Ecosyste.ms: Issues

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

GitHub / bodkan/slendr issues and pull requests

#160 - Reschedule finishing block to the `first()` phase of the final tick

Pull Request - State: closed - Opened by bodkan 24 days ago - 1 comment

#159 - problem with ts_eigenstrat

Issue - State: closed - Opened by Frasella 2 months ago - 4 comments

#158 - Update tskit to v0.5.7

Issue - State: closed - Opened by bodkan 5 months ago

#157 - Change handling of output paths

Pull Request - State: closed - Opened by bodkan 5 months ago - 1 comment

#155 - Support for non-neutral slendr/SLiM simulations via custom, user-defined SLiM code

Pull Request - State: closed - Opened by bodkan 7 months ago - 7 comments

#154 - slendr has trouble exporting conda paths

Issue - State: closed - Opened by janxkoci 8 months ago - 7 comments

#153 - Problem installing tskit (during setup_env())

Issue - State: closed - Opened by gsilvaarias 9 months ago - 8 comments

#152 - Fix SLiM-presence test in `check_dependencies()`

Issue - State: closed - Opened by bodkan 9 months ago - 1 comment

#150 - no attribute 'get_pedigree_ids'

Issue - State: closed - Opened by willright28 10 months ago - 17 comments

#149 - Add support for SLiM simulations on Windows

Pull Request - State: closed - Opened by bodkan 10 months ago - 38 comments

#148 - Avoid repeated resetting of spatial bounds (closes #147)

Pull Request - State: closed - Opened by bodkan 10 months ago - 1 comment

#147 - fixes for SLiM 4.1 changes to SpatialMap

Issue - State: closed - Opened by bhaller 10 months ago - 9 comments

#146 - A few questions regarding tspop integration into slendr

Issue - State: closed - Opened by bodkan 12 months ago - 9 comments

#145 - Implement experimental support for the tspop algorithm

Pull Request - State: closed - Opened by bodkan 12 months ago - 5 comments

#144 - Support for manually created tree sequences with spatial information

Pull Request - State: closed - Opened by bodkan about 1 year ago - 2 comments

#142 - Update engines.R

Pull Request - State: closed - Opened by GKresearch over 1 year ago - 7 comments

#140 - Controlling mutation rate?

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

#139 - remove rgdal asap

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

#138 - Implement rudimentary, experimental IBD squashing

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

#135 - Change the plot_model layout algorithm

Pull Request - State: closed - Opened by bodkan over 1 year ago - 7 comments

#134 - Fixing various gene flow errors

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

#132 - Incorrect error messages in `gene_flow()` caused by time errors

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

#131 - `plot_model()` does not adjust migration arrow ends when `log=TRUE`

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

#130 - Fixes for minor issues discovered during work on demografr and other things

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

#129 - Improve robustness of the "simulation finished" check in `slim()`

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

#128 - Implement interface to genealogical nearest neighbors

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

#126 - A fundamental design question for Slendr

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

#125 - Figure out a way to run SLiM-based simulations on Windows

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

#124 - slim binary not found

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

#123 - New ts_ibd function

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

#122 - Use NOT_CRAN=false on Windows-based GitHub Actions

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

#121 - Allow for the possibility to have non-spatial populations in an otherwise spatial model

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

#120 - Fix undesirable artefacts during map zooming/cropping for some CRS

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

#119 - Look into nicer reporting of errors after recent purrr changes

Issue - State: closed - Opened by bodkan almost 2 years ago

#117 - New error upon loading library

Issue - State: closed - Opened by hmoots almost 2 years ago - 4 comments

#116 - Strange things are happening with custom CRS projections in some corners of the world

Issue - State: closed - Opened by bodkan almost 2 years ago - 10 comments

#115 - Consider a balance between R-like NA values and -1 values in slendr tables

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

#113 - Correctly handle "truncated" models

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

#112 - Make serialization of slendr models to disk optional (for faster msprime coalescent runs)

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

#111 - Issues with replication of the explore_model() population history graph figure

Issue - State: closed - Opened by archgen about 2 years ago - 2 comments
Labels: documentation

#110 - library(slendr) throwing error after installing

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

#109 - Add SLiM's selfing rate function to slendR?

Issue - State: closed - Opened by ornobalam about 2 years ago - 3 comments
Labels: feature

#108 - Allow different mutation rate at different location on the demography ?

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

#107 - Fix passing of node times from tskit through `ts_phylo`

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

#105 - Implement ancestry tract detection mechanism

Issue - State: closed - Opened by bodkan over 2 years ago - 1 comment
Labels: feature

#104 - Port slendr to SLiM 4.0 and update Python dependencies

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

#102 - Windows port of the msprime functionality

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

#101 - Not getting an output when running slim

Issue - State: closed - Opened by AhmedSelim1997 over 2 years ago - 7 comments

#100 - Changing the way tree-sequence outputs are handled by default

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

#99 - Admixture in slendr vs msprime

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

#98 - Make sure slendr's SLiM back end can run both under SLiM 3 and SLiM 4

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

#97 - Add option to skip serialization of slendr configuration files

Issue - State: closed - Opened by bodkan over 2 years ago - 2 comments
Labels: feature

#96 - Could you allow non-uniform recombination rate in slendr?

Issue - State: open - Opened by dangliu over 2 years ago - 10 comments
Labels: feature

#93 - Installation issue "error: ModuleNotFoundError: No module named 'tskit'"

Issue - State: closed - Opened by awohns over 2 years ago - 11 comments

#92 - A few assorted usage issues: installation, visualization, distance units

Issue - State: closed - Opened by ornobalam over 2 years ago - 10 comments

#91 - Generalize the R-tskit interface towards non-slendr tree sequences

Pull Request - State: closed - Opened by bodkan over 2 years ago - 14 comments

#90 - Can we handle "failed to generate child after 1 million attempts" a bit more gracefully?

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

#89 - How to interpret location coordinates

Issue - State: closed - Opened by percyfal over 2 years ago - 6 comments
Labels: question

#88 - Add an option to automatically run simulation replicates (including parallel runs)

Issue - State: closed - Opened by bodkan over 2 years ago - 3 comments
Labels: feature

#87 - slim call throws conversion error

Issue - State: closed - Opened by percyfal over 2 years ago - 5 comments

#85 - Generalize the R-tskit interface towards non-slendr tree sequences

Issue - State: closed - Opened by bodkan over 2 years ago - 4 comments
Labels: feature

#84 - Installing requirements when using virtualenv

Issue - State: closed - Opened by DominikRafacz over 2 years ago - 9 comments

#83 - Failure with Python env install

Issue - State: closed - Opened by thijsjanzen over 2 years ago - 22 comments

#82 - Something very odd happened while running slendr

Issue - State: closed - Opened by jaurbanChicago over 2 years ago - 14 comments

#81 - Question about Sampling Process

Issue - State: closed - Opened by jaurbanChicago almost 3 years ago - 13 comments

#80 - Make the msprime backend first-class citizen in slendr

Pull Request - State: closed - Opened by bodkan almost 3 years ago - 1 comment

#79 - Save metadata to tree sequences produced by the msprime backend

Issue - State: closed - Opened by bodkan almost 3 years ago - 8 comments

#78 - Satisfy CRAN & Win-builder & R-hub check on macOS/Windows/Linux

Pull Request - State: closed - Opened by bodkan almost 3 years ago - 1 comment

#77 - Slim Simulations using SliM Genomic element types

Issue - State: closed - Opened by jaurbanChicago almost 3 years ago - 1 comment

#76 - Full implementation of the msprime back end for slendr models

Pull Request - State: closed - Opened by bodkan almost 3 years ago - 5 comments

#75 - The slim binary was not found in your $PATH variable.

Issue - State: closed - Opened by jaurbanChicago almost 3 years ago - 4 comments

#74 - Fix some minor issues (broken links etc.) described in a user report

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

#73 - Custom dispersal functions

Pull Request - State: closed - Opened by bodkan almost 3 years ago - 7 comments

#72 - deal with population overlap

Issue - State: open - Opened by petrelharp almost 3 years ago - 5 comments
Labels: enhancement

#71 - Spatial sampling

Pull Request - State: closed - Opened by bodkan almost 3 years ago

#70 - Fix two reported sampling issues

Pull Request - State: closed - Opened by bodkan almost 3 years ago

#69 - Remembered individuals missing despite being scheduled for sampling

Issue - State: closed - Opened by bodkan almost 3 years ago - 12 comments

#68 - Broken check for landscape intersection when population fills the whole world?

Issue - State: closed - Opened by bodkan about 3 years ago - 1 comment

#67 - Figure out a more convenient way to coalesce lineages in `ts_recapitate`

Issue - State: closed - Opened by bodkan about 3 years ago - 6 comments

#66 - Refactoring of the SLiM backend and some R internals

Pull Request - State: closed - Opened by bodkan about 3 years ago - 9 comments

#65 - A support for (partial) import of Demes models

Issue - State: closed - Opened by bodkan about 3 years ago - 2 comments
Labels: feature

#64 - Can we handle individual locations in SLiM directly in projected CRS units?

Issue - State: open - Opened by bodkan about 3 years ago - 5 comments
Labels: refactor, SLiM

#63 - Switch to new msprime.sim_mutations in ts_mutate

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

#62 - add slendr version number to top-level metadata

Issue - State: closed - Opened by petrelharp about 3 years ago

#61 - save raster information in top-level tree sequence metadata

Issue - State: closed - Opened by petrelharp about 3 years ago