Adding table getters and appenders, simplifying, sorting, and variants iterator

[LynxJinyangii]

No description provided.

[codecov]

Codecov Report

❌ Patch coverage is 99.89396% with 1 line in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
RcppTskit/src/RcppTskit.cpp	99.74%	1 Missing ⚠️

📢 Thoughts on this report? Let us know!

[gregorgorjanc]

I have rebased this to the most recent main branch that contains previous PRs.

[gregorgorjanc]

There is quite a bit to review in this PR, so best to make a list of new things! @LynxJinyangii I would appreciate such communication so it's easier to follow your work and thoughts etc. Best to err on the slight "over communication" that "no communication";) Even just copying NEWS.md entries or linking to them in the PR message would be fab.

From what I gather, this is the list of additions we should review:

• rtsk_table_collection_sort and TableCollection$sort related to Do we have to add TableCollection$sort() method? #99
• rtsk_treeseq_get_samples and TreeSeqeunce$samples (do we need samples for TableCollection then too? - best to discuss; edit - there is no such method for TableCollection)
• rtsk_node_table_get_row and TableCollection$node_table_get_row (do we need node_table_get_row for TreeSequence too? - best to discuss)
• rtsk_const_tsk_no_check_integrity
• rtsk_variant_iterator_init, rtsk_variant_iterator_next, and TreeSequence$variants

[gregorgorjanc]

@LynxJinyangii I have pushed changes to this branch/PR (rebased to main, which required sorting some merge conflicts; and come comments on sort), so best if you first pull before you start changes on your end.

[gregorgorjanc]

I have done some polishing of the code, docs, and terms in my recent commit&push. @LynxJinyangii make sure you git pull on your end so that you get these changes. I have reviewed all but variant/iteration stuff - that will take me more time - but you can work on the comments I provided above in the meantime and then we iterate.

[gregorgorjanc]

@bryo-han do you have capacity to go over this PR while I focus on teaching/course?

[gregorgorjanc]

@LynxJinyangii I have tagged you in a bunch of places where I don't see changes when I last reviewed certain parts. Remember to click on the > or v symbol next to file names to fold and unfold the file so you can see comments as you scroll through the files. Also, when the diff is large GitHub will not render the diff so you have to click on the file display to see diffs and comment sections.

[gregorgorjanc]

@LynxJinyangii Python API has None for all of these args so would be good to be consistent/in-line with that API here to. The Python API then checks the inputs and does what it does. Best to follow that style on our end too. So, put R_NilValue (or should it be NA_REAL?). We can come back to this once I review everything;)

[gregorgorjanc]

@LynxJinyangii I have now pushed my changes and squashed commits into one. I still have to review/polish the variants iterator, which will come as part (in sync) of AlphaSimR review.