Ecosyste.ms: Issues

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

GitHub / tskit-dev/tskit issues and pull requests

#2875 - Fix dep versions

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

#2872 - Topology counter not aligning with coalescent expectation

Issue - State: open - Opened by TymekPieszko 10 months ago - 10 comments

#2871 - Fix draw_svg warning for mutations above unplotted nodes

Pull Request - State: closed - Opened by duncanMR 11 months ago - 3 comments

#2870 - Warning for `draw_svg` plot uses `logging` module instead of `warnings`

Issue - State: open - Opened by duncanMR 11 months ago - 2 comments
Labels: bug

#2868 - leaks when loading tree sequence in SLiM

Issue - State: closed - Opened by bhaller 11 months ago - 26 comments

#2867 - Add tree_pos to tsk_tree_t struct

Pull Request - State: closed - Opened by duncanMR 11 months ago - 8 comments

#2866 - tmrca error when common ancestor does not exist

Issue - State: closed - Opened by daikitag 11 months ago - 2 comments

#2863 - Specify sites for two-site statistics

Pull Request - State: closed - Opened by lkirk 12 months ago - 16 comments

#2861 - Support all-nodes matching in LSHMM

Pull Request - State: open - Opened by jeromekelleher 12 months ago - 1 comment

#2860 - Add python 3.12 support

Pull Request - State: open - Opened by benjeffery 12 months ago - 1 comment

#2859 - Post release tasks

Pull Request - State: closed - Opened by benjeffery 12 months ago - 1 comment

#2858 - Prepare for 0.5.6 release

Pull Request - State: closed - Opened by benjeffery 12 months ago - 1 comment

#2857 - Update pypi release auth

Pull Request - State: closed - Opened by benjeffery 12 months ago - 1 comment

#2856 - Remove 3.7 and update pre-commit to 3.8

Pull Request - State: closed - Opened by benjeffery 12 months ago - 1 comment

#2855 - Python 3.12 support

Issue - State: open - Opened by benjeffery 12 months ago - 1 comment
Labels: Infrastructure and tools

#2853 - Add macros to LsHmm_forward_matrix and LsHmm_backward_matrix

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

#2852 - Mention bitwise flag values in nodes_flag and individuals_flag

Pull Request - State: closed - Opened by szhan 12 months ago - 1 comment

#2851 - Mention that node and individual flags are bitwise

Issue - State: closed - Opened by szhan 12 months ago - 3 comments
Labels: good first issue, documentation

#2850 - _tskit.lshmm doesn't take NaN in recombination rates

Issue - State: open - Opened by szhan 12 months ago
Labels: bug

#2849 - Fix numpy warnings

Pull Request - State: closed - Opened by benjeffery 12 months ago - 1 comment

#2848 - Use setup-python cache

Pull Request - State: closed - Opened by benjeffery 12 months ago - 3 comments

#2847 - Numpy deprecations

Issue - State: closed - Opened by benjeffery 12 months ago - 3 comments

#2846 - Install numpy with noblas

Pull Request - State: closed - Opened by benjeffery 12 months ago - 1 comment

#2845 - 32 bit CI broken when building numpy

Issue - State: closed - Opened by benjeffery 12 months ago

#2844 - Fix jsonschema validators error

Pull Request - State: closed - Opened by benjeffery 12 months ago - 3 comments

#2843 - Update data-model.md

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

#2842 - Add node metadata

Issue - State: closed - Opened by ShyamieG about 1 year ago - 15 comments

#2841 - Release GIL around tskit C API functions?

Issue - State: closed - Opened by benjeffery about 1 year ago - 4 comments
Labels: Python API

#2840 - Jsonschema >4.18.6 incompatibility

Issue - State: closed - Opened by alxsimon about 1 year ago - 1 comment
Labels: bug

#2838 - `write_vcf` returning position 0

Issue - State: closed - Opened by andrewkern about 1 year ago - 29 comments
Labels: bug

#2837 - Update mergify config

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

#2836 - Use default light code theme

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

#2835 - Release infrastructure update

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

#2834 - Refactor tsk_bit_array_* structures

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

#2833 - use restrict pointers in tsk_bit_array_* methods

Issue - State: open - Opened by jeromekelleher about 1 year ago
Labels: C API

#2832 - Multipopulation two-site statistics

Issue - State: open - Opened by lkirk about 1 year ago

#2831 - Handle missing data in two-locus statistics

Issue - State: open - Opened by lkirk about 1 year ago - 1 comment

#2830 - Windows/Site masking for two-site statistics

Issue - State: open - Opened by lkirk about 1 year ago - 10 comments

#2829 - Python interface for 2-locus statistics

Issue - State: open - Opened by lkirk about 1 year ago - 7 comments

#2828 - Switch to sphinx theme

Pull Request - State: closed - Opened by benjeffery about 1 year ago - 5 comments

#2827 - Random numba failures on python 3.7

Issue - State: closed - Opened by jeromekelleher about 1 year ago

#2826 - Test infrastructure maint

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

#2825 - Add tsk_tree_position_step function to C API

Issue - State: closed - Opened by duncanMR about 1 year ago
Labels: C API

#2824 - Change samples_only default for ``random_ploidy_individuals``to True

Issue - State: closed - Opened by jeromekelleher about 1 year ago
Labels: Python API

#2823 - Divmat sample_sets

Pull Request - State: closed - Opened by jeromekelleher about 1 year ago - 15 comments

#2820 - Add span normalise

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

#2819 - Add seek_backward function with tests

Pull Request - State: closed - Opened by duncanMR about 1 year ago - 7 comments

#2817 - Move C stats methods to ``stats.h``

Issue - State: open - Opened by jeromekelleher about 1 year ago - 2 comments
Labels: C API, Infrastructure and tools, refactoring

#2816 - normalization for two-locus, multiallelic stats?

Issue - State: open - Opened by petrelharp about 1 year ago - 1 comment

#2815 - Add tests for genotype imputation

Pull Request - State: open - Opened by szhan about 1 year ago - 17 comments

#2814 - Including the tests folder in the Pypi distribution

Issue - State: open - Opened by alxsimon about 1 year ago - 7 comments

#2813 - Better divmat site mode

Pull Request - State: open - Opened by jeromekelleher about 1 year ago - 5 comments

#2812 - Remove legacy h5py based formats

Issue - State: open - Opened by benjeffery about 1 year ago - 5 comments

#2811 - Fix 32bit CI

Pull Request - State: closed - Opened by benjeffery about 1 year ago - 6 comments

#2810 - Document use of the individual.parent pedigree structure

Issue - State: open - Opened by hyanwong about 1 year ago - 1 comment

#2809 - TableCollection method to adjust times

Issue - State: open - Opened by hyanwong about 1 year ago - 3 comments

#2808 - Multi-arg tMRCA

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

#2807 - Correct doc instances of "raises"

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

#2805 - Two Locus Statistics C API

Pull Request - State: closed - Opened by lkirk about 1 year ago - 15 comments

#2804 - Account for multiallelics in emission probabilities

Issue - State: open - Opened by astheeggeggs about 1 year ago - 1 comment

#2803 - Remove redundant compress() in backwards algorithm

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

#2802 - Add test_imputation.py file

Issue - State: open - Opened by jeromekelleher about 1 year ago - 27 comments

#2801 - Tree.tmrca error when MRCA does not exist

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

#2800 - Clarify tree.mrca if MRCA does not exist

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

#2799 - LS model refactoring

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

#2798 - Diploid testing: merge forward-backward and viterbi testing

Pull Request - State: closed - Opened by astheeggeggs about 1 year ago - 3 comments

#2797 - Remove tsk_diff_iter_t

Issue - State: open - Opened by jeromekelleher about 1 year ago - 4 comments
Labels: C API

#2796 - Update stats API algorithms to use tree_position_t

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

#2794 - Replace low-level tree positioning code with tsk_tree_position_t calls

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

#2793 - Update tskit-book-theme

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

#2792 - Characterise propagation up the tree performance with seeking

Issue - State: open - Opened by jeromekelleher about 1 year ago
Labels: enhancement, Performance

#2790 - Fix benchmark CI

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

#2789 - Error with Installing msprime

Issue - State: closed - Opened by AyomideOjo about 1 year ago - 8 comments

#2788 - Backwards algorithm (haploid) tree implementation and testing

Pull Request - State: closed - Opened by astheeggeggs about 1 year ago - 14 comments

#2786 - Modular incremental trees

Pull Request - State: closed - Opened by jeromekelleher about 1 year ago - 14 comments

#2785 - Tests and documentation for genetic_relatedness_weighted

Pull Request - State: closed - Opened by brieuclehmann about 1 year ago - 7 comments

#2784 - Add parallelism to stats API

Issue - State: open - Opened by jeromekelleher about 1 year ago
Labels: enhancement

#2783 - Use divergence_matrix for downstream statistics

Issue - State: open - Opened by jeromekelleher about 1 year ago - 3 comments

#2782 - Support windows in stats API that do not span whole genome

Issue - State: open - Opened by jeromekelleher about 1 year ago - 1 comment
Labels: enhancement

#2781 - Document divergence_matrix

Issue - State: open - Opened by jeromekelleher about 1 year ago - 1 comment
Labels: documentation

#2780 - Add support for ``individuals`` to divergence_matrix

Issue - State: open - Opened by jeromekelleher about 1 year ago
Labels: enhancement

#2779 - Improved algorithm for site-mode divergence matrix

Issue - State: open - Opened by jeromekelleher about 1 year ago - 2 comments
Labels: Performance

#2777 - add_pbs

Pull Request - State: open - Opened by atongsa about 1 year ago - 1 comment

#2776 - Add doc example of creating a matrix of all pairwise comparisons

Pull Request - State: open - Opened by hyanwong about 1 year ago - 2 comments

#2773 - Is tree.num_samples_array useful/worth it?

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

#2772 - CI-docs/requirements requires old version of tskit

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

#2771 - Add distance_between function and tests

Pull Request - State: open - Opened by Billyzhang1229 over 1 year ago

#2769 - Bump docs build cache

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

#2768 - CI failing to build docs

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

#2767 - added nodes time refactor code

Pull Request - State: closed - Opened by PalashLalwani over 1 year ago - 8 comments

#2766 - Avoid calling ``self.node()`` in max_root_time

Issue - State: closed - Opened by jeromekelleher over 1 year ago - 3 comments
Labels: good first issue, Python API, refactoring

#2765 - Returning the full ARG with ts.simplify()

Issue - State: open - Opened by kitchensjn over 1 year ago - 14 comments

#2764 - draw_svg() does not render on Mac OSX (via terminal)

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

#2763 - Remove package test from 32bit due to tricky dependancies

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

#2762 - Generic iterator class for trees and variants

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

#2761 - CI Fail: rust version

Issue - State: closed - Opened by benjeffery over 1 year ago - 2 comments
Labels: Infrastructure and tools

#2760 - Add method to impute mutation times

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