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* Modify quickrun to allow resuming * fix the gather tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add check for protocol_dag.json * add basic test * clearer language, hopefully * store protocol dag using transformation key * another tmpdir -> tmp_path fix * add error handling check * fix naming in test * add news item * use assert_click_success * add test for interrupted job * remove checkpoint when a job has completed successfully * add handling for checkpoint error handling without --resume * clean up logic * check for warning * add docs * make a cache dir * use clickexception * update error message * update kwarg * keep everything in the quickrun cache * clearer message * it's ProtocolDAG not protocolDAG * bump CI * bump CI * include output json in caching hash (#1890) * first pass at adding caching with output json * add (hopefully) helpful execution information * add resume command * fix testing path * check that output file isn't created early * clean up tests * line break * fix some comments to say cache instead of checkpoint * fix typo in news item --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Alyssa Travitz <alyssa.travitz@omsf.io> Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>