Refactoring and fixes for the `tutorial` branch

[kahaaga]

Some necessary changes to get #347 to pass CI and adhere to API.

• probabilities_and_outcomes and allprobabilities_and_outcomes are consistently the methods implemented, and probabilities/allprobabilities are just calls to those functions. The exception is if implementing the latter methods is faster.
• Fixed missing methods and exports (why were they removed to begin with, @Datseris? I'm thinking specifically of the allcounts etc methods that were generated previously)
• entropy(::Probabilities), which was used in the doc tutorial, is not a valid syntax. I am happy with that, since I like to specify which entropy one wants to compute. However, we can also dispatch automatically to entropy(Shannon(), p). Not sure what is the best. Here I just modified the examples in the tutorial to be explicit about using Shannon

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[kahaaga]

Fixed missing methods and exports (why were they removed to begin with, @Datseris? I'm thinking specifically of the allcounts etc methods that were generated previously)

If the purpose was to have fewer methods, I'm okay with dropping allprobabilities in favor of just having allprobabilities_and_outcomes. But then all references to the method has to be removed from both the docs, the docstrings, and the tests.

[kahaaga]

Otherwise I'm done here.

[Datseris]

• Not sure what is the best. Here I just modified the examples in the tutorial to be explicit about using Shannon

I disagree with that. entropy must default to Shannon. To my understanding so far in the wide literature of NLTS 99.9% of cases an entropy is computed, this is the Shannon entropy. Hence this is a sensible default.

For all the rest, okay!

[kahaaga]

I disagree with that. entropy must default to Shannon. To my understanding so far in the wide literature of NLTS 99.9% of cases an entropy is computed, this is the Shannon entropy. Hence this is a sensible default.

Ok, I'm fine with Shannon entropy being the default.

Should I implement it or will you do it? It's just a matter of removing the Shannon instances from the tutorial and changing the else case here

function entropy(args...)
    e = first(args)
    # Check the condition for throwing an error (if false)
    cond = if e isa ProbEstOrOutcomeSpace
        # Shannon is used as default information measure
        true
    elseif e isa InformationMeasure
        # Any subtype of entropy
        e isa Entropy
    elseif e isa InformationMeasureEstimator
        # Estimator is for any subtype of entropy
        e.definition isa Entropy
    else
        false
    end
    cond || throw(ArgumentError("""
        You have used `entropy` without an entropy definition
        ($(typeof(e))). Use `information` instead."""))
    return information(args...)
end

[Datseris]

• why were they removed to begin with, @Datseris?

That was when counts became the main method and counts_and_outcomes was in the deprecation file. Now of course this is incorrect, as the _and_outcomes is the correct method. Your changes are correct in any case!

---

Regarding allcounts: yes, neither allcounts nor allprobabilities should exist at all. Both must anwyays explicitly compute all outcomes, hence they have no reason to exist; they can never be optimized to not calculate outcomes. Hence, only the _and_outcomes versions should exist for both. So we should just add allcounts and allproabilities to deprecations file and simply remove all refernece of them from the docs! Let me mnow if you do this in this PR or we do it in the tutorial PR after merging this one in.

[kahaaga]

Regarding allcounts: yes, neither allcounts nor allprobabilities should exist at all. Both must anwyays explicitly compute all outcomes, hence they have no reason to exist; they can never be optimized to not calculate outcomes. Hence, only the _and_outcomes versions should exist for both. So we should just add allcounts and allproabilities to deprecations file and simply remove all refernece of them from the docs! Let me mnow if you do this in this PR or we do it in the tutorial PR after merging this one in.

I can add the deprecations here, no problem.

[Datseris]

Should I implement it or will you do it? It's just a matter of removing the Shannon instances from the tutorial and changing the else case here

Since in my branch Shannon was the default, please restore this behjavior before we merge your PR into mine.

[kahaaga]

Since in my branch Shannon was the default, please restore this behavior before we merge your PR into mine.

I haven't changed the behavior of the code, just the doc examples. Your doc build failed because entropy(p::Probabilities) isn't implemented. It also isn't tested for. But I'll fix both before merging here 👍

[Datseris]

ah sorry. ha my mind was stuck so far in the past where shannon was the default for entropy. that was proably so far in the past before even the information function.

[kahaaga]

ah sorry. ha my mind was stuck so far in the past where shannon was the default for entropy. that was proably so far in the past before even the information function.

Yes, I think this is from 1.X or so :D