Merge pull request #18 from matthiaskoenig/develop

changes for v0.3.2

.gitignore

@@ -4,4 +4,5 @@
 pyexsimo.egg-info/
 *.xlsx#
 .ipynb_checkpoints/
-__pycache__
+__pycache__
+*.h5

.travis.yml

@@ -1,6 +1,6 @@
 sudo: required
 language: python
-# cache: pip
+cache: pip
 python:
   - "3.6"
 

README.md

@@ -1,11 +1,11 @@
-<h1><img alt="EXSIMO logo" src="./docs/images/exsimo_logo_200.png" height="100" /> EXSIMO: EXecutable SImulation MOdel</h1>
+<h1><img src="./docs/images/exsimo_logo_200.png" height="100" /> EXSIMO: EXecutable SImulation MOdel</h1>
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3596068.svg)](https://doi.org/10.5281/zenodo.3596068)
 [![Build Status](https://travis-ci.org/matthiaskoenig/exsimo.svg?branch=develop)](https://travis-ci.org/matthiaskoenig/exsimo)
 [![GitHub version](https://badge.fury.io/gh/matthiaskoenig%2Fexsimo.svg)](https://badge.fury.io/gh/matthiaskoenig%2Fexsimo)
 [![codecov](https://codecov.io/gh/matthiaskoenig/exsimo/branch/develop/graph/badge.svg)](https://codecov.io/gh/matthiaskoenig/exsimo)
-![Docker Cloud Build Status](https://img.shields.io/docker/cloud/build/matthiaskoenig/exsimo)
-![Docker Pulls](https://img.shields.io/docker/pulls/matthiaskoenig/exsimo)
+[![Docker Cloud Build Status](https://img.shields.io/docker/cloud/build/matthiaskoenig/exsimo)](https://hub.docker.com/repository/docker/matthiaskoenig/exsimo)
+[![Docker Pulls](https://img.shields.io/docker/pulls/matthiaskoenig/exsimo)](https://hub.docker.com/repository/docker/matthiaskoenig/exsimo)
 
 <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>
 
@@ -16,9 +16,12 @@ Data, model and code for executable simulation model of hepatic glucose metaboli
 * `docs/models` - SBML model and model report
 * `pyexsimo` - python package (model generation, simulation experiments, tests, ...)
 
-Results of the executed model are available from https://matthiaskoenig.github.io/exsimo/ 
-
-Docker images available from https://hub.docker.com/repository/docker/matthiaskoenig/exsimo
+**Reports**: https://matthiaskoenig.github.io/exsimo/  
+**Docker images**: https://hub.docker.com/repository/docker/matthiaskoenig/exsimo  
+**Zenodo snapshots**: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3596068.svg)](https://doi.org/10.5281/zenodo.3596068)  
+**Github releases**: https://github.com/matthiaskoenig/exsimo/releases  
+
+<img src="./docs/images/exsimo_overview.png" width="600" />
 
 ## Setup local environment
 To run the analysis locally create a python virtual environment and install `pyexsimo`. 
@@ -44,7 +47,7 @@ docker run -it matthiaskoenig/exsimo:latest
 ```
 To run a specific model version use the respective tag
 ```bash
-docker run -it matthiaskoenig/exsimo:0.3.0
+docker run -it matthiaskoenig/exsimo:0.3.1
 ```
 To run the tests use `pytest`, to execute the analysis use `execute`.
 
@@ -57,7 +60,7 @@ pytest
 ## Run analysis
 The complete analysis can be run via
 ```
-(exsimo) execute
+execute
 ```
 which updates the results in the `./docs/` folder.
 

RELEASE.md

@@ -5,8 +5,10 @@ This document describes steps for releasing a new version
 ```
 git checkout develop
 ```
-## bump version
-Update version info in `_version.py`
+## bump version & requirements
+- update version info in `pyexsimo/_version.py`
+- check `sbmlsim` and `sbmlutils` hashes in `requirements.txt`
+
 ## run tests 
 ```
 (exsimo) pytest
@@ -30,6 +32,11 @@ Merge pull request in master. This triggers a zenodo update and the build of a n
 ## check online report
 [https://matthiaskoenig.github.io/exsimo/](https://matthiaskoenig.github.io/exsimo/)
 
+## upload tagged docker-container
+docker build -t matthiaskoenig/exsimo:${EXSIMO_VERSION} .
+docker login
+docker push matthiaskoenig/exsimo:${EXSIMO_VERSION}
+
 ## update develop branch
 ```
 git checkout master

docs/DoseResponseExperiment.md

@@ -12,10 +12,10 @@
 * [insulin.tsv](./sbmlsim/DoseResponseExperiment_data_insulin.tsv)
 
 ## Figures
-* [DoseResponseExperiment_fig1.png](DoseResponseExperiment_fig1.png)
+* [DoseResponseExperiment_fig1.svg](DoseResponseExperiment_fig1.svg)
 
 ### fig1
-![DoseResponseExperiment_fig1.png](DoseResponseExperiment_fig1.png)
+![DoseResponseExperiment_fig1.svg](DoseResponseExperiment_fig1.svg)
 
 
 ## Code