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Add non-forcefield-specific citations to the root of the data directory #655

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merged 10 commits into from
Feb 7, 2025

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@pckroon pckroon commented Jan 31, 2025

This is particularly useful for code that needs citing, such as MDTraj, and vermouth.

The vermouth citation gets formatted as

    INFO - general - Please cite: Kroon, P C; Grunewald, F; Barnoud, J; van Tilburg, M; Souza, P C; Wassenaar, T A; Marrink, S J;  elife 2024; 10.7554/elife.90627.2

Things got a bit more messy because of Molecules and Systems without forcefield (or, force_field=None), so I also did something sane with the defaults there.

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pckroon commented Feb 4, 2025

I'm not going to meet the patch test coverage; it's mostly because there's no tests for the Quote processor (and I don't care about that), and there's no tests for write_gmx_topology (and I don't have time to make those)

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lgtm, just one query about how mdtraj citations are now treated, because I think this now has the citation written regardless of whether it was used?

vermouth/gmx/topology.py Show resolved Hide resolved
@pckroon pckroon merged commit df2a554 into master Feb 7, 2025
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@pckroon pckroon deleted the common_citations branch February 7, 2025 10:45
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2 participants