Update website for v7.0.0

bodkan · Jun 26, 2023 · 9ec73ea · 9ec73ea
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 # slendr 0.7.0
 
-# slendr 0.6.1
-
-- Emergency upgrade to match the latest pyslim 1.0.3 due to a serious bug in recapitation (see [here](https://github.com/tskit-dev/pyslim/issues/307) and [here](https://github.com/bodkan/slendr/issues/141) for an extensive discussion. **This will require you to re-run `setup_env()` in order to update slendr's Python internals by creating a new internal Python virtual environment.** ([#45539a](https://github.com/bodkan/slendr/commit/45539a))
+- Emergency upgrade to match the latest pyslim 1.0.3 due to a serious bug in recapitation (see [here](https://github.com/tskit-dev/pyslim/issues/307) and [here](https://github.com/bodkan/slendr/issues/141) for an extensive discussion). **This will require you to re-run `setup_env()` in order to update slendr's Python internals by creating a new internal Python virtual environment.** ([#45539a](https://github.com/bodkan/slendr/commit/45539a))
 
 - A potential issue with a parent population being scheduled for removal before a daughter population splits from it is now caught at the moment of the daughter `population()` call rather than during a simulation `slim()` run. ([#0791b5](https://github.com/bodkan/slendr/commit/0791b5))
 
 - The function `plot_model()` has a new argument `gene_flow=<TRUE|FALSE>` which determines whether gene-flow arrows will be visualized or not. ([#104aa6](https://github.com/bodkan/slendr/commit/104aa6))
 
+- The possibility to perform recapitation, simplification, or mutation of a tree sequence right inside a call to `ts_load()` (by providing `recapitate = TRUE`, `simplify = TRUE`, and `mutate = TRUE`, together with their own arguments) has now been removed. The motivation for this change is the realization that there is no benefit of  doing things like `ts_load("<path>", recapitate = TRUE, Ne = ..., recombination_rate = ...)` over `ts_load("<path>") %>% ts_recapitate(Ne = ..., recombination_rate = ...)`, and the frequent confusion when `recapitate = TRUE` or other switches are forgotten by the user. All _slendr_ teaching material and most actively used research codebases I know of use the latter, more explicit, pipeline approach anyway, and this has been the one example where reduncancy does more harm than good. ([#ad82ee](https://github.com/bodkan/slendr/commit/ad82ee))
+
 **Loading `library(slendr)` will prompt a message _"The legacy packages maptools, rgdal, and rgeos, underpinning the sp package, which was just loaded, will retire in October 2023. [...]."_ This is an internal business of packages used by _slendr_ which unfortunately cannot be silenced from _slendr_'s side. There's no reason to panic, you can safely ignore them. Apologies for the unnecessary noise.**
 
 # slendr 0.6.0

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