molpopgen/fwdpy11 issues and pull requests

#1115 - Move c++ back end for internal function to core lib.

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1114 - New field for DiploidPopulation

Issue - State: closed - Opened by molpopgen over 1 year ago - 1 comment

#1113 - Fix error with mutation origin times

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1112 - Update test fixtures from #1110 to use default demographic model

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1111 - Updated mutation metadata scheme is needed

Issue - State: closed - Opened by molpopgen over 1 year ago - 2 comments

#1110 - Fix #1109

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1109 - Mutation metadata and starting simulations from an existing tree sequence.

Issue - State: closed - Opened by molpopgen over 1 year ago - 1 comment

#1108 - Drop Py 3.7 support. Add Py 3.11 support

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1107 - remove examples and manual sections related to old demography API

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1106 - potential fix for #1105

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1105 - ModelParams fails to properly validate non-Poisson crossover types

Issue - State: closed - Opened by molpopgen over 1 year ago
Labels: bug

#1104 - Rewrite vignette on importing mutations from tskit/msprime

Issue - State: closed - Opened by molpopgen over 1 year ago
Labels: documentation

#1103 - Pull more information from the rust back end during model setup.

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1102 - Tracking issue: requirements for 0.20.0 alpha release

Issue - State: closed - Opened by molpopgen over 1 year ago - 1 comment
Labels: tracking issue

#1101 - Use demes graphs directly during simulation

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1100 - use rust for size rounding

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1099 - test linear size changes

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1098 - add test of pickling ForwardDemesGraph

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1097 - Remove kwarg check_demographic_event_timings from fwdpy11.evolvets

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1096 - restore vignette fixed in #1094

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1095 - Remove outdated modules

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1094 - Track down conditional_models bug

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1093 - Bug in conditional_models

Issue - State: closed - Opened by molpopgen over 1 year ago
Labels: bug

#1092 - Remove obsolete modules

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1091 - refactor imports

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1090 - Remove modules made obsolete by demes

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1089 - Restore tests that are easy to restore.

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1088 - Fix bug where BinomialInterval and BinomialPoint always returned a breakpoint.

Pull Request - State: closed - Opened by molpopgen over 1 year ago
Labels: bug

#1087 - restore efficient genetic maps

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1086 - Improved ForwardDemesGraph testing

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1085 - restore tests of ancient samples

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1084 - Remove tests depending on behavior of old demography API

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1083 - Restore tests of evolving w/tree seq recording

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1082 - Recombination performance with very many "regions"

Issue - State: closed - Opened by molpopgen over 1 year ago
Labels: performance

#1081 - Delete C++/Python code for old demography API

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1080 - Add C++ tests of demes models with invalid epoch rounding

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1079 - Tracking issue: integrating demes into the back-end

Issue - State: closed - Opened by molpopgen over 1 year ago - 1 comment
Labels: tracking issue

#1078 - Add ForwardDemesGraph to Python public API

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1077 - Put the new C++ back end in place for Python.

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1076 - add start stop start tests

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1075 - Add tests of ancestry proportions

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1074 - Add simple test of size history correctness

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1073 - Add simple tests of new back end using island model.

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1072 - check pop generation time past end of model

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1071 - Enforce initial population deme sizes match the graph's expectations.

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1070 - Add back-end tests of simlen > length of demes graph.

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1069 - Use ForwardDemesGraph in refactored back end code.

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1068 - update README.rst

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1067 - Further prep for upcoming refactor.

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1066 - Add support for Python 3.11

Issue - State: closed - Opened by molpopgen over 1 year ago - 2 comments

#1065 - Drop support for Python 3.7

Issue - State: closed - Opened by molpopgen over 1 year ago - 1 comment

#1064 - Mark low-level discrete_demography API deprecated.

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1017 - Move C++ headers to project root

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#1003 - Add dependabot for github actions.

Pull Request - State: closed - Opened by molpopgen over 1 year ago

#960 - add demes-forward-capi submodule

Pull Request - State: closed - Opened by molpopgen almost 2 years ago - 1 comment

#951 - Outline of demes-like graph for forward-time models in C++.

Pull Request - State: closed - Opened by molpopgen about 2 years ago - 1 comment

#944 - Add explicit test of deme existence.

Pull Request - State: closed - Opened by molpopgen about 2 years ago - 1 comment

#934 - SimulationStatus semantics

Issue - State: closed - Opened by molpopgen about 2 years ago - 4 comments

#925 - Selfing rates of 0.

Issue - State: closed - Opened by molpopgen about 2 years ago - 3 comments
Labels: pending deprecation

#913 - Deprecate MassMigration class

Issue - State: closed - Opened by molpopgen over 2 years ago - 2 comments
Labels: demographic models, pending deprecation

#902 - Document how to do different "gvalue" object in different demes.

Issue - State: closed - Opened by molpopgen over 2 years ago
Labels: documentation

#901 - SetMigration rates post-init incorrectly handles demes field.

Issue - State: closed - Opened by molpopgen over 2 years ago - 2 comments
Labels: bug, pending deprecation

#895 - Demes vignette should be more explicit

Issue - State: closed - Opened by molpopgen over 2 years ago
Labels: documentation, demes integration

#780 - Missing test coverage

Issue - State: closed - Opened by molpopgen about 3 years ago
Labels: testing, tree sequences

#777 - Pickling DiscreteDemography does not round-trip the internal state of the model.

Issue - State: closed - Opened by molpopgen about 3 years ago - 4 comments
Labels: demographic models, tricky, pending deprecation

#768 - Add lazy parameter dict functions

Issue - State: closed - Opened by molpopgen about 3 years ago - 2 comments
Labels: enhancement, UI

#757 - Add property accessors to DemographicModelDetails.

Issue - State: closed - Opened by molpopgen about 3 years ago - 1 comment
Labels: enhancement

#718 - demes-related docs issue tracker

Issue - State: closed - Opened by molpopgen about 3 years ago - 1 comment
Labels: documentation, demographic models, demes integration

#644 - Improve performance of "ancient sample resetting"?

Issue - State: closed - Opened by molpopgen over 3 years ago - 1 comment
Labels: performance, tree sequences

#573 - Use typing.final where possible

Issue - State: closed - Opened by molpopgen almost 4 years ago - 4 comments

#476 - Performance issue in TreeIterator?

Issue - State: closed - Opened by molpopgen about 4 years ago - 3 comments
Labels: C++ back end, tree sequences

#463 - Reduce number of "GSS" classes in Python.

Issue - State: closed - Opened by molpopgen about 4 years ago
Labels: C++ back end, UI

GitHub / molpopgen/fwdpy11 issues and pull requests