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
#2874 - Add tree_pos to tsk_tree_t struct and change next, prev and seek_from_null to use tree_pos
Pull Request -
State: closed - Opened by duncanMR 10 months ago
- 25 comments
#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
#2795 - Replace calls to tsk_tree_position_t with the internal tree version
Issue -
State: closed - Opened by jeromekelleher about 1 year ago
#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
#2791 - New divergence_matrix function doesn't support string windows specifications
Issue -
State: closed - Opened by jeromekelleher about 1 year ago
Labels: bug
#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