Change handling of output paths

[bodkan]

Draft of the update for the NEWS file of what will eventually become v1.0.

The behavior previously implemented via the output = and ts = arguments of slim() (and msprime()) has been changed to facilitate more straightforward handling of output paths in user-defined SLiM extensions and other packages leveraging slendr for inference. This represents a breaking change in user interfaces of both slim() and msprime() functions:

• slim(): the ts argument is now logical. TRUE switches on tree-sequence recording, FALSE switches it off. If tree-sequence recording is on, the function automatically returns a tree-sequence R object. If users want to save it to a custom location, they should use the function ts_save(). If customized output files are to be simulated via user-defined extension scripts, those scripts can use a SLiM constant PATH, which can be set via slim(..., path = <path to a directory>) from R and is then automatically passed over to SLiM. This way, user-defined scripts don't have to deal with path management manually, but can specify output directory in R. In these case, the slim() function always returns that path back. If the path is set, slim() will not return a tree sequence object, but that object can be loaded by ts_load("<path to a directory>/slim.trees"). In other words, nothing changes for the usual SLiM-based slendr workflow, but for models generating custom output files, a small amount of work is needed to load the tree sequence -- the tree-sequence file outputs are therefore treated exactly the same way as non-tree-sequence user-defined output files. This function also no longer accepts a load = TRUE|FALSE argument for this exact reason.

• msprime(): Because customization of user outputs is only supported for SLiM models, msprime() still only ever simulates a tree sequence. Having a dedicated option to specify the path to a tree-sequence file is therefore redundant and when needed, tree sequences can be saved via the ts_save() function. This function also no longer accepts a load = TRUE|FALSE argument for this exact reason. The function also always simulates a tree sequence in memory, it never runs msprime on the command line in the background, regardless of whether a slendr model has been serialized or not.

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 90.41096% with 7 lines in your changes missing coverage. Please review.

Project coverage is 90.65%. Comparing base (6a1f090) to head (3a55cbe). Report is 33 commits behind head on main.

Files with missing lines	Patch %	Lines
R/slim.R	75.86%	7 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #157 +/- ## ========================================== + Coverage 90.57% 90.65% +0.08% ========================================== Files 11 11 Lines 3184 3190 +6 ========================================== + Hits 2884 2892 +8 + Misses 300 298 -2 ```

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