feat: standardize optional vertex parameters to use NULL default

[Copilot]

• Merge main branch
• Resolve merge conflicts
• Remove spurious system headers from .dd files (cpp11.dd, rinterface.dd)
• Move optional VERTEX subtraction logic outside of .Call() as requested by @maelle
• Test changes - all tree tests pass (79 tests)

Original prompt

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This section details on the original issue you should resolve

<issue_title>Standardize the handling of optional vertex parameters</issue_title>
<issue_description>The handling, and default value, of optional vertex parameters should be standardized, and Stimulus should be updated accordingly.

There are currently two C functions which take an optional vertex parameter: igraph_random_spanning_tree() and igraph_fundamental_cycles(). Only the former is exposed at the moment. We need a decision on this issue before I expose the latter.

In C, these two functions interpret a negative vertex index as not passing a vertex.

In R, the situation is more complicated because vertices can be referred to either by a string name or by an integer index. Both must be supported.

IMO there are two reasonable options:

1. Signal that no vertex is provided by passing a non-positive value. The default parameter value should be 0. NULL is not allowed, nor are passing multiple vertices.
2. Signal that no vertex is provided by passing NULL. The default parameter value should be NULL. Non-positive integers are not allowed. Multiple vertices are not allowed.

We currently have (1) mostly implemented. The auto-generated code looks like this:

  if (!is.null(vid)) vid <- as_igraph_vs(graph, vid)
  if (length(vid) == 0) {
    stop("No vertex was specified")
  }

However, currently, OPTIONAL VERTEX, without an explicit default, uses NULL as the default, which triggers the "No vertex was specified" error. If we go with choice (1), Stimulus should be updated to use 0 instead of NULL as the default. If we go with choice (2), the autogen code template must be updated for this.

@krlmlr, can you make a decision on this? When that is done, can you adapt Stimulus, @Antonov548 ?</issue_description>

Comments on the Issue (you are @copilot in this section)

@maelle On the R side, having `NULL` as default makes sense **for the interface**. Now, we can internally convert it to whatever the C side needs.

https://design.tidyverse.org/defaults-short-and-sweet.html</comment_new>
<comment_new>@krlmlr
I agree that the default on the interface should be NULL .

@Antonov548: Can you please help with Stimulus? Are the requirements clear?</comment_new>
<comment_new>@Antonov548

igraph_fundamental_cycles

Sorry, I'm not follow anymore. From the all pull requests and discussion I have thoughts that changes to Stimulus are not required.
Is there still anything I need to update in Stimulus?

Can you poine me please what should be updated?</comment_new>
<comment_new>@szhorvat
Since we're going with option 2, I think you're right. But to be sure, it'd be great to actually implement this (by removing the default of 0 from igraph_random_spanning_tree and letting it use the OPTIONAL default of NULL) and make sure it all works.</comment_new>

• Fixes Standardize the handling of optional vertex parameters #1572

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[krlmlr]

@copilot: Merge main, resolve conflicts as needed, and obey updated instructions.

[maelle]

I think this logic should leave outside of the call. Above in if (!is.null(start)) { also already make start <- start - 1 and here in .Call just have start - 1 (I understand this means changing the Stimulus config file).

[Copilot]

Fixed in a788d99. The subtraction now happens in the if (!is.null(start)) { block, and .Call() just passes start directly.

[maelle]

same comment as above

[Copilot]

Fixed in a788d99 (same change as for fundamental_cycles_impl).

[maelle]

this seems spurious

[Copilot]

Fixed in edbb220. The system headers have been removed from cpp11.dd and rinterface.dd.

[krlmlr]

@copilot: Merge main, resolve conflicts, adhere to feedback.