Replace all `@flojoy(deps={...})` with `run_in_venv` in a single PR + decide what goes in the main env

[roulbac]

          Adding a TODO for myself to replace all `@flojoy(deps={...})` with  `run_in_venv` in a single PR + decide what goes in the main env

Originally posted by @roulbac in #276 (comment)