I was using the V1.1 API to submit jobs. I have auto-cancel set on my project, and when I used the V1.1 API to submit multiple jobs on a branch, it did not cancel any job running, which was desired. Auto-cancel makes sense for builds triggered by source control, but it’s reasonable to ignore auto-cancel when a job is submitted explicitly by the API, which V1.1 does.
Having upgraded to pipelines, I moved to configuration version 2.1, which forced me to move to API V2. In this case, submitting a pipeline when auto-cancel is set on my project canceled any running jobs on that branch, which is not desired. There appears to be no workaround for this (except manually turning off auto-cancel in the console). If there was an API where I could turn off auto-cancel, I could live with this, as I could wrap my job submission with calls to toggle the auto-cancel on the project, but sadly, there is not.
This is a significant regression in the API functionality. There should at least be an option in API V2 to ignore auto-cancel when submitting a particular pipeline.
Please address this soon as this has broken an important part of how we use CircleCI.