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This is probably a bit speculative at this point, but it would be fairly simply to look at a Project.toml/Manifest.toml if one is specified via the --project command line arguments and see whether these specify a specific Julia version. If they do, run things in that specific version.
Of course, right now there is no official way to specify a Julia version in a Manifest.toml. For Project.toml, the situation is a bit different: at least for packages one can specify a version in the compat section. The mybinder integration for example looks for a julia entry in the compat section to decide what Julia version to use. We could do something similar, for example if there was an entry julia = "=1.3.1" in the Project.toml, we could start Julia 1.3.1.
But maybe this should also just wait until there is an official way to record Julia versions in Manifest.toml files.
NHDaly, StefanKarpinski, diversable, lmiq, kdheepak and 3 more