In MolSim/Deps.toml at d1e9159377bd685cf0c0a79f75043b482703b126 · JuliaMolSim/MolSim · GitHub you claim that JuLIP is a dependency for the version ranges [0-0.4) and [0.5.5-1.0) for SHIPs.jl. Note that the version 0.4 is excluded.
However, in MolSim/Compat.toml at d1e9159377bd685cf0c0a79f75043b482703b126 · JuliaMolSim/MolSim · GitHub you have a compatibility bound on JuLIP for [0.4 - 1.0) (0.4 included). So for v0.4 of SHIPs.jl you claim compatibility with a packages that is not listed as a a dependency.