Add MySQL connector

[Ullaakut]

Goal of this PR

Fixes #22

This PR implements a simple MySQL connector for Sroka. Just like other connectors, it supports fetching data into pandas dataframes as well as csv files.

It also:

• Adds mysql.connector to the requirements.txt file,
• Re-orders the requirements.txt file alphabetically, the way pip freeze normally sorts dependencies. Can be reverted if needed, since it is not part of the scope of the PR but is a side-effect,
• Adds MySQL connector configuration values to the sample configuration,
• Documents the MySQL connector in the README file,
• Adds a MySQL section and example to the sample Jupyter Notebook,
• Fixes the setup.py file which contained whitespaces at the end of the line 4, which prevented the pre-commit hook from letting commits pass.

How to test it

I personally tested this feature by using this public MySQL server. You can do the same by using the following configuration values in your config.ini file:

[mysql]
host=mysql-rfam-public.ebi.ac.uk
port=4497
unix_socket=
user=rfamro
password=
database=Rfam

Here is an example of running it in the sample Jupyter Notebook on this public database:

And here is the CSV file created when an argument is given for the filename:

Additional Notes

Feel free to be nit-picky about the PR, it's my first ever Python contribution so I don't know any of the best practices that are specific to Python.

[martynaut]

@Ullaakut could you please do a PR to dev branch? dev branch is where most recent code lives. We move code to master when we plan to do a release. I guess we need to make it clear for contributors in README.md to avoid future confusions. Sorry for that!

[Ullaakut]

@martynaut I changed the base of the PR and there are no conflicts. It should be okay now :)

[Ullaakut]

Pushed a fix for the path issues, did the following tests:

Ensure that it works when given a path to a folder that doesn't exist yet, and handles absolute paths

Ensure that relative paths are handled correctly

Ensure OS errors (no read/write access, file system errors, etc.) are caught properly