Metage2metabo

Add

* check for powergrasp and ete3 installations in m2m_analysis.

Fix

* compatibility with padmet 4.0.0.

Fix

* issues with malformatted SBML (issue 7).

Fix

* m2m tries to create a target sbml from an empty added value.

Add

* test for sbml conversion.
* tests for m2m_analysis.
* article seeds in article_data.

Fix

* issue with m2m recon and workflow when reconstructing a metabolic network from only one organism.

Update

* requirements.
* Singularity and Docker recipes.
* travis yml file with m2m_analysis dependencies.

Add

* log to m2m_analysis.
* keystone species to m2m log.

Fix

* m2m_analysis readthedocs.
* numerous issues with m2m_analysis.

Add

* **m2m_analysis**: optimal solutions enumeration, graph representation and compression into a powergraph.
* padmet creation after Pathway Tools reconstruction (wtih -p argument for m2m recon and workflow).
* statistics on genes/reactions/compounds in GSM after the reconstruction.

Fix

* miscoto and clyngor memory issue with solutions enumeration.

Update

* readthedocs by adding m2m_analysis.