DOC add command to run pre-commit checks to pull request template
I think we could add
```bash
passes `pre-commit run --from-ref=upstream/master --to-ref=HEAD --all-files`
```
to the pull request template (maybe it could even replace the current `black` and `flake8` ones).

The file to change would be
```
.github/PULL_REQUEST_TEMPLATE.md
```

Some of the contributing guide may also need updating if it mentions the `flake8 --diff` command.