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* Turn on 3 more CWL tests I can't get to reproducibly fail * Make promises say when they are being made and fulfilled * Fix promise ID reporting and add job generation reporting so we can catch stale reads more easily * Fix multiline f-string * Stop thinking the 0th local job also needs to run on Kubernetes * Fix log levels * Catch in advance if the worker is trying to use a file we never imported * Get the workflow to run through by processing the embedded tool's tool * Move all the imports back to the initial setup where they belong * Quiet debugging * Drop extra whitespace * Make error for an escaped import more decisive * Apply the longer conformance test timeout * Catch the new Kubernetes missing config exception in decorator * Say we have handled all CWL Process objects * Simplify dispatch * Recursively list directories in the input and in tools when setting up the workflow * Make sure to map everything in the listing and the shadow listing exactly once * Add a bunch of code to try and rewrite listings to stop CWL from looking at them * Come up with a method to send directory contents around that at least seems to work * Drop whitespace * Widen typing to better match what's actually passed * Remove some no longer useful debug prints * Just use the base Process class * Don't clear listings at the ends of jobs * Make the ToilPathMapper make directories * Document what visit() is supposed to do * Don't stage children when we stage parents, and go back to clearing listings * Steal cwltool's work of making the _: directories * Make stage_listing actually work * Remind the output file stager that it doesn't actually have the file store handy and skip exporting anything that's not a real file * Fix CWL test 87 by making sure Directory listings are in final output * Reorder job execution so we can rebuild the listing earlier * Revert "Reorder job execution so we can rebuild the listing earlier" This reverts commit a1fd2bd. * Use a single complex pass everywhere to encode directory contents without disturbing listings * Make sure listings' File and Directory objects get visited if they existed * Remove whitespace * Hackily propagate CWL unsupported feature detection back to cwltoil * fail_exit_code → failure_exit_code * Skip missing optional secondary files in workflow input * Accept optional secondary files in tool definitions * Allow bypassign the file store for in place update support * Reenable file staging postprocessing even when not using the FileStore; is it correct? * Test everything with file store bypass * Stage output files into place from per-job output temp directories * bump cwltool version * Filter secondary files always but tolerate file: * Try adding a toil imported flag for hiding illegitimate secondary files * Stop running all jobs as top level * Stop tagging files as imported * Document --bypass-file-store * Use the right name for the function * Fix check sense and assert variable names * Give a better message when using unsupported features. * Spell type constraint * Use toilfile: instead of toilfs: * Call job generations versions instead * Improve comments * Use the One True path_to_loc * Use more succinct human readable name finding * Link to CWL issue about the listing specs * Fix comment I stopped writing because it was wrong * Drop TODO that doesn't seem to break any conformance tests * Implement toildir: for output staging * Note when we think later on is * Break out CWL utilities and add tests for them * Get new unit tests to pass * Revert "Use the One True path_to_loc" This reverts commit 1feae24. * Fix lingering toilfs scheme name * Add download_structure test * Fix typo * Pass MyPy type checking * Drop trailing whitespace * Import moved function Co-authored-by: Michael R. Crusoe <[email protected]> Co-authored-by: Michael R. Crusoe <[email protected]>
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