Update dependency gemmi to >=0.5.5, <=0.5.5

rs-station / reciprocalspaceship

Tools for exploring reciprocal space

https://rs-station.github.io/reciprocalspaceship/

MIT License

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Update dependency gemmi to >=0.5.5, <=0.5.5 #158

Closed renovate[bot] closed 2 years ago

renovate[bot] commented 2 years ago

This PR contains the following updates:

Package	Change	Age	Adoption	Passing	Confidence
gemmi	`>=0.4.2, <=0.5.4` -> `>=0.5.5, <=0.5.5`

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JBGreisman commented 2 years ago

Summary: this PR updates reciprocalspaceship to use gemmi v0.5.5, and sets this to the new minimal version requirement due to the following changes to gemmi namespace:

gemmi.GroupOps.is_centric() was changed to gemmi.GroupOps.is_centrosymmetric(). This gets called in the multiplicity calculation in rs.utils
gemmi.Op.negated() was removed, and we instead use gemmi.Op.combine() with the Friedel operation -x,-y,-z. As commented above, Op.negated() had also negated the real-space translation of the symmetry operations, which impacted how phase shifts were compared in one test

JBGreisman commented 2 years ago

the is_centric() method was renamed to is_centrosymmetric(). Before, only the GroupOps object had this method, but now it is in the namespace of both SpaceGroup and GroupOps objects. Here, I opted to call it directly from the SpaceGroup, but either way could have worked -- the change in method name is certainly required though.