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Draft: One store : one run, and resume command

Louis Duchemin requested to merge store-rework into master

Major changes :

  • one store : one run, saved under the run key
  • improved store path parsing, relying on a Cmdliner converter to allow giving a path to either a store file or a directory that contains one. 4b5886bd is superseded by e26c80ba and should be squashed / ignored.
  • annotated tree of a run is now stored directly within the run record (see Store.Run), instead of a key to a Store.Annotated_tree_table (which was deleted). Relies on changes in Phylogenetics.Tree.t to include sexp derivations.

Remains to be done :

  • rework TSV outputs to take advantage of the single run store design
  • maybe remove best_sites field from records in Store.Run.(Discrete|Continuous) and generate it on-the-fly from processed_alignments
  • maybe add a status command that gives general infos on the run ? E.g its progression, number of alignments, model etc... Could be the default action for pelican store /some/store/ when no URI is provided.

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