added 'library' sample column#13
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As it was, the code relied on the
condition_precolumn in the sample and growth data frames to determine sample identity. This was implicit and relied on some fragile assumptions about how the user named those conditions. (For example,kanR-kanorkanR+kanrefers to the kano library with and without kanamycin. Further, to properly infer whether a condition was selective or not, we added a search for "-" or "+" in the condition string. Even more fragile.We broke out the
libraryinto its own column and separated it fromcondition_pre. This lets us avoid fragile assumptions about how the user names the columns.One knock-on effect was that we had to change the
sub_librarieslanguage in the simulation and raw processing config files totilesto avoid confusion. This is more precise anyway with our experimental design.Also did a bunch of docs/tests/CLAUDE.md cleanup.