Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / tskit-dev/msprime issues and pull requests

#2218 - No Sweep Model for Spatially Structured Populations

Issue - State: open - Opened by YuanboSong over 1 year ago - 1 comment

#2217 - Inconsistencies between algorithm.c and algorithm.py

Issue - State: open - Opened by YuanboSong over 1 year ago - 1 comment

#2216 - Fix docs build warning

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

#2214 - Update pedigree doc

Pull Request - State: closed - Opened by daikitag over 1 year ago - 4 comments

#2212 - Clarify the population size is diploid (by default)

Pull Request - State: closed - Opened by hyanwong over 1 year ago - 4 comments

#2211 - draw_pedigree documentation

Issue - State: closed - Opened by daikitag over 1 year ago - 3 comments

#2210 - Documentation for replicate_index

Issue - State: closed - Opened by daikitag over 1 year ago - 3 comments

#2208 - Update PyPI auth method

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

#2207 - Update pre commit

Pull Request - State: closed - Opened by benjeffery over 1 year ago - 3 comments

#2206 - Update deps, remove py37 and fix test warnings

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

#2205 - Update docs build

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

#2204 - Problem with Demography Debugger output

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

#2202 - Set favicon

Pull Request - State: closed - Opened by jeromekelleher over 1 year ago - 5 comments

#2201 - Clean up config and get version working

Pull Request - State: closed - Opened by jeromekelleher over 1 year ago - 3 comments

#2200 - Publish pip wheels for Windows

Issue - State: open - Opened by tomwhite over 1 year ago - 1 comment

#2199 - raise error when recording migrants

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

#2198 - The error for importing msprime

Issue - State: closed - Opened by frezaei98 over 1 year ago - 1 comment

#2197 - Change docs theme to sphinx-book-theme

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

#2195 - parent node having a time value <= to its child

Issue - State: closed - Opened by connor-french over 1 year ago - 8 comments

#2194 - update docs

Pull Request - State: closed - Opened by GertjanBisschop over 1 year ago - 4 comments

#2193 - Update docs config

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

#2192 - Update docs deps

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

#2190 - recording migrants with sweep model

Issue - State: closed - Opened by GertjanBisschop over 1 year ago - 3 comments

#2189 - Update intro.md to add tutorial links

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

#2187 - problems with gsl version in pyslim 1.0.3

Issue - State: closed - Opened by ShyamieG over 1 year ago - 6 comments

#2186 - Recording recombination events

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

#2185 - additional_nodes docs

Pull Request - State: closed - Opened by GertjanBisschop over 1 year ago - 2 comments

#2183 - auto_flush_edges

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

#2182 - Autoflush edges in the simulator

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

#2181 - Prototype

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

#2180 - Test and build wheels on 3.11

Pull Request - State: closed - Opened by benjeffery almost 2 years ago - 5 comments

#2177 - Python 3.11 wheels

Issue - State: closed - Opened by tomwhite almost 2 years ago - 1 comment

#2176 - Additional_nodes DTWF/FIXED_PEDIGREE

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

#2175 - doi for msprime 1.0 is not correct

Issue - State: closed - Opened by xin-huang almost 2 years ago - 2 comments
Labels: documentation

#2174 - modified stats test unary nodes

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

#2173 - clarification to migration documentation

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

#2170 - Fix codecov with token

Pull Request - State: closed - Opened by benjeffery almost 2 years ago - 5 comments

#2169 - Fix codecov

Pull Request - State: closed - Opened by benjeffery almost 2 years ago

#2168 - Update verification.py to use coalescent_segments_only flag

Issue - State: closed - Opened by GertjanBisschop almost 2 years ago - 1 comment

#2166 - Fix lint action

Pull Request - State: closed - Opened by benjeffery almost 2 years ago

#2165 - Update mergify config

Pull Request - State: closed - Opened by benjeffery almost 2 years ago

#2164 - clarify `coalescence_rate_trajectory`, closes #2163

Pull Request - State: closed - Opened by petrelharp almost 2 years ago - 3 comments

#2163 - Coalescence rate trajectory, more than two lineages

Issue - State: closed - Opened by trevorcousins almost 2 years ago - 5 comments

#2162 - new additional_nodes API

Pull Request - State: closed - Opened by GertjanBisschop almost 2 years ago - 11 comments

#2160 - change conda newick name; closes #2159

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

#2158 - Define global stopping condition

Issue - State: open - Opened by jeromekelleher almost 2 years ago

#2157 - Add option to simulate "above" local roots

Issue - State: open - Opened by jeromekelleher almost 2 years ago - 8 comments
Labels: enhancement

#2156 - Added tests for the distribution of nodes and edges in tree sequences…

Pull Request - State: closed - Opened by General-Solution almost 2 years ago - 6 comments

#2155 - Update conda instructions to use environment

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

#2154 - Fix docs

Pull Request - State: closed - Opened by benjeffery about 2 years ago - 2 comments

#2153 - Docs build broken

Issue - State: closed - Opened by jeromekelleher about 2 years ago - 1 comment
Labels: Infrastructure and tools

#2152 - extending tests record unary nodes

Pull Request - State: closed - Opened by GertjanBisschop about 2 years ago - 4 comments

#2151 - Add Software Heritage badge to README

Pull Request - State: closed - Opened by castedo about 2 years ago - 2 comments

#2150 - Building msprime from source results in ImportError: DLL load failed

Issue - State: closed - Opened by General-Solution about 2 years ago - 11 comments

#2147 - add Software Heritage badges to repo README file

Issue - State: closed - Opened by castedo about 2 years ago - 3 comments

#2146 - SMC with record_full_arg produces discontinuous nodes

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

#2145 - add keep_unary for pedigrees and dtwf

Pull Request - State: closed - Opened by GertjanBisschop about 2 years ago - 10 comments

#2144 - Clarify "transition matrix" in docs

Pull Request - State: closed - Opened by hyanwong about 2 years ago - 2 comments

#2143 - More helpful record_full_arg errors

Pull Request - State: closed - Opened by hyanwong about 2 years ago - 3 comments

#2140 - Documentation for "transition_matrix" of a mutation model

Issue - State: closed - Opened by hyanwong about 2 years ago - 3 comments

#2139 - Use state_independent in docs

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

#2138 - Fix doc build

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

#2137 - Test sim_mutations with unary nodes

Issue - State: closed - Opened by jeromekelleher about 2 years ago - 3 comments

#2136 - Test simulating with unary nodes on all ancestry models/processes

Issue - State: closed - Opened by jeromekelleher about 2 years ago - 1 comment

#2135 - Documentation for simulating with unary nodes

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

#2134 - Statistical testing with keep_unary

Issue - State: closed - Opened by jeromekelleher about 2 years ago - 16 comments

#2133 - Implement keep_unary for DTWF

Issue - State: closed - Opened by jeromekelleher about 2 years ago - 1 comment

#2132 - Review API around store_unary, store_full_arg etc

Issue - State: closed - Opened by jeromekelleher about 2 years ago - 9 comments

#2131 - Docs build broken

Issue - State: closed - Opened by jeromekelleher about 2 years ago - 1 comment

#2130 - first pass store unary

Pull Request - State: closed - Opened by GertjanBisschop about 2 years ago - 6 comments

#2129 - Keep all nodes in simulation from pedigree

Issue - State: closed - Opened by jeromekelleher about 2 years ago - 4 comments
Labels: enhancement

#2128 - Add an option to keep unary nodes

Issue - State: closed - Opened by jeromekelleher about 2 years ago - 5 comments
Labels: enhancement

#2127 - population-specific recombination rates?

Issue - State: open - Opened by gtsambos about 2 years ago - 10 comments

#2126 - update SLiM script for verification.py

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

#2125 - Fix and update lint

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

#2124 - Check for tree seqs without recombination nodes

Pull Request - State: closed - Opened by hyanwong about 2 years ago - 3 comments

#2123 - Raise error when calculating ARG likelihood on simplified tree seqs

Issue - State: closed - Opened by hyanwong over 2 years ago - 1 comment
Labels: enhancement

#2122 - Check performance implication of tracking breakpoints

Issue - State: open - Opened by jeromekelleher over 2 years ago - 1 comment
Labels: Performance

#2121 - Python algorithm without S avl tree

Pull Request - State: open - Opened by GertjanBisschop over 2 years ago - 21 comments

#2120 - Add Python 3.11 support

Pull Request - State: closed - Opened by benjeffery over 2 years ago - 2 comments

#2119 - Review microsat docs

Issue - State: closed - Opened by jeromekelleher over 2 years ago - 1 comment

#2118 - changed default value for min allele length to 1

Pull Request - State: closed - Opened by andrewkern over 2 years ago - 3 comments

#2116 - Update tskit requirement for Tree.num_children_array

Pull Request - State: closed - Opened by benjeffery over 2 years ago - 1 comment

#2114 - Check for valid input in ARG likelihood

Pull Request - State: closed - Opened by JereKoskela over 2 years ago - 5 comments

#2113 - add `stack_policy` argument to `SLiMMutationModel`

Issue - State: open - Opened by petrelharp over 2 years ago - 3 comments

#2112 - Add kastore to circle CI deps.

Pull Request - State: closed - Opened by benjeffery over 2 years ago - 1 comment

#2109 - small docfix

Pull Request - State: closed - Opened by petrelharp over 2 years ago - 11 comments

#2108 - Add tskit-book-theme to dev requirments

Pull Request - State: closed - Opened by benjeffery over 2 years ago - 3 comments

#2107 - segmentation fault when trying to run msprime.log_arg_likelihood()

Issue - State: closed - Opened by savitakartik over 2 years ago - 17 comments
Labels: bug

#2106 - Get population from Demography object by name

Issue - State: closed - Opened by hyanwong over 2 years ago - 3 comments

#2105 - Create names for individuals in SampleSet

Issue - State: closed - Opened by hyanwong over 2 years ago - 3 comments

#2104 - create `snakemake` wrapper for `msp`?

Issue - State: open - Opened by andrewkern over 2 years ago - 2 comments
Labels: enhancement

#2102 - New doc design

Pull Request - State: closed - Opened by benjeffery over 2 years ago - 4 comments

#2101 - slow simulation when recombination rate is high

Issue - State: closed - Opened by Devashish13 over 2 years ago - 1 comment

#2100 - Implement 2D stepping stone model

Issue - State: open - Opened by connor-french over 2 years ago - 3 comments
Labels: enhancement