Fix rate limiting calls following upstream API breakage

[sbesson]

PyGithub 1.43 introduces a breaking change in the RateLimit API modifying both the internal representation as well as the methods of the Rate objects - see https://github.com/PyGithub/PyGithub/commit/fd8a036 and https://github.com/PyGithub/PyGithub/pull/902. This causes scc to crash when the latest version of PyGithub (currently 1.43.1) is installed.

Rather than capping PyGithub or forcing an upgrade, this PR adds backwards-compatible support for the new rate limit API with the following changes:

• the get_rate_limits() method is deprecated
• a new get_rate_limit() method forwards the calls to GitHub.get_rate_limit()
• all internal usages of rate limits are updated to use get_rate_limit. A try/exept block is added to handle older and newer version of PyGithub and return the core rate as well as the search and graphql rates for recent versions.

To test this PR: 1- create a new virtualenv, install requirements.txt and check that e.g. scc rate fails with a KeyError 2- with the same virtualenv, run /path/to/venv/python/scc/main.py rate from this branch and check the command returns the core, search and graphql rates 3- check the backwards compatibility by downgrading PyGithub (or creating a new virtualenv) and check that /path/to/venv/python/scc/main.py rate returns the core rate only

Proposed tag: 0.10.1

[sbesson]

https://ci.openmicroscopy.org/job/SCC-merge/989/ is green with this included. Barring concerns, I would propose to include this as well as #235 in a patch release of scc to fix compatibility with the latest PyGithub release.

[joshmoore]

Tested this in a few starfish contexts (with and without submodules). :+1: