fwdpy11
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molpopgen
Forward-time simulation in Python using fwdpp
Currently, we specify dependencies in more than one place: 1. pyproject.toml 2. file in in requirements/ This redundancy leads to the obvious problems. We can solve the problem by: 1....
The C++ back end module (`fwdpy11._fwdpy11`) contains code in `cpp/ts/count_mutations.cc` that is not used anywhere in the Python API. We should either restore its visibility (see #1271, for example) or...
Recent discussions elsewhere demonstrate that the specification of the genetic value objects is confusing. Specifically, the `ndemes` field is a kludge. Ideally, `gvalue` would be a list of one object...
The C++ code is getting long and would be much more readable if we used functions instead of long control blocks. We may even get a compile-time speedup!
The change made in eed6689805d1719c67d934b2f7c68f182fc86c4b partially copy/pastes code found in `fwdpy11/evolvets/simplify_tables.hpp`. It would be nice to reduce the duplication.
We have a nice set of containerized workflows for verification. But they are only mentioned in a buried reference in the tutorial.
Need to describe optimal strategies for processing data sets w/"tons" of ancient samples and the resulting speed-vs-memory trade-off. These considerations are related to all sorts of things, including #387.
The recent attrs release deprecates `repr_ns`. We use this feature to facilitate separating the fwdpy11 namespace across multiple Python files. Such separation is NOT really supported by the language, meaning...
PR #1324 fixed an issue where fixations were not being "pruned" even when that option was `True`. With that fix, though, we have the following behaviors: * genetic values are...