Big changes to the way tree-sequence outputs are handled by slendr by default. See this comment for an extended description and examples of the change. (PR #100).
slendr’s tree-sequence R interface to the tskit Python module has been generalized to load, process, and analyze tree sequences from non-slendr models! This means that users can use the slendr R package even for analyzing tree sequences coming from standard msprime and SLiM scripts, including all spatial capabilities that have been only available for slendr tree sequences so far. Please note that this generalization is still rather experimental and there might be corner cases where a tree sequence from your msprime or SLiM script does not load properly or leads to other errors. If this happens, please open a GitHub issue with the script in question attached. (PR #91)
Removed functions and some function arguments originally
deprecated during the renaming phase of the pre-preprint refactoring.
This affects compile, boundary,
dispersal, expand, geneflow,
plot.slendr, plot_graph, read,
sampling, and shrink. Similarly, deprecated
dir argument of the compile_model is now
path, geneflow argument of
compile_model is now gene_flow, and the
_dist suffix was removed from
competition_dist, mate_dist, and
dispersal_dist. If you get an error about a missing
function or a function argument in code which used to work in an ancient
version of slendr, this is why. (#985b451)
When setting up an isolated Python environment using
setup_env(), slendr now makes a decision whether
to install Python dependencies using pip (critical on osx-arm64 for
which the conda msprime/tskit are unfortunately currently broken) or
with conda (every other platform). This can be still influenced by the
user using the pip = <TRUE|FALSE> argument, but we
now change the default behavior on ARM64 Mac. (#54a413d)
The name of the default slendr Python environment is now
shortened even more, and the redundant _pandas prefix is
now dropped. Users will be notified upon calling
library(slendr) that a new environment should be created.
This is OK, it’s not a bug. (#54a413d)
The format of the default slendr Python environment is
now
msprime-<version>_tskit-<version>_pyslim-<version>_pandas,
dropping the slendr_ prefix. This paves the way towards a
future non-slendr tskit R package, which will share the same
Python environment with slendr (because both R packages will go
hand in hand). This isn’t really a user-facing change, except that
calling setup_env() will suggests creating a new Python
environment and library(slendr) will appear as if a
slendr environment is not yet present. Calling
setup_env() and creating a new Python environment from
scratch will solve the problem. (#eb05180)
xrange and yrange parameters of
world() are now enforced to be two-dimensional numeric
vectors, avoiding unnecessary issues with misspecified
longitude/latitude (#df95369)
The argument sampling = in slim() and
msprime() is now renamed to samples = (#adf4e0d).
The automated setup_env() function for creating
dedicated mini Python environments for slendr now installs
packages using pip by default. Reason: The rate of conda
failures and dependency conflicts (even in the trivial case of
installing nothing more than msprime + tskit +
pyslim + pandas) is too high to rely on it. The option
to use conda for package installations with setup_env() is
still there, but the users must explicitly call
setup_env(pip = FALSE) to get this behavior. Note that
conda is still used as a means to install Python itself! This change
only affects the way how Python modules are installed into a dedicated
slendr Python environment, not the installation of Python
itself. (#81be1a7)
The name of the automatically created slendr-specific Python environment is now composed from the names and versions of Python modules installed. This makes it possible to naturally upgrade both slendr and its Python dependencies in case the tskit / msprime / pyslim folks upgrade some of those packages. In that case, if a slendr user upgrades the slendr package (and that new version requires newer versions of Python modules), slendr will simply recommend to create a new Python environment without additional effort on our part. (#81be1a7)
The code of setup_env() was simplified to bare
essentials. Now it only serves as a way to auto-setup a
dedicated, isolated Python installation and slendr environment.
The interface to install Python modules into custom-defined Python
environment created outside R has been removed because this
functionality is not necessary – these custom environments can be easily
activated by calling reticulate::use_virtualenv or
reticulate::use_condaenv. (#30f24b9)
If some Python users want to use custom Python environments with
msprime, tskit, and pyslim, they can silence
the suggestion to use setup_env() printed by the
library(slendr) call by setting
options(slendr.custom_env = TRUE). (#30f24b9)
The argument sim_length = is now renamed to
simulation_length =. Both are accepted for the moment and
using the old name will simply inform the user of the future
deprecation. (#56491fb)
Extensive set of runnable examples including figures and a built-in pre-compiled example model have been added to the documentation. (#395df62c)