Merge pull request #1006 from OpenFreeEnergy/release_prep_v1.2.0

Updated CHANGELOG for 1.2.0

Merge pull request #940 from OpenFreeEnergy/update-zenodo

Update CITATION.cff

Force the old LomapAtomMapper kwarg defaults on extra test (#862)

* Force the old LomapAtomMapper kwarg defaults on extra test

* Update environment a bit

Merge pull request #830 from OpenFreeEnergy/issue_803_userguide_resul…

…t_networks

docs: first pass at working with networks page

update LomapAtomMapper default settings to established best practices (…

…#730)

* update LomapAtomMapper default settings to established best practices

* fixup tests for relative_alchemical_network_planner following lomap default change

make these tests use the legacy default settings for Lomap, they're just smoke testing and the actual mappings don't matter

* fixup regression tests for command line plan-rbfe

these are different now that the lomap defaults have been changed for 1.0

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Co-authored-by: Mike Henry <[email protected]>

add missing path for result jsons for testing

Issue 335 float quantity in settings (#657)

* use FloatQuantity type annotation in Settings

this is different to `unit.Quantity` as it then allows the coercion of strings to correct values through a pydantic validator

will eventually aid in ingesting CLI inputs to Settings as strings can be passed directly onto Settings

* tests for setting fields in Settings via strings

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Co-authored-by: Mike Henry <[email protected]>

Add `gather --allow-partial`, improve related error message (#588)

* improve error message

* Add --allow-partial to gather

* use it for the other call as well

* ignore coverage on line that should never happen

* Make it possible to do both RHFE and RBFE

docs: fixup typo in tutorial links

add external edge files to MANIFEST