Metage2metabo

Fix

* Fix an issue with host keys ("host_prodtargets", "host_scope", "comhost_scope" and "host_unprodtargets") not appearing in `comm_scopes.json` file. But these keys used the old behavior of Metage2Metabo (possible unproducible seeds are contained in them). Host handling by Metage2Metabo will be modified in a future release.

WARNING: change for individual and community scopes:
* for individual scope: only seeds that are producible, ie associated with activated reactions are now shown in the results. Additional information on producible, non-producible and absent seeds are available in the json output. This requires MeneTools version >= `3.4.0`.
* for community scope: use of `miscoto focus` for computation in order to retrieve the metabolite producers in community. This requires MiSCoTo version >= `3.2.0`.

Add

* Test in m2m_analysis to check if combination of powergraph predicted by bubbletools is the same as the ones found in minimal communities.
* Creation of boolean equation summarizing the powergraph if it is simple enough.
* New option `--target-com-scope` to use all the community scope as targets for minimal community prediction (issue 21).
* Add a function to modify xml created by Pathway Tools (issue 60).
* Troubleshooting page in readthedocs (issue 24 and 25).
* Metadata json file created when using command line (both for `m2m` and `m2m_analysis`).
* Essential and alternative symbiont in `producibility_targets.json` (issue 19).
* Test for host for m2m metacom.

Fix

* Fix potential error when reading taxon_id file (issue 22).
* Fix issue with etree in reconstruction.
* Issues with readthedocs.
* GitHub Actions not working.

Modify

* Better deal with seeds that are absent from networks or not produced in iscope and also the seeds that are produced through interactions in cscope (issue 53).
* Exit m2m_analysis when there are unproducible targets (issue 23).
* Check forbidden characters during targets file creation.
* Do not allow abbreviation in command arguments by argparse (issue 54).
* Sanitize use of tarfile extractall (issue 55).
* Remove unused dependency.
* First step in replacing `pkg_resources` (which will become deprecated in the future) with `importlib.metadata` or import of \_\_version\_\_.
* Move from `setup.py`/`setup.cfg` to `pyproject.toml`.
* Update tutorial.
* Update docs and readme.
* Update license year and affiliation.
* Move support for CI to Python 3.8 and 3.9.
* Remove import in `__init__.py` to avoid loading m2m_analysis dependencies when using only m2m.
* Avoid using os.unlink() function on Windows as it can lead to Permission Error.

Fix

* Issues in html powergraph creation:
* some nodes are not indicated as alternative symbionts.
* colors are not applied to some nodes.
* the names of the nodes contain unicode ints.

Modify

* Update license year.

Fix

* Correctly fix the issue with the colors used for the powergraph.

Modify

* Change the shapes of the nodes in the html output of `m2m_analysis`: circle for essential symbionts and square for alternative symbionts.

Fix

* Issue with the number of colors used to color the taxon in the powergraph.

Fix

* issue in m2m_analysis where clyngor module uses the clingo module producing [ValueError](https://github.com/Aluriak/PowerGrASP/issues/1).
* issue in m2m_analysis when incorrect paths for seed and/or target files were given as input.