Metage2metabo

New features

* Provide a proxy to estimate functional redundancy in metabolite producibility by displaying, for each metabolite, all the metabolic networks that can produce it in the initial community. Outputs are a matrix in `indiv_scopes/rev_iscope.tsv` and in `indiv_scopes/rev_iscope.json`
* Provide a warning message + explanations in logs when one or several targets are also seeds.

Fix

* Enhance the readability of logs to clarify the producibility results of targets when a target file is given in inputs.
* Show all producible metabolites in `community_analysis/mincom.json` dict key "producible" so that when a target is also a seed, it appears under that key together with all other producible targets (a seed that is a target does not appear under the key `newly_producible`). Associated to updates in MiSCoTo (v2.1.2: this version is now a requirement).
* Fix the logs for the use case above
* Singularity image in Singularity Hub for `m2m` commands that do not require Pathway Tools
* Remove host keys in `community_analysis/comm_scopes.json` if no host is provided.

Doc

* New outputs in `indiv_scopes` to estimate functional redundancy
* Explanations about the new singularity image in Singularity Hub

CI

* Test for metabolite producers (reverse iscopes)
* Tests to account for the presence of targets that are also seeds

Add

* Targets option (`-t`) for cscope.
* New output file called `producibility_targets.json`, showing the producibility of each targets and by which organisms.
* Final producers for the target using miscoto 2.1.1. The final producers are the organisms able to produce the target in full community or in minimal communities.
* New page in the readthedocs with all the output of m2m.
* Seeds from the diabetes metagenomic analysis of the paper.

Modification

* Remove sbml conversion, as it seems that menetools and miscoto can handle SBML 3.

Fix

* Issue with m2m test and `-t` option.

Update

* Doc and README and fix numerous typos.

CI

* Test for cscope, the new output file and final producers given by miscoto.

Add

* Targets option (`-t`) for metacom and workflow. By using this option, m2m will replace the added-value targets by the user targets.
* Use Miscoto function to_json to create mincom json, this fix issue with the formatting of the json. M2M now requires Miscoto >= 2.1.0.

Fix

* Oog.jar is now also check in `__main_analysis__` to show if there is an error with the Oog.jar file earlier.
* Issue with logs especially mpwt logs not showing off.

Update

* Doc and README and fix numerous typos.

CI
* Do not launch the CI if the commit modify only the readme or the docs.

Add

* Error messages during compounds sbml creation.

Fix

* Issue with mpwt results check.

New features

* `m2m metacom` to run the whole workflow *except* metabolic network reconstruction
* Add a log file by default in the results directory
* Add a quiet option `- q` that write in the log file and streams to stdout logs from warning level
* Create a json output file when calling `m2m addedvalue`
* Add a new option `-p` in recon to create padmet files.
* Create a `targets.sbml` file when running `addedvalue` in `output folder/community_analysis`

Fix

* Typos in doc, README
* Logger issues
* Build of the package in ReadTheDoc
* Behaviour of the programme when using empty metabolic networks
* Retrieve the caught exceptions from the dependencies to give more information for troubleshooting (especially useful for mpwt and Pathway Tools)

Update

* Doc and README with
* more details on the modelling of producibility
* documentation of new functionalities (`metacom`, quiet option...)
* Compatibility with mpwt 0.5.4


CI

* Use of Github Actions instead of Travis
* Test for `m2m metacom`
* Fix and customise existing tests

Fix

* compatibility with mpwt 0.5.3.
* typos.