Metage2metabo

This release focuses on `m2m_analysis` by adding new option, new output files,more documentation and refactoring some functions and output files.

There is also a complete refactoring on the structure of m2m repository: the two big scripts (`m2m_workflow.py` and `m2m_analysis.py`) are now split in multiple scripts in two folders ( `m2m` and `m2m_analysis`).

Add

* New option for `m2m_analysis`: `--level` to select the taxonomy level (phylum, class, order, family, genus or species) that will be used in the following steps of m2m_analysis, by default, it is phylum.
* HTML output for `m2m_analysis`. HTML visualization is interactive and nodes are coloured (by key species types or taxon).
* Error message with incorrect SBML file format.
* Log files for `m2m_analysis`.
* New tests for `m2m_analysis`.
* Documentation about `m2m_analysis` output files.
* Citation to eLife article.
* Tutorial with a jupyter notebook about `m2m metacom` methods.

Modify

* Add colours (by key species types or taxon) to `m2m_analysis` svg.
* Modify `m2m_analysis` output files.
* Replace GPL license by LGPL license.
* Complete refactoring of m2m repository structure: `m2m_workflow.py` and `m2m_analysis.py` have been split into multiple scripts contained inside `m2m` and `m2m_analysis` folders.

Remove

* Delete `m2m_analysis stats` because it is no more useful with the changes made to `m2m_analysis`.

Add

* Clarified logs when some target metabolites are also part of the seeds. Indications to which file one must refer in order to check the individual producibility of such seeds by organisms.

**Warning**: the version 1.4.0 of m2m needs updated version of its dependencies:
- menetools >= 3.1.0.
- miscoto >= 3.0.3.
- mpwt >= 0.6.0.

Add

* Multiprocessing for `m2m iscope` and `m2m metacom`, wich can be called using the options `-c`.
* New option `--pwt-xml` for `m2m recon` and `m2m workflow`: this option extracts the XML file created by MetaFlux (a module of Pathway Tools) so it can be used as input for m2m instead of extracting the `.dat` files and using padmet to create the SBML input (using mpwt 0.6.0).
* Scripts and data for diversity analysis in article data.
* New output file "indiv_produced_seeds.json" showing if seeds are producible by individual organisms (using menetools 3.1.0).

Fix

* Issue with seeds in individual_producers.
* SBML and padmet stats computation for `m2m recon` and `m2m workflow` so it can count correctly reactions, metabolites and genes in XML from MetaFlux.

Modify

* Update article data, scripts and jupyter notebook.
* Update readme and docs.
* Update requirements.txt and delete redundant files.
* Replace `keystone species` by `key species` (also modified in miscoto 3.0.3).

Add

* Windows and MacOS tests in GitHub Actions.
* Windows compatibility for `m2m metacom` using menetools 3.0.2 and miscoto 3.0.2.

Fix

* Issue with warning message (about compounds being both in seeds and targets) always showing.

Fix

* Seeds file validation broke for m2m options that did not require seeds (no "seeds" in args namespace", e.g `m2m recon`)

Add

* data and scripts associated to the manuscript in the Github repository