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
#2159 - species_tree.py check_newick_import(): update conda install message
Issue -
State: closed - Opened by isaacovercast over 1 year ago
#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
#2115 - Add tskit version requirement to dev requirements and check setup.cfg requirements.
Issue -
State: closed - Opened by benjeffery over 1 year ago
#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
#2093 - Unable to run msprime after installling on Windows via conda; get error with msprime._msprime not being found.
Issue -
State: closed - Opened by HadiKhan-dev almost 2 years ago
- 6 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
#2087 - Add example working out NaN bits when working with multiple chromosomes
Issue -
State: open - Opened by jeromekelleher almost 2 years ago
#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