Species rename

[shyuep]

Summary

Include a summary of major changes in bullet points:

• Rename Specie and DummySpecie to Species and DummySpecies
• Specie and DummySpecie is allowed as a mapping for backwards compatibility.
• Corresponding changes to doc where possible.
• Pylint does not pass because of refactoring in chemenv and defects and abinit packages. These are unrelated to the changes made.

Additional dependencies introduced (if any)

TODO (if any)

Checklist

Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request title.

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• [X ] Code is in the standard Python style.
  Run pycodestyle and flake8
  on your local machine.
• [ X] Docstrings have been added in the Google docstring format.
  Run pydocstyle on your code.
• Type annotations are highly encouraged. Run mypy
  to type check your code.
• Tests have been added for any new functionality or bug fixes.
• All existing tests pass.

[shyuep]

@mkhorton Pls review.

[mkhorton]

I'm fine merging this since the original Specie and DummySpecie are not deprecated but will remain as simple subclasses, so net disruption to the end user should be minimal.

However, I'm mixed overall since it seems like the change doesn't produce net benefit, but will result in e.g. schemas becoming more complicated, teaching materials becoming out of date. I'm more of a lingustic descriptivist than a prescriptivist, so although I concede the original usage has always been technically incorrect, that doesn't necessarily mean it's wrong.