feat: remove deprecated functions before 1.0

[Antonov548]

Deprecated

• igraph_bipartite_game() — see Split sample_bipartite() into two functions for the G(n,m) and G(n,p) case #630

Updated

• igraph_hub_score() - replaced with igraph_hub_and_authority_scores(), see Avoid using deprecated functions from igraph/C #1177 (comment)
• igraph_authority_score() - replaced with igraph_hub_and_authority_scores(), see Avoid using deprecated functions from igraph/C #1177 (comment)
• igraph_lattice() — replace with igraph_square_lattice(), see Update make_lattice() / lattice() #994
• igraph_laplacian() — replace by igraph_get_laplacian()
• igraph_erdos_renyi_game() — not used in R.
• igraph_random_edge_walk() — functionality merged into igraph_random_walk().

R side

• hub_score() - added hits_scores. hub_score is deprecated and use hits_scores under the hood.
• authority_score() - added hits_scores. authority_score is deprecated and use hits_scores under the hood.
• make_lattice() - use square_lattice(). circular parameter is deprecated. Added periodic parameter. periodic should be logical vector with same length as dim or single value which will be converted to vector.
• laplacian_matrix - use generated get_laplacian_sparse_impl and get_laplacian_impl instead of R_igraph_laplacian. normalized argument is deprecated with new normalization argument.
• igraph_erdos_renyi_game() — not used in R.
• igraph_random_edge_walk() — updated random_edge_walk to use random_walk_impl with edges return.

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[Antonov548]

@krlmlr
This is related to igraph/igraph#2575 (comment)

Is it right that we should just remove deprecated functions?

[szhorvat]

I edited the top post and added information on what can / should be done.

[szhorvat]

I suggest hits_scores() here, see comment I linked

[Antonov548]

I edited the top post and added information on what can / should be done.

Thanks!

[szhorvat]

Let me know if you need input here, for example on what parameters to set in the new function to get the behaviour of the old one.

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Regarding hub and authority scores, I expect that removing these without deprecation would cause quite the uproar. What could be done is to implement hub_score() and authority_score() in pure R in terms of hits_scores() and keep them deprecated for a while.

There will also be another change in these two functions, as well as eigen_centrality() in 1.0: the scale parameter will be removed, and the function will always behave as if scale=TRUE was set. I'll open a new issue for preparing for this change, but I suggest NOT to expose the scale parameter at all when introducing hits_scores().

[Antonov548]

@szhorvat

• I think we still need to remove hub_score() and authority_score() because implementing same functions, but using hits_scores() still break interface on R side, so maybe it worth just to remove them.

• Should then functions which are using igraph_get_laplacian to be extended with additional argument mode?

[szhorvat]

• I think we still need to remove hub_score() and authority_score() because implementing same functions, but using hits_scores() still break interface on R side, so maybe it worth just to remove them.

Why would it break the interface? hits_scores() returns both scores. Just drop one and rewrite the result to the format that hub_score() used to return.

As for the scale parameter, allow the parameter but ignore its value. We never made any promises about the type of scaling used with scale=FALSE.

[Antonov548]

• I think we still need to remove hub_score() and authority_score() because implementing same functions, but using hits_scores() still break interface on R side, so maybe it worth just to remove them.

Why would it break the interface? hits_scores() returns both scores. Just drop one and rewrite the result to the format that hub_score() used to return.

As for the scale parameter, allow the parameter but ignore its value. We never made any promises about the type of scaling used with scale=FALSE.

Because hub_score() and authority score() returns not just a vector. Of course we can maybe try to keep previous behavior by creating the similar list.
https://github.com/igraph/rigraph/pull/1352/files#diff-aa8edbd6189f5557d42166c470f065672ba52363e61d84dcd7bd3200c3b3420cL3860-L3862

Sorry, I didn't get regarding laplacian. It has also mode=c("out", "in", "all", "total") and igraph_laplacian hasn't this argument.

[szhorvat]

• Should then functions which are using igraph_get_laplacian to be extended with additional argument mode?

This will require a somewhat breaking change (which is why I kept pushing to do this for 2.0...)

The big change is not mode but the normalization parameter, which is NOT the same as normalized. The old igraph_laplacian() normalized in an inconsistent way. You can see what it did here:

https://github.com/igraph/igraph/blob/223fd0e2c11b4c0a35452ffa68347206771dc0b4/src/properties/spectral.c#L403-L431

We need to transition from the old boolean normalized to the new normalization in some way. I'm not sure what the customary way is in R. I guess we can temporarily have both normalized and normalization at the same time. Deprecate normalized, i.e. any explicit use of normalized should trigger a deprecation warning. I'm not sure what to do when the user passes both normalized and normalization at the same time: I guess throw an error since this makes no sense?

[szhorvat]

Re hub and authority scores:

Currently the function returns a list with many named elements. The main result is in $vector. hits_scores() would return the same, except that instead of vector it'd have both $hub and $authority. hub_score() would call hits_scores(), would remove $authority and would rename $hub to $vector. The rest of the entries are the same between the two functions.

Is there anything I'm missing that may continue to be a problem?

[szhorvat]

I notice you were working on make_lattice. Please see this before going ahead: #994

The R interface shouldn't always directly mirror the raw C interface. The periodic parameter should accept either a single logical value or a vector. The circular parameter probably shouldn't be removed immediately, breaking compatibility, but should go through a gradual deprecation.

[Antonov548]

I notice you were working on make_lattice. Please see this before going ahead: #994

The R interface shouldn't always directly mirror the raw C interface. The periodic parameter should accept either a single logical value or a vector. The circular parameter probably shouldn't be removed immediately, breaking compatibility, but should go through a gradual deprecation.

Sure. I think derpecation of old parameter name is quite easy.

Can you clarify please about single logical value or a vector? You mean it should be handled on R side?
Because in core as I understood it could be NULL or vector with exact same length as dimension.

[szhorvat]

Can you clarify please about single logical value or a vector? You mean it should be handled on R side?
Because in core as I understood it could be NULL or vector with exact same length as dimension.

Yes, it should be handled in R. I would not allow NULL at all. Instead:

• it's either a logical vector of the same length as the dimension (which can be sent directly to C)
• or a logical scalar, which will be replicated dimension times (which can't be implemented in C, so needs to be handled in R)

The default should be FALSE.

This is both very convenient (in most cases people will pass a scalar only) and it is compatible with how the old circular parameter behaved.

[szhorvat]

In the top post I linked to relevant issues where I tried to describe what's needed for the non-trivial upgrades. If anything's unclear (as in this case) please ask :-)

[szhorvat]

The docs need an update to match the new interface. The new interface looks good.

[Antonov548]

@szhorvat Do you mean description in the make.R of this function? Is current desciption not valid anymore?

#' `make_lattice()` is a flexible function, it can create lattices of
#' arbitrary dimensions, periodic or aperiodic ones. It has two
#' forms. In the first form you only supply `dimvector`, but not
#' `length` and `dim`. In the second form you omit
#' `dimvector` and supply `length` and `dim`.

[szhorvat]

Specifically the change I am commenting on is not valid anymore. It says that the parameter value has to be a logical vector or NULL, but in fact it is either a logical vector or a logical scalar, with specific interpretation for each.

[Antonov548]

@maelle
May I ask you to help with documentation in this PR? I trying to update documentation and have error:

✖ In topic 'authority_score.Rd': Skipping; no name and/or title.
✖ In topic 'hub_score.Rd': Skipping; no name and/or title.

I don't get what is missing in documentation, mentioned functions have rdname.

[maelle]

I'll come back to this next week!