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

#2164 - clarify `coalescence_rate_trajectory`, closes #2163

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

#2163 - Coalescence rate trajectory, more than two lineages

Issue - State: closed - Opened by trevorcousins over 1 year ago - 5 comments

#2162 - new additional_nodes API

Pull Request - State: closed - Opened by GertjanBisschop over 1 year ago - 11 comments

#2160 - change conda newick name; closes #2159

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

#2158 - Define global stopping condition

Issue - State: open - Opened by jeromekelleher over 1 year ago

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

Issue - State: open - Opened by jeromekelleher over 1 year 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 over 1 year ago - 6 comments

#2155 - Update conda instructions to use environment

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

#2154 - Fix docs

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

#2153 - Docs build broken

Issue - State: closed - Opened by jeromekelleher over 1 year ago - 1 comment
Labels: Infrastructure and tools

#2152 - extending tests record unary nodes

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

#2151 - Add Software Heritage badge to README

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

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

Issue - State: closed - Opened by General-Solution over 1 year ago - 11 comments

#2147 - add Software Heritage badges to repo README file

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

#2146 - SMC with record_full_arg produces discontinuous nodes

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

#2145 - add keep_unary for pedigrees and dtwf

Pull Request - State: closed - Opened by GertjanBisschop over 1 year ago - 10 comments

#2144 - Clarify "transition matrix" in docs

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

#2143 - More helpful record_full_arg errors

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

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

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

#2139 - Use state_independent in docs

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

#2138 - Fix doc build

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

#2137 - Test sim_mutations with unary nodes

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

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

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

#2135 - Documentation for simulating with unary nodes

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

#2134 - Statistical testing with keep_unary

Issue - State: closed - Opened by jeromekelleher over 1 year ago - 16 comments

#2133 - Implement keep_unary for DTWF

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

#2132 - Review API around store_unary, store_full_arg etc

Issue - State: closed - Opened by jeromekelleher over 1 year ago - 9 comments

#2131 - Docs build broken

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

#2130 - first pass store unary

Pull Request - State: closed - Opened by GertjanBisschop over 1 year ago - 6 comments

#2129 - Keep all nodes in simulation from pedigree

Issue - State: closed - Opened by jeromekelleher over 1 year ago - 4 comments
Labels: enhancement

#2128 - Add an option to keep unary nodes

Issue - State: closed - Opened by jeromekelleher over 1 year ago - 5 comments
Labels: enhancement

#2127 - population-specific recombination rates?

Issue - State: open - Opened by gtsambos over 1 year ago - 10 comments

#2126 - update SLiM script for verification.py

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

#2125 - Fix and update lint

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

#2124 - Check for tree seqs without recombination nodes

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

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

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

#2122 - Check performance implication of tracking breakpoints

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

#2121 - Python algorithm without S avl tree

Pull Request - State: open - Opened by GertjanBisschop over 1 year ago - 21 comments

#2120 - Add Python 3.11 support

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

#2119 - Review microsat docs

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

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

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

#2116 - Update tskit requirement for Tree.num_children_array

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

#2114 - Check for valid input in ARG likelihood

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

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

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

#2112 - Add kastore to circle CI deps.

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

#2109 - small docfix

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

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

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

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

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

#2106 - Get population from Demography object by name

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

#2105 - Create names for individuals in SampleSet

Issue - State: open - Opened by hyanwong almost 2 years ago - 3 comments

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

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

#2102 - New doc design

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

#2101 - slow simulation when recombination rate is high

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

#2100 - Implement 2D stepping stone model

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

#2098 - simulating genome-wide SNPs

Issue - State: closed - Opened by mandresapata almost 2 years ago - 3 comments

#2095 - Docs: add warning to not install to conda root

Issue - State: closed - Opened by jeromekelleher almost 2 years ago
Labels: documentation

#2094 - Small update to error message for MSP_ERR_TIME_TRAVEL

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

#2092 - flake8 line length recs from Black have changed-- update this?

Issue - State: closed - Opened by andrewkern almost 2 years ago - 4 comments
Labels: Infrastructure and tools

#2091 - Issue importing msprime into Python

Issue - State: closed - Opened by asadrh8 almost 2 years ago - 9 comments

#2090 - Use new logo

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

#2086 - Change microsat default for lo to 1

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

#2085 - Microsat verify

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

#2084 - Rework sectioning in mutations page

Issue - State: open - Opened by jeromekelleher about 2 years ago
Labels: documentation

#2083 - Docs for simulating multiple chromosomes with pedigrees

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

#2082 - Update docs on simulating multiple chromosomes

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

#2080 - clean up of microsatellite documentation and defaults

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

#2079 - Review interface and documentation.

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

#2078 - Justify default values for lo and hi

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

#2077 - Documentation for EL2 contradicts signature

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

#2076 - More details on defaults for EL2

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

#2075 - More details on defaults for TPM

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

#2074 - Review and document default params for microsat models

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

#2073 - Validation of microsat mutation models

Issue - State: closed - Opened by jeromekelleher about 2 years ago - 13 comments

#2071 - Microsatellite mutations models

Pull Request - State: closed - Opened by andrewkern about 2 years ago - 21 comments

#2061 - Update to tskit C API 1.0.0

Pull Request - State: closed - Opened by benjeffery about 2 years ago - 8 comments

#2060 - Update to tskit C 1.0

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

#2048 - Fix non-MassMigration edge case in from_old_style()

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

#2044 - Simulating sex chromosomes

Issue - State: open - Opened by LukeAndersonTrocme about 2 years ago - 9 comments
Labels: help wanted, question

#2013 - adding microsatellite mutation models

Issue - State: closed - Opened by andrewkern over 2 years ago - 13 comments

#1993 - Use ``ancestral_to`` field on segments instead of global lookup table.

Issue - State: closed - Opened by jeromekelleher over 2 years ago - 3 comments
Labels: Performance

#1952 - Remove tests/data directory

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

#1931 - Add special case for merging non-overlapping segments

Issue - State: closed - Opened by jeromekelleher over 2 years ago - 4 comments
Labels: Performance

#1862 - Add support for ``store_full_arg`` option to pedigree sims.

Issue - State: closed - Opened by jeromekelleher over 2 years ago - 3 comments
Labels: enhancement

#1855 - Support internal samples in simulation through pedigree

Issue - State: open - Opened by jeromekelleher over 2 years ago - 16 comments
Labels: enhancement

#1762 - GenicSelection model cannot complete a sweep with a neutral trajectory.

Issue - State: open - Opened by molpopgen almost 3 years ago - 23 comments
Labels: bug

#1653 - Integration of Selfing and Dormancy

Issue - State: open - Opened by TPPSellinger about 3 years ago - 9 comments
Labels: enhancement

#1485 - "Sandbox violation" with meson 0.57

Issue - State: closed - Opened by jeromekelleher over 3 years ago - 4 comments
Labels: bug, Infrastructure and tools

#1346 - Read hapmap reworking

Pull Request - State: closed - Opened by hyanwong over 3 years ago - 7 comments

#1299 - Docs for simulating with multiple chromosomes

Pull Request - State: closed - Opened by apragsdale over 3 years ago - 26 comments

#1087 - Mutation model conditioned on specific ancestral sequence

Issue - State: open - Opened by jeromekelleher about 4 years ago - 1 comment

#1065 - implementation of AA models

Pull Request - State: closed - Opened by GertjanBisschop about 4 years ago - 14 comments

#1037 - Remove extra parameter in DemographicEvent.get_ll_representation

Issue - State: open - Opened by jeromekelleher about 4 years ago - 2 comments

#1032 - Compare msprime against seq-gen #1018

Pull Request - State: closed - Opened by GertjanBisschop about 4 years ago - 67 comments