I like to use magit to interact with git. I wanted to figure out how exactly the command-line version of git (which magit is running under the hood) interacts with pull requests on GitHub, because the workflow at my job is to make commits on feature branches, then merge them onto develop following a PR (which provides time for code review.)
I'm making the assumption you have a PR to merge a branch test onto a branch develop, with some linked issues. Here's how you close PR when you merge. Note that this doesn't close the associated issues. First, checkout your local copy of develop: b c develop, then and pull any changes from your remote with F origin/develop. Merge test into develop with m m test. Finally, push the changes to the remote: p origin/develop.
To get the issues to close, you must edit the commit message for the merge with m e test after checking out develop. The merge commit must mention each of the issues you wish to close. I usually go for a commit message like this:
Merge branch 'test'
* test:
commit 1
Closes #14
Closes #16Sadly, you can't use the PR number in the Closes string to close the associated issues. You have to enumerate the issues explicitly. You also can't do Closes #1, #2, #3. Each issue has to have its own closing keyword.