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Command line tool and API consistency

Javier Duarte requested to merge github/fork/vloncar/cnn_stream into master

Created by: vloncar

Currently, when using API to write projects the projects don't keep the yml config in the output directory, so they can't be used by hls4ml build command. The changes ensure that we always write the yml in the output dir. I also made the minor change to get rid of the warning newer Python produces about comparing to a literal value.

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