make SBML simulations great again
+
+The idea of sbmlsim is to provide a simple abstraction layer for running
+simulations with SBML models in python.
+
+**Simplicity**
+- make it easy to encode simple simulation experiments with a focus
+    on numerical ODE simulations 
+
+**Simulation**
+- timecourse simulations
+- combined simulation experiments (combination of changes)
+- parameter scans
+- parameter sensitivity analysis
+
+**Visualization**
+- interactive plots (altair)
+
+**Parallelization**
+-  simple parallelization of multiple simulation, collection of results
+
+**Parameter fitting**
+- helpers for using model + data to run simulations on a cluster
+
+**Unit support**
+

requirements-docs.txt

@@ -0,0 +1,3 @@
+sphinx
+recommonmark
+sphinx-rtd-theme