Analysis options overridden by default options

[yaelbh]

Still need to verify that there is really a bug here. It looks like this from the following lines, taken from BaseAnalysis.run:

        analysis_options = self._default_options()
        analysis_options.update_options(**options)

I see two potential issues here:

• The first line retrieves the default options instead of the current ones, hence overriding the current options by the default ones.
• Possibly the second line overrides the default options.

[yaelbh]

Closing because it was fixed, apparently in #39