Miscoto

New

- `CHANGLEOG.md` showing the different versions and the associated changes.

Modify

- Miscoto focus can be run from a LP instance (issue 17).
- Copy but do not modify given instance in miscoto scopes and mincom (issue 8).
- Replace use of pkg_resources that will become deprecated.
- Update license year.
- Modify if statement that will be deprecated in the future.
- Move from `setup.py`/`setup.cfg` to `pyproject.toml`.

New

- `miscoto focus` can now be run systematically for all species with the `--all` option

Fix

- Latest clyngor versions led to errors that can be preventing by not using the clingo module when calling solver 14

Test

- Tests are no longer done for Python 3.6 but for versions 3.7, 3.8, 3.9

Doc

- Update `miscoto focus` section

CI

- Mirror to Inria Gitlab

New

`miscoto focus` calculates the producible metabolites for one metabolic network of interest in two conditions. First when considered alone in the given nutritional conditions. Secondly, among its community, in the same nutritional conditions but those are necesarily altered by what other species are likely to produce.

Doc

* usage of `miscoto focus`
* fix docstringd

Tests

* test `miscoto focus`

Licence

MiSCoTo is now under the LGPL licence

Fix

* consider reversible reactions to characterise target_producer_coop_initcom
* remove adding a host fact in `miscoto instance`when no host argument was provided

Test

* test the second fix

Add

* test for key species in mincom.

Replace

* "keystone species" by "key species".

Add

* Windows and MacOS tests in GitHub Actions.
* Windows compatibility.