implement prior generation

This MR implements parsing a mixture of specified priors, fixed parameters and then adding in defaults.

There's a new function in prior.py and a couple of changes to run_sampler.py.

An example of the new usage is shown in BasicTutorial.py and Injection.py.

Thoughts @paul-lasky @gregory.ashton @moritz.huebner?

I'm afraid I'm not a fan of having 'fixed_parameters' and 'priors', I don't see why they need to be separated. From a 'big picture' point of view, they are not different, one is just a delta function, the other is something else (i.e. uniform or Gaussian etc). One a pragmatic level, if I want to quickly fix a parameter and rerun something, I now have to add it to a list of fixed parameters which takes longer and is more error prone. Sorry if I'm missing something.

Separating the fixed_parameters is just a convenient way to pass a bunch of them at once. The function turns them all into delta function parameters.

You can still fix parameters by specifying it as a DeltaFunction, or however it was possible to before.

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• f6be258e - get rid of 'fixed parameters'

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• a525af7b - update to make tests.py run, change internal logic

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@gregory.ashton does this look better? It also has the ability to remove junk (waveform approximant strings) that happen to have been left in the prior.

added 7 commits

• a525af7b...65603c50 - 6 commits from branch master
• 3edddccd - Merge branch 'master' into 'fill_prior'

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• 3edddccd...553a3ad2 - 3 commits from branch master
• f4a12805 - Merge branch 'master' into 'fill_prior'

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added 3 commits

• cfbbc2cc - update tests.py syntax
• e4c3f8d8 - merge waveform_genrerator from master
• f749916e - update 150914 tutorial

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• f749916e...22874e1b - 7 commits from branch master
• 89871f3d - Merge branch 'master' into 'fill_prior'

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added 7 commits

• 87151c7e - update syntax in Injection.py tutorial
• c282847a - merge detector.py from master
• 33059813 - Merge branch 'fill_prior' of git.ligo.org:Monash/peyote into fill_prior
• 40937470 - fix fill_priors to deal with bad waveform generator variables
• 82cf5813 - add function to write prior distribution to file
• 8ae58ed7 - make sampler write the prior to file
• 0fd899cf - update Injection tutorial to new prior interface

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changed the description

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• 44480cef - update printing of prior
• dbf11786 - rename parameters of powerlaw and uniform parameters
• 337751e9 - use default mass prior
• ad489a53 - update basic tutorial
• ccf6fef5 - trivial change

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added 4 commits

• ec2965a1 - update tests for new prior parameters
• 692041f9 - update custom source tutorial for new prior parameters
• 5bc131c1 - typo fix
• 7605f685 - add docstring for prior filling

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The changes in prior.py are now pretty extensive, including some changes to the names of parameters of prior models, most notably, PowerLaw and Uniform.

@gregory.ashton or @paul-lasky can this be merged in?

This now fills in the prior and also adds functionality to print the prior to file and does this before starting the sampler.

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• 7605f685...57f16cf5 - 8 commits from branch master
• 1041a950 - Merge branch 'master' into 'fill_prior'

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enabled an automatic merge when the pipeline for 1041a950 succeeds

This is being merged in. This allows for pretty extreme changes in usage, watch out.

added 1 commit

• 8828f254 - Fix bug in prior

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enabled an automatic merge when the pipeline for 8828f254 succeeds

merged

mentioned in commit a92343dc