Merge pull request #5 from matthiaskoenig/develop

Changes for 0.1.0a1

Author: matthiaskoenig

.travis.yml

@@ -0,0 +1,23 @@
+language: python
+matrix:
+  include:
+    - os: linux
+      sudo: required
+      python: 3.6
+
+
+before_install:
+   sudo apt-get install -y libhdf5-serial-dev
+
+install:
+  pip install -r requirements.txt
+
+script:
+  pytest --cov=sbmlsim
+
+after_success:
+   pip install codecov; codecov
+
+cache:
+  directories:
+    - $HOME/.cache/pip

README.md

@@ -1,15 +1,53 @@
 
+[![Build Status](https://travis-ci.org/matthiaskoenig/sbmlsim.svg?branch=develop)](https://travis-ci.org/matthiaskoenig/sbmlsim)
+[![Documentation Status](https://readthedocs.org/projects/sbmlsim/badge/?version=latest)](https://sbmlsim.readthedocs.io/en/latest/)
+[![License (LGPL version 3)](https://img.shields.io/badge/license-LGPLv3.0-blue.svg?style=flat-square)](http://opensource.org/licenses/LGPL-3.0)
+
 <h1>sbmlsim: SBML simulation made easy</h1>
-<b><a href="https://orcid.org/0000-0003-1725-179X" title="https://orcid.org/0000-0003-1725-179X"><img src="./docs/images/orcid.png" height="15"/></a> Matthias König</b>
+<b><a href="https://orcid.org/0000-0003-1725-179X" title="https://orcid.org/0000-0003-1725-179X"><img src="./docs/static/images/orcid.png" height="15"/></a> Matthias König</b>
 
 `sbmlsim`: SBML simulation made easy
 
+For documentation and examples see https://sbmlsim.readthedocs.io
+
 ### License
 * Source Code: [LGPLv3](http://opensource.org/licenses/LGPL-3.0)
 * Documentation: [CC BY-SA 4.0](http://creativecommons.org/licenses/by-sa/4.0/)
 
-## Funding
+### Funding
 Matthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany)
 within the research network Systems Medicine of the Liver (**LiSyM**, grant number 031L0054).
 
+## Installation
+`sbmlsim` currently works only python3.6.
+
+HDF5 support is required which can be installed via
+```
+sudo apt-get install -y libhdf5-serial-dev
+```
+
+Best install `sbmlsim` in a virtual environment via pip
+```bash
+# checkout code
+git clone https://github.com/matthiaskoenig/sbmlsim.git
+
+# virtualenv
+cd sbmlsim
+mkvirtualenv sbmlsim --python=python3.6
+(sbmlsim) pip install -e .
+```
+The notebook support can be installed via
+```bash
+(sbmlsim) pip install jupyter jupyterlab
+(sbmlsim) python -m ipykernel install --user --name sbmlsim
+```
+Notebooks are available in
+- `docs/notebooks` (notebooks used in documentation on https://sbmlsim.readthedocs.io/en/latest/)
+- `notebooks`
+
+and can be started from within `jupyterlab`
+```
+(sbmlsim) jupyter lab
+```
+
 &copy; 2019 Matthias König

codecov.yml

@@ -0,0 +1,2 @@
+codecov:
+  branch: develop

docs/conf.py

@@ -14,6 +14,8 @@
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
 
+import os
+on_rtd = os.environ.get('READTHEDOCS') == 'True'
 
 # -- Project information -----------------------------------------------------
 
@@ -30,15 +32,25 @@
 extensions = [
     'recommonmark',
     'sphinx_rtd_theme',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.autosectionlabel',
+    'IPython.sphinxext.ipython_console_highlighting',  # https://github.com/jupyter/nbconvert/issues/528
 ]
 
+master_doc = 'index'
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
 # 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']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'README.md']
 
 
 # -- Options for HTML output -------------------------------------------------
@@ -51,4 +63,4 @@
 # 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_static_path = ['static']

docs/index.rst

@@ -1,16 +1,15 @@
-.. 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!
 ===================================
 
+``sbmlsim``: Python utilities for simulating `SBML <http://www.sbml.org>`_ models available at
+`https://github.com/matthiaskoenig/sbmlsim <https://github.com/matthiaskoenig/sbmlsim>`_.
+
+Contents:
+
 .. toctree::
    :maxdepth: 2
-   :caption: Contents:
 
-   overview
+   introduction
    notebooks/simjson.rst
 
 

docs/overview.md docs/introduction.mddocs/overview.md renamed to docs/introduction.md

@@ -1,4 +1,4 @@
-# Overview
+# Introduction
 
 **Mission**: make SBML simulations great again
 
@@ -15,6 +15,9 @@ simulations with SBML models in python.
 - parameter scans
 - parameter sensitivity analysis
 
+A simplified exchange language based on JSON is part of `sbmlsim` 
+
+
 **Visualization**
 - interactive plots (altair)
 

docs/make_docs.sh

@@ -18,7 +18,6 @@ echo "--------------------------------------"
 echo "remove old documentation"
 echo "--------------------------------------"
 rm -rf _built
-rm -rf _static
 rm -rf _templates
 rm -rf _notebooks
 
@@ -35,7 +34,8 @@ echo "--------------------------------------"
 echo "postprocessing notebooks rst"
 echo "--------------------------------------"
 # remove the following lines from the documentation
-# sed -i '/%matplotlib inline/d' ./*.rst
+sed -i '/%load_ext autoreload/d' $NBDIR/*.rst
+sed -i '/%autoreload 2/d' $NBDIR/*.rst
 
 # change the image locations (FIXME)
 sed -i -- 's/.. image:: /.. image:: notebooks\/docs\//g' ./*.rst

docs/notebooks/json_examples/example_1.json

@@ -0,0 +1,13 @@
+{
+  "timecourses": [
+    {
+      "start": 0,
+      "end": 60,
+      "steps": 60,
+      "changes": {},
+      "model_changes": {}
+    }
+  ],
+  "selections": null,
+  "reset": true
+}