Closed bluegenes closed 5 years ago
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.
@ctb - @charlesreid1 added a testing framework! Works and looks good to me, but your review would be helpful
I think I already merged it?
it was merged into this branch/PR, not into master i think...?
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!
-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/dib-lab/eelpond/pull/69#issuecomment-460387667 -- C. Titus Brown, ctbrown@ucdavis.edu
it was merged into this branch/PR, not into master i think...?
yup, that's right - the inspiration for the tests was testing the new --dagfile
and --dagpng
flags so I added it into the DAG-related pull requests. Thanks for merging!
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.dot
or
./run_eelpond examples/nema.yaml default --dag | dot -Tpng > dagfile.png
addresses #11 - provides all the functionality, though it doesn't enable an easy
--dagfile FILENAME
flag. Thoughts @charlesreid1?