[MRG] Better dag handling #69
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This wraps the Snakemake API call in a custom context manager class that checks if we are printing a DAG, and if we are, when we enter the context, sets up stdout to be a file buffer, and assembles the buffer contents into a list when done.
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I think having the --dag flag to dump straight to output is a good idea, so that you can pipe it to scripts or other command line utilities, but I also think it's good to have a flag to dump to a file or to a png. I implemented a context manager that will capture stdout when the user is creating the directed acyclic graph, and either prints it to the screen (in the case of --dag, which will continue to work as you implemented it), or prints it to a file (if the user passes the --dagfile flag), or uses dot to convert the dotfile into a png file (if the user passes the --dagpng flag). I opened a pull request (#73) against this pull request so you can take a look. I'll also add a few tests of the new functionality. |
* Add eelpond tests/ directory This adds individual unit tests for each of eelpond's flags. Not all of these flag unit tests are implemented yet, but the --dag and --dagfile flags are tested, as are the --help and --dry-run flags, to demonstrate how to do it. * fill in --dagpng test. clean up test_flags test * add pytest to environment.yml, add pytest command to travis
Further improvements to DAG handling
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@ctb - @charlesreid1 added a testing framework! Works and looks good to me, but your review would be helpful |
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I think I already merged it?
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it was merged into this branch/PR, not into master i think...? |
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oh. well, I reviewed it already :)
On Mon, Feb 04, 2019 at 11:51:03AM -0800, Tessa Pierce wrote:
it was merged into this branch/PR, not into master!
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#69 (comment)
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C. Titus Brown, ctbrown@ucdavis.edu
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yup, that's right - the inspiration for the tests was testing the new |
Don't print to stdout if building a
dag. This change means that we can redirect the output directly to a dot file, or use graphviz to get an image (rather than needing to delete the extra lines first)../run_eelpond examples/nema.yaml default --dag > dagfile.dotor
./run_eelpond examples/nema.yaml default --dag | dot -Tpng > dagfile.pngaddresses #11 - provides all the functionality, though it doesn't enable an easy
--dagfile FILENAMEflag. Thoughts @charlesreid1?